Sample records for salen type ligand
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Effects of axial coordination on immobilized Mn(salen) catalysts.
Teixeira, Filipe; Mosquera, Ricardo A; Melo, André; Freire, Cristina; Cordeiro, M Natália D S
2014-11-13
The consequences of anchoring Mn(salen) catalysts onto a supporting material using one of the vacant positions of the metal center are tackled by studying several Mn(salen) complexes with different axial ligands attached. This is accomplished using Density Functional Theory at the X3LYP/Triple-ζ level of theory and the Atom In Molecules formalism. The results suggest that both Mn(salen) complexes and their oxo derivatives should lie in a triplet ground state. Also, the choice of the axial ligand bears a moderate effect on the energy involved in the oxidation of the former to oxo-Mn(salen) complexes, as well as in the stability of such complexes toward ligand removal by HCl. AIM analysis further suggests that the salen ligand acts as a "charge reservoir" for the metal center, with strong correlations being obtained between the charge of salen and the electron population donated by the axial ligand to the metal center. Moreover, the results suggest that the Mn atom in Mn(salen) complexes holds different hybridization of its valence orbitals depending on the type of axial ligand present in the system.
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Darensbourg, Donald J; Mackiewicz, Ryan M; Rodgers, Jody L; Fang, Cindy C; Billodeaux, Damon R; Reibenspies, Joseph H
2004-09-20
A detailed mechanistic study into the copolymerization of CO2 and cyclohexene oxide utilizing CrIII(salen)X complexes and N-methylimidazole, where H2salen = N,N'-bis(3,5-di-tert-butylsalicylidene)-1,2-ethylenediimine and other salen derivatives and X = Cl or N3, has been conducted. By studying salen ligands with various groups on the diimine backbone, we have observed that bulky groups oriented perpendicular to the salen plane reduce the activity of the catalyst significantly, while such groups oriented parallel to the salen plane do not retard copolymer formation. This is not surprising in that the mechanism for asymmetric ring opening of epoxides was found to occur in a bimetallic fashion, whereas these perpendicularly oriented groups along with the tert-butyl groups on the phenolate rings produce considerable steric requirements for the two metal centers to communicate and thus initiate the copolymerization process. It was also observed that altering the substituents on the phenolate rings of the salen ligand had a 2-fold effect, controlling both catalyst solubility as well as electron density around the metal center, producing significant effects on the rate of copolymer formation. This and other data discussed herein have led us to propose a more detailed mechanistic delineation, wherein the rate of copolymerization is dictated by two separate equilibria. The first equilibrium involves the initial second-order epoxide ring opening and is inhibited by excess amounts of cocatalyst. The second equilibrium involves the propagation step and is enhanced by excess cocatalyst. This gives the [cocatalyst] both a positive and negative effect on the overall rate of copolymerization. Copyright 2004 American Chemical Society
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In situ formation of heterobimetallic salen complexes containing titanium and/or vanadium ions.
Belokon, Yuri N; Harrington, Ross W; North, Michael; Young, Carl
2008-05-05
A combination of high-resolution electrospray mass spectrometry and (1)H NMR spectroscopy has been used to prove that when a mixture of [(salen)TiO]2 complexes containing two different salen ligands (salen and salen') is formed, an equilibrium is established between the homodimers and the heterodimer [(salen)TiO2Ti(salen')]. Depending upon the structure and stereochemistry of the two salen ligands, the equilibrium may favor either the homodimers or the heterodimer. Extension of this process to mixtures of titanium(salen) complexes [(salen)TiO]2 and vanadium (V)(salen') complexes [(salen')VO] (+)Cl (-) allowed the in situ formation of the heterobimetallic complex [(salen)TiO2V(salen')] (+)X (-) to be confirmed for all combinations of salen ligands studied except when the salen ligand attached to titanium contained highly electron-withdrawing nitro-groups. The rate of equilibration between heterobimetallic complexes is faster than that between two titanium complexes as determined by line broadening in the (1)H NMR spectra. These structural results explain the strong rate-inhibiting effect of vanadium (V)(salen) complexes in asymmetric cyanohydrin synthesis catalyzed by [(salen)TiO]2 complexes. It has also been demonstrated for the first time that the titanium and vanadium complexes can undergo exchange of salen ligands and that this is catalyzed by protic solvents. However, the ligand exchange is relatively slow (occurring on a time scale of days at room temperature) and so does not complicate studies aimed at using heterobimetallic titanium and vanadium salen complexes as asymmetric catalysts. Attempts to obtain a crystal structure of a heterobimetallic salen complex led instead to the isolation of a trinuclear titanium(salen) complex, the formation of which is also consistent with the catalytic results obtained previously.
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Karukurichi, Kannan R.; Fei, Xiang; Swyka, Robert A.; Broussy, Sylvain; Shen, Weijun; Dey, Sangeeta; Roy, Sandip K.; Berkowitz, David B.
2015-01-01
This study introduces new methods of screening for and tuning chiral space and in so doing identifies a promising set of chiral ligands for asymmetric synthesis. The carbafructopyranosyl-1,2-diamine(s) and salens constructed therefrom are particularly compelling. It is shown that by removing the native anomeric effect in this ligand family, one can tune chiral ligand shape and improve chiral bias. This concept is demonstrated by a combination of (i) x-ray crystallographic structure determination, (ii) assessment of catalytic performance, and (iii) consideration of the anomeric effect and its underlying dipolar basis. The title ligands were identified by a new mini version of the in situ enzymatic screening (ISES) procedure through which catalyst-ligand combinations are screened in parallel, and information on relative rate and enantioselectivity is obtained in real time, without the need to quench reactions or draw aliquots. Mini-ISES brings the technique into the nanomole regime (200 to 350 nmol catalyst/20 μl organic volume) commensurate with emerging trends in reaction development/process chemistry. The best-performing β-d-carbafructopyranosyl-1,2-diamine–derived salen ligand discovered here outperforms the best known organometallic and enzymatic catalysts for the hydrolytic kinetic resolution of 3-phenylpropylene oxide, one of several substrates examined for which the ligand is “matched.” This ligand scaffold defines a new swath of chiral space, and anomeric effect tunability defines a new concept in shaping that chiral space. Both this ligand set and the anomeric shape-tuning concept are expected to find broad application, given the value of chiral 1,2-diamines and salens constructed from these in asymmetric catalysis. PMID:26501130
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The effect of axial ligand on the oxidation of syringyl alcohol by Co(salen) adducts
Thomas Elder; Joseph Bozell; Diana Cedeno
2013-01-01
Experimental work on the oxidation of the lignin model, syringyl alcohol, using oxygen and a Co(salen) catalyst has revealed variations in yield with different imidazole-based axial ligands. A reasonable linear relationship was found between product yield and pKa of the axial ligand. The current work, using density functional calculations, examined geometric,...
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The preparation and use of metal salen complexes derived from cyclobutane diamine
NASA Astrophysics Data System (ADS)
Patil, Smita
The helix is an important chiral motif in nature, there is increasing development in field of helical transition metal complexes and related supramolecular structures. Hence, the goals of this work are to apply the principles of helicity in order to produce metal complexes with predictable molecular shapes and to study their properties as asymmetric catalysts. Computational studies suggest that the (1R,2 R)-cyclobutyldiamine unit can produce highly twisted salen complexes with a large energy barrier between the M and P helical forms. To test this prediction, the tartrate salt of (1R,2R)-cyclobutyldiamine was synthesized and condensed with a series of saliclaldehydes to produce novel salen ligands. The salicylaldehydes chosen have extended phenanthryl or benz[a]anthryl sidearms to encourage formation of helical coordination complexes. These ligands were metallated with zinc, iron and manganese salts to produce salen metal complexes which were characterized by NMR analysis, high-resolution mass spectrometry, and IR spectroscopy. A second ligand type, neutral bis(pyridine-imine) has also been synthesized from (1R,2R)-cyclobutyldiamine and quinolylaldehydes. The synthesis of bis(pyridine-imine) ligands was conducted using greener method, solvent assisted grinding. These ligands, in-situ with nickel metal salts, showed good catalytic activity for asymmetric Diels-Alder reactions. The third ligand type studied was chiral acid-functionalized Schiff-base ligands. These were synthesized by the condensation of 3-formyl-5-methyl salicylic acid and (1R,2R)-cyclobutyldiamine. With this type of ligand, there is possibility of producing both mono and dinuclear metal complexes. In our studies, we were only able to synthesize mononuclear complexs. These were tested as catalysts for asymmetric direct Mannich-type reaction, but were found to be ineffective.
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Kurahashi, Takuya; Fujii, Hiroshi
2011-06-01
Ligand radicals from salen complexes are unique mixed-valence compounds in which a phenoxyl radical is electronically linked to a remote phenolate via a neighboring redox-active metal ion, providing an opportunity to study electron transfer from a phenolate to a phenoxyl radical mediated by a redox-active metal ion as a bridge. We herein synthesize one-electron-oxidized products from electronically diverse manganese(III) salen complexes in which the locus of oxidation is shown to be ligand-centered, not metal-centered, affording manganese(III)-phenoxyl radical species. The key point in the present study is an unambiguous assignment of intervalence charge transfer bands by using nonsymmetrical salen complexes, which enables us to obtain otherwise inaccessible insight into the mixed-valence property. A d(4) high-spin manganese(III) ion forms a Robin-Day class II mixed-valence system, in which electron transfer is occurring between the localized phenoxyl radical and the phenolate. This is in clear contrast to a d(8) low-spin nickel(II) ion with the same salen ligand, which induces a delocalized radical (Robin-Day class III) over the two phenolate rings, as previously reported by others. The present findings point to a fascinating possibility that electron transfer could be drastically modulated by exchanging the metal ion that bridges the two redox centers. © 2011 American Chemical Society
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Specklin, David; Fliedel, Christophe; Hild, Frédéric; Mameri, Samir; Karmazin, Lydia; Bailly, Corinne; Dagorne, Samuel
2017-10-03
A series of mononuclear salen-supported gallium amido/alkoxide derivatives were prepared and structurally characterized and subsequently used as initiators in rac-lactide ring-opening polymerisation (ROP). The reaction of variously substituted salen ligands (1a-1f) with 0.5 equiv. of Ga 2 (NMe 2 ) 6 allowed the isolation of the corresponding (salen)Ga-NMe 2 chelates (2b-2d, 2f) via an amine elimination route, as poorly soluble compounds in common solvents. The (salen)Ga-OBn derivatives (3a-3e) may be readily accessed by an amine-elimination/alcoholysis sequence and the molecular structures of 3a, 3d and 3e were confirmed through X-ray crystallography diffraction analysis. The present (salen)Ga-X species may effectively mediate the iso-selective ROP of rac-LA in a controlled manner (P m up to 0.77 using a 1/1 2f/BnOH mixture as ROP initiator), with a ROP activity greatly dependent upon steric hindrance and geometrical constraints imposed by the variously substituted salen ligands. Based on the present study, salen ligands with limited steric hindrance and a certain degree of flexibility appear best suited for iso-selective ROP by (salen)Ga chelates. The salen-gallium complex 3a is also effective for the controlled ROP of ε-caprolactone (CL) and the production of PCL-b-PLA copolymers.
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Principal component analysis of Mn(salen) catalysts.
Teixeira, Filipe; Mosquera, Ricardo A; Melo, André; Freire, Cristina; Cordeiro, M Natália D S
2014-12-14
The theoretical study of Mn(salen) catalysts has been traditionally performed under the assumption that Mn(acacen') (acacen' = 3,3'-(ethane-1,2-diylbis(azanylylidene))bis(prop-1-en-olate)) is an appropriate surrogate for the larger Mn(salen) complexes. In this work, the geometry and the electronic structure of several Mn(salen) and Mn(acacen') model complexes were studied using Density Functional Theory (DFT) at diverse levels of approximation, with the aim of understanding the effects of truncation, metal oxidation, axial coordination, substitution on the aromatic rings of the salen ligand and chirality of the diimine bridge, as well as the choice of the density functional and basis set. To achieve this goal, geometric and structural data, obtained from these calculations, were subjected to Principal Component Analysis (PCA) and PCA with orthogonal rotation of the components (rPCA). The results show the choice of basis set to be of paramount importance, accounting for up to 30% of the variance in the data, while the differences between salen and acacen' complexes account for about 9% of the variance in the data, and are mostly related to the conformation of the salen/acacen' ligand around the metal centre. Variations in the spin state and oxidation state of the metal centre also account for large fractions of the total variance (up to 10% and 9%, respectively). Other effects, such as the nature of the diimine bridge or the presence of an alkyl substituent in the 3,3 and 5,5 positions of the aldehyde moiety, were found to be less important in terms of explaining the variance within the data set. A matrix of discriminants was compiled using the loadings of the principal and rotated components that best performed in the classification of the entries in the data. The scores obtained from its application to the data set were used as independent variables for devising linear models of different properties, with satisfactory prediction capabilities.
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Kasumov, Veli T; Yerli, Yusuf; Kutluay, Aysegul; Aslanoglu, Mehmet
2013-03-01
New salen type ligands, N,N'-bis(X-3-tert-butylsalicylidene)-4,4'-ethylenedianiline [(X=H (1), 5-tert-butyl (2)] and N,N'-bis(X-3-tert-butylsalicylidene)-4,4'-amidedianiline [X=H (3), 5-tert (4)] and their copper(II) complexes 5-8, have been synthesized. Their spectroscopic (IR, (1)H NMR, UV/vis, ESR) properties, as well as magnetic and redox-reactivity behavior are reported. IR spectra of 7 and 8 indicate the coordination of amide oxygen atoms of 3 and 4 ligands to Cu(II). The solid state ESR spectra of 5-8 exhibits less informative exchange narrowed isotropic or anisotropic signals with weak unresolved low field patterns. The magnetic moments of 5 (2.92 μ(B) per Cu(II)) and 6 (2.79 μ(B) per Cu(II)) are unusual for copper(II) complexes and considerably higher than those for complexes 7 and 8. Cryogenic measurements (300-10 K) show weak antiferromagnetic exchange interactions between the copper(II) centers in complexes 6 and 8. The results of electrochemical and chemical redox-reactivity studies are discussed. Copyright © 2012 Elsevier B.V. All rights reserved.
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Miranda, James A; Wade, Carolyn J; Little, R Daniel
2005-09-30
[Chemical reaction: See text] We describe efforts to achieve the electroreductive cyclization (ERC) and the electrohydrocyclization (EHC) reactions using catalytic nickel(II) salen as a mediator. While nickel(II) salen proved effective, the analogous cobalt complex as well as nickel(II) cyclam were not. The transformations were achieved in yields ranging from 60 to 94% using either a mercury pool or an environmentally preferable reticulated vitreous carbon (RVC) cathode. These examples represent the first instances wherein a nickel salen complex has been used in this manner. Clear differences between the voltammetric behavior of the ERC and EHC substrates were observed. The bisenoate 14, for example, displays a substantially larger catalytic current. When the structurally modified mediator 31 was used, the electron-transfer pathway shuts down. Instead, the reduced form of 31 behaves as an electrogenerated base, leading to the formation of the intramolecular Michael adduct 23. Presumably, the methyl groups of the modified ligand diminish the ability of the reduced form of the complex to serve as a nucleophile but not as a base. Aldehyde 23 was also characterized as a side product of the nickel(II) salen mediated electroreductive cyclization of 11. Given that it is absent from nonmediated processes, its formation is linked to the presence of the mediator. To account for the results, we favor the existence of a mechanistic continuum involving an equilibrium between nickel(II) salen (15) and two reduced forms, one being the metal-centered species 16, the other being a ligand-centered species 17. We postulate that one form may be more prominently involved with the chemistry than another, depending upon the electronic properties/requirements of the substrate, and suggest that the equilibrium will shift to accommodate the need. Thus, for a hard electrophile like an alkyl halide, the properties of 16 ought to dominate, whereas 17 ought to predominate as the reactive
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C-N bond cleavage of anilines by a (salen)ruthenium(VI) nitrido complex.
Man, Wai-Lun; Xie, Jianhui; Pan, Yi; Lam, William W Y; Kwong, Hoi-Ki; Ip, Kwok-Wa; Yiu, Shek-Man; Lau, Kai-Chung; Lau, Tai-Chu
2013-04-17
We report experimental and computational studies of the facile oxidative C-N bond cleavage of anilines by a (salen)ruthenium(VI) nitrido complex. We provide evidence that the initial step involves nucleophilic attack of aniline at the nitrido ligand of the ruthenium complex, which is followed by proton and electron transfer to afford a (salen)ruthenium(II) diazonium intermediate. This intermediate then undergoes unimolecular decomposition to generate benzene and N2.
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Man, Wai-Lun; Kwong, Hoi-Ki; Lam, William W Y; Xiang, Jing; Wong, Tsz-Wing; Lam, Wing-Hong; Wong, Wing-Tak; Peng, Shie-Ming; Lau, Tai-Chu
2008-07-07
Reaction of [Ru (VI)(N)(L (1))(MeOH)] (+) (L (1) = N, N'-bis(salicylidene)- o-cyclohexylenediamine dianion) with excess pyridine in CH 3CN produces [Ru (III)(L (1))(py) 2] (+) and N 2. The proposed mechanism involves initial equilibrium formation of [Ru (VI)(N)(L (1))(py)] (+), which undergoes rapid N...N coupling to produce [(py)(L (1))Ru (III) N N-Ru (III)(L (1))(py)] (2+); this is followed by pyridine substituion to give the final product. This ligand-induced N...N coupling of Ru (VI)N is utilized in the preparation of a series of new ruthenium(III) salen complexes, [Ru (III)(L)(X) 2] (+/-) (L = salen ligand; X = H 2O, 1-MeIm, py, Me 2SO, PhNH 2, ( t )BuNH 2, Cl (-) or CN (-)). The structures of [Ru (III)(L (1))(NH 2Ph) 2](PF 6) ( 6), K[Ru (III)(L (1))(CN) 2] ( 9), [Ru (III)(L (2))(NCCH 3) 2][Au (I)(CN) 2] ( 11) (L (2) = N, N'-bis(salicylidene)- o-phenylenediamine dianion) and [N ( n )Bu 4][Ru (III)(L (3))Cl 2] ( 12) (L (3) = N, N'-bis(salicylidene)ethylenediamine dianion) have been determined by X-ray crystallography.
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Electron transfer reaction of oxo(salen)chromium(V) ion with anilines.
Premsingh, Sundarsingh; Venkataramanan, Natarajan Sathiyamoorthy; Rajagopal, Seenivasan; Mirza, Shama P; Vairamani, Mariappanadar; Rao, P Sambasiva; Velavan, K
2004-09-06
The kinetics of oxidation of 16 meta-, ortho-, and para-substituted anilines with nine oxo(salen)chromium(V) ions have been studied by spectrophotometric, ESIMS, and EPR techniques. During the course of the reaction, two new peaks with lambda(max) at 470 and 730 nm appear in the absorption spectrum, and these peaks are due to the formation of emeraldine forms of oligomers of aniline supported by the ESIMS peaks with m/z values 274 and 365 (for the trimer and tetramer of aniline). The rate of the reaction is highly sensitive to the change of substituents in the aryl moiety of aniline and in the salen ligand of chromium(V) complexes. Application of the Hammett equation to analyze kinetic data yields a rho value of -3.8 for the substituent variation in aniline and +2.2 for the substituent variation in the salen ligand of the metal complex. On the basis of the spectral, kinetic, and product analysis studies, a mechanism involving an electron transfer from the nitrogen of aniline to the metal complex in the rate controlling step has been proposed. The Marcus equation has been successfully applied to this system, and the calculated values are compliant with the measured values.
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NASA Astrophysics Data System (ADS)
Wu, Qiong; Wu, Wei; Wu, Yongmei; Li, Weili; Qiao, Yongfeng; Wang, Ying; Wang, Baoling
2018-04-01
By the reaction of manganese-Schiff-base complexes with penta-anionic Anderson heteropolyanion, a new supramolecular architecture [Mn2(Salen)2(H2O)2][Mn(Salen)(H2O)2]2Na[IMo6O24]·8H2O (1) (salen = N,N‧-ethylene-bis (salicylideneiminate) has been isolated. Compound 1 was characterized by the single-crystal X-ray diffraction, elemental, IR and thermal gravimetric analyses. Structural analysis reveals that the unit cell simultaneously contains MnIII-Salen dimer and monomer cation fragments, for which the Anderson-type polyanions serve as counter anions. In the packing arrangement, all the MnIII dimers are well separated by polyoxometalate units and form tertiary structure together with MnIII monomers. Interestingly, different from the previous work, in the exact same reaction conditions, we are able to template MnIII-Salen complexes into different configurations by varying the charge state of polyanions. Besides, the magnetic properties of 1 were also examined by using both dc and ac magnetic field of the superconducting quantum interference devices. Most importantly, our fitting of the experimental data to a Heisenberg-type spin model shows that there exists a ferromagnetic exchange interaction ∼5 K between the spins (S = 2) on MnIII in the dimer, while antiferromagnetic ones exist among monomers and dimer (∼2 K). This meta-magnetic state could induce a slight spin frustration at low temperature, which would in turn affect the magnetic behavior. In addition, our ac field measurement of the susceptibilities suggests a typical signature for a single-molecule magnet.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Szajna-Fuller, Ewa; Huang, Yulin; Rapp, Jennifer L.
2009-03-09
A comparative study of catalytic activity under homogeneous and heterogeneous conditions was carried out using the (salen)Cr{sup III}-catalyzed oxidation of tetramethylbenzidine (TMB) with iodosobenzene as a model reaction. Amine-functionalized mesoporous silica nanoparticles (MSN) were synthesized in a co-condensation reaction and functionalized with salen via a covalent Si-C bond. A Cr(III) complex of this supported ligand, MSN-(salen)Cr{sup III}, was prepared and characterized. Data from powder XRD, BET isotherms and BJH pore size distribution all showed that MSN-(salen)Cr{sup III} still had the typical MSN high surface area, narrow pore size distribution, and ordered hexagonal pore structure, which were further confirmed by transmissionmore » electron microscopy (TEM) images. {sup 13}C and {sup 29}Si solid-state NMR data provided structural information about the catalyst and verified successful functionalization of the salen ligand and coordination to Cr(III). No unreacted salen or Cr(III) were observed. The loadings of salen and salen-Cr{sup III} complex were determined via TGA and EDX, respectively. Both measurements indicated that approximately 0.5 mmol/g of catalyst was loaded on the surface of MSN. The oxidation of TMB with iodosobenzene using MSN-(salen)Cr{sup III} as a heterogeneous catalyst exhibited both similarities and differences with the analogous homogeneous reaction using (salen)Cr{sup III}(H{sub 2}O){sup +} as a catalyst in aqueous acetonitrile. In the presence of 0.10 M HClO{sub 4}, the two catalytic reactions proceeded at similar rates and generated the doubly oxidized product TMB{sup 2+}. In the absence of acid, the radical cation TMB{sup +} was produced. The kinetics of the heterogeneous reaction in the absence of added acid responded to concentrations of all three reagents, i.e. (salen)Cr{sup III}, TMB, and PhIO.« less
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Song, Jintong; Wang, Man; Zhou, Xiangge; Xiang, Haifeng
2018-05-17
A series of chiral and helical Pt II -Salen complexes with 1,1'-binaphthyl linkers were synthesized and characterized. Owing to the restriction of intramolecular motions of central 1,1'-binaphthyls, the complexes exhibit unusual near-infrared aggregation-induced phosphorescence (AIP). The (R)/(S) enantiopure complexes were characterized by X-ray diffraction, circular dichroism spectra, time-dependent density functional theory calculations, and circularly polarized luminescence (CPL). The present work explores the use of tetradentate ligands that can be easily prepared from commercially available enantiopure compounds, and the subsequent preparation of stable CPL-active square planar Pt II complexes with AIP effect that may have interest in many applications. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Brown, M. Kevin; Blewett, Megan M.; Colombe, James R.; Corey, E. J.
2010-01-01
The experiments described here clarify the mechanism and origin of the enantioselectivity of the oxidation of racemic secondary alcohols catalyzed by chiral Mn(III)–salen complexes using HOBr, Br2/H2O/KOAc or PhI(OAc)2/H2O/KBr as a stoichiometric oxidant. Key points of the proposed pathway include (1) the formation of a Mn(V)–salen dibromide, (2) its subsequent reaction with the alcohol to give an alkoxy-Mn(V) species, and (3) carbonyl-forming elimination to produce the ketone via a highly organized transition state with intramolecular transfer of hydrogen from carbon to an oxygen of the salen ligand. PMID:20666410
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NASA Astrophysics Data System (ADS)
Li, F. H.; Bi, H.; Huang, D. X.; Zhang, M.; Song, Y. B.
2018-01-01
Co(II), Mn(II), Cu(II) and Cr(III) salen type complexes were synthesized in situ in Y zeolite by the reaction of ion-exchanged metal ions with the flexible ligand molecules that had diffused into the cavities. Data of characterization indicates the formation of metal salen complexes in the pores without affecting the zeolite framework structure, the absence of any extraneous species and the geometry of encapsulated complexes. The catalytic activity results show that Cosalcyen Y exhibited higher catalytic activity in the water phase selective oxidation of benzyl alcohol, which could be attributed to their geometry and the steric environment of the metal actives sites.
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Ford, David D.; Nielsen, Lars P. C.; Zuend, Stephan J.; Jacobsen, Eric N.
2013-01-01
In the (salen)Co(III)-catalyzed hydrolytic kinetic resolution (HKR) of terminal epoxides, the rate- and stereoselectivity-determining epoxide ring-opening step occurs by a cooperative bimetallic mechanism with one Co(III) complex acting as a Lewis acid and another serving to deliver the hydroxide nucleophile. In this paper, we analyze the basis for the extraordinarily high stereoselectivity and broad substrate scope observed in the HKR. We demonstrate that the stereochemistry of each of the two (salen)Co(III) complexes in the rate-determining transition structure is important for productive catalysis: a measurable rate of hydrolysis occurs only if the absolute stereochemistry of each of these (salen)Co(III) complexes is the same. Experimental and computational studies provide strong evidence that stereochemical communication in the HKR is mediated by the stepped conformation of the salen ligand, and not the shape of the chiral diamine backbone of the ligand. A detailed computational analysis reveals that the epoxide binds the Lewis acidic Co(III) complex in a well-defined geometry imposed by stereoelectronic, rather than steric effects. This insight serves as the basis of a complete stereochemical and transition structure model that sheds light on the reasons for the broad substrate generality of the HKR. PMID:24041239
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Ford, David D; Nielsen, Lars P C; Zuend, Stephan J; Musgrave, Charles B; Jacobsen, Eric N
2013-10-16
In the (salen)Co(III)-catalyzed hydrolytic kinetic resolution (HKR) of terminal epoxides, the rate- and stereoselectivity-determining epoxide ring-opening step occurs by a cooperative bimetallic mechanism with one Co(III) complex acting as a Lewis acid and another serving to deliver the hydroxide nucleophile. In this paper, we analyze the basis for the extraordinarily high stereoselectivity and broad substrate scope observed in the HKR. We demonstrate that the stereochemistry of each of the two (salen)Co(III) complexes in the rate-determining transition structure is important for productive catalysis: a measurable rate of hydrolysis occurs only if the absolute stereochemistry of each of these (salen)Co(III) complexes is the same. Experimental and computational studies provide strong evidence that stereochemical communication in the HKR is mediated by the stepped conformation of the salen ligand, and not the shape of the chiral diamine backbone of the ligand. A detailed computational analysis reveals that the epoxide binds the Lewis acidic Co(III) complex in a well-defined geometry imposed by stereoelectronic rather than steric effects. This insight serves as the basis of a complete stereochemical and transition structure model that sheds light on the reasons for the broad substrate generality of the HKR.
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NASA Astrophysics Data System (ADS)
Ghaffari, Abolfazl; Behzad, Mahdi; Pooyan, Mahsa; Amiri Rudbari, Hadi; Bruno, Giuseppe
2014-04-01
Three new nickel(II) complexes of a series of methoxy substituted salen type Schiff base ligands were synthesized and characterized by IR, UV-Vis and 1H NMR spectroscopy and elemental analysis. The ligands were synthesized from the condensation of meso-1,2-diphenyl-1,2-ethylenediamine with n-methoxysalicylaldehyde (n = 3, 4 and 5). Crystal structures of these complexes were determined. Electrochemical behavior of the complexes was studied by means of cyclic voltammetry in DMSO solutions. Catalytic performance of the complexes was studied in the epoxidation of cyclooctene using tert-butylhydroperoxide (TBHP) as oxidant under various conditions to find the optimum operating parameters. Low catalytic activity with moderate epoxide selectivity was observed in in-solvent conditions but in the solvent-free conditions, enhanced catalytic activity with high epoxide selectivity was achieved.
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Rashid, Zahra; Ghahremanzadeh, Ramin; Nejadmoghaddam, Mohammad-Reza; Nazari, Mahboobeh; Shokri, Mohammad-Reza; Naeimi, Hossein; Zarnani, Amir-Hassan
2017-03-24
In this research, a simple, efficient, inexpensive, rapid and high yield method for the purification of 6×histidine-tagged recombinant protein was developed. For this purpose, manganese ferrite magnetic nanoparticles (MNPs) were synthesized through a co-precipitation method and then they were conveniently surface-modified with tetraethyl orthosilicate (TEOS) in order to prevent oxidation and form high density of hydroxyl groups. Next, the salen ligand was prepared from condensation reaction of salicylaldehyde and 3-aminopropyl (trimethoxy) silane (APTMS) in 1:1 molar ratio; followed by complexation with Ni(OAc) 2 .4H 2 O. Finally, the prepared Ni(II)-salen complex conjugated to silica coated MNPs and MnFe 2 O 4 @SiO 2 @Ni-Salen complex nanoparticles were obtained. The functionalized nanoparticles were spherical with an average diameter around 70nm. The obtained MNPs had a saturation magnetization about 54 emu/g and had super paramagnetic character. These MNPs were used efficiently to enrich recombinant histidine-tagged (His-tagged) protein-A from bacterial cell lysate. In about 45min, highly pure His-tagged recombinant protein was obtained, as judged by SDS-PAGE analysis and silver staining. The amount of target protein in flow through and washing fractions was minimal denoting the high efficiency of purification process. The average capacity of the matrix was found to be high and about 180±15mgg -1 (protein/MnFe 2 O 4 @SiO 2 @Ni-Salen complex). Collectively, purification process with MnFe 2 O 4 @SiO 2 @Ni-Salen complex nanoparticles is rapid, efficient, selective and whole purification can be carried out in only a single tube without the need for expensive systems. Copyright © 2017 Elsevier B.V. All rights reserved.
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Man, Wai-Lun; Lam, William W Y; Kwong, Hoi-Ki; Peng, Shie-Ming; Wong, Wing-Tak; Lau, Tai-Chu
2010-01-04
The reaction of [Ru(VI)(N)(L)(MeOH)](PF(6)) [1; L = N,N'-bis(salicylidene)-o-cyclohexyldiamine dianion] with a stoichiometric amount of RSH in CH(3)CN gives the corresponding (salen)ruthenium(IV) sulfilamido species [Ru(IV){N(H)SR}(L)(NCCH(3))](PF(6)) (2a, R = (t)Bu; 2b, R = Ph). Metathesis of 2a with NaN(3) in methanol affords [Ru(IV){N(H)S(t)Bu}(L)(N(3))] (2c). 2a undergoes further reaction with 1 equiv of RSH to afford a (salen)ruthenium(III) sulfilamine species, [Ru(III){N(H)(2)S(t)Bu}(L)(NCCH(3))](PF(6)) (3). On the other hand, 2b reacts with 2 equiv of PhSH to give a (salen)ruthenium(III) ammine species [Ru(III)(NH(3))(L)(NCCH(3))](PF(6)) (4); this species can also be prepared by treatment of 1 with 3 equiv of PhSH. The X-ray structures of 2c and 4 have been determined. Kinetic studies of the reaction of 1 with excess RSH indicate the following schemes: 1 --> 2a --> 3 (R = (t)Bu), 1 --> 2b --> 4 (R = Ph). The conversion of 1 to 2 probably involves nucleophilic attack of RSH at the nitrido ligand, followed by a proton shift. The conversions of 2a to 3 and 2b to 4 are proposed to involve rate-limiting H-atom abstraction from RSH by 2a or 2b. 2a and 2b are also able to abstract H atoms from hydrocarbons with weak C-H bonds. These reactions occur with large deuterium isotope effects; the kinetic isotope effect values for the oxidation of 9,10-dihydroanthracene, 1,4-cyclohexadiene, and fluorene by 2a are 51, 56, and 11, respectively.
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Tang, Xiaoshuang; Jia, Jing; Li, Feng; Liu, Wei; Yang, Chao; Jin, Bin; Shi, Qi; Wang, Xinyang; He, Dalin; Guo, Peng
2017-01-01
Currently only docetaxel has been approved to be used in the chemotherapy of prostate cancer and new drugs are urgent need. Salen-Mn is a novel type of synthetic reagent bionic and exerts remarkable anticancer activities. However, the effect of Salen-Mn on human prostate cancer has not been elucidated yet. In this study, we found that treatment of PC-3 and DU145 human prostate cancer cells with Salen-Mn inhibited cell growth in dose and time dependent manner. Moreover, Salen-Mn induced cell apoptosis, and increased the expression of apoptotic proteins, such as cleaved caspase-3, cleaved PARP, and Bax, in PC-3 and DU145 prostate cancer cells. Furthermore, we found that Salen-Mn induced expression of LC3-I/II, which is protein marker of cell autophagy, in both dose and time dependent manners; in addition, Salen-Mn increased the phosphorylation of AMPK, suggesting that Salen-Mn increase cell autophagy through activating AMPK pathway. On the other hand, when PC-3 and DU145 cells were treated with Salen-Mn and 3-MA, an inhibitor of cell autophagy, the inhibitory effect of Salen-Mn on cell growth and the induction of apoptotic proteins were decreased. In addition, we found that Salen-Mn inhibited the growth of PC-3 cell xenografts in nude mice. In summary, our results indicate that Salen-Mn suppresses cell growth through inducing AMPK activity and autophagic cell death related cell apoptosis in prostate cancer cells and suggest that Salen-Mn and its derivatives could be new options for the chemical therapeutics in the treatment of prostate cancer. PMID:29156794
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Spectroscopic, thermal analysis and DFT computational studies of salen-type Schiff base complexes.
Ebrahimi, Hossein Pasha; Hadi, Jabbar S; Abdulnabi, Zuhair A; Bolandnazar, Zeinab
2014-01-03
A new series of metal(II) complexes of Co(II), Ni(II), Cu(II), Zn(II), and Pb(II) have been synthesized from a salen-type Schiff base ligand derived from o-vanillin and 4-methyl-1,2-phenylenediamine and characterized by elemental analysis, spectral (IR, UV-Vis, (1)H NMR, (13)C NMR and EI-mass), molar conductance measurements and thermal analysis techniques. Coats-Redfern method has been utilized to calculate the kinetic and thermodynamic parameters of the metal complexes. The molecular geometry, Mulliken atomic charges of the studied compounds were investigated theoretically by performing density functional theory (DFT) to access reliable results to the experimental values. The theoretical (13)C chemical shift results of the studied compounds have been calculated at the B3LYP, PBEPBE and PW91PW91 methods and standard 6-311+G(d,p) basis set starting from optimized geometry. The comparison of the results indicates that B3LYP/6-311+G(d,p) yields good agreement with the observed chemical shifts. The measured low molar conductance values in DMF indicate that the metal complexes are non-electrolytes. The spectral and thermal analysis reveals that all complexes have octahedral geometry except Cu(II) complex which can attain the square planner arrangement. The presence of lattice and coordinated water molecules are indicated by thermograms of the complexes. The thermogravimetric (TG/DTG) analyses confirm high stability for all complexes followed by thermal decomposition in different steps. Copyright © 2013 Elsevier B.V. All rights reserved.
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Paramagnetic Europium Salen Complex and Sickle-Cell Anemia
NASA Astrophysics Data System (ADS)
Wynter, Clive I.; Ryan, D. H.; May, Leopold; Oliver, F. W.; Brown, Eugene; Hoffman, Eugene J.; Bernstein, David
2005-04-01
A new europium salen complex, Eu(salen)2NH4, was synthesized, and its composition was confirmed by chemical analysis and infrared spectroscopy. Further characterization was carried out by 151 Eu Mössbauer spectroscopy and magnetic susceptibility measurements. Mössbauer spectroscopic measurements were made at varying temperatures between 9 K and room temperature and a value of Debye temperature of 133 ±5 K was computed. Both Mössbauer and magnetic susceptibility measurements confirmed the paramagnetic behavior of this complex and the trivalent state of the europium ion. In view of the fact that the "odd" paramagnetic molecule NO has been shown to reverse sickling of red blood cells in sickle cell anemia, the interaction between the paramagnetic europium salen complex and sickle cells was examined after incubation with this europium complex and shown to have similar effects.
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Nielsen, Lars P. C.; Zuend, Stephan J.; Ford, David D.; Jacobsen, Eric N.
2012-01-01
The (salen)Co(III)-catalyzed hydrolytic kinetic resolution (HKR) of terminal epoxides is a bimetallic process with a rate controlled by partitioning between a nucleophilic (salen)Co–OH catalyst and a Lewis acidic (salen)Co–X catalyst. The commonly used (salen)Co–OAc and (salen)Co–Cl precatalysts undergo complete and irreversible counterion addition to epoxide during the course of the epoxide hydrolysis reaction, resulting in quantitative formation of weakly Lewis acidic (salen)Co–OH, and severely diminished reaction rates in the late stages of HKR reactions. In contrast, (salen)Co–OTs maintains high reactivity over the entire course of HKR reactions. We describe here an investigation of catalyst partitioning with different (salen)Co–X precatalysts, and demonstrate that counterion addition to epoxide is reversible in the case of the (salen)Co–OTs. This reversible counterion addition results in stable partitioning between nucleophilic and Lewis acidic catalyst species, allowing highly efficient catalysis throughout the course of the HKR reaction. PMID:22292515
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Nielsen, Lars P C; Zuend, Stephan J; Ford, David D; Jacobsen, Eric N
2012-03-02
The (salen)Co(III)-catalyzed hydrolytic kinetic resolution (HKR) of terminal epoxides is a bimetallic process with a rate controlled by partitioning between a nucleophilic (salen)Co-OH catalyst and a Lewis acidic (salen)Co-X catalyst. The commonly used (salen)Co-OAc and (salen)Co-Cl precatalysts undergo complete and irreversible counterion addition to epoxide during the course of the epoxide hydrolysis reaction, resulting in quantitative formation of weakly Lewis acidic (salen)Co-OH and severely diminished reaction rates in the late stages of HKR reactions. In contrast, (salen)Co-OTs maintains high reactivity over the entire course of HKR reactions. We describe here an investigation of catalyst partitioning with different (salen)Co-X precatalysts and demonstrate that counterion addition to epoxide is reversible in the case of the (salen)Co-OTs. This reversible counterion addition results in stable partitioning between nucleophilic and Lewis acidic catalyst species, allowing highly efficient catalysis throughout the course of the HKR reaction.
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Alborés, Pablo; Seeman, Johanna; Rentschler, Eva
2009-10-07
The synthesis, crystal structure, and magneto-chemical characterization of two new unprecedented -phenoxo--carboxylato heterodinuclear complexes based on the Cr(salen) moiety (salen = N,N-bis(salicylidene)ethylenediamine), [MII(O2C(CH3)3)(OH2)2(mu-O2C(CH3)3)(-salen)CrIII(O2C(CH3)3)], M = Ni (2), Co(3) are reported. The dinuclear complexes were obtained starting from the mononuclear trans-[Cr(salen)(CN)2]PPh4 (1), whose crystal structure is also reported. They show a trans arrangement of the Cr(salen) unit, bridging through the phenolate O atoms to a second metal center. An additional 2-O2-carboxylato bridge and a further monodentating carboxylate ligand complete the roughly octahedral Cr(III) coordination sphere. The highly distorted octahedral M(II) coordination environment is completed by two coordinated water molecules and an additional monodentating carboxylate. Variable-temperature solid-state DC magnetization studies were carried out in the 2.0-300 K range. Ferromagnetic isotropic pairwise exchange parameters were found with values of J = 4.1 cm-1 (2) and J = 2.1 cm-1 (3). Additionally, for complex 3, a ZFS parameter, D, was employed to properly fit the experimental data. Magnetization (M) vs. field (H) and temperature (T) data further support the presence of this anisotropic component and confirm ground states S = 5/2 and S = 3 for 2 and 3, respectively. Broken symmetry DFT calculations properly reproduce the experimental J values supporting the ferromagnetic exchange interaction experimentally observed. No out of phase susceptibility signal was observed in 0 DC magnetic field for both complexes. However, in the case of complex 3 a non-zero is observed when a small external field is applied below 3 K, suggesting slow relaxation of the magnetization which at 0 DC field is suppressed, probably due to efficient tunnelling relaxation pathways. The low symmetry of the Co(II) site in complex 3 may lead to the presence of transversal anisotropic components which
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Salen complexes with dianionic counterions
Job, Gabriel E.; Farmer, Jay J.; Cherian, Anna E.
2016-08-02
The present invention describes metal salen complexes having dianionic counterions. Such complexes can be readily precipitated and provide an economical method for the purification and isolation of the complexes, and are useful to prepare novel polymer compositions.
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Induction of apoptosis by Fe(salen)Cl through caspase-dependent pathway specifically in tumor cells.
Pradhan, Nitika; Pratheek, B M; Garai, Antara; Kumar, Ashutosh; Meena, Vikram S; Ghosh, Shyamasree; Singh, Sujay; Kumari, Shikha; Chandrashekar, T K; Goswami, Chandan; Chattopadhyay, Subhasis; Kar, Sanjib; Maiti, Prasanta K
2014-10-01
Iron-based compounds possess the capability of inducing cell death due to their reactivity with oxidant molecules, but their specificity towards cancer cells and the mechanism of action are hitherto less investigated. A Fe(salen)Cl derivative has been synthesized that remains active in monomer form. The efficacy of this compound as an anti-tumor agent has been investigated in mouse and human leukemia cell lines. Fe(salen)Cl induces cell death specifically in tumor cells and not in primary cells. Mouse and human T-cell leukemia cell lines, EL4 and Jurkat cells are found to be susceptible to Fe(salen)Cl and undergo apoptosis, but normal mouse spleen cells and human peripheral blood mononuclear cells (PBMC) remain largely unaffected by Fe(salen)Cl. Fe(salen)Cl treated tumor cells show significantly higher expression level of cytochrome c that might have triggered the cascade of reactions leading to apoptosis in cancer cells. A significant loss of mitochondrial membrane potential upon Fe(salen)Cl treatment suggests that Fe(salen)Cl induces apoptosis by disrupting mitochondrial membrane potential and homeostasis, leading to cytotoxity. We also established that apoptosis in the Fe(salen)Cl-treated tumor cells is mediated through caspase-dependent pathway. This is the first report demonstrating that Fe(salen)Cl can specifically target the tumor cells, leaving the primary cells least affected, indicating an excellent potential for this compound to emerge as a next-generation anti-tumor drug. © 2014 International Federation for Cell Biology.
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Man, Wai-Lun; Lam, William W Y; Kwong, Hoi-Ki; Yiu, Shek-Man; Lau, Tai-Chu
2012-09-03
Kinetic and mechanistic studies on the intermolecular activation of strong C-H bonds of alkanes by a (salen)ruthenium(VI) nitride were performed. The initial, rate-limiting step, the hydrogen atom transfer (HAT) from the alkane to Ru(VI)≡N, generates Ru(V)=NH and RC·HCH(2)R. The following steps involve N-rebound and desaturation. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Kar, Paramita; Biswas, Rituparna; Drew, Michael G B; Ida, Yumi; Ishida, Takayuki; Ghosh, Ashutosh
2011-04-07
The preparation, crystal structures and magnetic properties of two new isoelectronic and isomorphous formate- and nitrite-bridged 1D chains of Mn(III)-salen complexes, [Mn(salen)(HCOO)](n) (1) and [Mn(salen)(NO(2))](n) (2), where salen is the dianion of N,N'-bis(salicylidene)-1,2-diaminoethane, are presented. The structures show that the salen ligand coordinates to the four equatorial sites of the metal ion and the formate or nitrite ions coordinate to the axial positions to bridge the Mn(III)-salen units through a syn-antiμ-1κO:2κO' coordination mode. Such a bridging mode is unprecedented in Mn(III) for formate and in any transition metal ion for nitrite. Variable-temperature magnetic susceptibility measurements of complexes 1 and 2 indicate the presence of ferromagnetic exchange interactions with J values of 0.0607 cm(-1) (for 1) and 0.0883 cm(-1) (for 2). The ac measurements indicate negligible frequency dependence for 1 whereas compound 2 exhibits a decrease of χ(ac)' and a concomitant increase of χ(ac)'' on elevating frequency around 2 K. This finding is an indication of slow magnetization reversal characteristic of single-chain magnets or spin-glasses. The μ-nitrito-1κO:2κO' bridge seems to be a potentially superior magnetic coupler to the formate bridge for the construction of single-molecule/-chain magnets as its coupling constant is greater and the χ(ac)' and χ(ac)'' show frequency dependence. © The Royal Society of Chemistry 2011
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Ramgobin, Aditya; Fontaine, Gaëlle; Penverne, Christophe; Bourbigot, Serge
2017-01-01
This study deals with the synthesis and evaluation of salen based derivatives as fire retardants in thermoplastic polyurethane. Salens, hydroxysalens and their first row transition metal complexes (salen-M) were synthesized (Copper, Manganese, Nickel and Zinc). They were then incorporated in thermoplastic polyurethane (TPU) with a loading as low as 10:1 weight ratio. The thermal stability as well as the fire properties of the formulations were evaluated. Thermogravimetric analysis (TGA) showed that different coordination metals on the salen could induce different decomposition pathways when mixed with TPU. The Pyrolysis Combustion Flow Calorimetry (PCFC) results showed that some M-salen have the ability to significantly decrease the peak heat release rate (−61% compared to neat TPU) and total heat released (−63% compared to neat TPU) when formulated at 10:1 wt % ratio in TPU. Mass Loss Cone Calorimetry (MLC) results have shown that some additives (salen-Cu and salen-Mn) exhibit very promising performance and they are good candidates as flame-retardants for TPU. PMID:28773025
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Mir, Jan Mohammad; Jain, N; Jaget, P S; Maurya, R C
2017-09-01
Photodynamic therapy (PDT) is a treatment that uses photosensitizing agents to kill cancer cells. Scientific community has been eager for decades to design an efficient PDT drug. Under such purview, the current report deals with the computational photodynamic behavior of ruthenium(II) nitrosyl complex containing N, N'-salicyldehyde-ethylenediimine (SalenH 2 ), the synthesis and X-ray crystallography of which is already known [Ref. 38,39]. Gaussian 09W software package was employed to carry out the density functional (DFT) studies. DFT calculations with Becke-3-Lee-Yang-Parr (B3LYP)/Los Alamos National Laboratory 2 Double Z (LanL2DZ) specified for Ru atom and B3LYP/6-31G(d,p) combination for all other atoms were used using effective core potential method. Both, the ground and excited states of the complex were evolved. Some known photosensitizers were compared with the target complex. Pthalocyanine and porphyrin derivatives were the compounds selected for the respective comparative study. It is suggested that effective photoactivity was found due to the presence of ruthenium core in the model complex. In addition to the evaluation of theoretical aspects in vitro anticancer aspects against COLO-205 human cancer cells have also been carried out with regard to the complex. More emphasis was laid to extrapolate DFT to depict the chemical power of the target compound to release nitric oxide. A promising visible light triggered nitric oxide releasing power of the compound has been inferred. In vitro antiproliferative studies of [RuCl 3 (PPh 3 ) 3 ] and [Ru(NO)(Salen)(Cl)] have revealed the model complex as an excellent anticancer agent. From IC 50 values of 40.031mg/mL in former and of 9.74mg/mL in latter, it is established that latter bears more anticancer potentiality. From overall study the DFT based structural elucidation and the efficiency of NO, Ru and Salen co-ligands has shown promising drug delivery property and a good candidacy for both chemotherapy as well as
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Digital logic circuit based on two component molecular systems of BSA and salen
NASA Astrophysics Data System (ADS)
Hai-Bin, Lin; Feng, Chen; Hong-Xu, Guo
2018-02-01
A new fluorescent molecular probe 1 was designed and constructed by combining bovine serum albumin (BSA) and N,N‧-bis(salicylidene)ethylenediamine (salen). Stimulated by Zn2 +, tris, or EDTAH2Na2, the distance between BSA and salen was regulated, which was accompanied by an obvious change in the fluorescence intensity at 350 or 445 nm based on Förster resonance energy transfer. Moreover, based on the encoding binary digits in these inputs and outputs applying positive logic conventions, a monomolecular circuit integrating one OR, three NOT, and three YES gates, was successfully achieved.
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Red Luminescent Eu(III) Coordination Bricks Excited on Blue LED Chip.
Koizuka, Toru; Yanagisawa, Kei; Hirai, Yuichi; Kitagawa, Yuichi; Nakanishi, Takayuki; Fushimi, Koji; Hasegawa, Yasuchika
2018-06-18
Three types of red luminescent Eu(III) complexes with Schiff base and hfa ligands (hfa: hexafluoroacetylacetonate), mononuclear [Eu(hfa) 2 (OAc)(salen) 2 ] (OAc: acetate anion, salen: N,N'-bis(salicylidene)ethylenediamine), brick-type [Eu 2 (hfa) 4 (OAc) 2 (salbn) 2 ] (salbn: N,N'-bis(salicylidene)-1,4-butanediamine), and polynuclear [Eu(hfa) 2 (OAc)(salhen)] n (salhen: N,N'-bis(salicylidene)-1,6-hexanediamine) are reported for white light-emitting diode (LED) devices. Among these complexes, brick-type [Eu 2 (hfa) 4 (OAc) 2 (salbn) 2 ] excited by blue light (460 nm) exhibits the photosensitized quantum yield (Φ π-π* = 47%) and remarkably high efficiency of sensitization (η sens = 96%). The efficiency of sensitization is caused by the excited state based on ligand-ligand interaction between the Schiff base and hfa ligands in Eu(III) complexes. To fabricate LED devices, the red luminescent [Eu 2 (hfa) 4 (OAc) 2 (salbn) 2 ] was mounted on an InGaN blue LED chip.
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2016-01-01
Aluminum alkoxide complexes (2) of salen ligands with a three-carbon linker and para substituents having variable electron-withdrawing capabilities (X = NO2, Br, OMe) were prepared, and the kinetics of their ring-opening polymerization (ROP) of ε-caprolactone (CL) were investigated as a function of temperature, with the aim of drawing comparisons to similar systems with two-carbon linkers investigated previously (1). While 1 and 2 exhibit saturation kinetics and similar dependences of their ROP rates on substituents X (invariant Keq, similar Hammett ρ = +1.4(1) and 1.2(1) for k2, respectively), ROP by 2 was significantly faster than for 1. Theoretical calculations confirm that, while the reactant structures differ, the transition state geometries are quite similar, and by analyzing the energetics of the involved distortions accompanying the structural changes, a significant contribution to the basis for the rate differences was identified. Using this knowledge, a simplified computational method for evaluating ligand structural influences on cyclic ester ROP rates is proposed that may have utility for future catalyst design. PMID:26900488
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Zhang, Guangbin; Tang, Yuhai; Sun, Yang; Yu, Hua; Du, Wei; Fu, Qiang
2016-02-01
A water-soluble sulphonato-(salen)manganese(III) complex with excellent catalytic properties was synthesized and demonstrated to greatly enhance the chemiluminescence signal of the hydrogen peroxide - luminol reaction. Coupled with flow-injection technique, a simple and sensitive chemiluminescence method was first developed to detect hydroquinone based on the chemiluminescence system of the hydrogen peroxide-luminol-sulphonato-(salen)manganese(III) complex. Under optimal conditions, the assay exhibited a wide linear range from 0.1 to 10 ng mL(-1) with a detection limit of 0.05 ng mL(-1) for hydroquinone. The method was applied successfully to detect hydroquinone in tap-water and mineral-water, with a sampling frequency of 120 times per hour. The relative standard deviation for determination of hydroquinone was less than 5.6%, and the recoveries ranged from 96.8 to 103.0%. The ultraviolet spectra, chemiluminescence spectra, and the reaction kinetics for the peroxide-luminol-sulphonato-(salen)manganese(III) complex system were employed to study the possible chemiluminescence mechanism. The proposed chemiluminescence analysis technique is rapid and sensitive, with low cost, and could be easily extended and applied to other compounds. Copyright © 2015 John Wiley & Sons, Ltd.
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NASA Astrophysics Data System (ADS)
Azam, Mohammad; Dwivedi, Sourabh; Al-Resayes, Saud I.; Adil, S. F.; Islam, Mohammad Shahidul; Trzesowska-Kruszynska, Agata; Kruszynski, Rafal; Lee, Dong-Ung
2017-02-01
The catalytic property of a mononuclear Cu(II) salen complex in Chan-Lam coupling reaction with phenyl boronic acid at room temperature is reported. The studied complex is found to be potential catalyst in the preparation of carbon-heteroatom bonds with excellent yields. The studied Cu(II) salen complex is monoclinic with cell parameters, a = 9.6807(5) (α 90°), (b = 17.2504(8) (β 112.429 (2), c = 11.1403 (6) (γ = 90°), and has distorted square planar environment around Cu(II) ion. Furthermore, there is no π⋯π interactions in the reported complex due to large distance between the centroid of aromatic rings. In addition, DNA binding study of Cu(II) salen complex by fluorescence and absorption spectroscopy is also reported. Moreover, the reported Cu(II) salen complex exhibits significant anticancer activity against MCF-7 cancer cell lines, and displays potential antimicrobial biofilm activity against P. aeruginosa, suggesting antimicrobial biofilm an important tool for suppression of resistant infections caused by P. aeruginosa.
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Martín, Carmen
2014-01-01
Summary Zn(salen) complexes have been employed as active catalysts for the formation of cyclic carbonates from epoxides and CO2. A series of kinetic experiments was carried out to obtain information about the mechanism for this process catalyzed by these complexes and in particular about the order-dependence in catalyst. A comparative analysis was done between the binary catalyst system Zn(salphen)/NBu4I and a bifunctional system Zn(salpyr)·MeI with a built-in nucleophile. The latter system demonstrates an apparent second-order dependence on the bifunctional catalyst concentration and thus follows a different, bimetallic mechanism as opposed to the binary catalyst that is connected with a first-order dependence on the catalyst concentration and a monometallic mechanism. PMID:25161742
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Pointillart, Fabrice; Bernot, Kevin; Sorace, Lorenzo; Sessoli, Roberta; Gatteschi, Dante
2007-07-07
The reaction between [Ru(salen)(PPh3)Cl] and the 4-pyridyl-substituted nitronyl nitroxide radical (NITpPy) leads to the [Ru(salen)(PPh3)(NITpPy)](ClO4)(H2O)2 complex while the reaction with the azido anion (N3-) leads to the [Ru(salen)(PPh3)(N3)] complex 2 (where salen2- = N,N'-ethan-1,2-diylbis(salicylidenamine) and PPh3 = triphenylphosphine). Both compounds have been characterized by single crystal X-ray diffraction. The two crystal structures are composed by a [Ru(III)(salen)(PPh3)]+ unit where the Ru(III) ion is coordinated to a salen2- ligand and one PPh3 ligand in axial position. In 1 the Ru(III) ion is coordinated to the 4-pyridyl-substituted nitronyl nitroxide radical whereas in 2 the second axial position is occupied by the azido ligand. In both complexes the Ru(III) ions are in the same environment RuO2N3P, in a tetragonally elongated octhaedral geometry. The crystal packing of 1 reveals pi-stacking in pairs. While antiferromagnetic intermolecular interaction (J2 = 5.0 cm(-1)) dominates at low temperatures, ferromagnetic intramolecular interaction (J1 = -9.0 cm(-1)) have been found between the Ru(III) ion and the coordinated NITpPy.
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Prevention of nonalcoholic steatohepatitis in rats by two manganese-salen complexes.
Rezazadeh, Alireza; Yazdanparast, Razieh
2014-01-01
Nonalcoholic steatohepatitis (NASH), a progressive stage of nonalcoholic fatty liver disease (NAFLD), is characterized by steatosis with inflammation. Investigations have suggested that oxidative stress may play an important role in the progress of NAFLD to NASH. To provide further insights into beneficial effects of antioxidants in NASH prevention, we employed two manganese-superoxide dismutase/catalase mimetics, manganese N,N`-bis(salicyldene) ethylene diamine chloride (EUK-8) and manganese-3-methoxy N,N`-bis(salicyldene)ethylenediamine chloride (EUK-134), as two salen representatives and vitamin C as the standard antioxidant. Experimental NASH was induced in Male N-Mary rats by feeding a methionine/choline-deficient (MCD) diet to rats for 10 weeks. The rats (n = 5, 30 mg/kg/day) were randomly assigned to receive vitamin C, EUK-8, EUK-134 or vehicle orally. Administration of salens together with the MCD diet reduced the serum aminotransferases, glutathione transferase and alkaline phosphatase, cholesterol, and LDL contents. In addition, the EUK-8 and EUK-134 improved NASH pathological features in liver of MCD-fed rats. EUK-8 and EUK-134 supplementation reduces NASH-induced abnormalities, pointing out that antioxidant strategy could be beneficial for prevention of NASH.
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Clegg, William; Harrington, Ross W; North, Michael; Villuendas, Pedro
2010-09-17
The combined use of the bimetallic aluminum(salen) complex [Al(salen)](2)O and tetrabutylammonium bromide (or tributylamine) is found to catalyze the reaction between epoxides and carbon disulfide. In most cases, at 50 °C, the reaction produces 1,3-oxathiolane-2-thiones, while at 90 °C, 1,3-dithiolane-2-thiones are the main product. The structure and stereochemistry of three of the 1,3-dithiolane-2-thiones is unambiguously determined by X-ray crystallographic analysis, and this is used to correct errors in the literature concerning the synthesis of cyclic di- and trithiocarbonates. The kinetics of 1,3-oxathiolane-2-thione synthesis are determined, and the resulting rate equation, along with a stereochemical analysis of the reaction and catalyst modification studies, is used to determine a mechanism for the synthesis of 1,3-oxathiolane-2-thiones which contrasts with the mechanism previously determined for cyclic carbonate synthesis using the same bimetallic aluminum(salen) complex.
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Prevention of Nonalcoholic Steatohepatitis in Rats by Two Manganese-Salen Complexes
Rezazadeh, Alireza; Yazdanparast, Razieh
2014-01-01
Background: Nonalcoholic steatohepatitis (NASH), a progressive stage of nonalcoholic fatty liver disease (NAFLD), is characterized by steatosis with inflammation. Investigations have suggested that oxidative stress may play an important role in the progress of NAFLD to NASH. To provide further insights into beneficial effects of antioxidants in NASH prevention, we employed two manganese-superoxide dismutase/catalase mimetics, manganese N,N`-bis(salicyldene) ethylene diamine chloride (EUK-8) and manganese-3-methoxy N,N`-bis(salicyldene)ethylenediamine chloride (EUK-134), as two salen representatives and vitamin C as the standard antioxidant. Methods: Experimental NASH was induced in Male N-Mary rats by feeding a methionine/choline-deficient (MCD) diet to rats for 10 weeks. The rats (n = 5, 30 mg/kg/day) were randomly assigned to receive vitamin C, EUK-8, EUK-134 or vehicle orally. Results: Administration of salens together with the MCD diet reduced the serum aminotransferases, glutathione transferase and alkaline phosphatase, cholesterol, and LDL contents. In addition, the EUK-8 and EUK-134 improved NASH pathological features in liver of MCD-fed rats. Conclusion: EUK-8 and EUK-134 supplementation reduces NASH-induced abnormalities, pointing out that antioxidant strategy could be beneficial for prevention of NASH. PMID:24375162
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Cheng, Jinghui; Gou, Fei; Zhang, Xiaohong; Shen, Guangyu; Zhou, Xiangge; Xiang, Haifeng
2016-09-19
We report a class of multiresponsive colorimetric and fluorescent pH probes based on three different reaction mechanisms including cation exchange, protonation, and hydrolysis reaction of K(I), Ca(II), Zn(II), Cu(II), Al(III), and Pd(II) Salen complexes. Compared with traditional pure organic pH probes, these complex-based pH probes exhibited a much better selectivity due to the shielding function of the filled-in metal ion in the complex. Their pH sensing performances were affected by the ligand structure and the central metal ion. This work is the first report of "off-on-on'-off" colorimetric and fluorescent pH probes that possess three different reaction mechanisms and should inspire the design of multiple-responsive probes for important analytes in biological systems.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Greathouse, Jeffery A.; Boyle, Timothy J.; Kemp, Richard A.
Molecular tracers that can be selectively placed underground and uniquely identified at the surface using simple on-site spectroscopic methods would significantly enhance subsurface fluid monitoring capabilities. To ensure their widespread utility, the solubility of these tracers must be easily tuned to oil- or water-wet conditions as well as reducing or eliminating their propensity to adsorb onto subsurface rock and/or mineral phases. In this work, molecular dynamics simulations were used to investigate the relative solubilities and mineral surface adsorption properties of three candidate tracer compounds comprising Mg–salen derivatives of varying degrees of hydrophilic character. Simulations in water–toluene liquid mixtures indicate thatmore » the partitioning of each Mg–salen compound relative to the interface is strongly influenced by the degree of hydrophobicity of the compound. Simulations of these complexes in fluid-filled mineral nanopores containing neutral (kaolinite) and negatively charged (montmorillonite) mineral surfaces reveal that adsorption tendencies depend upon a variety of parameters, including tracer chemical properties, mineral surface type, and solvent type (water or toluene). Simulation snapshots and averaged density profiles reveal insight into the solvation and adsorption mechanisms that control the partitioning of these complexes in mixed liquid phases and nanopore environments. As a result, this work demonstrates the utility of molecular simulation in the design and screening of molecular tracers for use in subsurface applications.« less
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Greathouse, Jeffery A.; Boyle, Timothy J.; Kemp, Richard A.
2018-04-11
Molecular tracers that can be selectively placed underground and uniquely identified at the surface using simple on-site spectroscopic methods would significantly enhance subsurface fluid monitoring capabilities. To ensure their widespread utility, the solubility of these tracers must be easily tuned to oil- or water-wet conditions as well as reducing or eliminating their propensity to adsorb onto subsurface rock and/or mineral phases. In this work, molecular dynamics simulations were used to investigate the relative solubilities and mineral surface adsorption properties of three candidate tracer compounds comprising Mg–salen derivatives of varying degrees of hydrophilic character. Simulations in water–toluene liquid mixtures indicate thatmore » the partitioning of each Mg–salen compound relative to the interface is strongly influenced by the degree of hydrophobicity of the compound. Simulations of these complexes in fluid-filled mineral nanopores containing neutral (kaolinite) and negatively charged (montmorillonite) mineral surfaces reveal that adsorption tendencies depend upon a variety of parameters, including tracer chemical properties, mineral surface type, and solvent type (water or toluene). Simulation snapshots and averaged density profiles reveal insight into the solvation and adsorption mechanisms that control the partitioning of these complexes in mixed liquid phases and nanopore environments. As a result, this work demonstrates the utility of molecular simulation in the design and screening of molecular tracers for use in subsurface applications.« less
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NASA Astrophysics Data System (ADS)
Salavati-Niasari, Masoud; Bazarganipour, Mehdi
2009-06-01
Hydroxyl functionalized copper(II) Schiff-base, N,N'-bis(4-hydroxysalicylidene)-ethylene-1,2-diaminecopper(II), [Cu((OH) 2-salen)], has been covalently anchored on modified MWCNTs. The new modified MWCNTs ([Cu((OH) 2-salen)]-MWCNTs) have been characterized by TEM, thermal analysis, XRD, XPS, UV-vis, DRS, FT-IR spectroscopy and elemental analysis. The modified copper(II) MWCNTs solid was used to affect the catalytic oxidation of ethylbenzene with tert-butylhydroperoxide as the oxidant at 333 K. The system is truly heterogeneous (no leaching observed) and reusable (no decrease in activity) in three consecutive runs. Acetophenone was the major product though small amounts of o- and p-hydroxyacetophenones were also formed revealing that C-H bond activation takes place both at benzylic and aromatic ring carbon atoms. Ring hydroxylation was more over the "neat" complexes than over the encapsulated complexes.
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Field induced 4f5d [Re(salen)]2O3[Dy(hfac)3(H2O)]2 single molecule magnet.
Pointillart, Fabrice; Bernot, K; Sessoli, R; Gatteschi, D
2010-05-03
The reaction between the mononuclear [ReO(salen)(OMe)] (salen(2-) = N,N'-ethan-1,2-diylbis(salicylidenamine) dianion) and Dy(hfac)(3).2H(2)O (hfac(-) = 1,1,1,5,5,5-hexafluoroacetylacetonate anion) complexes lead to the formation of a compound with the formula {[Re(salen)](2)O(3)[Dy(hfac)(3)(H(2)O)](2)}(CHCl(3))(2)(CH(2)Cl(2))(2) noted (Dy(2)Re(2)). This compound has been characterized by single crystal and powder X-ray diffraction and has been found isostructural to the Y(III) derivative (Y(2)Re(2)) that we previously reported. The cyclic voltammetry demonstrates the redox activity of the system. The characterization of both static and dynamic magnetic properties is reported. Static magnetic data has been analyzed after the cancellation of the crystal field contribution by two different methods. Weak ferromagnetic exchange interactions between the Dy(III) ions are highlighted. The compound Dy(2)Re(2) displays slow relaxation of the magnetization when an external magnetic field is applied. Alternating current susceptibility shows a thermally activated behavior with pre-exponential factors of 7.13 (+/-0.10) x 10(-6) and 5.76 (+/-0.27) x 10(-7) s, and energy barriers of 4.19 (+/-0.02) and 8.52 (+/-0.55) K respectively for low and high temperature regimes.
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Bogaerts, Thomas; Van Yperen-De Deyne, Andy; Liu, Ying-Ya; Lynen, Frederic; Van Speybroeck, Veronique; Van Der Voort, Pascal
2013-09-21
An enantioselective catalyst, consisting of a chiral Mn(III)salen complex entrapped in the MIL-101 metal organic framework, is reported. For the first time, we assemble a robust MOF-cage around a chiral complex. The heterogeneous catalyst shows the same selectivity as the homogeneous complex and is fully recyclable. Theoretical calculations provide insight into this retention of selectivity.
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Raymundo-Pereira, Paulo A; Teixeira, Marcos F S; Fatibello-Filho, Orlando; Dockal, Edward R; Bonifácio, Viviane Gomes; Marcolino, Luiz H
2013-10-01
The preparation and electrochemical characterization of a carbon paste electrode modified with the N,N-ethylene-bis(salicyllideneiminato)oxovanadium (IV) complex ([VO(salen)]) as well as its application for ranitidine determination are described. The electrochemical behavior of the modified electrode for the electroreduction of ranitidine was investigated using cyclic voltammetry, and analytical curves were obtained for ranitidine using linear sweep voltammetry (LSV) under optimized conditions. The best voltammetric response was obtained for an electrode composition of 20% (m/m) [VO(salen)] in the paste, 0.10 mol L(-1) of KCl solution (pH 5.5 adjusted with HCl) as supporting electrolyte and scan rate of 25 mV s(-1). A sensitive linear voltammetric response for ranitidine was obtained in the concentration range from 9.9×10(-5) to 1.0×10(-3) mol L(-1), with a detection limit of 6.6×10(-5) mol L(-1) using linear sweep voltammetry. These results demonstrated the viability of this modified electrode as a sensor for determination, quality control and routine analysis of ranitidine in pharmaceutical formulations. Copyright © 2013. Published by Elsevier B.V.
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The Movable Type Method Applied to Protein-Ligand Binding.
Zheng, Zheng; Ucisik, Melek N; Merz, Kenneth M
2013-12-10
Accurately computing the free energy for biological processes like protein folding or protein-ligand association remains a challenging problem. Both describing the complex intermolecular forces involved and sampling the requisite configuration space make understanding these processes innately difficult. Herein, we address the sampling problem using a novel methodology we term "movable type". Conceptually it can be understood by analogy with the evolution of printing and, hence, the name movable type. For example, a common approach to the study of protein-ligand complexation involves taking a database of intact drug-like molecules and exhaustively docking them into a binding pocket. This is reminiscent of early woodblock printing where each page had to be laboriously created prior to printing a book. However, printing evolved to an approach where a database of symbols (letters, numerals, etc.) was created and then assembled using a movable type system, which allowed for the creation of all possible combinations of symbols on a given page, thereby, revolutionizing the dissemination of knowledge. Our movable type (MT) method involves the identification of all atom pairs seen in protein-ligand complexes and then creating two databases: one with their associated pairwise distant dependent energies and another associated with the probability of how these pairs can combine in terms of bonds, angles, dihedrals and non-bonded interactions. Combining these two databases coupled with the principles of statistical mechanics allows us to accurately estimate binding free energies as well as the pose of a ligand in a receptor. This method, by its mathematical construction, samples all of configuration space of a selected region (the protein active site here) in one shot without resorting to brute force sampling schemes involving Monte Carlo, genetic algorithms or molecular dynamics simulations making the methodology extremely efficient. Importantly, this method explores the free
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Solution structure of the chick TGFbeta type II receptor ligand-binding domain.
Marlow, Michael S; Brown, Christopher B; Barnett, Joey V; Krezel, Andrzej M
2003-02-28
The transforming growth factor beta (TGFbeta) signaling pathway influences cell proliferation, immune responses, and extracellular matrix reorganization throughout the vertebrate life cycle. The signaling cascade is initiated by ligand-binding to its cognate type II receptor. Here, we present the structure of the chick type II TGFbeta receptor determined by solution NMR methods. Distance and angular constraints were derived from 15N and 13C edited NMR experiments. Torsion angle dynamics was used throughout the structure calculations and refinement. The 20 final structures were energy minimized using the generalized Born solvent model. For these 20 structures, the average backbone root-mean-square distance from the average structure is below 0.6A. The overall fold of this 109-residue domain is conserved within the superfamily of these receptors. Chick receptors fully recognize and respond to human TGFbeta ligands despite only 60% identity at the sequence level. Comparison with the human TGFbeta receptor determined by X-ray crystallography reveals different conformations in several regions. Sequence divergence and crystal packing interactions under low pH conditions are likely causes. This solution structure identifies regions were structural changes, however subtle, may occur upon ligand-binding. We also identified two very well conserved molecular surfaces. One was found to bind ligand in the crystallized human TGFbeta3:TGFbeta type II receptor complex. The other, newly identified area can be the interaction site with type I and/or type III receptors of the TGFbeta signaling complex.
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Adam, Waldemar; Roschmann, Konrad J; Saha-Möller, Chantu R; Seebach, Dieter
2002-05-08
cis-Stilbene (1) has been epoxidized by a set of diverse oxygen donors [OxD], catalyzed by the Mn(III)(salen)X complexes 3 (X = Cl, PF(6)), to afford a mixture of cis- and trans-epoxides 2. The cis/trans ratios range from 29:71 (extensive isomerization) to 92:8, which depends both on the oxygen source [OxD] and on the counterion X of the catalyst. When (1 alpha,2 beta,3 alpha)-(2-ethenyl-3-methoxycyclopropyl)-benzene (4) is used as substrate, a mechanistic probe which differentiates between radical and cationic intermediates, no cationic ring-opening products are found in this epoxidation reaction; thus, isomerized epoxide product arises from intermediary radicals. The dependence of the diastereoselectivity on the oxygen source is rationalized in terms of a bifurcation step in the catalytic cycle, in which concerted Lewis-acid-activated oxygen transfer competes with stepwise epoxidation by the established Mn(V)(oxo) species. The experimental counterion effect is attributed to the computationally assessed ligand-dependent reaction profiles and stereoselectivities of the singlet, triplet, and quintet spin states available to the manganese species.
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Canaj, Angelos B; Siczek, Milosz; Otręba, Marta; Lis, Tadeusz; Lorusso, Giulia; Evangelisti, Marco; Milios, Constantinos J
2016-11-22
A solvothermal reaction between Ln(NO 3 ) 3 ·6H 2 O (Ln: Gd, Tb and Dy), 2-hydroxy-1-naphthaldehyde, 2-OH-naphth, and ethylenediamine, en, in MeOH in the presence of a base, NEt 3 , led to the formation of the 1D coordination polymers [Ln(L)(MeO)(MeOH) 0.5 ] n ·MeOH (Ln = Gd (1·MeOH), Tb(2), Dy (3·MeOH); H 2 L = 1,1'-((1E,1'E)-(ethane-1,2-diylbis(azanylylidene))bis(methanylylidene))bis(naphthalen-2-ol), the Schiff-base ligand derived from the condensation of 2-OH-naphth and en), while a similar reaction in an excess of NaN 3 yielded 1D coordination polymers [Ln(L)(N 3 ) 0.75 (MeO) 0.25 (MeOH)] n (Ln = Gd (4), Tb (5), Dy (6)). Finally, upon replacing ethylenediamine with o-phenylenediamine, o-phen, we managed to isolate the discrete dimers [Dy 2 (L') 3 (MeOH)]·2MeOH (7·2MeOH) and [Gd 2 (L') 3 (MeOH)]·2MeOH (8·2MeOH) (H 2 L' = 1,1'-((1E,1'E)-(1,2-phenylenebis(azanylylidene))bis(methanylylidene))bis (naphthalen-2-ol), the Schiff-base ligand from the condensation of 2-OH-naphth and o-phen). Polymers 1-3 describe one-dimensional chains, containing alternating seven- and eight-coordinate Ln III metal centers, polymers 4-6 contain eight-coordinate lanthanide ions, while in both 7 and 8 the two Ln III centers are eight- and seven-coordinate, adopting square antiprismatic and "piano-stool" geometry, respectively. The magnetocaloric properties of the three Gd III analogues were determined from magnetic measurements, yielding the magnetic entropy change -ΔS m = 21.8, 23.0 and 16.0 J kg -1 K -1 at T = 3.0 K on demagnetization of 7 T to 0, for 1, 4 and 8, respectively. The study of the magnetic properties also revealed that all three Dy III analogues (3, 6 and 7) display out-of-phase signals, therefore suggesting slow magnetic relaxation, while such behaviour was not established in the Tb III analogues.
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Tong, Yi-Ping; Lin, Yan-Wen
2011-02-01
Two Ga(III) complexes with main ligand, 2-(2-hydroxyphenyl)benzothiazole (HL'), namely mixed-ligand ML2X-type [GaL'2X'] (1) (HX'=acetic acid, as ancillary ligand) and the meridianal tris-chelate [GaL'3] (2) have been investigated by the density functional theory (DFT/TDDFT) level calculations. Both 1 and 2 can be presented as a similar "mixed-ligand ML2X-type" species. The molecular geometries, electronic structures, metal-ligand bonding property of Ga-O (N) (main ligand), Ga-O (N) (ancillary ligand) interactions, and the ancillary ligand effect on their HOMO-LUMO gap, their absorption/emission property, and their absorption/emission wavelengths/colors for them have been discussed in detail based on the orbital interactions, the partial density of states (PDOS), and so on. The current investigation also indicates that it is quite probable that by introduction of different ancillary ligands, a series of new mixed-ligand ML2X-type complexes for group 13 metals can be designed with their absorption/emission property and the absorption/emission wavelengths and colors being tuned. Copyright © 2011 Elsevier B.V. All rights reserved.
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Castro-Osma, José A; North, Michael; Offermans, Willem K; Leitner, Walter; Müller, Thomas E
2016-04-21
The mechanism by which [Al(salen)]2 O complexes catalyse the synthesis of cyclic carbonates from epoxides and carbon dioxide in the absence of a halide cocatalyst has been investigated. Density functional theory (DFT) studies, mass spectrometry and (1) H NMR, (13) C NMR and infrared spectroscopies provide evidence for the formation of an unprecedented carbonato bridged bimetallic aluminium complex which is shown to be a key intermediate for the halide-free synthesis of cyclic carbonates from epoxides and carbon dioxide. Deuterated and enantiomerically-pure epoxides were used to study the reaction pathway. Based on the experimental and theoretical results, a catalytic cycle is proposed. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Structural studies of P-type ATPase–ligand complexes using an X-ray free-electron laser
Bublitz, Maike; Nass, Karol; Drachmann, Nikolaj D.; ...
2015-06-11
Membrane proteins are key players in biological systems, mediating signalling events and the specific transport ofe.g.ions and metabolites. Consequently, membrane proteins are targeted by a large number of currently approved drugs. Understanding their functions and molecular mechanisms is greatly dependent on structural information, not least on complexes with functionally or medically important ligands. Structure determination, however, is hampered by the difficulty of obtaining well diffracting, macroscopic crystals. Here, the feasibility of X-ray free-electron-laser-based serial femtosecond crystallography (SFX) for the structure determination of membrane protein–ligand complexes using microcrystals of various native-source and recombinant P-type ATPase complexes is demonstrated. The data revealmore » the binding sites of a variety of ligands, including lipids and inhibitors such as the hallmark P-type ATPase inhibitor orthovanadate. By analyzing the resolution dependence of ligand densities and overall model qualities, SFX data quality metrics as well as suitable refinement procedures are discussed. Even at relatively low resolution and multiplicity, the identification of ligands can be demonstrated. This makes SFX a useful tool for ligand screening and thus for unravelling the molecular mechanisms of biologically active proteins.« less
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Schön, Eva; Zhang, Xiangyang; Zhou, Zhiping; Chisholm, Malcolm H; Chen, Peter
2004-11-15
The gas-phase reactions of a series of mass-selected mononuclear and dinuclear Cr(salen) complexes with propylene oxide suggest that the enhanced reactivity of the dinuclear complexes in gas-phase and in solution may derive from a dicationic mechanism in which the alkoxide chain is mu(2)-coordinated to two Lewis acidic metal centers. The double coordination is proposed to suppress backbiting, and hence chain-transfer in the gas-phase homopolymerization of epoxides.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Hawkins, Cory A.; Bustillos, Christian G.; May, Iain
Conventional solvent extraction of selected f-element cations by bis(2-ethylhexyl)phosphoric acid (HDEHP) yields increased extraction from aqueous to organic solution along the series Np(V) < Cm(III) < Eu(III) < U(VI), with distribution ratios all within two orders of magnitude. However, in the presence of the water-soluble tetradentate Schiff base (N,N'-bis(5-sulfonatosalicylidene)-ethylenediamine or H 2salenSO 3), selective complexation of the two actinyl cations (Np(V) and U(VI)) resulted in an extraction order of Np(V) < U(VI) << Eu(III) < Cm(III). The extraction of neither Cm(III) or Eu(III) by HDEHP are significantly impacted by the presence of the aqueous phase Schiff base. Despite observed hydrolyticmore » decomposition of H 2salenSO 3 in aqueous solutions, the calculated high conditional stability constant (β 11 = 26) for the complex [UO 2(salenSO 3)] 2- demonstrates its capacity for aqueous hold-back of U(VI). UV-visible-NIR spectroscopy of solutions prepared with a Np(VI) stock and H 2salenSO 3 suggest that reduction of Np(VI) to Np(V) by the ligand was rapid, resulting in a pentavalent Np complex that was substantially retained in the aqueous phase. Lastly, results from 1H NMR of aqueous solutions of H 2salenSO 3 with U(VI) and La(III), Eu(III), and Lu(III) provides additional evidence that the ligand readily chelates U(VI), but has only weak interactions with trivalent lanthanide ions.« less
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Water-soluble Schiff base-actinyl complexes and their effect on the solvent extraction of f-elements
Hawkins, Cory A.; Bustillos, Christian G.; May, Iain; ...
2016-09-07
Conventional solvent extraction of selected f-element cations by bis(2-ethylhexyl)phosphoric acid (HDEHP) yields increased extraction from aqueous to organic solution along the series Np(V) < Cm(III) < Eu(III) < U(VI), with distribution ratios all within two orders of magnitude. However, in the presence of the water-soluble tetradentate Schiff base (N,N'-bis(5-sulfonatosalicylidene)-ethylenediamine or H 2salenSO 3), selective complexation of the two actinyl cations (Np(V) and U(VI)) resulted in an extraction order of Np(V) < U(VI) << Eu(III) < Cm(III). The extraction of neither Cm(III) or Eu(III) by HDEHP are significantly impacted by the presence of the aqueous phase Schiff base. Despite observed hydrolyticmore » decomposition of H 2salenSO 3 in aqueous solutions, the calculated high conditional stability constant (β 11 = 26) for the complex [UO 2(salenSO 3)] 2- demonstrates its capacity for aqueous hold-back of U(VI). UV-visible-NIR spectroscopy of solutions prepared with a Np(VI) stock and H 2salenSO 3 suggest that reduction of Np(VI) to Np(V) by the ligand was rapid, resulting in a pentavalent Np complex that was substantially retained in the aqueous phase. Lastly, results from 1H NMR of aqueous solutions of H 2salenSO 3 with U(VI) and La(III), Eu(III), and Lu(III) provides additional evidence that the ligand readily chelates U(VI), but has only weak interactions with trivalent lanthanide ions.« less
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The salen based chemosensors for highly selective recognition of Zn2+ ion.
Zhu, Wenkai; Du, LongChao; Li, Wensheng; Zuo, Jinyan; Shan, Jingrui
2018-06-03
Two novel salen based chemosensors have been successfully synthesized. UV-vis absorption, fluorescence emission spectroscopy and cyclic voltammetry (CV) were exploited to investigate their recognition toward various metal ions, including Na + , K + , Mg 2+ , Al 3+ , Zn 2+ , Ag + , Pb 2+ , Co 2+ , Li + , Ba 2+ , Ca 2+ , Cd 2+ , La 3+ , Cu 2+ and Mn 2+ ions. The results indicated that the sensor L1 and L2 exhibited highly selective and sensitive recognition for Zn 2+ ions. The binding stoichiometry ratio of L1-Zn 2+ /L2-Zn 2+ were recognized as 4:1 by the method of Job's plot. Meanwhile, this investigation is confirmed by 1 H NMR. These results indicated that L1 and L2 can be applied as chemosensor for the detection of Zn 2+ ion. Copyright © 2018 Elsevier B.V. All rights reserved.
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Homoleptic nickel(II) complexes of redox-tunable pincer-type ligands.
Hewage, Jeewantha S; Wanniarachchi, Sarath; Morin, Tyler J; Liddle, Brendan J; Banaszynski, Megan; Lindeman, Sergey V; Bennett, Brian; Gardinier, James R
2014-10-06
Different synthetic methods have been developed to prepare eight new redox-active pincer-type ligands, H(X,Y), that have pyrazol-1-yl flanking donors attached to an ortho-position of each ring of a diarylamine anchor and that have different groups, X and Y, at the para-aryl positions. Together with four previously known H(X,Y) ligands, a series of 12 Ni(X,Y)2 complexes were prepared in high yields by a simple one-pot reaction. Six of the 12 derivatives were characterized by single-crystal X-ray diffraction, which showed tetragonally distorted hexacoordinate nickel(II) centers. The nickel(II) complexes exhibit two quasi-reversible one-electron oxidation waves in their cyclic voltammograms, with half-wave potentials that varied over a remarkable 700 mV range with the average of the Hammett σ(p) parameters of the para-aryl X, Y groups. The one- and two-electron oxidized derivatives [Ni(Me,Me)2](BF4)n (n = 1, 2) were prepared synthetically, were characterized by X-band EPR, electronic spectroscopy, and single-crystal X-ray diffraction (for n = 2), and were studied computationally by DFT methods. The dioxidized complex, [Ni(Me,Me)2](BF4)2, is an S = 2 species, with nickel(II) bound to two ligand radicals. The mono-oxidized complex [Ni(Me,Me)2](BF4), prepared by comproportionation, is best described as nickel(II) with one ligand centered radical. Neither the mono- nor the dioxidized derivative shows any substantial electronic coupling between the metal and their bound ligand radicals because of the orthogonal nature of their magnetic orbitals. On the other hand, weak electronic communication occurs between ligands in the mono-oxidized complex as evident from the intervalence charge transfer (IVCT) transition found in the near-IR absorption spectrum. Band shape analysis of the IVCT transition allowed comparisons of the strength of the electronic interaction with that in the related, previously known, Robin-Day class II mixed valence complex, [Ga(Me,Me)2](2+).
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Kianfar, Ali Hossein; Mahmood, Wan Ahmad Kamil; Dinari, Mohammad; Azarian, Mohammad Hossein; Khafri, Fatemeh Zare
2014-06-05
The [Co(Me(2)Salen)(PBu(3))(OH(2))]BF4 and [Co(Me(2)Salen)(PPh(3))(Solv)]BF(4), complexes were synthesized and characterized by FT-IR, UV-Vis, (1)H NMR spectroscopy and elemental analysis techniques. The coordination geometry of [Co(Me(2)Salen)(PPh(3))(H(2)O)]BF(4) was determined by X-ray crystallography. It has been found that the complex is containing [Co(Me(2)Salen)(PPh(3))(H(2)O)]BF(4) and [Co(Me(2)Salen)(PPh(3))(EtOH)]BF(4) hexacoordinate species in the solid state. Cobalt atom exhibits a distorted octahedral geometry and the Me(2)Salen ligand has the N2O2 coordinated environment in the equatorial plane. The [Co(Me(2)Salen)(PPh(3))(H(2)O)]BF(4) complex shows a dimeric structure via hydrogen bonding between the phenolate oxygen and hydrogens of coordinated H2O molecule. These complexes were incorporated into Montmorillonite-K10 nanoclay. The modified clays were identified by FT-IR, XRD, EDX, TGA/DTA, SEM and TEM techniques. According to the XRD results of the new nanohybrid materials, the Schiff base complexes are intercalated in the interlayer spaces of the clay. SEM and TEM micrographs show that the resulting hybrid nanomaterials have layer structures. Also, TGA/DTG results show that the intercalation reaction was taken place successfully. Copyright © 2014. Published by Elsevier B.V.
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NASA Astrophysics Data System (ADS)
Sheng, Xia; Alvarez-Gallego, Yolanda; Dominguez-Benetton, Xochitl; Baert, Kitty; Hubin, Annick; Zhao, Hailiang; Mihaylov, Tzvetan T.; Pierloot, Kristine; Vankelecom, Ivo F. J.; Pescarmona, Paolo P.
2018-06-01
Carbon-supported iron complexes were investigated as electrocatalysts for the reduction of nitric oxide (NO) in a H2-NO fuel cell conceived for the production of hydroxylamine (NH2OH) with concomitant generation of electricity. Two types of iron complexes with tetradentate ligands, namely bis(salicylidene)ethylenediimine (Salen) and phthalocyanine (Pc), supported on activated carbon or graphite were prepared and evaluated as electrocatalysts, either without further treatment or after pyrolysis at 700 °C. The performance in the reduction of NO of gas diffusion cathodes based on these electrocatalysts was investigated in an electrochemical half cell (3-electrode configuration) using linear sweep voltammetry (LSV). The most promising electrocatalysts were studied further by chronoamperometric experiments in a H2-NO fuel cell, which allowed comparison in terms of power output and hydroxylamine production. Depending on the concentration of the NO feed (6 or 18%), the best electrocatalytic performance was delivered either by FePc or FeSalen. The gas diffusion electrode based on FeSalen supported on activated carbon with 0.3 wt% Fe-loading provided the highest current density (86 A/m2) and the best current efficiency (43%) towards the desired NH2OH when operating at the higher NO concentration (18%). Moreover, FeSalen offers the advantage of being cheaper than FePc. The experimental work was complemented by density functional theory (DFT) calculations, which allowed to shed more light on the reaction mechanism for the reduction of nitric oxide at the atomistic level.
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Nomura, Wataru; Aikawa, Haruo; Taketomi, Shohei; Tanabe, Miho; Mizuguchi, Takaaki; Tamamura, Hirokazu
2015-11-01
We have previously used poly-L-proline linkers for the development of bivalent-type ligands for the chemokine receptor, CXCR4. The bivalent ligands with optimum linkers showed specific binding to CXCR4, suggesting the existence of CXCR4 possibly as a dimer on the cell membrane, and enabled definition of the amount of CXCR4 expressed. This paper reports the synthesis by a copper-catalyzed azide-alkyne cycloaddition reaction as the key reaction, of bivalent CXCR4 ligands with near infrared (NIR) dyes at the terminus or the center of the poly-L-proline linker. Some of the NIR-labeled ligands, which would be valuable probes useful in studies of the behavior of cells expressing CXCR4, have been obtained. The information concerning the effects of the labeling positions of NIR dyes on their binding properties is useful for the design of modified bivalent-type CXCR4 ligands. Copyright © 2015 Elsevier Ltd. All rights reserved.
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Light activated nitric oxide releasing materials
NASA Astrophysics Data System (ADS)
Muizzi Casanas, Dayana Andreina
The ability to control the location and dosage of biologically active molecules inside the human body can be critical to maximizing effective treatment of cardiovascular diseases like angina. The current standard of treatment relies on the metabolism of organonitrate drugs into nitric oxide (NO), which are not specific, and also show problems with densitization with long-term use. There is a need then to create a treatment method that gives targeted release of NO. Metal-nitrosyl (M-NO) complexes can be used for delivery of NO since the release of NO can be controlled with light. However, the NO-releasing drug must be activated with red light to ensure maximum penetration of light through tissue. However, the release of NO from M-NO complexes with red-light activation is a significant challenge since the energy required to break the metal-NO bond is usually larger than the energy provided by red light. The goal of this project was to create red- sensitive, NO-releasing materials based on Ru-salen-nitrosyl compounds. Our approach was to first modify Ru salen complexes to sensitize the photochemistry for release of NO after red light irradiation. Next, we pursued polymerization of the Ru-salen complexes. We report the synthesis and quantitative photochemical characterization of a series of ruthenium salen nitrosyl complexes. These complexes were modified by incorporating electron donating groups in the salen ligand structure at key locations to increase electron density on the Ru. Complexes with either an --OH or --OCH3 substituent showed an improvement in the quantum yield of release of NO upon blue light irradiation compared to the unmodified salen. These --OH and --OCH3 complexes were also sensitized for NO release after red light activation, however the red-sensitive complexes were unstable and showed ligand substitution on the order of minutes. The substituted complexes remained sensitive for NO release, but only after blue light irradiation. The Ru
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Yang, Haixia; Xiao, Lei; Wang, Nanping
2017-04-01
Peroxisome proliferator-activated receptor α (PPARα) plays a key role in lipid metabolism and glucose homeostasis and a crucial role in the prevention and treatment of metabolic diseases. Natural dietary compounds, including nutrients and phytochemicals, are PPARα ligands or modulators. High-throughput screening assays have been developed to screen for PPARα ligands and modulators in our diet. In the present review, we discuss recent advances in our knowledge of PPARα, including its structure, function, and ligand and modulator screening assays, and summarize the different types of dietary PPARα ligands and modulators. © 2016 Ruijin Hospital, Shanghai Jiaotong University School of Medicine and John Wiley & Sons Australia, Ltd.
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Shin, Jae-Min; Cho, Doo-Ho
2005-01-01
PDB-Ligand (http://www.idrtech.com/PDB-Ligand/) is a three-dimensional structure database of small molecular ligands that are bound to larger biomolecules deposited in the Protein Data Bank (PDB). It is also a database tool that allows one to browse, classify, superimpose and visualize these structures. As of May 2004, there are about 4870 types of small molecular ligands, experimentally determined as a complex with protein or DNA in the PDB. The proteins that a given ligand binds are often homologous and present the same binding structure to the ligand. However, there are also many instances wherein a given ligand binds to two or more unrelated proteins, or to the same or homologous protein in different binding environments. PDB-Ligand serves as an interactive structural analysis and clustering tool for all the ligand-binding structures in the PDB. PDB-Ligand also provides an easier way to obtain a number of different structure alignments of many related ligand-binding structures based on a simple and flexible ligand clustering method. PDB-Ligand will be a good resource for both a better interpretation of ligand-binding structures and the development of better scoring functions to be used in many drug discovery applications.
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Li, Wenhui; Xu, Jiachao; Kou, Xiaolong; Zhao, Rong; Zhou, Wei; Fang, Xiaohong
2018-05-01
Angiotensin II type 1 receptor (AT1R), a typical G protein-coupled receptor, plays a key role in regulating many cardiovascular functions. Different ligands can bind with AT1R to selectively activate either G protein (Gq) or β-arrestin (β-arr) pathway, or both pathways, but the molecular mechanism is not clear yet. In this work, we used, for the first time, atomic force microscopy-based single molecule force spectroscopy (SMFS) to study the interactions of AT1R with three types of ligands, balanced ligand, Gq-biased ligand, and β-arr-biased ligand, in living cells. The results revealed their difference in binding force and binding stability. The complex of the Gq-biased ligand-AT1R overcame two energy barriers with an intermediate state during dissociation, whereas that of β-arr-biased ligand-AT1R complex overcame one energy barrier. This indicated that AT1R had different ligand-binding conformational substates and underwent different structural changes to activate downstream signaling pathways with variable agonist efficacies. Quantitative analysis of AT1R-ligand binding in living cells at the single-molecule level offers a new tool to study the molecular mechanism of AT1R biased activation. Graphical Abstract Single-molecule force measurement on the living cell expressing AT1R-eGFP with a ligand modified AFM tip (left), the dynamic force spectra of β-arrestin biased ligands-AT1R (middle), and Gq-biased ligands-AT1R (right). The complexes of β-arr-biased ligand-AT1R overcame one energy barrier, with one linear region in the spectra, whereas the Gq-biased ligand-AT1R complexes overcame two energy barriers with two linear regions.
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Najar, Adel M; Tidmarsh, Ian S; Adams, Harry; Ward, Michael D
2009-12-21
Reaction of two structurally related bridging ligands L(26Py) and L(13Ph), in which two bidentate chelating pyrazolyl-pyridine units are connected to either a 2,6-pyridine-diyl or 1,3-benzene-diyl central group via methylene spacers, with first-row transition metal dications, results in a surprising variety of structures. The commonest is that of an octanuclear coordination cage [M(8)L(12)]X(16) [M = Co(II) or Zn(II); X = perchlorate or tetrafluoroborate] in which a metal ion is located at each of the eight vertices of an approximate cube, and one bis-bidentate bridging ligand spans each edge. The arrangement of fac and mer tris-chelate metal centers around the inversion center results in approximate (non-crystallographic) S(6) symmetry. Another structural type observed in the solid state is a hexanuclear complex [Co(6)(L(13Ph))(9)](ClO(4))(12) in which the six metal ions are in a rectangular array (two rows of three), folded about the central Co-Co vector like a partially open book, with each metal-metal edge containing one bridging ligand apart from the two outermost metal-metal edges which are spanned by a pair of bridging ligands in a double helical array. The final structural type we observed is a tetranuclear square [Ni(4)(L(26Py))(6)](BF(4))(8), with the four Ni-Ni edges spanned alternately by one and two bridging ligand such that it effectively consists of two dinuclear double helicates cross-linked by additional bridging ligands. A balance between the "cube" and "book" forms, which varied from compound to compound, was observed in solution in many cases by (1)H NMR and ES mass spectrometry studies.
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Caputo, Christopher B; Vukotic, V Nicholas; Sirizzotti, Natalie M; Loeb, Stephen J
2011-08-14
A new tetradentate, pyridine ligand with a rigid tetrahedral core can be prepared in good yield by a cross-coupling methodology. Two metal organic framework structures of Cu(II) with PtS-type topology having a carbon atom as the tetrahedral node have been characterized utilising this ligand. This journal is © The Royal Society of Chemistry 2011
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NASA Astrophysics Data System (ADS)
Gao, Baojiao; Zhang, Dandan; Li, Yanbin
2018-03-01
Luminescent polymer-rare earth complexes are an important class of photoluminescence and electroluminescence materials. Via molecular design, two furfural-based bidentate Schiff base ligands, furfural-aniline (FA) type ligand and furfural-cyclohexylamine (FC) type ligand, were bonded on the side chains of polysulfone (PSF), respectively, forming two functionalized macromolecules, PSF-FA and PSF-FC. And then through respective coordination reactions of the two functionalized macromolecules with Eu(Ⅲ) ion and Tb(Ⅲ) ion, novel luminescent binary and ternary (with 1,10-phenanthroline as the second ligand) polymer-rare earth complexes were synthesized. For these complexes, on basis of the characterization of their chemical structures, they photoluminescence properties were main researched, and the relationship between their luminescent properties and structures was explored. The experimental results show that the complexes coming from PSF-FA and Eu(Ⅲ) ion including binary and ternary complexes emit strong red luminescence, indicating that the bonded bidentate Schiff base ligand FA can sensitize the fluorescence emission of Eu(III) ion. While the complexes coming from PSF-FC and Tb(Ⅲ) ion produce green luminescence, displaying that the bonded bidentate Schiff base ligand FC can sensitize the fluorescence emission of Tb(Ⅲ) ion. The fluorescence emission intensities of the ternary complexes were stronger than that of binary complexes, reflecting the important effect of the second ligand. The fluorescence emission of the solid film of complexes is much stronger than that of the solutions of complexes. Besides, by comparison, it is found that the furfural (as a heteroaromatic compound)-based Schiff base type polymer-rare earth complexes have stronger fluorescence emission and higher energy transfer efficiency than salicylaldehyde (as a common aromatic compound)-based Schiff base type polymer-rare earth complexes.
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Kume, Satoshi; Lee, Young-Ho; Nakatsuji, Masatoshi; Teraoka, Yoshiaki; Yamaguchi, Keisuke; Goto, Yuji; Inui, Takashi
2014-03-18
The hydrophobic cavity of lipocalin-type prostaglandin D synthase (L-PGDS) has been suggested to accommodate various lipophilic ligands through hydrophobic effects, but its energetic origin remains unknown. We characterized 18 buffer-independent binding systems between human L-PGDS and lipophilic ligands using isothermal titration calorimetry. Although the classical hydrophobic effect was mostly detected, all complex formations were driven by favorable enthalpic gains. Gibbs energy changes strongly correlated with the number of hydrogen bond acceptors of ligand. Thus, the broad binding capability of L-PGDS for ligands should be viewed as hydrophilic interactions delicately tuned by enthalpy-entropy compensation using combined effects of hydrophilic and hydrophobic interactions. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.
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Weitman, Efraim; Bachar, Etty; Suissa, Yaron; Cohen, Guy; Schyr, Rachel Ben-Haroush; Sabanay, Helena; Horwitz, Elad; Glaser, Benjamin; Dor, Yuval; Pribluda, Ariel; Hanna, Jacob H.
2013-01-01
NK cells rapidly kill tumor cells, virus infected cells and even self cells. This is mediated via killer receptors, among which NKp46 (NCR1 in mice) is prominent. We have recently demonstrated that in type 1 diabetes (T1D) NK cells accumulate in the diseased pancreas and that they manifest a hyporesponsive phenotype. In addition, we found that NKp46 recognizes an unknown ligand expressed by beta cells derived from humans and mice and that blocking of NKp46 activity prevented diabetes development. Here we investigated the properties of the unknown NKp46 ligand. We show that the NKp46 ligand is mainly located in insulin granules and that it is constitutively secreted. Following glucose stimulation the NKp46 ligand translocates to the cell membrane and its secretion decreases. We further demonstrate by using several modalities that the unknown NKp46 ligand is not insulin. Finally, we studied the expression of the NKp46 ligand in type 2 diabetes (T2D) using 3 different in vivo models and 2 species; mice and gerbils. We demonstrate that the expression of the NKp46 ligand is decreased in all models of T2D studied, suggesting that NKp46 is not involved in T2D. PMID:24009765
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Surprisingly facile CO2 insertion into cobalt alkoxide bonds: A theoretical investigation.
Offermans, Willem K; Bizzarri, Claudia; Leitner, Walter; Müller, Thomas E
2015-01-01
Exploiting carbon dioxide as co-monomer with epoxides in the production of polycarbonates is economically highly attractive. More effective catalysts for this reaction are intensively being sought. To promote better understanding of the catalytic pathways, this study uses density functional theory calculations to elucidate the reaction step of CO2 insertion into cobalt(III)-alkoxide bonds, which is also the central step of metal catalysed carboxylation reactions. It was found that CO2 insertion into the cobalt(III)-alkoxide bond of [(2-hydroxyethoxy)Co(III)(salen)(L)] complexes (salen = N,N"-bis(salicyliden-1,6-diaminophenyl)) is exothermic, whereby the exothermicity depends on the trans-ligand L. The more electron-donating this ligand is, the more exothermic the insertion step is. Interestingly, we found that the activation barrier decreases with increasing exothermicity of the CO2 insertion. Hereby, a linear Brønsted-Evans-Polanyi relationship was found between the activation energy and the reaction energy.
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NASA Astrophysics Data System (ADS)
Richter, David; Moraga, Ignacio; Winkelmann, Hauke; Birkholz, Oliver; Wilmes, Stephan; Schulte, Markos; Kraich, Michael; Kenneweg, Hella; Beutel, Oliver; Selenschik, Philipp; Paterok, Dirk; Gavutis, Martynas; Schmidt, Thomas; Garcia, K. Christopher; Müller, Thomas D.; Piehler, Jacob
2017-07-01
The spatiotemporal organization of cytokine receptors in the plasma membrane is still debated with models ranging from ligand-independent receptor pre-dimerization to ligand-induced receptor dimerization occurring only after receptor uptake into endosomes. Here, we explore the molecular and cellular determinants governing the assembly of the type II interleukin-4 receptor, taking advantage of various agonists binding the receptor subunits with different affinities and rate constants. Quantitative kinetic studies using artificial membranes confirm that receptor dimerization is governed by the two-dimensional ligand-receptor interactions and identify a critical role of the transmembrane domain in receptor dimerization. Single molecule localization microscopy at physiological cell surface expression levels, however, reveals efficient ligand-induced receptor dimerization by all ligands, largely independent of receptor binding affinities, in line with the similar STAT6 activation potencies observed for all IL-4 variants. Detailed spatiotemporal analyses suggest that kinetic trapping of receptor dimers in actin-dependent microcompartments sustains robust receptor dimerization and signalling.
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Zhang, Dandan; Gao, Baojiao; Li, Yanbin
2017-08-01
Using molecular design and polymer reactions, two types of bidentate Schiff base ligands, salicylaldehyde-aniline (SAN) and salicylaldehyde-cyclohexylamine (SCA), were synchronously synthesized and bonded onto the side chain of polysulfone (PSF), giving two bidentate Schiff base ligand-functionalized PSFs, PSF-SAN and PSF-SCA, referred to as macromolecular ligands. Following coordination reactions between the macromolecular ligands and Eu(III) and Tb(III) ions (the reaction occurred between the bonded ligands SAN or SCA and the lanthanide ion), two series of luminescent polymer-rare earth complexes, PSF-SAN-Eu(III) and PSF-SCA-Tb(III), were obtained. The two macromolecular ligands were fully characterized by Fourier transform infrared (FTIR), 1 H NMR and UV absorption spectroscopy, and the prepared complexes were also characterized by FTIR, UV absorption spectroscopy and thermo-gravity analysis. On this basis, the photoluminescence properties of these complexes and the relationships between their structure and luminescence were investigated in depth. The results show that the bonded bidentate Schiff base ligands, SAN and SCA, can effectively sensitize the fluorescence emission of Eu(III) and Tb(III) ions, respectively. PSF-SAN-Eu(III) series complexes, namely the binary complex PSF-(SAN) 3 -Eu(III) and the ternary complex PSF-(SAN) 3 -Eu(III)-(Phen) 1 (Phen is the small-molecule ligand 1,10-phenanthroline), produce strong red luminescence, suggesting that the triplet state energy level of SAN is lower and well matched with the resonant energy level of the Eu(III) ion. By contrast, PSF-SAN-Eu(III) series complexes, namely the binary complex PSF-(SCA) 3 -Tb(III) and the ternary complex PSF-(SCA) 3 -Tb(III)-(Phen) 1 , display strong green luminescence, suggesting that the triplet state energy level of SCA is higher and is well matched with the resonant energy level of Tb(III). Copyright © 2017 John Wiley & Sons, Ltd.
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Karabal, Pratibha U; Kamble, Dayanand A; Sudalai, Arumugam
2014-04-21
The salen Co(III)-catalyzed phenolic kinetic resolution of racemic anti- or syn-azido and benzyloxy epoxides provides a practical route to a range of enantioenriched anti- or syn-1-aryloxy-3-azido or benzyloxy-2-alcohols in excellent yields and ees. The synthetic potential of this protocol is illustrated with an enantioselective synthesis of ICI-118,551, a β-blocker, in a highly optically pure form (99% ee).
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A ferromagnetic compound with anti-cancer proeprties for controlled drug delivery and imaging
Eguchi, Haruki; Hirata, Kunio; Kurotani, Reiko; ...
2015-03-17
New anticancer agents and modalities for their use are of great interest. Recent studies have demonstrated the presence of anti-cancer properties in salen derivatives. We found that an iron salen derivative, i.e., [Fe(salen)] 2O, displays ferromagnetic order above room temperature and shows spontaneous field-dependent magnetization and hysteresis. Understanding of this magnetic property is provided by first-principles calculations based on structures obtained by X-ray crystallography. [Fe(salen)] 2O exhibited potent anti-cancer properties against various cancer cell types and was readily attracted by even moderate-strength permanent magnets in vitro. We demonstrated that the delivery of [Fe(salen)] 2O to melanoma tissues transplanted into themore » tails of mice using a permanent magnet leads to a robust decrease in tumor size. The local accumulation of [Fe(salen)] 2O was visualized by MRI. Thus, [Fe(salen)] 2O acted as an anti-cancer and MRI contrast compound that has a pharmacological effect that is delivered in a controlled manner, suggesting new strategies for anti-cancer drug development.« less
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A ferromagnetic compound with anti-cancer proeprties for controlled drug delivery and imaging
DOE Office of Scientific and Technical Information (OSTI.GOV)
Eguchi, Haruki; Hirata, Kunio; Kurotani, Reiko
New anticancer agents and modalities for their use are of great interest. Recent studies have demonstrated the presence of anti-cancer properties in salen derivatives. We found that an iron salen derivative, i.e., [Fe(salen)] 2O, displays ferromagnetic order above room temperature and shows spontaneous field-dependent magnetization and hysteresis. Understanding of this magnetic property is provided by first-principles calculations based on structures obtained by X-ray crystallography. [Fe(salen)] 2O exhibited potent anti-cancer properties against various cancer cell types and was readily attracted by even moderate-strength permanent magnets in vitro. We demonstrated that the delivery of [Fe(salen)] 2O to melanoma tissues transplanted into themore » tails of mice using a permanent magnet leads to a robust decrease in tumor size. The local accumulation of [Fe(salen)] 2O was visualized by MRI. Thus, [Fe(salen)] 2O acted as an anti-cancer and MRI contrast compound that has a pharmacological effect that is delivered in a controlled manner, suggesting new strategies for anti-cancer drug development.« less
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Adam, W; Humpf, H U; Roschmann, K J; Saha-Möller, C R
2001-08-24
A set of aryl-substituted allylic alcohols rac-2 has been epoxidized by chiral Mn(salen*) complexes 1 as the catalyst and iodosyl benzene (PhIO) as the oxygen source. Whereas one enantiomer of the allylic alcohol 2 is preferentially epoxidized to give the threo- or cis-epoxy alcohol 3 (up to 80% ee) as the main product (dr up to >95:5), the other enantiomer of 2 is enriched (up to 53% ee). In the case of 1,1-dimethyl-1,2-dihydronaphthalen-2-ol (2c), the CH oxidation to the enone 4c proceeds enantioselectively and competes with the epoxidation. The absolute configurations of the allylic alcohols 2 and their epoxides 3 have been determined by chemical correlation or CD spectroscopy. The observed diastereo- and enantioselectivities in the epoxidation reactions are rationalized in terms of a beneficial interplay between the hydroxy-directing effect and the attack along the Katsuki trajectory.
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Martínez-Rodríguez, Luis; Bandeira, Nuno A G; Bo, Carles; Kleij, Arjan W
2015-05-04
A calix[4]arene host equipped with two bis-[Zn(salphen)] complexes self-assembles into a capsular complex in the presence of a chiral diamine guest with an unexpected 2:1 ratio between the host and the guest. Effective chirality transfer from the diamine to the calix-salen hybrid host is observed by circular dichroism (CD) spectroscopy, and a high stability constant K2,1 of 1.59×10(11) M(-2) for the assembled host-guest ensemble has been determined with a substantial cooperativity factor α of 6.4. Density functional calculations are used to investigate the origin of the stability of the host-guest system and the experimental CD spectrum compared with those calculated for both possible diastereoisomers showing that the M,M isomer is the one that is preferentially formed. The current system holds promise for the chirality determination of diamines, as evidenced by the investigated substrate scope and the linear relationship between the ee of the diamine and the amplitude of the observed Cotton effects. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Akdemir, Atilla; De Monte, Celeste; Carradori, Simone; Supuran, Claudiu T
2015-02-01
In previous work, 14 salen and tetrahydrosalen compounds have been synthesized and tested in enzyme inhibition assays against cytosolic human carbonic anhydrase isozymes I and II (hCA I and II) and tumor-associated isozymes IX and XII (hCA IX and XII). These compounds show selectivity against hCA XII over hCA I, II and IX. In this study, molecular modeling and docking studies were applied to understand this preference of the compounds for hCA XII. Most likely, the compounds can displace the zinc-bound water molecule of hCA XII to form a direct interaction with the Zn(2+) ion. In the other isozymes, the compounds might not be able to displace the water molecule nor are they expected to interact with the Zn(2+) ion.
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Notch-ligand expression by NALT dendritic cells regulates mucosal Th1- and Th2-type responses
DOE Office of Scientific and Technical Information (OSTI.GOV)
Fukuyama, Yoshiko; Tokuhara, Daisuke; Division of Mucosal Immunology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639
Highlights: Black-Right-Pointing-Pointer Nasal Ad-FL effectively up-regulates APC function by CD11c{sup +} DCs in mucosal tissues. Black-Right-Pointing-Pointer Nasal Ad-FL induces Notch ligand (L)-expressing CD11c{sup +} DCs. Black-Right-Pointing-Pointer Notch L-expressing DCs support the induction of Th1- and Th2-type cytokine responses. -- Abstract: Our previous studies showed that an adenovirus (Ad) serotype 5 vector expressing Flt3 ligand (Ad-FL) as nasal adjuvant activates CD11c{sup +} dendritic cells (DCs) for the enhancement of antigen (Ag)-specific IgA antibody (Ab) responses. In this study, we examined the molecular mechanism for activation of CD11c{sup +} DCs and their roles in induction of Ag-specific Th1- and Th2-cell responses. Ad-FLmore » activated CD11c{sup +} DCs expressed increased levels of the Notch ligand (L)-expression and specific mRNA. When CD11c{sup +} DCs from various mucosal and systemic lymphoid tissues of mice given nasal OVA plus Ad-FL were cultured with CD4{sup +} T cells isolated from non-immunized OVA TCR-transgenic (OT II) mice, significantly increased levels of T cell proliferative responses were noted. Furthermore, Ad-FL activated DCs induced IFN-{gamma}, IL-2 and IL-4 producing CD4{sup +} T cells. Of importance, these APC functions by Ad-FL activated DCs were down-regulated by blocking Notch-Notch-L pathway. These results show that Ad-FL induces CD11c{sup +} DCs to the express Notch-ligands and these activated DCs regulate the induction of Ag-specific Th1- and Th2-type cytokine responses.« less
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Amino acid ionic liquids as chiral ligands in ligand-exchange chiral separations.
Liu, Qian; Wu, Kangkang; Tang, Fei; Yao, Lihua; Yang, Fei; Nie, Zhou; Yao, Shouzhuo
2009-09-28
Recently, amino acid ionic liquids (AAILs) have attracted much research interest. In this paper, we present the first application of AAILs in chiral separation based on the chiral ligand exchange principle. By using 1-alkyl-3-methylimidazolium L-proline (L-Pro) as a chiral ligand coordinated with copper(II), four pairs of underivatized amino acid enantiomers-dl-phenylalanine (dl-Phe), dl-histidine (dl-His), dl-tryptophane (dl-Trp), and dl-tyrosine (dl-Tyr)-were successfully separated in two major chiral separation techniques, HPLC and capillary electrophoresis (CE), with higher enantioselectivity than conventionally used amino acid ligands (resolution (R(s))=3.26-10.81 for HPLC; R(s)=1.34-4.27 for CE). Interestingly, increasing the alkyl chain length of the AAIL cation remarkably enhanced the enantioselectivity. It was inferred that the alkylmethylimidazolium cations and L-Pro form ion pairs on the surface of the stationary phase or on the inner surface of the capillary. The ternary copper complexes with L-Pro are consequently attached to the support surface, thus inducing an ion-exchange type of retention for the dl-enantiomers. Therefore, the AAIL cation plays an essential role in the separation. This work demonstrates that AAILs are good alternatives to conventional amino acid ligands for ligand-exchange-based chiral separation. It also reveals the tremendous application potential of this new type of task-specific ILs.
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NASA Astrophysics Data System (ADS)
Mahlooji, Niloofar; Behzad, Mahdi; Tarahhomi, Atekeh; Maroney, Michael; Rudbari, Hadi Amiri; Bruno, Giuseppe; Ghanbari, Bahram
2016-04-01
Two new heteronuclear Nickel(II)/Sodium(I) complexes of a side-off compartmental Schiff base ligand were synthesized and characterized by spectroscopic methods. Crystal structures of both of the complexes were also obtained. The Schiff base ligand was synthesized from the condensation of meso-1,2-diphenyl-1,2-ethylenediamine with 2-hydroxy-3-methoxybenzaldehyde. In both of the complexes the Ni(II) ion is coordinated to the inner N2O2 coordination sphere with square-planar geometry and the Na(I) ion is coordinated to the outer O2 O2‧ coordination sphere. In Complex (1) with general formula [Ni(L)Na(CH3OH)(ClO4)] the sodium ion is seven coordinated while in (2) with general formula [{Ni(L)Na(OH2)}2(μ-Ni(CN)4)] the sodium ion is six coordinated. Intermolecular interactions in two studied complexes were analyzed using 3D Hirshfeld surfaces and corresponding 2D fingerprint plots. This analysis showed that the H … H and C … H/H … C contacts for both structures (altogether 67.5% of total Hirshfeld surface area for (1) and 77.6% for (2)) and the O … H/H … O (24.2%) for (1) and the N … H/H … N (8.1%) contacts for (2) were the characteristic intermolecular contacts in the related crystal structures.
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Gao, Baojiao; Zhang, Liqin; Zhang, Dandan
2018-02-07
Two kinds of bidentate Schiff base ligands derived from benzaldehyde, benzaldehyde/m-aminophenol (BAMA) type and benzaldehyde/glutamic acid (BAGL) type ligands, were synchronously synthesized and bonded on the backbone of polysulfone (PSF) through molecular design and by polymer reactions, and two functional polymers, PSF-BAMA and PSF-BAGL, were obtained. Then two series of novel luminescent Schiff base-type polymer-rare earth complexes were prepared via coordination reactions. In this work, the effects of the structures of the bonded ligands on the photoluminescence performance of the complexes were investigated in detail, and for the different photophysical properties of the prepared complexes, relevant theoretical explanations were given. The experimental results show that the bonded ligand BAMA can strongly sensitize the fluorescence emission of Eu(iii) ions, and the binary complex PSF-(BAMA) 3 -Eu(iii) emits strong red fluorescence under UV light. The reason for this lies in the fact that a larger conjugate π-bond system is contained in the structure of BAMA, and so the triplet state of BAMA can be matched with the resonant energy level of the Eu(iii) ion. While the bonded ligand BAGL can effectively sensitize the fluorescence emission of Tb(iii) ions, the binary complex PSF-(BAGL) 3 -Tb(iii) exhibits very strong green fluorescence under UV light. The reason is that a smaller conjugate π-bond system is contained in the structure of BAGL and there is a good energy level matching between the triplet state of BAGL and the resonant energy level of the Tb(iii) ion. The fluorescence intensities of the two ternary complexes, PSF-(BAMA) 3 -Eu(iii)-(Phen) 1 (phenanthroline, Phen) and PSF-(BAGL) 3 -Tb(iii)-(Phen) 1 , are much stronger than that of the corresponding binary complex because Phen as the second ligand has two effects, the effect of synergistic coordination with the first ligand and the effect of replacing the coordinated water around the central ion, and
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The future of type 1 cannabinoid receptor allosteric ligands.
Alaverdashvili, Mariam; Laprairie, Robert B
2018-02-01
Allosteric modulation of the type 1 cannabinoid receptor (CB1R) holds great therapeutic potential. This is because allosteric modulators do not possess intrinsic efficacy, but instead augment (positive allosteric modulation) or diminish (negative allosteric modulation) the receptor's response to endogenous ligand. Consequently, CB1R allosteric modulators have an effect ceiling which allows for the tempering of CB1R signaling without the desensitization, tolerance, dependence, and psychoactivity associated with orthosteric compounds. Pain, movement disorders, epilepsy, obesity are all potential therapeutic targets for CB1R allosteric modulation. Several challenges exist for the development of CB1R allosteric modulators, such as receptor subtype specificity, translation to in vivo systems, and mixed allosteric/agonist/inverse agonist activity. Despite these challenges, elucidation of crystal structures of CB1R and compound design based on structure-activity relationships will advance the field. In this review, we will cover recent progress for CB1R allosteric modulators and discuss the future promise of this research.
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NASA Technical Reports Server (NTRS)
Miskowski, Vincent M.; Houlding, Virginia H.
1989-01-01
Two types of emission behavior for Pt(II) complexes containing alpha-diimine ligands have been observed in dilute solution. If the complex also has weak field ligands such as chloride, ligand field (d-d) excited states become the lowest energy excited states. If only strong field ligands are present, a diimine 3(pi-pi/asterisk/) state becomes the lowest. In none of the cases studied did metal-to-ligand charge transfer excited state lie lowest.
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Refat, Moamen S; El-Korashy, Sabry A; Kumar, Deo Nandan; Ahmed, Ahmed S
2008-09-01
Complexes of ruthenium(III) with N,N'-disalicylidene-l,2-phenylenediamine (H2dsp), N,N'-disalicylidene-3,4-diaminotoluene (H2dst), 4-nitro-N,N'-disalicylidene-1,2-phenylenediamine (H2ndsp) and N,N'-disalicylidene ethylenediamine (H2salen) have been prepared and characterized by elemental analysis, molar conductivity, spectral methods (mid-infrared, 1H NMR and UV-vis spectra) and simultaneous thermal analysis (TG and DTG) techniques. The molar conductance measurements proved that all these complexes are non-electrolytes. The electronic spectra measurements were used to infer the structures. The IR spectra of the ligands and their complexes are used to identify the type of bonding. The kinetic thermodynamic parameters such as: E*, DeltaH*, DeltaS* and DeltaG* are estimated from the DTG curves. The four ligands and their complexes have been studied for their possible biological antifungal activity.
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Ilgü, Hüseyin; Jeckelmann, Jean-Marc; Colas, Claire; Ucurum, Zöhre; Schlessinger, Avner; Fotiadis, Dimitrios
2018-01-01
The l-arginine/agmatine transporter AdiC is a prokaryotic member of the SLC7 family, which enables pathogenic enterobacteria to survive the extremely acidic gastric environment. Wild-type AdiC from Escherichia coli, as well as its previously reported point mutants N22A and S26A, were overexpressed homologously and purified to homogeneity. A size-exclusion chromatography-based thermostability assay was used to determine the melting temperatures (Tms) of the purified AdiC variants in the absence and presence of the selected ligands l-arginine (Arg), agmatine, l-arginine methyl ester, and l-arginine amide. The resulting Tms indicated stabilization of AdiC variants upon ligand binding, in which Tms and ligand binding affinities correlated positively. Considering results from this and previous studies, we revisited the role of AdiC residue S26 in Arg binding and proposed interactions of the α-carboxylate group of Arg exclusively with amide groups of the AdiC backbone. In the context of substrate binding in the human SLC7 family member l-type amino acid transporter-1 (LAT1; SLC7A5), an analogous role of S66 in LAT1 to S26 in AdiC is discussed based on homology modeling and amino acid sequence analysis. Finally, we propose a binding mechanism for l-amino acid substrates to LATs from the SLC7 family. PMID:29558430
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Vijver, Martina G; De Koning, Arjan; Peijnenburg, Willie J G M
2008-11-01
One of the aims of the Water Framework Directive is to derive Europe-wide environmental quality standards that are scientifically based and protective of surface waters. Accounting for water type-specific bioavailability corrections presents challenges and opportunities for metals research. In this study, we present generally applicable approaches for tiered risk assessment of chemicals for prospective use. The objective of the present study was to derive water type-specific dissolved copper criteria for Dutch surface waters. The intent was to show the utility of accounting for bioavailability by using biotic ligand models (BLMs) and two different ways of extrapolating these BLMs in order to obtain reliable bioavailability-corrected species sensitivity distributions. Water type-specific criteria estimations were generated for six different water quality conditions. Average hazard concentrations as calculated using the BLMs and the two alternate normalization scenarios varied significantly among the different water types, from 5.6 to 73.6 microg/L. Water types defined as large rivers, sandy springs, and acid ponds were most sensitive for Cu. Streams and brooks had the highest hazard concentrations. The two different options examined for toxicity data normalization did impact the calculated hazard concentrations for each water type.
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Wu, Si-Hai; Zhong, Yu-Wu; Yao, Jiannian
2013-07-01
A new bridging ligand, 2,3-di(2-pyridyl)-5-phenylpyrazine (dpppzH), has been synthesized. This ligand was designed so that it could bind two metals through a NN-CNN-type coordination mode. The reaction of dpppzH with cis-[(bpy)2RuCl2] (bpy = 2,2'-bipyridine) affords monoruthenium complex [(bpy)2Ru(dpppzH)](2+) (1(2+)) in 64 % yield, in which dpppzH behaves as a NN bidentate ligand. The asymmetric biruthenium complex [(bpy)2Ru(dpppz)Ru(Mebip)](3+) (2(3+)) was prepared from complex 1(2+) and [(Mebip)RuCl3] (Mebip = bis(N-methylbenzimidazolyl)pyridine), in which one hydrogen atom on the phenyl ring of dpppzH is lost and the bridging ligand binds to the second ruthenium atom in a CNN tridentate fashion. In addition, the RuPt heterobimetallic complex [(bpy)2Ru(dpppz)Pt(C≡CPh)](2+) (4(2+)) has been prepared from complex 1(2+), in which the bridging ligand binds to the platinum atom through a CNN binding mode. The electronic properties of these complexes have been probed by using electrochemical and spectroscopic techniques and studied by theoretical calculations. Complex 1(2+) is emissive at room temperature, with an emission λmax = 695 nm. No emission was detected for complex 2(3+) at room temperature in MeCN, whereas complex 4(2+) displayed an emission at about 750 nm. The emission properties of these complexes are compared to those of previously reported Ru and RuPt bimetallic complexes with a related ligand, 2,3-di(2-pyridyl)-5,6-diphenylpyrazine. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Ilgü, Hüseyin; Jeckelmann, Jean-Marc; Colas, Claire; Ucurum, Zöhre; Schlessinger, Avner; Fotiadis, Dimitrios
2018-03-20
The l-arginine/agmatine transporter AdiC is a prokaryotic member of the SLC7 family, which enables pathogenic enterobacteria to survive the extremely acidic gastric environment. Wild-type AdiC from Escherichia coli, as well as its previously reported point mutants N22A and S26A, were overexpressed homologously and purified to homogeneity. A size-exclusion chromatography-based thermostability assay was used to determine the melting temperatures ( T m s) of the purified AdiC variants in the absence and presence of the selected ligands l-arginine (Arg), agmatine, l-arginine methyl ester, and l-arginine amide. The resulting T m s indicated stabilization of AdiC variants upon ligand binding, in which T m s and ligand binding affinities correlated positively. Considering results from this and previous studies, we revisited the role of AdiC residue S26 in Arg binding and proposed interactions of the α-carboxylate group of Arg exclusively with amide groups of the AdiC backbone. In the context of substrate binding in the human SLC7 family member l-type amino acid transporter-1 (LAT1; SLC7A5), an analogous role of S66 in LAT1 to S26 in AdiC is discussed based on homology modeling and amino acid sequence analysis. Finally, we propose a binding mechanism for l-amino acid substrates to LATs from the SLC7 family.
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Kremer, Alexandre B; Andrews, Ryan J; Milner, Matthew J; Zhang, Xu R; Ebrahimi, Tannaz; Patrick, Brian O; Diaconescu, Paula L; Mehrkhodavandi, Parisa
2017-02-06
The impact of the metal size and Lewis acidity on the polymerization activity of group 13 metal complexes was studied, and it was shown that, within the same ligand family, indium complexes are far more reactive and selective than their gallium analogues. To this end, gallium and aluminum complexes supported by a tridentate diaminophenolate ligand, as well as gallium complexes supported by N,N'-ethylenebis(salicylimine)(salen) ligands, were synthesized and compared to their indium analogues. Using the tridentate ligand set, it was possible to isolate the gallium chloride complexes 3 and (±)-4 and the aluminum analogues 5 and (±)-6. The alkoxygallium complex (±)-2, supported by a salen ligand, was also prepared and characterized and, along with the three-component system GaCl 3 /BnOH/NEt 3 , was tested for the ring-opening polymerization of lactide and ε-caprolactone. The polymerization rates and selectivities of both systems were significantly lower than those for the indium analogues. The reaction of (±)-2 with 1 equiv of lactide forms the first insertion product, which is stable in solution and can be characterized at room temperature. In order to understand the differences of the reactivity within the group 13 metal complexes, a Lewis acidity study using triethylphosphine oxide (the Gutmann-Beckett method) was undertaken for a series of aluminum, gallium, and indium halide complexes; this study shows that indium halide complexes are less Lewis acidic than their aluminum and gallium analogues. Density functional theory calculations show that the Mulliken charges for the indium complexes are higher than those for the gallium analogues. These data suggest that the impact of ligands on the reactivity is more significant than that of the metal Lewis acidity.
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Sorai, Michio; Burriel, Ramón; Westrum, Edgar F; Hendrickson, David N
2008-04-10
Magnetic and thermal properties of the iron(III) spin crossover complex [Fe(3MeO-salenEt)(2)]PF(6) are very sensitive to mechanochemical perturbations. Heat capacities for unperturbed and differently perturbed samples were precisely determined by adiabatic calorimetry at temperatures in the 10-300 K range. The unperturbed compound shows a cooperative spin crossover transition at 162.31 K, presenting a hysteresis of 2.8 K. The anomalous enthalpy and entropy contents of the transition were evaluated to be Delta(trs)H = 5.94 kJ mol(-1) and Delta(trs)S = 36.7 J K(-1) mol(-1), respectively. By mechanochemical treatments, (1) the phase transition temperature was lowered by 1.14 K, (2) the enthalpy and entropy gains at the phase transition due to the spin crossover phenomenon were diminished to Delta(trs)H = 4.94 kJ mol(-1) and Delta(trs)S = 31.1 J K(-1) mol(-1), and (3) the lattice heat capacities were larger than those of the unperturbed sample over the whole temperature range. In spite of different mechanical perturbations (grinding with a mortar and pestle and grinding in a ball-mill), two sets of heat capacity measurements provided basically the same results. The mechanochemical perturbation exerts its effect more strongly on the low-spin state than on the high-spin state. It shows a substantial increase of the number of iron(III) ions in the high-spin state below the transition temperature. The heat capacities of the diamagnetic cobalt(III) analogue [Co(3MeO-salenEt)(2)]PF(6) also were measured. The lattice heat capacity of the iron compounds has been estimated from either the measurements on the cobalt complex using a corresponding states law or the effective frequency distribution method. These estimations have been used for the evaluation of the transition anomaly.
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Clinical Use of PPARγ Ligands in Cancer
Hatton, Jennifer L.; Yee, Lisa D.
2008-01-01
The role of PPARγ in adipocyte differentiation has fueled intense interest in the function of this steroid nuclear receptor for regulation of malignant cell growth and differentiation. Given the antiproliferative and differentiating effects of PPARγ ligands on liposarcoma cells, investigation of PPARγ expression and ligand activation in other solid tumors such as breast, colon, and prostate cancers ensued. The anticancer effects of PPARγ ligands in cell culture and rodent models of a multitude of tumor types suggest broad applicability of these agents to cancer therapy. This review focuses on the clinical use of PPARγ ligands, specifically the thiazolidinediones, for the treatment and prevention of cancer. PMID:19125177
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NASA Astrophysics Data System (ADS)
Armstrong, Craig G.; Toghill, Kathryn E.
2017-05-01
A single species redox flow battery employing a new class of cobalt(II) complexes with 'tunable' tridentate azole-pyridine type ligands is reported. Four structures were synthesised and their electrochemical, physical and battery characteristics were investigated as a function of successive substitution of the ligand terminal pyridyl donors. The Co(II/I) and Co(III/II) couples are stable and quasi-reversible on gold and glassy carbon electrodes, however redox potentials are tunable allowing the cobalt potential difference to be preferentially increased from 1.07 to 1.91 V via pyridine substitution with weaker σ-donating/π-accepting 3,5-dimethylpyrazole groups. The charge-discharge properties of the system were evaluated using an H-type glass cell and graphite rod electrodes. The complexes delivered high Coulombic efficiencies of 89.7-99.8% and very good voltaic efficiencies of 70.3-81.0%. Consequently, energy efficiencies are high at 63.1-80.8%, marking an improvement on other similar non-aqueous systems. Modification of the ligands also improved solubility from 0.18 M to 0.50 M via pyridyl substitution with 3,5-dimethylpyrazole, though the low solubility of the complexes limits the overall energy capacity to between 2.58 and 12.80 W h L-1. Preliminary flow cell studies in a prototype flow cell are also demonstrated.
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Reaction chemistry and ligand exchange at cadmium selenide nanocrystal surfaces
DOE Office of Scientific and Technical Information (OSTI.GOV)
Owen, Jonathan; Park, Jungwon; Trudeau, Paul-Emile
Chemical modification of nanocrystal surfaces is fundamentally important to their assembly, their implementation in biology and medicine, and greatly impacts their electrical and optical properties. However, it remains a major challenge owing to a lack of analytical tools to directly determine nanoparticle surface structure. Early nuclear magnetic resonance (NMR) and X-ray photoelectron spectroscopy (XPS) studies of CdSe nanocrystals prepared in tri-n-octylphosphine oxide (1) and tri-n-octylphosphine (2), suggested these coordinating solvents are datively bound to the particle surface. However, assigning the broad NMR resonances of surface-bound ligands is complicated by significant concentrations of phosphorus-containing impurities in commercial sources of 1, andmore » XPS provides only limited information about the nature of the phosphorus containing molecules in the sample. More recent reports have shown the surface ligands of CdSe nanocrystals prepared in technical grade 1, and in the presence of alkylphosphonic acids, include phosphonic and phosphinic acids. These studies do not, however, distinguish whether these ligands are bound datively, as neutral, L-type ligands, or by X-type interaction of an anionic phosphonate/phosphinate moiety with a surface Cd{sup 2+} ion. Answering this question would help clarify why ligand exchange with such particles does not proceed generally as expected based on a L-type ligand model. By using reagents with reactive silicon-chalcogen and silicon-chlorine bonds to cleave the ligands from the nanocrystal surface, we show that our CdSe and CdSe/ZnS core-shell nanocrystal surfaces are likely terminated by X-type binding of alkylphosphonate ligands to a layer of Cd{sup 2+}/Zn{sup 2+} ions, rather than by dative interactions. Further, we provide spectroscopic evidence that 1 and 2 are not coordinated to our purified nanocrystals.« less
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Metallosupramolecular Architectures Obtained from Poly-N-heterocyclic Carbene Ligands.
Sinha, Narayan; Hahn, F Ekkehardt
2017-09-19
Over the past two decades, self-assembly of supramolecular architectures has become a field of intensive research due to the wide range of applications for the resulting assemblies in various fields such as molecular encapsulation, supramolecular catalysis, drug delivery, metallopharmaceuticals, chemical and photochemical sensing, and light-emitting materials. For these purposes, a large number of coordination-driven metallacycles and metallacages featuring different sizes and shapes have been prepared and investigated. Almost all of these are Werner-type coordination compounds where metal centers are coordinated by nitrogen and/or oxygen donors of polydentate ligands. With the evolving interest in the coordination chemistry of N-heterocyclic carbenes (NHCs), discrete supramolecular complexes held together by M-C NHC bonds have recently become of interest. The construction of such metallosupramolecular assemblies requires the synthesis of suitable poly-NHC ligands where the NHC donors form labile bonds with metal centers thus enabling the formation of the thermodynamically most stable reaction product. In organometallic chemistry, these conditions are uniquely met by the combination of poly-NHCs and silver(I) ions where the resulting assemblies also offer the possibility to generate new structures by transmetalation of the poly-NHC ligands to additional metal centers forming more stable C NHC -M bonds. Stable metallosupramolecular assemblies obtained from poly-NHC ligands feature special properties such as good solubility in many less polar organic solvents and the presence of the often catalyticlly active {M(NHC) n } moiety as building block. In this Account, we review recent developments in organometallic supramolecular architectures derived from poly-NHC ligands. We describe dinuclear (M = Ag I , Au I , Cu I ) tetracarbene complexes obtained from bis-NHC ligands with an internal olefin or two external coumarin pendants and their postsynthetic modification via a
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LigandRNA: computational predictor of RNA–ligand interactions
Philips, Anna; Milanowska, Kaja; Łach, Grzegorz; Bujnicki, Janusz M.
2013-01-01
RNA molecules have recently become attractive as potential drug targets due to the increased awareness of their importance in key biological processes. The increase of the number of experimentally determined RNA 3D structures enabled structure-based searches for small molecules that can specifically bind to defined sites in RNA molecules, thereby blocking or otherwise modulating their function. However, as of yet, computational methods for structure-based docking of small molecule ligands to RNA molecules are not as well established as analogous methods for protein-ligand docking. This motivated us to create LigandRNA, a scoring function for the prediction of RNA–small molecule interactions. Our method employs a grid-based algorithm and a knowledge-based potential derived from ligand-binding sites in the experimentally solved RNA–ligand complexes. As an input, LigandRNA takes an RNA receptor file and a file with ligand poses. As an output, it returns a ranking of the poses according to their score. The predictive power of LigandRNA favorably compares to five other publicly available methods. We found that the combination of LigandRNA and Dock6 into a “meta-predictor” leads to further improvement in the identification of near-native ligand poses. The LigandRNA program is available free of charge as a web server at http://ligandrna.genesilico.pl. PMID:24145824
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Li, Tong; Khah, Massoud Kheir; Slavnic, Snjezana; Johansson, Ingegerd; Strömberg, Nicklas
2001-01-01
Actinomyces spp. exhibit type 1 fimbria-mediated adhesion to salivary acidic proline-rich proteins (PRPs) and statherin ligands. Actinomyces spp. with different animal and tissue origins belong to three major adhesion types as relates to ligand specificity and type 1 fimbria genes. (i) In preferential acidic-PRP binding, strains of Actinomyces naeslundii genospecies 1 and 2 from human and monkey mouths displayed at least three ligand specificities characterized by preferential acidic-PRP binding. Slot blot DNA hybridization showed seven highly conserved type 1 fimbria genes (orf1- to -6 and fimP) in genospecies 1 and 2 strains, except that orf5 and orf3 were divergent in genospecies 1. (ii) In preferential statherin binding, oral Actinomyces viscosus strains of rat and hamster origin (and strain 19246 from a human case of actinomycosis) bound statherin preferentially. DNA hybridization and characterization of the type 1 fimbria genes from strain 19246 revealed a homologous gene cluster of four open reading frames (orfA to -C and fimP). Bioinformatics suggested sortase (orfB, orf4, and part of orf5), prepilin peptidase (orfC and orf6), fimbria subunit (fimP), and usher- and autotransporter-like (orfA and orf1 to -3) functions. Those gene regions corresponding to orf3 and orf5 were divergent, those corresponding to orf2, orf1, and fimP were moderately conserved, and those corresponding to orf4 and orf6 were highly conserved. Restriction fragment length polymorphism analyses using a fimP probe separated human and monkey and rat and hamster strains into phylogenetically different groups. (iii) In statherin-specific binding, strains of A. naeslundii genospecies 1 from septic and other human infections displayed a low-avidity binding to statherin. Only the orf4 and orf6 gene regions were highly conserved. Finally, rat saliva devoid of statherin bound bacterial strains avidly irrespective of ligand specificity, and specific antisera detected either type 1, type 2, or both
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Collagen type I as a ligand for receptor-mediated signaling
NASA Astrophysics Data System (ADS)
Boraschi-Diaz, Iris; Wang, Jennifer; Mort, John S.; Komarova, Svetlana V.
2017-05-01
Collagens form the fibrous component of the extracellular matrix in all multi-cellular animals. Collagen type I is the most abundant collagen present in skin, tendons, vasculature, as well as the organic portion of the calcified tissue of bone and teeth. This review focuses on numerous receptors for which collagen acts as a ligand, including integrins, discoidin domain receptors DDR1 and 2, OSCAR, GPVI, G6b-B and Lair-1 of the leukocyte receptor complex and mannose family receptor uPARAP/Endo 180. We explore the process of collagen production and self-assembly, as well as its degradation by collagenases and gelatinases in order to predict potential temporal and spatial sites of action of different collagen receptors. While the interactions of the mature collagen matrix with integrins and DDR are well-appreciated, potential signals from immature matrix as well as collagen degradation products are possible but not yet described. The role of multiple collagen receptors in physiological processes and their contribution to pathophysiology of diseases affecting collagen homeostasis require further studies.
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Analysis of macromolecules, ligands and macromolecule-ligand complexes
Von Dreele, Robert B [Los Alamos, NM
2008-12-23
A method for determining atomic level structures of macromolecule-ligand complexes through high-resolution powder diffraction analysis and a method for providing suitable microcrystalline powder for diffraction analysis are provided. In one embodiment, powder diffraction data is collected from samples of polycrystalline macromolecule and macromolecule-ligand complex and the refined structure of the macromolecule is used as an approximate model for a combined Rietveld and stereochemical restraint refinement of the macromolecule-ligand complex. A difference Fourier map is calculated and the ligand position and points of interaction between the atoms of the macromolecule and the atoms of the ligand can be deduced and visualized. A suitable polycrystalline sample of macromolecule-ligand complex can be produced by physically agitating a mixture of lyophilized macromolecule, ligand and a solvent.
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Synthesis and characterization β-ketoamine ligands
NASA Astrophysics Data System (ADS)
Zaid, Nurzati Amani Mohamed; Hassan, Nur Hasyareeda; Karim, Nurul Huda Abd
2018-04-01
β-ketoamine ligands are important members of heterodonor ligand because of their ease of preparation and modification of both steric and/or electronic effects. Complexes with β-ketoamine has received much less attention and there has been no study about this complex with β-ketoamine in ionic liquid reported. Two type of β-ketoamine ligands which are 4-amino-3-pentene-2-onato (A) and 3-amino-2-butenoic acid methyl ester (B) have been synthesized in this work. The resulting compound formed was characterized using standard spectroscopic and structural techniques which includes 1H and 13C, NMR spectroscopy and FTIR spectroscopy. The 1H and 13C NMR spectrum displayed all the expected signals with correct integration and multiplicity. And it is proved that there are some differences between two ligands as observed in NMR and FTIR spectrum.
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da Costa, Leonardo Moreira; de Mesquita Carneiro, José Walkimar; Paes, Lilian Weitzel Coelho
2011-08-01
DFT (B3LYP/6-31+G(d)) calculations of Mg(2+) affinities for a set of phosphoryl ligands were performed. Two types of ligands were studied: a set of trivalent [O = P(R)] and a set of pentavalent phosphoryl ligands [O = P(R)(3)] (R = H, F, Cl, Br, OH, OCH(3), CH(3), CN, NH(2) and NO(2)), with R either bound directly to the phosphorus atom or to the para position of a phenyl ring. The affinity of the Mg(2+) cation for the ligands was quantified by means of the enthalpy for the substitution of one water molecule in the [Mg(H(2)O)(6)](2+) complex for a ligand. The enthalpy of substitution was correlated with electronic and geometric parameters. Electron-donor groups increase the interaction between the cation and the ligand, while electron-acceptor groups decrease the interaction enthalpy.
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The effect of ligand affinity on integrins' lateral diffusion in cultured cells.
Mainali, Dipak; Smith, Emily A
2013-04-01
The role of ligand affinity in altering αPS2CβPS integrins' lateral mobility was studied using single particle tracking (SPT) with ligand-functionalized quantum dots (QDs) and fluorescence recovery after photobleaching (FRAP) with fluorescent protein tagged integrins. Integrins are ubiquitous transmembrane proteins that are vital for numerous cellular functions, including bidirectional signaling and cell anchorage. Wild-type and high ligand affinity mutant (αPS2CβPS-V409D) integrins were studied in S2 cells. As measured by SPT, the integrin mobile fraction decreased by 22% and had a 4× slower diffusion coefficient for αPS2CβPS-V409D compared to wild-type integrins. These differences are partially the result of αPS2CβPS-V409D integrins' increased clustering. For the wild-type integrins, the average of all diffusion coefficients measured by SPT was statistically similar to the ensemble FRAP results. A 75% slower average diffusion coefficient was measured by SPT compared to FRAP for αPS2CβPS-V409D integrins, and this may be the result of SPT measuring only ligand-bound integrins, in contrast all ligand-bound and ligand-unbound integrins are averaged in FRAP measurements. Specific binding of the ligand-functionalized QDs was 99% for integrin expressing cells. The results prove that the ligand binding affinity affects the lateral dynamics of a subset of integrins based on the complementary SPT and FRAP data.
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Chelating ligands for nanocrystals' surface functionalization.
Querner, Claudia; Reiss, Peter; Bleuse, Joël; Pron, Adam
2004-09-22
A new family of ligands for the surface functionalization of CdSe nanocrystals is proposed, namely alkyl or aryl derivatives of carbodithioic acids (R-C(S)SH). The main advantages of these new ligands are as follows: they nearly quantitatively exchange the initial surface ligands (TOPO) in very mild conditions; they significantly improve the resistance of nanocrystals against photooxidation because of their ability of strong chelate-type binding to metal atoms; their relatively simple preparation via Grignard intermediates facilitates the development of new bifunctional ligands containing, in addition to the anchoring carbodithioate group, a second function, which enables the grafting of molecules or macromolecules of interest on the nanocrystal surface. To give an example of this approach, we report, for the first time, the grafting of an electroactive oligomer from the polyaniline family-aniline tetramer-on CdSe nanocrystals after their functionalization with 4-formyldithiobenzoic acid. The grafting proceeds via a condensation reaction between the aldehyde group of the ligand and the terminal primary amine group of the tetramer. The resulting organic/inorganic hybrid exhibits complete extinction of the fluorescence of its constituents, indicating efficient charge or energy transfer between the organic and the inorganic semiconductors.
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Embryonic expression of the transforming growth factor beta ligand and receptor genes in chicken.
Cooley, James R; Yatskievych, Tatiana A; Antin, Parker B
2014-03-01
Transforming growth factor-beta (TGFβ) signaling regulates a myriad of biological processes during embryogenesis, in the adult, and during the manifestation of disease. TGFβ signaling is propagated through one of three TGFβ ligands interacting with Type I and Type II receptors, and Type III co-receptors. Although TGFβ signaling is regulated partly by the combinatorial expression patterns of TGFβ receptors and ligands, a comprehensive gene expression analysis has not been published. Here we report the embryonic mRNA expression patterns in chicken embryos of the canonical TGFβ ligands (TGFB1, TGFB2, and TGFB3) and receptors (TGFBR1, TGFBR2, TGFBR3), plus the Activin A receptor, type 1 (ACVR1) and co receptor Endoglin (ENG) that also transduce TGFβ signaling. TGFB ligands and receptors show dynamic and frequently overlapping expression patterns in numerous embryonic cell layers and structures. Integrating expression information identifies combinations of ligands and receptors that are involved in specific developmental processes including somitogenesis, cardiogenesis and vasculogenesis. Copyright © 2013 Wiley Periodicals, Inc.
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Muto, S; Takada, T; Matsumoto, K
2001-07-02
The biological activities of mannose-binding lectin (MBL) which binds to different ligands on mammalian cells were examined using two types of Colo205 cells, a human colon adenocarcinoma cell line: one naturally expressing Lewis A and Lewis B antigens as ligands for MBL (NT-Colo205), and the other modified to express high-mannose type oligosaccharides by treatment with benzyl-2-acetamide-2-deoxy-alpha-galactopyranoside and 1-deoxymannojirimycin (Bz+dMM-Colo205). Although the final lysis was not observed, the deposition of C4 and C3 was observed on both types of Colo205 cells after treatment with MBL and complements as a result of complement activation by MBL. MBL bound to Bz+dMM-Colo205 could also activate human peripheral blood leukocytes and induce superoxide production; however, MBL bound to NT-Colo205 could not. This may be explained by the lower affinity of MBL to Lewis A and Lewis B antigens than to high-mannose type oligosaccharides under physiological conditions, since MBL bound to NT-Colo205 was more easily released from the cell surface than that bound to Bz+dMM-Colo205 at 37 degrees C. These findings suggest that the difference in the affinity of MBL to its ligands could influence the expression of some biological activities of MBL.
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NASA Astrophysics Data System (ADS)
Baret, P.; Beaujolais, V.; Bougault, C.; Gaude, D.; Pierre, J.-L.
1998-01-01
^1H NMR studies of the diamagnetic gallium (III) and paramagnetic iron (III) complexes of a chiral macrobicyclic ligand of bicapped tris (binaphtol) type are described. The study of the gallium complex emphasizes: (i) that the inversion of the octahedral center is not observed and: (ii) the absence of exchange between free ligand and complex, at room temperature. In the case of the iron complex, assignments of the hyperfine shifted resolved resonances are achieved, based on temperature-behavior studies, which evidence the D3 symmetry of the complex. These assignments are in complete agreement with measured T1 values and proton-to-iron distances obtained from molecular modelling. Les complexes du gallium (III) et du fer (III) d'un ligand macrobicyclique chiral impliquant trois sous-unités de type binaphtol sont étudiés en RMN du proton en solution méthanolique. L'étude du complexe (diamagnétique) du gallium permet de montrer que le complexe : (i) ne subit pas d'inversion de la configuration (Δ/Λ) du site octaédrique et : (ii) qu'il n'y a pas d'échange entre ligand libre et complexe à la température ambiante. L'évolution du spectre du complexe paramagnétique du fer avec la température permet une attribution des protons du ligand et met en évidence la symétrie D3 du complexe. Une bonne corrélation est obtenue entre la distance fer-proton (donnée par la modélisation moléculaire) et le T1 du proton considéré.
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Cell-specific targeting by heterobivalent ligands.
Josan, Jatinder S; Handl, Heather L; Sankaranarayanan, Rajesh; Xu, Liping; Lynch, Ronald M; Vagner, Josef; Mash, Eugene A; Hruby, Victor J; Gillies, Robert J
2011-07-20
Current cancer therapies exploit either differential metabolism or targeting to specific individual gene products that are overexpressed in aberrant cells. The work described herein proposes an alternative approach--to specifically target combinations of cell-surface receptors using heteromultivalent ligands ("receptor combination approach"). As a proof-of-concept that functionally unrelated receptors can be noncovalently cross-linked with high avidity and specificity, a series of heterobivalent ligands (htBVLs) were constructed from analogues of the melanocortin peptide ligand ([Nle(4), dPhe(7)]-α-MSH) and the cholecystokinin peptide ligand (CCK-8). Binding of these ligands to cells expressing the human Melanocortin-4 receptor and the Cholecystokinin-2 receptor was analyzed. The MSH(7) and CCK(6) were tethered with linkers of varying rigidity and length, constructed from natural and/or synthetic building blocks. Modeling data suggest that a linker length of 20-50 Å is needed to simultaneously bind these two different G-protein coupled receptors (GPCRs). These ligands exhibited up to 24-fold enhancement in binding affinity to cells that expressed both (bivalent binding), compared to cells with only one (monovalent binding) of the cognate receptors. The htBVLs had up to 50-fold higher affinity than that of a monomeric CCK ligand, i.e., Ac-CCK(6)-NH(2). Cell-surface targeting of these two cell types with labeled heteromultivalent ligand demonstrated high avidity and specificity, thereby validating the receptor combination approach. This ability to noncovalently cross-link heterologous receptors and target individual cells using a receptor combination approach opens up new possibilities for specific cell targeting in vivo for therapy or imaging.
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Cell-Specific Targeting by Heterobivalent Ligands
Josan, Jatinder S.; Handl, Heather L.; Sankaranarayanan, Rajesh; Xu, Liping; Lynch, Ronald M.; Vagner, Josef; Mash, Eugene A.; Hruby, Victor J.; Gillies, Robert J.
2012-01-01
Current cancer therapies exploit either differential metabolism or targeting to specific individual gene products that are overexpressed in aberrant cells. The work described herein proposes an alternative approach—to specifically target combinations of cell-surface receptors using heteromultivalent ligands (“receptor combination approach”). As a proof-of-concept that functionally unrelated receptors can be noncovalently cross-linked with high avidity and specificity, a series of heterobivalent ligands (htBVLs) were constructed from analogues of the melanocortin peptide ligand ([Nle4, DPhe7]-α-MSH) and the cholecystokinin peptide ligand (CCK-8). Binding of these ligands to cells expressing the human Melanocortin-4 receptor and the Cholecystokinin-2 receptor was analyzed. The MSH(7) and CCK(6) were tethered with linkers of varying rigidity and length, constructed from natural and/or synthetic building blocks. Modeling data suggest that a linker length of 20–50 Å is needed to simultaneously bind these two different G-protein coupled receptors (GPCRs). These ligands exhibited up to 24-fold enhancement in binding affinity to cells that expressed both (bivalent binding), compared to cells with only one (monovalent binding) of the cognate receptors. The htBVLs had up to 50-fold higher affinity than that of a monomeric CCK ligand, i.e., Ac-CCK(6)-NH2. Cell-surface targeting of these two cell types with labeled heteromultivalent ligand demonstrated high avidity and specificity, thereby validating the receptor combination approach. This ability to noncovalently cross-link heterologous receptors and target individual cells using a receptor combination approach opens up new possibilities for specific cell targeting in vivo for therapy or imaging. PMID:21639139
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Fathima, Nishtar Nishad; Aravindhan, Rathinam; Rao, Jonnalagadda Raghava; Nair, Balachandran Unni
2008-01-01
Catalytic wet hydrogen peroxide oxidation of an anionic dye has been explored in this study. Copper(II) complex of NN'-ethylene bis(salicylidene-aminato) (salenH2) has been encapsulated in super cages of zeolite-Y by flexible ligand method. The catalyst has been characterized by Fourier transforms infra red spectroscopy, X-ray powder diffractograms, Thermo-gravimetric and differential thermal analysis and nitrogen adsorption studies. The effects of various parameters such as pH, catalyst and hydrogen peroxide concentration on the oxidation of dye were studied. The results indicate that complete removal of color has been obtained after a period of less than 1h at 60 degrees C, 0.175M H2O2 and 0.3g l(-1) catalyst. More than 95% dye removal has been achieved using this catalyst for commercial effluent. These studies indicate that copper salen complex encapsulated in zeolite framework is a potential heterogeneous catalyst for removal of color from wastewaters.
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Photo-activation of Single Molecule Magnet Behavior in a Manganese-based Complex
NASA Astrophysics Data System (ADS)
Fetoh, Ahmed; Cosquer, Goulven; Morimoto, Masakazu; Irie, Masahiro; El-Gammal, Ola; El-Reash, Gaber Abu; Breedlove, Brian K.; Yamashita, Masahiro
2016-03-01
A major roadblock to fully realizing molecular electronic devices is the ability to control the properties of each molecule in the device. Herein we report the control of the magnetic properties of single-molecule magnets (SMMs), which can be used in memory devices, by using a photo-isomerizable diarthylenthene ligand. Photo-isomerization of the diarylethene ligand bridging two manganese salen complexes with visible light caused a significant change in the SMM behavior due to opening of the six-membered ring of diarylethene ligand, accompanied by reorganization of the entire molecule. The ring-opening activated the frequency-dependent magnetization of the complex. Our results are a major step towards the realization of molecular memory devices composed of SMMs because the SMM behaviour can be turned on and off simply by irradiating the molecule.
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Woo, James A; Chen, Hong; Snyder, Mark A; Chai, Yiming; Frost, Russell G; Cramer, Steven M
2015-08-14
A homologous ligand library based on the commercially-available Nuvia cPrime ligand was generated to systematically explore various features of a multimodal cation-exchange ligand and to identify structural variants that had significantly altered chromatographic selectivity. Substitution of the polar amide bond with more hydrophobic chemistries was found to enhance retention while remaining hydrophobically-selective for aromatic residues. In contrast, increasing the solvent exposure of the aromatic ring was observed to strengthen the ligand affinity for both types of hydrophobic residues. An optimal linker length between the charged and hydrophobic moieties was also observed to enhance retention, balancing the steric accessibility of the hydrophobic moiety with its ability to interact independently of the charged group. The weak pKa of the carboxylate charge group was found to have a notable impact on protein retention on Nuvia cPrime at lower pH, increasing hydrophobic interactions with the protein. Substituting the charged group with a sulfonic acid allowed this strong MM ligand to retain its electrostatic-dominant character in this lower pH range. pH gradient experiments were also carried out to further elucidate this pH dependent behavior. A single QSAR model was generated using this accumulated experimental data to predict protein retention across a range of multimodal and ion exchange systems. This model could correctly predict the retention of proteins on resins that were not included in the original model and could prove quite powerful as an in silico approach toward designing more effective and differentiated multimodal ligands. Copyright © 2015. Published by Elsevier B.V.
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Denizli, A; Pişkin, E
2001-10-30
Dye-ligands have been considered as one of the important alternatives to natural counterparts for specific affinity chromatography. Dye-ligands are able to bind most types of proteins, in some cases in a remarkably specific manner. They are commercially available, inexpensive, and can easily be immobilized, especially on matrices bearing hydroxyl groups. Although dyes are all synthetic in nature, they are still classified as affinity ligands because they interact with the active sites of many proteins mimicking the structure of the substrates, cofactors, or binding agents for those proteins. A number of textile dyes, known as reactive dyes, have been used for protein purification. Most of these reactive dyes consist of a chromophore (either azo dyes, anthraquinone, or phathalocyanine), linked to a reactive group (often a mono- or dichlorotriazine ring). The interaction between the dye ligand and proteins can be by complex combination of electrostatic, hydrophobic, hydrogen bonding. Selection of the supporting matrix is the first important consideration in dye-affinity systems. There are several methods for immobilization of dye molecules onto the support matrix, in which usually several intermediate steps are followed. Both the adsorption and elution steps should carefully be optimized/designed for a successful separation. Dye-affinity systems in the form of spherical sorbents or as affinity membranes have been used in protein separation.
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NASA Astrophysics Data System (ADS)
Saini, Anoop Kumar; Sharma, Vinay; Mathur, Pradeep; Shaikh, Mobin M.
2016-10-01
The morphology of nucleus and nucleolus is powerful indicator of physiological and pathological conditions. The specific staining of nucleolus recently gained much attention due to the limited and expensive availability of the only existing stain “SYTO RNA-Select”. Here, a new multifunctional salen type ligand (L1) and its Al3+ complex (1) are designed and synthesized. L1 acts as a chemosensor for Al3+ whereas 1 demonstrates specific staining of nucleus as well as nucleoli. The binding of 1 with nucleic acid is probed by DNase and RNase digestion in stained cells. 1 shows an excellent photostability, which is a limitation for existing nucleus stains during long term observations. 1 is assumed to be a potential candidate as an alternative to expensive commercial dyes for nucleus and nucleoli staining.
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Saini, Anoop Kumar; Sharma, Vinay; Mathur, Pradeep; Shaikh, Mobin M
2016-10-10
The morphology of nucleus and nucleolus is powerful indicator of physiological and pathological conditions. The specific staining of nucleolus recently gained much attention due to the limited and expensive availability of the only existing stain "SYTO RNA-Select". Here, a new multifunctional salen type ligand (L 1 ) and its Al 3+ complex (1) are designed and synthesized. L 1 acts as a chemosensor for Al 3+ whereas 1 demonstrates specific staining of nucleus as well as nucleoli. The binding of 1 with nucleic acid is probed by DNase and RNase digestion in stained cells. 1 shows an excellent photostability, which is a limitation for existing nucleus stains during long term observations. 1 is assumed to be a potential candidate as an alternative to expensive commercial dyes for nucleus and nucleoli staining.
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Ligand placement based on prior structures: the guided ligand-replacement method
DOE Office of Scientific and Technical Information (OSTI.GOV)
Klei, Herbert E.; Bristol-Myers Squibb, Princeton, NJ 08543-4000; Moriarty, Nigel W., E-mail: nwmoriarty@lbl.gov
2014-01-01
A new module, Guided Ligand Replacement (GLR), has been developed in Phenix to increase the ease and success rate of ligand placement when prior protein-ligand complexes are available. The process of iterative structure-based drug design involves the X-ray crystal structure determination of upwards of 100 ligands with the same general scaffold (i.e. chemotype) complexed with very similar, if not identical, protein targets. In conjunction with insights from computational models and assays, this collection of crystal structures is analyzed to improve potency, to achieve better selectivity and to reduce liabilities such as absorption, distribution, metabolism, excretion and toxicology. Current methods formore » modeling ligands into electron-density maps typically do not utilize information on how similar ligands bound in related structures. Even if the electron density is of sufficient quality and resolution to allow de novo placement, the process can take considerable time as the size, complexity and torsional degrees of freedom of the ligands increase. A new module, Guided Ligand Replacement (GLR), was developed in Phenix to increase the ease and success rate of ligand placement when prior protein–ligand complexes are available. At the heart of GLR is an algorithm based on graph theory that associates atoms in the target ligand with analogous atoms in the reference ligand. Based on this correspondence, a set of coordinates is generated for the target ligand. GLR is especially useful in two situations: (i) modeling a series of large, flexible, complicated or macrocyclic ligands in successive structures and (ii) modeling ligands as part of a refinement pipeline that can automatically select a reference structure. Even in those cases for which no reference structure is available, if there are multiple copies of the bound ligand per asymmetric unit GLR offers an efficient way to complete the model after the first ligand has been placed. In all of these applications
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Human Group C Rotavirus VP8*s Recognize Type A Histo-Blood Group Antigens as Ligands.
Sun, Xiaoman; Wang, Lihong; Qi, Jianxun; Li, Dandi; Wang, Mengxuan; Cong, Xin; Peng, Ruchao; Chai, Wengang; Zhang, Qing; Wang, Hong; Wen, Hongling; Gao, George F; Tan, Ming; Duan, Zhaojun
2018-06-01
Group/species C rotaviruses (RVCs) have been identified as important pathogens of acute gastroenteritis (AGE) in children, family-based outbreaks, as well as animal infections. However, little is known regarding their host-specific interaction, infection, and pathogenesis. In this study, we performed serial studies to characterize the function and structural features of a human G4P[2] RVC VP8* that is responsible for the host receptor interaction. Glycan microarrays demonstrated that the human RVC VP8* recognizes type A histo-blood group antigens (HBGAs), which was confirmed by synthetic glycan-/saliva-based binding assays and hemagglutination of red blood cells, establishing a paradigm of RVC VP8*-glycan interactions. Furthermore, the high-resolution crystal structure of the human RVC VP8* was solved, showing a typical galectin-like structure consisting of two β-sheets but with significant differences from cogent proteins of group A rotaviruses (RVAs). The VP8* in complex with a type A trisaccharide displays a novel ligand binding site that consists of a particular set of amino acid residues of the C-D, G-H, and K-L loops. RVC VP8* interacts with type A HBGAs through a unique mechanism compared with that used by RVAs. Our findings shed light on the host-virus interaction and the coevolution of RVCs and will facilitate the development of specific antivirals and vaccines. IMPORTANCE Group/species C rotaviruses (RVCs), members of Reoviridae family, infect both humans and animals, but our knowledge about the host factors that control host susceptibility and specificity is rudimentary. In this work, we characterized the glycan binding specificity and structural basis of a human RVC that recognizes type A HBGAs. We found that human RVC VP8*, the rotavirus host ligand binding domain that shares only ∼15% homology with the VP8* domains of RVAs, recognizes type A HBGA at an as-yet-unknown glycan binding site through a mechanism distinct from that used by RVAs. Our new
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da Costa, Leonardo Moreira; Carneiro, José Walkimar de Mesquita; Romeiro, Gilberto Alves; Paes, Lilian Weitzel Coelho
2011-02-01
The affinity of the Ca(2+) ion for a set of substituted carbonyl ligands was analyzed with both the DFT (B3LYP/6-31+G(d)) and semi-empirical (PM6) methods. Two types of ligands were studied: a set of monosubstituted [O=CH(R)] and a set of disubstituted ligands [O=C(R)(2)] (R=H, F, Cl, Br, OH, OCH(3), CH(3), CN, NH(2) and NO(2)), with R either directly bound to the carbonyl carbon atom or to the para position of a phenyl ring. The interaction energy was calculated to quantify the affinity of the Ca(2+) cation for the ligands. Geometric and electronic parameters were correlated with the intensity of the metal-ligand interaction. The electronic nature of the substituent is the main parameter that determines the interaction energy. Donor groups make the interaction energy more negative (stabilizing the complex formed), while acceptor groups make the interaction energy less negative (destabilizing the complex formed).
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West, Graham M.; Willard, Francis S.; Sloop, Kyle W.; Showalter, Aaron D.; Pascal, Bruce D.; Griffin, Patrick R.
2014-01-01
Activation of the glucagon-like peptide-1 receptor (GLP-1R) in pancreatic β-cells potentiates insulin production and is a current therapeutic target for the treatment of type 2 diabetes mellitus (T2DM). Like other class B G protein-coupled receptors (GPCRs), the GLP-1R contains an N-terminal extracellular ligand binding domain. N-terminal truncations on the peptide agonist generate antagonists capable of binding to the extracellular domain, but not capable of activating full length receptor. The main objective of this study was to use Hydrogen/deuterium exchange (HDX) to identify how the amide hydrogen bonding network of peptide ligands and the extracellular domain of GLP-1R (nGLP-1R) were altered by binding interactions and to then use this platform to validate direct binding events for putative GLP-1R small molecule ligands. The HDX studies presented here for two glucagon-like peptide-1 receptor (GLP-1R) peptide ligands indicates that the antagonist exendin-4[9-39] is significantly destabilized in the presence of nonionic detergents as compared to the agonist exendin-4. Furthermore, HDX can detect stabilization of exendin-4 and exendin-4[9-39] hydrogen bonding networks at the N-terminal helix [Val19 to Lys27] upon binding to the N-terminal extracellular domain of GLP-1R (nGLP-1R). In addition we show hydrogen bonding network stabilization on nGLP-1R in response to ligand binding, and validate direct binding events with the extracellular domain of the receptor for putative GLP-1R small molecule ligands. PMID:25180755
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Scoring ligand similarity in structure-based virtual screening.
Zavodszky, Maria I; Rohatgi, Anjali; Van Voorst, Jeffrey R; Yan, Honggao; Kuhn, Leslie A
2009-01-01
Scoring to identify high-affinity compounds remains a challenge in virtual screening. On one hand, protein-ligand scoring focuses on weighting favorable and unfavorable interactions between the two molecules. Ligand-based scoring, on the other hand, focuses on how well the shape and chemistry of each ligand candidate overlay on a three-dimensional reference ligand. Our hypothesis is that a hybrid approach, using ligand-based scoring to rank dockings selected by protein-ligand scoring, can ensure that high-ranking molecules mimic the shape and chemistry of a known ligand while also complementing the binding site. Results from applying this approach to screen nearly 70 000 National Cancer Institute (NCI) compounds for thrombin inhibitors tend to support the hypothesis. EON ligand-based ranking of docked molecules yielded the majority (4/5) of newly discovered, low to mid-micromolar inhibitors from a panel of 27 assayed compounds, whereas ranking docked compounds by protein-ligand scoring alone resulted in one new inhibitor. Since the results depend on the choice of scoring function, an analysis of properties was performed on the top-scoring docked compounds according to five different protein-ligand scoring functions, plus EON scoring using three different reference compounds. The results indicate that the choice of scoring function, even among scoring functions measuring the same types of interactions, can have an unexpectedly large effect on which compounds are chosen from screening. Furthermore, there was almost no overlap between the top-scoring compounds from protein-ligand versus ligand-based scoring, indicating the two approaches provide complementary information. Matchprint analysis, a new addition to the SLIDE (Screening Ligands by Induced-fit Docking, Efficiently) screening toolset, facilitated comparison of docked molecules' interactions with those of known inhibitors. The majority of interactions conserved among top-scoring compounds for a given scoring
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Drawing Mononuclear Octahedral Coordination Compounds Containing Tridentate Chelating Ligands
ERIC Educational Resources Information Center
Mohamadou, Aminou; Ple, Karen; Haudrechy, Arnaud
2011-01-01
Complexes with tridentate ligands of the type [M(A-B-C)2], where A [not equal to] B [not equal to] C and with an imposed bonding sequence A-B-C, require special attention to draw all possible stereoisomers. Depending on the nature of the central donor atom B of the tridentate ligand, an easy drawing method is presented that shows seven chiral…
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Two novel mixed-ligand complexes containing organosulfonate ligands.
Li, Mingtian; Huang, Jun; Zhou, Xuan; Fang, Hua; Ding, Liyun
2008-07-01
The structures reported herein, viz. bis(4-aminonaphthalene-1-sulfonato-kappaO)bis(4,5-diazafluoren-9-one-kappa(2)N,N')copper(II), [Cu(C(10)H(8)NO(3)S)(2)(C(11)H(6)N(2)O)(2)], (I), and poly[[[diaquacadmium(II)]-bis(mu-4-aminonaphthalene-1-sulfonato)-kappa(2)O:N;kappa(2)N:O] dihydrate], {[Cd(C(10)H(8)NO(3)S)(2)(H(2)O)(2)].2H(2)O}(n), (II), are rare examples of sulfonate-containing complexes where the anion does not fulfill a passive charge-balancing role, but takes an active part in coordination as a monodentate and/or bridging ligand. Monomeric complex (I) possesses a crystallographic inversion center at the Cu(II) atom, and the asymmetric unit contains one-half of a Cu atom, one complete 4-aminonaphthalene-1-sulfonate (ans) ligand and one 4,5-diazafluoren-9-one (DAFO) ligand. The Cu(II) atom has an elongated distorted octahedral coordination geometry formed by two O atoms from two monodentate ans ligands and by four N atoms from two DAFO molecules. Complex (II) is polymeric and its crystal structure is built up by one-dimensional chains and solvent water molecules. Here also the cation (a Cd(II) atom) lies on a crystallographic inversion center and adopts a slightly distorted octahedral geometry. Each ans anion serves as a bridging ligand linking two Cd(II) atoms into one-dimensional infinite chains along the [010] direction, with each Cd(II) center coordinated by four ans ligands via O and N atoms and by two aqua ligands. In both structures, there are significant pi-pi stacking interactions between adjacent ligands and hydrogen bonds contribute to the formation of two- and three-dimensional networks.
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Glukhova, Xenia A; Trizna, Julia A; Proussakova, Olga V; Gogvadze, Vladimir; Beletsky, Igor P
2018-01-22
Fas-ligand/CD178 belongs to the TNF family proteins and can induce apoptosis through death receptor Fas/CD95. The important requirement for Fas-ligand-dependent cell death induction is its localization to rafts, cholesterol- and sphingolipid-enriched micro-domains of membrane, involved in regulation of different signaling complexes. Here, we demonstrate that Fas-ligand physically associates with caveolin-1, the main protein component of rafts. Experiments with cells overexpressing Fas-ligand revealed a FasL N-terminal pre-prolin-rich region, which is essential for the association with caveolin-1. We found that the N-terminal domain of Fas-ligand bears two caveolin-binding sites. The first caveolin-binding site binds the N-terminal domain of caveolin-1, whereas the second one appears to interact with the C-terminal domain of caveolin-1. The deletion of both caveolin-binding sites in Fas-ligand impairs its distribution between cellular membranes, and attenuates a Fas-ligand-induced cytotoxicity. These results demonstrate that the interaction of Fas-ligand and caveolin-1 represents a molecular basis for Fas-ligand translocation to rafts, and the subsequent induction of Fas-ligand-dependent cell death. A possibility of a similar association between other TNF family members and caveolin-1 is discussed.
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Effects of electrostatic interactions on ligand dissociation kinetics
NASA Astrophysics Data System (ADS)
Erbaş, Aykut; de la Cruz, Monica Olvera; Marko, John F.
2018-02-01
We study unbinding of multivalent cationic ligands from oppositely charged polymeric binding sites sparsely grafted on a flat neutral substrate. Our molecular dynamics simulations are suggested by single-molecule studies of protein-DNA interactions. We consider univalent salt concentrations spanning roughly a 1000-fold range, together with various concentrations of excess ligands in solution. To reveal the ionic effects on unbinding kinetics of spontaneous and facilitated dissociation mechanisms, we treat electrostatic interactions both at a Debye-Hückel (DH) (or implicit ions, i.e., use of an electrostatic potential with a prescribed decay length) level and by the more precise approach of considering all ionic species explicitly in the simulations. We find that the DH approach systematically overestimates unbinding rates, relative to the calculations where all ion pairs are present explicitly in solution, although many aspects of the two types of calculation are qualitatively similar. For facilitated dissociation (FD) (acceleration of unbinding by free ligands in solution) explicit-ion simulations lead to unbinding at lower free-ligand concentrations. Our simulations predict a variety of FD regimes as a function of free-ligand and ion concentrations; a particularly interesting regime is at intermediate concentrations of ligands where nonelectrostatic binding strength controls FD. We conclude that explicit-ion electrostatic modeling is an essential component to quantitatively tackle problems in molecular ligand dissociation, including nucleic-acid-binding proteins.
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Ravindranath, Pradeep Anand; Sanner, Michel F.
2016-01-01
Motivation: The identification of ligand-binding sites from a protein structure facilitates computational drug design and optimization, and protein function assignment. We introduce AutoSite: an efficient software tool for identifying ligand-binding sites and predicting pseudo ligand corresponding to each binding site identified. Binding sites are reported as clusters of 3D points called fills in which every point is labelled as hydrophobic or as hydrogen bond donor or acceptor. From these fills AutoSite derives feature points: a set of putative positions of hydrophobic-, and hydrogen-bond forming ligand atoms. Results: We show that AutoSite identifies ligand-binding sites with higher accuracy than other leading methods, and produces fills that better matches the ligand shape and properties, than the fills obtained with a software program with similar capabilities, AutoLigand. In addition, we demonstrate that for the Astex Diverse Set, the feature points identify 79% of hydrophobic ligand atoms, and 81% and 62% of the hydrogen acceptor and donor hydrogen ligand atoms interacting with the receptor, and predict 81.2% of water molecules mediating interactions between ligand and receptor. Finally, we illustrate potential uses of the predicted feature points in the context of lead optimization in drug discovery projects. Availability and Implementation: http://adfr.scripps.edu/AutoDockFR/autosite.html Contact: sanner@scripps.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27354702
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Fully Flexible Docking of Medium Sized Ligand Libraries with RosettaLigand
DeLuca, Samuel; Khar, Karen; Meiler, Jens
2015-01-01
RosettaLigand has been successfully used to predict binding poses in protein-small molecule complexes. However, the RosettaLigand docking protocol is comparatively slow in identifying an initial starting pose for the small molecule (ligand) making it unfeasible for use in virtual High Throughput Screening (vHTS). To overcome this limitation, we developed a new sampling approach for placing the ligand in the protein binding site during the initial ‘low-resolution’ docking step. It combines the translational and rotational adjustments to the ligand pose in a single transformation step. The new algorithm is both more accurate and more time-efficient. The docking success rate is improved by 10–15% in a benchmark set of 43 protein/ligand complexes, reducing the number of models that typically need to be generated from 1000 to 150. The average time to generate a model is reduced from 50 seconds to 10 seconds. As a result we observe an effective 30-fold speed increase, making RosettaLigand appropriate for docking medium sized ligand libraries. We demonstrate that this improved initial placement of the ligand is critical for successful prediction of an accurate binding position in the ‘high-resolution’ full atom refinement step. PMID:26207742
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NALDB: nucleic acid ligand database for small molecules targeting nucleic acid.
Kumar Mishra, Subodh; Kumar, Amit
2016-01-01
Nucleic acid ligand database (NALDB) is a unique database that provides detailed information about the experimental data of small molecules that were reported to target several types of nucleic acid structures. NALDB is the first ligand database that contains ligand information for all type of nucleic acid. NALDB contains more than 3500 ligand entries with detailed pharmacokinetic and pharmacodynamic information such as target name, target sequence, ligand 2D/3D structure, SMILES, molecular formula, molecular weight, net-formal charge, AlogP, number of rings, number of hydrogen bond donor and acceptor, potential energy along with their Ki, Kd, IC50 values. All these details at single platform would be helpful for the development and betterment of novel ligands targeting nucleic acids that could serve as a potential target in different diseases including cancers and neurological disorders. With maximum 255 conformers for each ligand entry, our database is a multi-conformer database and can facilitate the virtual screening process. NALDB provides powerful web-based search tools that make database searching efficient and simplified using option for text as well as for structure query. NALDB also provides multi-dimensional advanced search tool which can screen the database molecules on the basis of molecular properties of ligand provided by database users. A 3D structure visualization tool has also been included for 3D structure representation of ligands. NALDB offers an inclusive pharmacological information and the structurally flexible set of small molecules with their three-dimensional conformers that can accelerate the virtual screening and other modeling processes and eventually complement the nucleic acid-based drug discovery research. NALDB can be routinely updated and freely available on bsbe.iiti.ac.in/bsbe/naldb/HOME.php. Database URL: http://bsbe.iiti.ac.in/bsbe/naldb/HOME.php. © The Author(s) 2016. Published by Oxford University Press.
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NALDB: nucleic acid ligand database for small molecules targeting nucleic acid
Kumar Mishra, Subodh; Kumar, Amit
2016-01-01
Nucleic acid ligand database (NALDB) is a unique database that provides detailed information about the experimental data of small molecules that were reported to target several types of nucleic acid structures. NALDB is the first ligand database that contains ligand information for all type of nucleic acid. NALDB contains more than 3500 ligand entries with detailed pharmacokinetic and pharmacodynamic information such as target name, target sequence, ligand 2D/3D structure, SMILES, molecular formula, molecular weight, net-formal charge, AlogP, number of rings, number of hydrogen bond donor and acceptor, potential energy along with their Ki, Kd, IC50 values. All these details at single platform would be helpful for the development and betterment of novel ligands targeting nucleic acids that could serve as a potential target in different diseases including cancers and neurological disorders. With maximum 255 conformers for each ligand entry, our database is a multi-conformer database and can facilitate the virtual screening process. NALDB provides powerful web-based search tools that make database searching efficient and simplified using option for text as well as for structure query. NALDB also provides multi-dimensional advanced search tool which can screen the database molecules on the basis of molecular properties of ligand provided by database users. A 3D structure visualization tool has also been included for 3D structure representation of ligands. NALDB offers an inclusive pharmacological information and the structurally flexible set of small molecules with their three-dimensional conformers that can accelerate the virtual screening and other modeling processes and eventually complement the nucleic acid-based drug discovery research. NALDB can be routinely updated and freely available on bsbe.iiti.ac.in/bsbe/naldb/HOME.php. Database URL: http://bsbe.iiti.ac.in/bsbe/naldb/HOME.php PMID:26896846
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PLIP: fully automated protein-ligand interaction profiler.
Salentin, Sebastian; Schreiber, Sven; Haupt, V Joachim; Adasme, Melissa F; Schroeder, Michael
2015-07-01
The characterization of interactions in protein-ligand complexes is essential for research in structural bioinformatics, drug discovery and biology. However, comprehensive tools are not freely available to the research community. Here, we present the protein-ligand interaction profiler (PLIP), a novel web service for fully automated detection and visualization of relevant non-covalent protein-ligand contacts in 3D structures, freely available at projects.biotec.tu-dresden.de/plip-web. The input is either a Protein Data Bank structure, a protein or ligand name, or a custom protein-ligand complex (e.g. from docking). In contrast to other tools, the rule-based PLIP algorithm does not require any structure preparation. It returns a list of detected interactions on single atom level, covering seven interaction types (hydrogen bonds, hydrophobic contacts, pi-stacking, pi-cation interactions, salt bridges, water bridges and halogen bonds). PLIP stands out by offering publication-ready images, PyMOL session files to generate custom images and parsable result files to facilitate successive data processing. The full python source code is available for download on the website. PLIP's command-line mode allows for high-throughput interaction profiling. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
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Sun, Xianfeng; Zhou, Le; Li, Wei; Zhang, Xumu
2008-02-01
A convenient, divergent strategy for the synthesis of a series of modular and fine-tunable C3-TunePhos-type chiral diphosphine ligands and their applications in highly efficient Ru-catalyzed asymmetric hydrogenations were explored. Up to 97 and 99% ee values were achieved for the enantioselective synthesis of beta-methyl chiral amines and alpha-hydroxy acid derivatives, respectively.
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Yu, Xiaochun; Sharma, Kailash D.; Takahashi, Tsuyoshi; Iwamoto, Ryo; Mekada, Eisuke
2002-01-01
Dimerization and phosphorylation of the epidermal growth factor (EGF) receptor (EGFR) are the initial and essential events of EGF-induced signal transduction. However, the mechanism by which EGFR ligands induce dimerization and phosphorylation is not fully understood. Here, we demonstrate that EGFRs can form dimers on the cell surface independent of ligand binding. However, a chimeric receptor, comprising the extracellular and transmembrane domains of EGFR and the cytoplasmic domain of the erythropoietin receptor (EpoR), did not form a dimer in the absence of ligands, suggesting that the cytoplasmic domain of EGFR is important for predimer formation. Analysis of deletion mutants of EGFR showed that the region between 835Ala and 918Asp of the EGFR cytoplasmic domain is required for EGFR predimer formation. In contrast to wild-type EGFR ligands, a mutant form of heparin-binding EGF-like growth factor (HB2) did not induce dimerization of the EGFR-EpoR chimeric receptor and therefore failed to activate the chimeric receptor. However, when the dimerization was induced by a monoclonal antibody to EGFR, HB2 could activate the chimeric receptor. These results indicate that EGFR can form a ligand-independent inactive dimer and that receptor dimerization and activation are mechanistically distinct and separable events. PMID:12134089
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Differential hydrogen/deuterium exchange mass spectrometry analysis of protein–ligand interactions
Chalmers, Michael J; Busby, Scott A; Pascal, Bruce D; West, Graham M; Griffin, Patrick R
2011-01-01
Functional regulation of ligand-activated receptors is driven by alterations in the conformational dynamics of the protein upon ligand binding. Differential hydrogen/deuterium exchange (HDX) coupled with mass spectrometry has emerged as a rapid and sensitive approach for characterization of perturbations in conformational dynamics of proteins following ligand binding. While this technique is sensitive to detecting ligand interactions and alterations in receptor dynamics, it also can provide important mechanistic insights into ligand regulation. For example, HDX has been used to determine a novel mechanism of ligand activation of the nuclear receptor peroxisome proliferator activated receptor-γ, perform detailed analyses of binding modes of ligands within the ligand-binding pocket of two estrogen receptor isoforms, providing insight into selectivity, and helped classify different types of estrogen receptor-α ligands by correlating their pharmacology with the way they interact with the receptor based solely on hierarchical clustering of receptor HDX signatures. Beyond small-molecule–receptor interactions, this technique has also been applied to study protein–protein complexes, such as mapping antibody–antigen interactions. In this article, we summarize the current state of the differential HDX approaches and the future outlook. We summarize how HDX analysis of protein–ligand interactions has had an impact on biology and drug discovery. PMID:21329427
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Ligand Depot: a data warehouse for ligands bound to macromolecules.
Feng, Zukang; Chen, Li; Maddula, Himabindu; Akcan, Ozgur; Oughtred, Rose; Berman, Helen M; Westbrook, John
2004-09-01
Ligand Depot is an integrated data resource for finding information about small molecules bound to proteins and nucleic acids. The initial release (version 1.0, November, 2003) focuses on providing chemical and structural information for small molecules found as part of the structures deposited in the Protein Data Bank. Ligand Depot accepts keyword-based queries and also provides a graphical interface for performing chemical substructure searches. A wide variety of web resources that contain information on small molecules may also be accessed through Ligand Depot. Ligand Depot is available at http://ligand-depot.rutgers.edu/. Version 1.0 supports multiple operating systems including Windows, Unix, Linux and the Macintosh operating system. The current drawing tool works in Internet Explorer, Netscape and Mozilla on Windows, Unix and Linux.
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Kroupa, Daniel M.; Anderson, Nicholas C.; Castaneda, Chloe V.; ...
2016-11-07
Here, we employed quantitative NMR spectroscopy and spectrophotometric absorbance titration to study a quantum dot X-type ligand exchange reaction. We find that the exchange is highly cooperative, where at low extents of exchange the change in free energy of the reaction, Δ G XC, is ~11 kJ mol –1 while at higher extents of exchange Δ G XC saturates to ~–4 kJ mol –1. A modified Fowler binding isotherm is developed to describe the reaction.
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Architecture effects on multivalent interactions by polypeptide-based multivalent ligands
NASA Astrophysics Data System (ADS)
Liu, Shuang
Multivalent interactions are characterized by the simultaneous binding between multiple ligands and multiple binding sites, either in solutions or at interfaces. In biological systems, most multivalent interactions occur between protein receptors and carbohydrate ligands through hydrogen-bonding and hydrophobic interactions. Compared with weak affinity binding between one ligand and one binding site, i.e. monovalent interaction, multivalent interactioins provide greater avidity and specificity, and therefore play unique roles in a broad range of biological activities. Moreover, the studies of multivalent interactions are also essential for producing effective inhibitors and effectors of biological processes that could have important therapeutic applications. Synthetic multivalent ligands have been designed to mimic the biological functions of natural multivalent interactions, and various types of scaffolds have been used to display multiple ligands, including small molecules, linear polymers, dendrimers, nanoparticle surfaces, monolayer surfaces and liposomes. Studies have shown that multivalent interactions can be highly affected by various architectural parameters of these multivalent ligands, including ligand identities, valencies, spacing, ligand densities, nature of linker arms, scaffold length and scaffold conformation. Most of these multivalent ligands are chemically synthesized and have limitations of controlling over sequence and conformation, which is a barrier for mimicking ordered and controlled natural biological systems. Therefore, multivalent ligands with precisely controlled architecture are required for improved structure-function relationship studies. Protein engineering methods with subsequent chemical coupling of ligands provide significant advantages of controlling over backbone conformation and functional group placement, and therefore have been used to synthesize recombinant protein-based materials with desired properties similar to natural
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Bassner, S.L.; Morrison, E.D.; Geoffroy, G.L.
1986-08-20
Free ketene is a valuable organic synthetic reagent, but its utility is somewhat limited by its high reactivity and tendency to dimerize to yield diketene. The ketene ligand is obviously stabilized by metal coordination in a variety of bonding modes, but it is not yet known how coordination influences the chemistry of this important molecule. The authors have studied the reactivity of the coordinated ketene ligand of type II found in the anionic cluster compound (PPN)(Os/sub 3/(CO)/sub 10/(..mu..-I)(..mu..-CH/sub 2/CO)) (1) (PPN/sup +/ = (Ph/sub 3/P)/sub 2/N/sup +/) and herein show that this ligand is readily converted into eta-enolate ligands uponmore » reaction with simple nucleophiles and into vinyl and acetyl ligands upon reaction with electrophiles.« less
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Impact of protein and ligand impurities on ITC-derived protein-ligand thermodynamics.
Grüner, Stefan; Neeb, Manuel; Barandun, Luzi Jakob; Sielaff, Frank; Hohn, Christoph; Kojima, Shun; Steinmetzer, Torsten; Diederich, François; Klebe, Gerhard
2014-09-01
The thermodynamic characterization of protein-ligand interactions by isothermal titration calorimetry (ITC) is a powerful tool in drug design, giving valuable insight into the interaction driving forces. ITC is thought to require protein and ligand solutions of high quality, meaning both the absence of contaminants as well as accurately determined concentrations. Ligands synthesized to deviating purity and protein of different pureness were titrated by ITC. Data curation was attempted also considering information from analytical techniques to correct stoichiometry. We used trypsin and tRNA-guanine transglycosylase (TGT), together with high affinity ligands to investigate the effect of errors in protein concentration as well as the impact of ligand impurities on the apparent thermodynamics. We found that errors in protein concentration did not change the thermodynamic properties obtained significantly. However, most ligand impurities led to pronounced changes in binding enthalpy. If protein binding of the respective impurity is not expected, the actual ligand concentration was corrected for and the thus revised data compared to thermodynamic properties obtained with the respective pure ligand. Even in these cases, we observed differences in binding enthalpy of about 4kJ⋅mol(-1), which is considered significant. Our results indicate that ligand purity is the critical parameter to monitor if accurate thermodynamic data of a protein-ligand complex are to be recorded. Furthermore, artificially changing fitting parameters to obtain a sound interaction stoichiometry in the presence of uncharacterized ligand impurities may lead to thermodynamic parameters significantly deviating from the accurate thermodynamic signature. Copyright © 2014 Elsevier B.V. All rights reserved.
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Group Additivity in Ligand Binding Affinity: An Alternative Approach to Ligand Efficiency.
Reynolds, Charles H; Reynolds, Ryan C
2017-12-26
Group additivity is a concept that has been successfully applied to a variety of thermochemical and kinetic properties. This includes drug discovery, where functional group additivity is often assumed in ligand binding. Ligand efficiency can be recast as a special case of group additivity where ΔG/HA is the group equivalent (HA is the number of non-hydrogen atoms in a ligand). Analysis of a large data set of protein-ligand binding affinities (K i ) for diverse targets shows that in general ligand binding is distinctly nonlinear. It is possible to create a group equivalent scheme for ligand binding, but only in the context of closely related proteins, at least with regard to size. This finding has broad implications for drug design from both experimental and computational points of view. It also offers a path forward for a more general scheme to assess the efficiency of ligand binding.
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Differential TAM receptor-ligand-phospholipid interactions delimit differential TAM bioactivities.
Lew, Erin D; Oh, Jennifer; Burrola, Patrick G; Lax, Irit; Zagórska, Anna; Través, Paqui G; Schlessinger, Joseph; Lemke, Greg
2014-09-29
The TAM receptor tyrosine kinases Tyro3, Axl, and Mer regulate key features of cellular physiology, yet the differential activities of the TAM ligands Gas6 and Protein S are poorly understood. We have used biochemical and genetic analyses to delineate the rules for TAM receptor-ligand engagement and find that the TAMs segregate into two groups based on ligand specificity, regulation by phosphatidylserine, and function. Tyro3 and Mer are activated by both ligands but only Gas6 activates Axl. Optimal TAM signaling requires coincident TAM ligand engagement of both its receptor and the phospholipid phosphatidylserine (PtdSer): Gas6 lacking its PtdSer-binding 'Gla domain' is significantly weakened as a Tyro3/Mer agonist and is inert as an Axl agonist, even though it binds to Axl with wild-type affinity. In two settings of TAM-dependent homeostatic phagocytosis, Mer plays a predominant role while Axl is dispensable, and activation of Mer by Protein S is sufficient to drive phagocytosis.
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Ligand-independent pathway that controls stability of interferon alpha receptor
Liu, Jianghuai; Plotnikov, Alexander; Banerjee, Anamika; Kumar, K.G. Suresh; Ragimbeau, Josiane; Marijanovic, Zrinka; Baker, Darren P.; Pellegrini, Sandra; Fuchs, Serge Y.
2008-01-01
SUMMARY Ligand-specific negative regulation of cytokine-induced signaling relies on down regulation of the cytokine receptors. Down regulation of the IFNAR1 sub-unit of the Type I interferon (IFN) receptor proceeds via lysosomal receptor proteolysis, which is triggered by ubiquitination that depends on IFNAR1 serine phosphorylation. While IFN-inducible phosphorylation, ubiquitination and degradation requires the catalytic activity of the Tyk2 Janus kinase, here we found the ligand- and Tyk2-independent pathway that promotes IFNAR1 phosphorylation, ubiquitination, and degradation when IFNAR1 is expressed at high levels. A major cellular kinase activity that is responsible for IFNAR1 phosphorylation in vitro does not depend on either ligand or Tyk2 activity. Inhibition of ligand-independent IFNAR1 degradation suppresses cell proliferation. We discuss the signaling events that might lead to ubiquitination and degradation of IFNAR1 via ligand-dependent and independent pathways and their potential physiologic significance. PMID:18166147
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A mixed valence zinc dithiolene system with spectator metal and reactor ligands.
Ratvasky, Stephen C; Mogesa, Benjamin; van Stipdonk, Michael J; Basu, Partha
2016-08-16
Neutral complexes of zinc with N,N'-diisopropylpiperazine-2,3-dithione ( i Pr 2 Dt 0 ) and N,N'-dimethylpiperazine-2,3-dithione (Me 2 Dt 0 ) with chloride or maleonitriledithiolate (mnt 2- ) as coligands have been synthesized and characterized. The molecular structures of these zinc complexes have been determined using single crystal X-ray diffractometry. Complexes recrystallize in monoclinic P type systems with zinc adopting a distorted tetrahedral geometry. Two zinc complexes with mixed-valent dithiolene ligands exhibit ligand-to-ligand charge transfer bands. Optimized geometries, molecular vibrations and electronic structures of charge-transfer complexes were calculated using density functional theory (B3LYP/6-311G+(d,p) level). Redox orbitals are shown to be almost exclusively ligand in nature, with a HOMO based heavily on the electron-rich maleonitriledithiolate ligand, and a LUMO comprised mostly of the electron-deficient dithione ligand. Charge transfer is thus believed to proceed from dithiolate HOMO to dithione LUMO, showing ligand-to-ligand redox interplay across a d 10 metal.
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Characterization of Colloidal Quantum Dot Ligand Exchange by X-ray Photoelectron Spectroscopy
NASA Astrophysics Data System (ADS)
Atewologun, Ayomide; Ge, Wangyao; Stiff-Roberts, Adrienne D.
2013-05-01
Colloidal quantum dots (CQDs) are chemically synthesized semiconductor nanoparticles with size-dependent wavelength tunability. Chemical synthesis of CQDs involves the attachment of long organic surface ligands to prevent aggregation; however, these ligands also impede charge transport. Therefore, it is beneficial to exchange longer surface ligands for shorter ones for optoelectronic devices. Typical characterization techniques used to analyze surface ligand exchange include Fourier-transform infrared spectroscopy, x-ray diffraction, transmission electron microscopy, and nuclear magnetic resonance spectroscopy, yet these techniques do not provide a simultaneously direct, quantitative, and sensitive method for evaluating surface ligands on CQDs. In contrast, x-ray photoelectron spectroscopy (XPS) can provide nanoscale sensitivity for quantitative analysis of CQD surface ligand exchange. A unique aspect of this work is that a fingerprint is identified for shorter surface ligands by resolving the regional XPS spectrum corresponding to different types of carbon bonds. In addition, a deposition technique known as resonant infrared matrix-assisted pulsed laser evaporation is used to improve the CQD film uniformity such that stronger XPS signals are obtained, enabling more accurate analysis of the ligand exchange process.
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Parkesh, Raman; Childs-Disney, Jessica L.; Nakamori, Masayuki; Kumar, Amit; Wang, Eric; Wang, Thomas; Hoskins, Jason; Tran, Tuan; Housman, David; Thornton, Charles A.; Disney, Matthew D.
2012-01-01
Myotonic dystrophy type 1 (DM1) is a triplet repeating disorder caused by expanded CTG repeats in the 3′ untranslated region of the dystrophia myotonica protein kinase (DMPK) gene. The transcribed repeats fold into an RNA hairpin with multiple copies of a 5′CUG/3′GUC motif that binds the RNA splicing regulator muscleblind-like 1 protein (MBNL1). Sequestration of MBNL1 by expanded r(CUG) repeats causes splicing defects in a subset of pre-mRNAs including the insulin receptor, the muscle-specific chloride ion channel, Sarco(endo)plasmic reticulum Ca2+ ATPase 1 (Serca1/Atp2a1), and cardiac troponin T (cTNT). Based on these observations, the development of small molecule ligands that target specifically expanded DM1 repeats could serve as therapeutics. In the present study, computational screening was employed to improve the efficacy of pentamidine and Hoechst 33258 ligands that have been shown previously to target the DM1 triplet repeat. A series of inhibitors of the RNA-protein complex with low micromolar IC50’s, which are >20-fold more potent than the query compounds, were identified. Importantly, a bis-benzimidazole identified from the Hoechst query improves DM1-associated pre-mRNA splicing defects in cell and mouse models of DM1 (when dosed with 1 mM and 100 mg/kg, respectively). Since Hoechst 33258 was identified as a DM1 binder through analysis of an RNA motif-ligand database, these studies suggest that lead ligands targeting RNA with improved biological activity can be identified by using a synergistic approach that combines analysis of known RNA-ligand interactions with virtual screening. PMID:22300544
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Algarra, Andrés G; Basallote, Manuel G; Fernandez-Trujillo, M J; Llusar, Rosa; Pino-Chamorro, Jose A; Sorribes, Ivan; Vicent, Cristian
2010-04-21
The synthesis, crystal structure and solution characterization of the cubane-type [Mo(3)(FeCl)S(4)(dmpe)(3)Cl(3)] (1) (dmpe = 1,2-bis(dimethylphophane-ethane)) cluster are reported and the ligand substitution processes of chloride by thiophenolate investigated. The kinetics and the intimate mechanism of these substitutions reveal that compound 1 undergoes a number of Fe and Mo site specific ligand substitution reactions in acetonitrile solutions. In particular, PhS(-) coordination at the tetrahedral Fe site proceeds in a single resolved kinetic step whereas such substitutions at the Mo sites proceed more slowly. The effect of the presence of acids in the reaction media is also investigated and reveals that an acid excess hinders substitution reactions both at the Fe and Mo sites; however, an acid-promoted solvolysis of the Fe-Cl bonds is observed. Electrospray ionization (ESI) and tandem (ESI-MS/MS) mass spectrometry allow the identification of all the reaction intermediates proposed on the basis of stopped-flow measurements. The distinctive site specific reactivity made it possible to isolate two new clusters of the Mo(3)FeS(4)(4+) family featuring mixed chlorine/thiophenolate ligands, namely Mo(3)S(4)(FeSPh)(dmpe)(3)Cl(3) (2) and [Mo(3)S(4)(FeSPh)(dmpe)(3)(SPh)(3)] (3). A detailed computational study has also been carried out to understand the details of the mechanism of substitution at the M-Cl (M = Mo and Fe) bonds as well as the solvolysis at the Fe-Cl sites, with particular emphasis on the role of acids on the substitution process. The results of the calculations are in agreement with the experimental observations, thus justifying the non-existence of an accelerating effect of acids on the thiophenolate substitution reaction, which differs from previous proposals for the Fe(4)S(4) and MoFe(3)S(4) clusters and some related compounds.
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Activin receptor ligand traps in chronic kidney disease.
Jelkmann, Wolfgang
2018-05-29
Sotatercept and luspatercept are recombinant soluble activin type-II receptor-IgG-Fc fusion proteins that are tested in clinical trials for the treatment of various types of anemias, including renal anemia. The mechanism of the action of the novel drugs is incompletely understood, but it seems to be based on the inactivation of soluble proteins of the transforming growth factor-ß (TGFß) family. This review considers pros and cons of the clinical use of the drugs in reference to the current therapy with recombinant erythropoiesis-stimulating agents (ESAs). One or more activin type-II receptor (ActRII) ligands appear to inhibit erythroid precursors, for example growth and differentiation factor 11. Trapping of these ligands by the recombinant ActRII fusion proteins, sotatercept and luspatercept increases red blood cell numbers and hemoglobin levels in humans. Reportedly, the novel compounds were well tolerated in trials on healthy volunteers and patients suffering from anemia due to chronic kidney disease or malignancies. On approval, the drugs may prove particularly useful in patients suffering from ineffective erythropoiesis, such as in myelodysplastic syndrome, multiple myeloma or ß-thalassemia, where ESAs are of little use. Independent of their effect on erythropoiesis, ActRII ligand traps were found to exert beneficial effects on renal tissue in experimental animals. ESAs are likely to remain standard of care in renal anemia. There is a need for a better understanding of the effects of ActRII ligand traps on TGFß-like proteins. The novel drugs have not been approved for sale as therapeutics so far. Their long-term efficacy and safety still needs to be proven, particularly with respect to immunogenicity. Antifibrotic effects may be worthy to be investigated in humans.
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NASA Astrophysics Data System (ADS)
Cholko, Timothy; Chen, Wei; Tang, Zhiye; Chang, Chia-en A.
2018-05-01
Abnormal activity of cyclin-dependent kinase 8 (CDK8) along with its partner protein cyclin C (CycC) is a common feature of many diseases including colorectal cancer. Using molecular dynamics (MD) simulations, this study determined the dynamics of the CDK8-CycC system and we obtained detailed breakdowns of binding energy contributions for four type-I and five type-II CDK8 inhibitors. We revealed system motions and conformational changes that will affect ligand binding, confirmed the essentialness of CycC for inclusion in future computational studies, and provide guidance in development of CDK8 binders. We employed unbiased all-atom MD simulations for 500 ns on twelve CDK8-CycC systems, including apoproteins and protein-ligand complexes, then performed principal component analysis (PCA) and measured the RMSF of key regions to identify protein dynamics. Binding pocket volume analysis identified conformational changes that accompany ligand binding. Next, H-bond analysis, residue-wise interaction calculations, and MM/PBSA were performed to characterize protein-ligand interactions and find the binding energy. We discovered that CycC is vital for maintaining a proper conformation of CDK8 to facilitate ligand binding and that the system exhibits motion that should be carefully considered in future computational work. Surprisingly, we found that motion of the activation loop did not affect ligand binding. Type-I and type-II ligand binding is driven by van der Waals interactions, but electrostatic energy and entropic penalties affect type-II binding as well. Binding of both ligand types affects protein flexibility. Based on this we provide suggestions for development of tighter-binding CDK8 inhibitors and offer insight that can aid future computational studies.
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Seth, P; Ganapathy, M E; Conway, S J; Bridges, C D; Smith, S B; Casellas, P; Ganapathy, V
2001-07-25
The type 1 sigma receptor (sigmaR1) has been shown to participate in a variety of functions in the central nervous system. To identify the specific regions of the brain that are involved in sigmaR1 function, we analyzed the expression pattern of the receptor mRNA in the mouse brain by in situ hybridization. SigmaR1 mRNA was detectable primarily in the cerebral cortex, hippocampus, and Purkinje cells of cerebellum. To identify the critical anionic amino acid residues in the ligand-binding domain of sigmaR1, we employed two different approaches: chemical modification of anionic amino acid residues and site-directed mutagenesis. Chemical modification of anionic amino acids in sigmaR1 with 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide reduced the ligand-binding activity markedly. Since it is known that a splice variant of this receptor which lacks exon 3 does not have the ability to bind sigma ligands, the ligand-binding domain with its critical anionic amino acid residues is likely to be present in or around the region coded by exon 3. Therefore, each of the anionic amino acids in this region was mutated individually and the influence of each mutation on ligand binding was assessed. These studies have identified two anionic amino acids, D126 and E172, that are obligatory for ligand binding. Even though the ligand-binding function was abolished by these two mutations, the expression of these mutants was normal at the protein level. These results show that sigmaR1 is expressed at high levels in specific areas of the brain that are involved in memory, emotion and motor functions. The results also provide important information on the chemical nature of the ligand-binding site of sigmaR1 that may be of use in the design of sigmaR1-specific ligands with potential for modulation of sigmaR1-related brain functions.
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A new test set for validating predictions of protein-ligand interaction.
Nissink, J Willem M; Murray, Chris; Hartshorn, Mike; Verdonk, Marcel L; Cole, Jason C; Taylor, Robin
2002-12-01
We present a large test set of protein-ligand complexes for the purpose of validating algorithms that rely on the prediction of protein-ligand interactions. The set consists of 305 complexes with protonation states assigned by manual inspection. The following checks have been carried out to identify unsuitable entries in this set: (1) assessing the involvement of crystallographically related protein units in ligand binding; (2) identification of bad clashes between protein side chains and ligand; and (3) assessment of structural errors, and/or inconsistency of ligand placement with crystal structure electron density. In addition, the set has been pruned to assure diversity in terms of protein-ligand structures, and subsets are supplied for different protein-structure resolution ranges. A classification of the set by protein type is available. As an illustration, validation results are shown for GOLD and SuperStar. GOLD is a program that performs flexible protein-ligand docking, and SuperStar is used for the prediction of favorable interaction sites in proteins. The new CCDC/Astex test set is freely available to the scientific community (http://www.ccdc.cam.ac.uk). Copyright 2002 Wiley-Liss, Inc.
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Ligand migration in the truncated hemoglobin of Mycobacterium tuberculosis.
Heroux, Maxime S; Mohan, Anne D; Olsen, Kenneth W
2011-03-01
The truncated hemoglobin of Mycobacterium tuberculosis (Mt-trHbO) is a small heme protein belonging to the hemoglobin superfamily. Truncated hemoglobins (trHbs) are believed to have functional roles such as terminal oxidases and oxygen sensors involved in the response to oxidative and nitrosative stress, nitric oxide (NO) detoxification, O₂/NO chemistry, O₂ delivery under hypoxic conditions, and long-term ligand storage. Based on sequence similarities, they are classified into three groups. Experimental studies revealed that all trHbs display a 2-on-2 α-helical sandwich fold rather than the 3-on-3 α-helical sandwich fold of the classical hemoglobin fold. Using locally enhanced sampling (LESMD) molecular dynamics, the ligand-binding escape pathways from the distal heme binding cavity of Mt-trHbO were determined to better understand how this protein functions. The importance of specific residues, such as the group II and III invariant W(G8) residue, can be seen in terms of ligand diffusion pathways and ligand dynamics. LESMD simulations show that the wild-type Mt-trHbO has three diffusion pathways while the W(G8)F Mt-trHbO mutant has only two. The W(G8) residue plays a critical role in ligand binding and stabilization and helps regulate the rate of ligand escape from the distal heme pocket. Thus, this invariant residue is important in creating ligand diffusion pathways and possibly in the enzymatic functions of this protein. Copyright © 2011 Wiley Periodicals, Inc.
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Capping Ligand Vortices as "Atomic Orbitals" in Nanocrystal Self-Assembly.
Waltmann, Curt; Horst, Nathan; Travesset, Alex
2017-11-28
We present a detailed analysis of the interaction between two nanocrystals capped with ligands consisting of hydrocarbon chains by united atom molecular dynamics simulations. We show that the bonding of two nanocrystals is characterized by ligand textures in the form of vortices. These results are generalized to nanocrystals of different types (differing core and ligand sizes) where the structure of the vortices depends on the softness asymmetry. We provide rigorous calculations for the binding free energy, show that these energies are independent of the chemical composition of the cores, and derive analytical formulas for the equilibrium separation. We discuss the implications of our results for the self-assembly of single-component and binary nanoparticle superlattices. Overall, our results show that the structure of the ligands completely determines the bonding of nanocrystals, fully supporting the predictions of the recently proposed Orbifold topological model.
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Pérot, Stéphanie; Regad, Leslie; Reynès, Christelle; Spérandio, Olivier; Miteva, Maria A; Villoutreix, Bruno O; Camproux, Anne-Claude
2013-01-01
Pockets are today at the cornerstones of modern drug discovery projects and at the crossroad of several research fields, from structural biology to mathematical modeling. Being able to predict if a small molecule could bind to one or more protein targets or if a protein could bind to some given ligands is very useful for drug discovery endeavors, anticipation of binding to off- and anti-targets. To date, several studies explore such questions from chemogenomic approach to reverse docking methods. Most of these studies have been performed either from the viewpoint of ligands or targets. However it seems valuable to use information from both ligands and target binding pockets. Hence, we present a multivariate approach relating ligand properties with protein pocket properties from the analysis of known ligand-protein interactions. We explored and optimized the pocket-ligand pair space by combining pocket and ligand descriptors using Principal Component Analysis and developed a classification engine on this paired space, revealing five main clusters of pocket-ligand pairs sharing specific and similar structural or physico-chemical properties. These pocket-ligand pair clusters highlight correspondences between pocket and ligand topological and physico-chemical properties and capture relevant information with respect to protein-ligand interactions. Based on these pocket-ligand correspondences, a protocol of prediction of clusters sharing similarity in terms of recognition characteristics is developed for a given pocket-ligand complex and gives high performances. It is then extended to cluster prediction for a given pocket in order to acquire knowledge about its expected ligand profile or to cluster prediction for a given ligand in order to acquire knowledge about its expected pocket profile. This prediction approach shows promising results and could contribute to predict some ligand properties critical for binding to a given pocket, and conversely, some key pocket
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Reynès, Christelle; Spérandio, Olivier; Miteva, Maria A.; Villoutreix, Bruno O.; Camproux, Anne-Claude
2013-01-01
Pockets are today at the cornerstones of modern drug discovery projects and at the crossroad of several research fields, from structural biology to mathematical modeling. Being able to predict if a small molecule could bind to one or more protein targets or if a protein could bind to some given ligands is very useful for drug discovery endeavors, anticipation of binding to off- and anti-targets. To date, several studies explore such questions from chemogenomic approach to reverse docking methods. Most of these studies have been performed either from the viewpoint of ligands or targets. However it seems valuable to use information from both ligands and target binding pockets. Hence, we present a multivariate approach relating ligand properties with protein pocket properties from the analysis of known ligand-protein interactions. We explored and optimized the pocket-ligand pair space by combining pocket and ligand descriptors using Principal Component Analysis and developed a classification engine on this paired space, revealing five main clusters of pocket-ligand pairs sharing specific and similar structural or physico-chemical properties. These pocket-ligand pair clusters highlight correspondences between pocket and ligand topological and physico-chemical properties and capture relevant information with respect to protein-ligand interactions. Based on these pocket-ligand correspondences, a protocol of prediction of clusters sharing similarity in terms of recognition characteristics is developed for a given pocket-ligand complex and gives high performances. It is then extended to cluster prediction for a given pocket in order to acquire knowledge about its expected ligand profile or to cluster prediction for a given ligand in order to acquire knowledge about its expected pocket profile. This prediction approach shows promising results and could contribute to predict some ligand properties critical for binding to a given pocket, and conversely, some key pocket
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Role of ligand-ligand vs. core-core interactions in gold nanoclusters.
Milowska, Karolina Z; Stolarczyk, Jacek K
2016-05-14
The controlled assembly of ligand-coated gold nanoclusters (NCs) into larger structures paves the way for new applications ranging from electronics to nanomedicine. Here, we demonstrate through rigorous density functional theory (DFT) calculations employing novel functionals accounting for van der Waals forces that the ligand-ligand interactions determine whether stable assemblies can be formed. The study of NCs with different core sizes, symmetry forms, ligand lengths, mutual crystal orientations, and in the presence of a solvent suggests that core-to-core van der Waals interactions play a lesser role in the assembly. The dominant interactions originate from combination of steric effects, augmented by ligand bundling on NC facets, and related to them changes in electronic properties induced by neighbouring NCs. We also show that, in contrast to standard colloidal theory approach, DFT correctly reproduces the surprising experimental trends in the strength of the inter-particle interaction observed when varying the length of the ligands. The results underpin the importance of understanding NC interactions in designing gold NCs for a specific function.
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Decatur, S M; DePillis, G D; Boxer, S G
1996-04-02
A variety of heterocyclic ligands can be exchanged into the proximal cavity of sperm whale myoglobin mutant H93G, providing a simple method for introduction of the equivalent of unnatural amino acid side chains into a functionally critical location in this protein. These modified proteins bind CO on the distal side. 1H NMR data on H93G(Im)CO, where Im is imidazole, demonstrate that the structure of the distal heme pocket in H93G(Im)CO is very similar to that of wild type; thus, the effects of the proximal ligand's properties on CO binding can be studied with minimal perturbation of distal pocket structure. The exogenous proximal ligands used in this study include imidazole (Im), 4-methylimidazole (4-MeIm), 4-bromoimidazole (4-BrIm), N-methylimidazole (N-MeIm), pyridine (Pyr), and 3-fluoropyridine (3-FPyr). Substitution of the proximal ligand is found to produce substantial changes in the CO on and off rates, the equilibrium binding constant, and the vibrational stretch frequency of CO. Many of the changes are as large as those reported for distal pocket mutants prepared by site-directed mutagenesis. The ability to systematically vary the nature of the proximal ligand is exploited to test the effects of particular properties of the proximal ligand on CO binding. For example, 4-MeIm and 4-BrIm are similar in size and shape but differ significantly in pKa. The same relationship is true for Pyr and 3-FPyr. By comparison of the IR spectra and CO recombination kinetics of these complexes, the effects of proximal ligand pKa on the CO binding are assessed. Likewise, N-MeIm and 4-MeIm are similar in size and pKa but differ in their ability to hydrogen bond to amino acid residues in the proximal cavity. Comparisons of IR spectra and CO binding kinetics in these complexes reveal that proximal ligand conformation and hydrogen bonding affect the kinetics of CO binding. The mechanism of proximal ligand exchange between solution and the proximal cavity in CO complexes was
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Ligand solvation in molecular docking.
Shoichet, B K; Leach, A R; Kuntz, I D
1999-01-01
Solvation plays an important role in ligand-protein association and has a strong impact on comparisons of binding energies for dissimilar molecules. When databases of such molecules are screened for complementarity to receptors of known structure, as often occurs in structure-based inhibitor discovery, failure to consider ligand solvation often leads to putative ligands that are too highly charged or too large. To correct for the different charge states and sizes of the ligands, we calculated electrostatic and non-polar solvation free energies for molecules in a widely used molecular database, the Available Chemicals Directory (ACD). A modified Born equation treatment was used to calculate the electrostatic component of ligand solvation. The non-polar component of ligand solvation was calculated based on the surface area of the ligand and parameters derived from the hydration energies of apolar ligands. These solvation energies were subtracted from the ligand-receptor interaction energies. We tested the usefulness of these corrections by screening the ACD for molecules that complemented three proteins of known structure, using a molecular docking program. Correcting for ligand solvation improved the rankings of known ligands and discriminated against molecules with inappropriate charge states and sizes.
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Parkesh, Raman; Childs-Disney, Jessica L; Nakamori, Masayuki; Kumar, Amit; Wang, Eric; Wang, Thomas; Hoskins, Jason; Tran, Tuan; Housman, David; Thornton, Charles A; Disney, Matthew D
2012-03-14
Myotonic dystrophy type 1 (DM1) is a triplet repeating disorder caused by expanded CTG repeats in the 3'-untranslated region of the dystrophia myotonica protein kinase (DMPK) gene. The transcribed repeats fold into an RNA hairpin with multiple copies of a 5'CUG/3'GUC motif that binds the RNA splicing regulator muscleblind-like 1 protein (MBNL1). Sequestration of MBNL1 by expanded r(CUG) repeats causes splicing defects in a subset of pre-mRNAs including the insulin receptor, the muscle-specific chloride ion channel, sarco(endo)plasmic reticulum Ca(2+) ATPase 1, and cardiac troponin T. Based on these observations, the development of small-molecule ligands that target specifically expanded DM1 repeats could be of use as therapeutics. In the present study, chemical similarity searching was employed to improve the efficacy of pentamidine and Hoechst 33258 ligands that have been shown previously to target the DM1 triplet repeat. A series of in vitro inhibitors of the RNA-protein complex were identified with low micromolar IC(50)'s, which are >20-fold more potent than the query compounds. Importantly, a bis-benzimidazole identified from the Hoechst query improves DM1-associated pre-mRNA splicing defects in cell and mouse models of DM1 (when dosed with 1 mM and 100 mg/kg, respectively). Since Hoechst 33258 was identified as a DM1 binder through analysis of an RNA motif-ligand database, these studies suggest that lead ligands targeting RNA with improved biological activity can be identified by using a synergistic approach that combines analysis of known RNA-ligand interactions with chemical similarity searching.
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2013-01-01
A total of four biferrocene-based Walphos-type ligands have been synthesized, structurally characterized, and tested in the rhodium-, ruthenium- and iridium-catalyzed hydrogenation of alkenes and ketones. Negishi coupling conditions allowed the biferrocene backbone of these diphosphine ligands to be built up diastereoselectively from the two nonidentical and nonracemic ferrocene fragments (R)-1-(N,N-dimethylamino)ethylferrocene and (SFc)-2-bromoiodoferrocene. The molecular structures of (SFc)-2-bromoiodoferrocene, the coupling product, two ligands, and the two complexes ([PdCl2(L)] and [RuCl(p-cymene)(L)]PF6) were determined by X-ray diffraction. The structural features of complexes and the catalysis results obtained with the newly synthesized biferrocene-based ligands were compared with those of the corresponding Walphos ligands. PMID:23457421
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Ligand interaction scan: a general method for engineering ligand-sensitive protein alleles.
Erster, Oran; Eisenstein, Miriam; Liscovitch, Mordechai
2007-05-01
The ligand interaction scan (LIScan) method is a general procedure for engineering small molecule ligand-regulated forms of a protein that is complementary to other 'reverse' genetic and chemical-genetic methods for drug-target validation. It involves insertional mutagenesis by a chemical-genetic 'switch', comprising a genetically encoded peptide module that binds with high affinity to a small-molecule ligand. We demonstrated the method with TEM-1 beta-lactamase, using a tetracysteine hexapeptide insert and a biarsenical fluorescein ligand (FlAsH).
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pKa based protonation states and microspecies for protein-ligand docking
NASA Astrophysics Data System (ADS)
ten Brink, Tim; Exner, Thomas E.
2010-11-01
In this paper we present our reworked approach to generate ligand protonation states with our structure preparation tool SPORES (Structure PrOtonation and REcognition System). SPORES can be used for the preprocessing of proteins and protein-ligand complexes as e.g. taken from the Protein Data Bank as well as for the setup of 3D ligand databases. It automatically assigns atom and bond types, generates different protonation, tautomeric states as well as different stereoisomers. In the revised version, pKa calculations with the ChemAxon software MARVIN are used either to determine the likeliness of a combinatorial generated protonation state or to determine the titrable atoms used in the combinatorial approach. Additionally, the MARVIN software is used to predict microspecies distributions of ligand molecules. Docking studies were performed with our recently introduced program PLANTS (Protein-Ligand ANT System) on all protomers resulting from the three different selection methods for the well established CCDC/ASTEX clean data set demonstrating the usefulness of especially the latter approach.
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Translating in vitro ligand bias into in vivo efficacy.
Luttrell, Louis M; Maudsley, Stuart; Gesty-Palmer, Diane
2018-01-01
It is increasingly apparent that ligand structure influences both the efficiency with which G protein-coupled receptors (GPCRs) engage their downstream effectors and the manner in which they are activated. Thus, 'biased' agonists, synthetic ligands whose intrinsic efficacy differs from the native ligand, afford a strategy for manipulating GPCR signaling in ways that promote beneficial signals while blocking potentially deleterious ones. Still, there are significant challenges in relating in vitro ligand efficacy, which is typically measured in heterologous expression systems, to the biological response in vivo, where the ligand is acting on natively expressed receptors and in the presence of the endogenous ligand. This is particularly true of arrestin pathway-selective 'biased' agonists. The type 1 parathyroid hormone receptor (PTH 1 R) is a case in point. Parathyroid hormone (PTH) is the principal physiological regulator of calcium homeostasis, and PTH 1 R expressed on cells of the osteoblast lineage are an established therapeutic target in osteoporosis. In vitro, PTH 1 R signaling is highly sensitive to ligand structure, and PTH analogs that affect the selectivity/kinetics of G protein coupling or that engage arrestin-dependent signaling mechanisms without activating heterotrimeric G proteins have been identified. In vivo, intermittent administration of conventional PTH analogs accelerates the rate of osteoblastic bone formation, largely through known cAMP-dependent mechanisms. Paradoxically, both intermittent and continuous administration of an arrestin pathway-selective PTH analog, which in vivo would be expected to antagonize endogenous PTH 1 R-cAMP signaling, also increases bone mass. Transcriptomic analysis of tissue from treated animals suggests that conventional and arrestin pathway-selective PTH1R ligands act in largely different ways, with the latter principally affecting pathways involved in the regulation of cell cycle, survival, and migration
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Dean, Rebecca K; Devaine-Pressing, Katalin; Dawe, Louise N; Kozak, Christopher M
2013-07-07
A diamine-bis(phenolate) chromium(III) complex, {CrCl[O2NN'](BuBu)}2 catalyzes the copolymerization of propylene oxide with carbon dioxide. The synthesis of this metal complex is straightforward and it can be obtained in high yields. This catalyst incorporates a tripodal amine-bis(phenolate) ligand, which differs from the salen or salan ligands typically used with Cr and Co complexes that have been employed as catalysts for the synthesis of such polycarbonates. The catalyst reported herein yields low molecular weight polymers with narrow polydispersities when the reaction is performed at room temperature. Performing the reaction at elevated temperatures causes the selective synthesis of propylene carbonate. The copolymerization activity for propylene oxide and carbon dioxide, as well as the coupling of carbon dioxide and styrene oxide to give styrene carbonate are presented.
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Impact of copper ligand mutations on a cupredoxin with a green copper center.
Roger, Magali; Sciara, Giuliano; Biaso, Frédéric; Lojou, Elisabeth; Wang, Xie; Bauzan, Marielle; Giudici-Orticoni, Marie-Thérèse; Vila, Alejandro J; Ilbert, Marianne
2017-05-01
Mononuclear cupredoxins contain a type 1 copper center with a trigonal or tetragonal geometry usually maintained by four ligands, a cystein, two histidines and a methionine. The recent discovery of new members of this family with unusual properties demonstrates, however, the versatility of this class of proteins. Changes in their ligand set lead to drastic variation in their metal site geometry and in the resulting spectroscopic and redox features. In our work, we report the identification of the copper ligands in the recently discovered cupredoxin AcoP. We show that even though AcoP possesses a classical copper ligand set, it has a highly perturbed copper center. In depth studies of mutant's properties suggest a high degree of constraint existing in the copper center of the wild type protein and even the addition of exogenous ligands does not lead to the reconstitution of the initial copper center. Not only the chemical nature of the axial ligand but also constraints brought by its covalent binding to the protein backbone might be critical to maintain a green copper site with high redox potential. This work illustrates the importance of experimentally dissecting the molecular diversity of cupredoxins to determine the molecular determinants responsible for their copper center geometry and redox potential. Copyright © 2017 Elsevier B.V. All rights reserved.
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Ertem, Mehmed Zahid; Suna, Yuki; Himeda, Yuichiro; ...
2017-10-06
Pentamethylcyclopentadienyl iridium (Cp*Ir) complexes with bidentate ligands consisting of a pyridine ring and an electron-rich diazole ring were prepared. Their catalytic activity towards CO 2 hydrogenation in 2.0 M KHCO 3 aqueous solutions (pH 8.5) at 50 °C, under 1.0 MPa CO 2/H 2 (1:1) have been reported as an alternative to photo- and electrochemical CO 2 reduction. Bidentate ligands incorporating an electron-rich diazole ring improved the catalytic performance of the Ir complexes compared to the bipyridine ligand. Complexes 2, 4 and 6, possessing both a hydroxy group and an uncoordinated NH group, which are proton-responsive and capable of generatingmore » pendent-bases in basic media, recorded high initial TOF values of 1300 h -1, 1550 h -1 and 2000 h -1, respectively. Here, spectroscopic and computational investigations revealed that the reversible deprotonation changes the electronic properties of the complexes and causes interactions between pendent base and substrate and/or solvent water molecules, resulting in the high catalytic performance in basic media.« less
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Suna, Yuki; Himeda, Yuichiro; Fujita, Etsuko; Muckerman, James T; Ertem, Mehmed Z
2017-11-23
Pentamethylcyclopentadienyl iridium (Cp*Ir) complexes with bidentate ligands consisting of a pyridine ring and an electron-rich diazole ring were prepared. Their catalytic activity toward CO 2 hydrogenation in 2.0 m KHCO 3 aqueous solutions (pH 8.5) at 50 °C, under 1.0 MPa CO 2 /H 2 (1:1) have been reported as an alternative to photo- and electrochemical CO 2 reduction. Bidentate ligands incorporating an electron-rich diazole ring improved the catalytic performance of the Ir complexes compared to the bipyridine ligand. Complexes 2, 4, and 6, possessing both a hydroxy group and an uncoordinated NH group, which are proton-responsive and capable of generating pendent bases in basic media, recorded high initial turnover frequency values of 1300, 1550, and 2000 h -1 , respectively. Spectroscopic and computational investigations revealed that the reversible deprotonation changes the electronic properties of the complexes and causes interactions between pendent base and substrate and/or solvent water molecules, resulting in high catalytic performance in basic media. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Schulte, Marianne; Panwalkar, Vineet; Freischem, Stefan; Willbold, Dieter; Dingley, Andrew J
2018-04-19
Sequence alignment of the four WW domains from human Nedd4-1 (neuronal precursor cell expressed developmentally down-regulated gene 4-1) reveals that the highest sequence diversity exists in loop I. Three residues in this type I β-turn interact with the PPxY motif of the human epithelial Na + channel (hENaC) subunits, indicating that peptide affinity is defined by the loop I sequence. The third WW domain (WW3*) has the highest ligand affinity and unlike the other three hNedd4-1 WW domains or other WW domains studied contains the highly statistically preferred proline at the ( i + 1) position found in β-turns. In this report, molecular dynamics simulations and experimental data were combined to characterize loop I stability and dynamics. Exchange of the proline to the equivalent residue in WW4 (Thr) results in the presence of a predominantly open seven residue Ω loop rather than the type I β-turn conformation for the wild-type apo-WW3*. In the presence of the ligand, the structure of the mutated loop I is locked into a type I β-turn. Thus, proline in loop I ensures a stable peptide binding-competent β-turn conformation, indicating that amino acid sequence modulates local flexibility to tune binding preferences and stability of dynamic interaction motifs.
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Tang, Xiao-Yan; Wang, Yong-Xia; Liu, San-Rong; Liu, Jing-Yu; Li, Yue-Sheng
2013-01-14
A series of novel monochloro half-zirconocene complexes containing phosphine oxide-(thio)phenolate chelating ligands of the type, ClCp'Zr[X-2-R(1)-4-R(2)-6-(Ph(2)P=O)C(6)H(2)](2) (Cp' = C(5)H(5), 2a: X = O, R(1) = Ph, R(2) = H; 2b: X = O, R(1) = F, R(2) = H; 2c: X = O, R(1) = (t)Bu, R(2) = H; 2d: X = O, R(1) = R(2) = (t)Bu; 2e: X = O, R(1) = SiMe(3), R(2) = H; 2f: X = S, R(1) = SiMe(3), R(2) = H; Cp' = C(5)Me(5), 2g: X = O, R(1) = SiMe(3), R(2) = H), have been synthesized in high yields. These complexes were identified by (1)H {(13)C} NMR and elemental analyses. Structures for 2b, 2c and 2f were further confirmed by X-ray crystallography. Structural characterization of these complexes reveals crowded environments around the zirconium. Complexes 2b and 2c adopt six-coordinate, distorted octahedral geometry around the zirconium center, in which the equatorial positions are occupied by three oxygen atoms of two chelating phosphine oxide-bridged phenolate ligands and a chlorine atom. The cyclopentadienyl ring and one oxygen atom of the ligand are coordinated on the axial position. Complex 2f also folds a six-coordinate, distorted octahedral geometry around the Zr center, consisting of a Cp-Zr-O (in P=O) axis [177.16°] and a distorted plane of two sulfur atoms and one oxygen atom of two chelating phosphine oxide-bridged thiophenolate ligands as well as a chlorine atom. When activated by modified methylaluminoxane (MMAO), all the complexes exhibited high activities towards ethylene polymerization at high temperature (75 °C), giving high molecular weight polymers with unimodal molecular weight distribution. The formation of 14-electron, cationic metal alkyl species might come from the Zr-O (in phenol ring) bond cleavage based on the DFT calculations study.
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NASA Astrophysics Data System (ADS)
Córdova-Sintjago, Tania; Villa, Nancy; Fang, Lijuan; Booth, Raymond G.
2014-02-01
The serotonin (5-hydroxytryptamine, 5-HT) 5-HT2 G protein-coupled receptor (GPCR) family consists of types 2A, 2B, and 2C that share ∼75% transmembrane (TM) sequence identity. Agonists for 5-HT2C receptors are under development for psychoses; whereas, at 5-HT2A receptors, antipsychotic effects are associated with antagonists - in fact, 5-HT2A agonists can cause hallucinations and 5-HT2B agonists cause cardiotoxicity. It is known that 5-HT2A TM6 residues W6.48, F6.51, and F6.52 impact ligand binding and function; however, ligand interactions with these residues at the 5-HT2C receptor have not been reported. To predict and validate molecular determinants for 5-HT2C-specific activation, results from receptor homology modelling, ligand docking, and molecular dynamics simulation studies were compared with experimental results for ligand binding and function at wild type and W6.48A, F6.51A, and F6.52A point-mutated 5-HT2C receptors.
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Increased Accuracy of Ligand Sensing by Receptor Internalization and Lateral Receptor Diffusion
NASA Astrophysics Data System (ADS)
Aquino, Gerardo; Endres, Robert
2010-03-01
Many types of cells can sense external ligand concentrations with cell-surface receptors at extremely high accuracy. Interestingly, ligand-bound receptors are often internalized, a process also known as receptor-mediated endocytosis. While internalization is involved in a vast number of important functions for the life of a cell, it was recently also suggested to increase the accuracy of sensing ligand as overcounting of the same ligand molecules is reduced. A similar role may be played by receptor diffusion om the cell membrane. Fast, lateral receptor diffusion is known to be relevant in neurotransmission initiated by release of neurotransmitter glutamate in the synaptic cleft between neurons. By binding ligand and removal by diffusion from the region of release of the neurotransmitter, diffusing receptors can be reasonably expected to reduce the local overcounting of the same ligand molecules in the region of signaling. By extending simple ligand-receptor models to out-of-equilibrium thermodynamics, we show that both receptor internalization and lateral diffusion increase the accuracy with which cells can measure ligand concentrations in the external environment. We confirm this with our model and give quantitative predictions for experimental parameters values. We give quantitative predictions, which compare favorably to experimental data of real receptors.
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CO 2 hydrogenation catalyzed by iridium complexes with a proton-responsive ligand
Onishi, Naoya; Xu, Shaoan; Manaka, Yuichi; ...
2015-02-18
In this study, the catalytic cycle for the production of formic acid by CO₂ hydrogenation and the reverse reaction has received renewed attention because they are viewed as offering a viable scheme for hydrogen storage and release. In this Forum Article, CO₂ hydrogenation catalyzed by iridium complexes bearing N^N-bidentate ligands is reported. We describe how a ligand containing hydroxyl groups as proton-responsive substituents enhances catalytic performance by an electronic effect of the oxyanions and a pendent-base effect through secondary coordination sphere interaction. In particular, [(Cp*IrCl)₂(TH2BPM)]Cl₂ (Cp* = pentamethyl cyclopentadienyl, TH2BPM = 4,4',6,6'-tetrahydroxy-2,2'-bipyrimidine) promotes enormously the catalytic hydrogenation of CO₂ bymore » these synergistic effects under atmospheric pressure and at room temperature. Additionally, newly designed complexes with azole-type ligands are applied to CO₂ hydrogenation. The catalytic efficiencies of the azole-type complexes are much higher than that of the unsubstituted bipyridine complex [Cp*Ir(bpy)(OH₂)]SO₄. Furthermore, the introduction of one or more hydroxyl groups into ligands such as 2-pyrazolyl-6-hydroxypyridine, 2-pyrazolyl-4,6-dihydroxyl pyrimidine, and 4-pyrazolyl-2,6-dihydroxyl pyrimidine enhanced catalytic activity. It is clear that the incorporation of electron-donating hydroxyl groups into proton-responsive ligands is effective for promoting the hydrogenation of CO₂.« less
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Classification of ligand molecules in PDB with fast heuristic graph match algorithm COMPLIG.
Saito, Mihoko; Takemura, Naomi; Shirai, Tsuyoshi
2012-12-14
A fast heuristic graph-matching algorithm, COMPLIG, was devised to classify the small-molecule ligands in the Protein Data Bank (PDB), which are currently not properly classified on structure basis. By concurrently classifying proteins and ligands, we determined the most appropriate parameter for categorizing ligands to be more than 60% identity of atoms and bonds between molecules, and we classified 11,585 types of ligands into 1946 clusters. Although the large clusters were composed of nucleotides or amino acids, a significant presence of drug compounds was also observed. Application of the system to classify the natural ligand status of human proteins in the current database suggested that, at most, 37% of the experimental structures of human proteins were in complex with natural ligands. However, protein homology- and/or ligand similarity-based modeling was implied to provide models of natural interactions for an additional 28% of the total, which might be used to increase the knowledge of intrinsic protein-metabolite interactions. Copyright © 2012 Elsevier Ltd. All rights reserved.
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Quantitative analysis of protein-ligand interactions by NMR.
Furukawa, Ayako; Konuma, Tsuyoshi; Yanaka, Saeko; Sugase, Kenji
2016-08-01
to analyze population-averaged NMR quantities. Essentially, to apply NMR successfully, both the type of experiment and equation to fit the data must be carefully and specifically chosen for the protein-ligand interaction under analysis. In this review, we first explain the exchange regimes and kinetic models of protein-ligand interactions, and then describe the NMR methods that quantitatively analyze these specific interactions. Copyright © 2016 Elsevier B.V. All rights reserved.
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Marsh, Lorraine
2015-01-01
Many systems in biology rely on binding of ligands to target proteins in a single high-affinity conformation with a favorable ΔG. Alternatively, interactions of ligands with protein regions that allow diffuse binding, distributed over multiple sites and conformations, can exhibit favorable ΔG because of their higher entropy. Diffuse binding may be biologically important for multidrug transporters and carrier proteins. A fine-grained computational method for numerical integration of total binding ΔG arising from diffuse regional interaction of a ligand in multiple conformations using a Markov Chain Monte Carlo (MCMC) approach is presented. This method yields a metric that quantifies the influence on overall ligand affinity of ligand binding to multiple, distinct sites within a protein binding region. This metric is essentially a measure of dispersion in equilibrium ligand binding and depends on both the number of potential sites of interaction and the distribution of their individual predicted affinities. Analysis of test cases indicates that, for some ligand/protein pairs involving transporters and carrier proteins, diffuse binding contributes greatly to total affinity, whereas in other cases the influence is modest. This approach may be useful for studying situations where "nonspecific" interactions contribute to biological function.
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Scognamiglio, Giosuè; De Chiara, Anna; Di Bonito, Maurizio; Tatangelo, Fabiana; Losito, Nunzia Simona; Anniciello, Annamaria; De Cecio, Rossella; D’Alterio, Crescenzo; Scala, Stefania; Cantile, Monica; Botti, Gerardo
2016-01-01
In normal cell physiology, programmed death 1 (PD-1) and its ligand, PD-L1, play an immunoregulatory role in T-cell activation, tolerance, and immune-mediated tissue damage. The PD-1/PD-L1 pathway also plays a critical role in immune escape of tumor cells and has been demonstrated to correlate with a poor prognosis of patients with several types of cancer. However, recent reports have revealed that the immunohistochemical (IHC) expression of the PD-L1 in tumor cells is not uniform for the use of different antibodies clones, with variable specificity, often doubtful topographical localization, and with a score not uniquely defined. The purpose of this study was to analyze the IHC expression of PD-L1 on a large series of several human tumors to correctly define its staining in different tumor tissues. PMID:27213372
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A systematic analysis of atomic protein-ligand interactions in the PDB.
Ferreira de Freitas, Renato; Schapira, Matthieu
2017-10-01
As the protein databank (PDB) recently passed the cap of 123 456 structures, it stands more than ever as an important resource not only to analyze structural features of specific biological systems, but also to study the prevalence of structural patterns observed in a large body of unrelated structures, that may reflect rules governing protein folding or molecular recognition. Here, we compiled a list of 11 016 unique structures of small-molecule ligands bound to proteins - 6444 of which have experimental binding affinity - representing 750 873 protein-ligand atomic interactions, and analyzed the frequency, geometry and impact of each interaction type. We find that hydrophobic interactions are generally enriched in high-efficiency ligands, but polar interactions are over-represented in fragment inhibitors. While most observations extracted from the PDB will be familiar to seasoned medicinal chemists, less expected findings, such as the high number of C-H···O hydrogen bonds or the relatively frequent amide-π stacking between the backbone amide of proteins and aromatic rings of ligands, uncover underused ligand design strategies.
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NASA Astrophysics Data System (ADS)
Hassan, Hassan M. A.; Betiha, Mohamed A.; Mohamed, Shaimaa K.; El-Sharkawy, E. A.; Ahmed, Emad A.
2017-08-01
The synthesis of metal-organic frameworks (MOFs), porous coordination polymers with functional groups has received immense interest due to the functional groups can offer desirable properties and allow post-synthetic modification. Herein, for the first time, Zr(IV)-Sal Schiff base complex incorporated into amino-functionalized MIL-101(Cr) framework by salicylaldehyde condensing to amino group, and coordinating Zr(IV) ion have been successfully synthesized. The worthiness of the synthesized material as a catalyst has been examined for the esterification of oleic acid (free fatty acid) with methanol producing biodiesel (methyl oleate), Knoveonagel condensation reaction of aldehydes and Friedel-Crafts acylation of anisole. Our findings demonstrated that Salen-Zr(IV) grafted to framework of NH2-MIL-101(Cr) as a solid acid catalyst exhibited distinct catalytic performance for the production of biodiesel by esterification of oleic acid with methanol, Knoveonagel condensation and Friedel-Crafts acylation. These could be attributed to high surface area which allow high distribution of Zr(IV) species lead to a sufficient contact with the reactants species. Furthermore, the catalyst showed excellent recycling efficiency due to the strong interaction between the Zr(IV) ions and chelating groups in the NH2-MIL-101(Cr)-Sal.
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pK(a) based protonation states and microspecies for protein-ligand docking.
ten Brink, Tim; Exner, Thomas E
2010-11-01
In this paper we present our reworked approach to generate ligand protonation states with our structure preparation tool SPORES (Structure PrOtonation and REcognition System). SPORES can be used for the preprocessing of proteins and protein-ligand complexes as e.g. taken from the Protein Data Bank as well as for the setup of 3D ligand databases. It automatically assigns atom and bond types, generates different protonation, tautomeric states as well as different stereoisomers. In the revised version, pKa calculations with the ChemAxon software MARVIN are used either to determine the likeliness of a combinatorial generated protonation state or to determine the titrable atoms used in the combinatorial approach. Additionally, the MARVIN software is used to predict microspecies distributions of ligand molecules. Docking studies were performed with our recently introduced program PLANTS (Protein-Ligand ANT System) on all protomers resulting from the three different selection methods for the well established CCDC/ASTEX clean data set demonstrating the usefulness of especially the latter approach.
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Synthesis and Characterization of PEGylated Toll Like Receptor 7 Ligands
Chan, Michael; Hayashi, Tomoko; Mathewson, Richard D.; Yao, Shiyin; Gray, Christine; Tawatao, Rommel; Kalenian, Kevin; Zhang, Yanmei; Hayashi, Yuki; Lao, Fitzgerald S.; Cottam, Howard B.; Carson, Dennis A.
2011-01-01
Toll like receptor 7 (TLR7) is located in the endosomal compartment of immune cells. Signaling through TLR7, mediated by the adaptor protein MyD88, stimulates the innate immune system and shapes adaptive immune responses. Previously, we characterized TLR7 ligands conjugated to protein, lipid or polyethylene glycol (PEG). Among the TLR7 ligand conjugates, the addition of PEG chains reduced the agonistic potency. PEGs are safe in humans and widely used for improvement of pharmacokinetics in existing biologics and some low molecular weight compounds. PEGylation could be a feasible method to alter the pharmacokinetics and pharmacodynamics of TLR7 ligands. In this study, we systematically studied the influence of PEG chain length on the in vitro and in vivo properties of potent TLR7 ligands. PEGylation increased solubility of the TLR7 ligands and modulated protein binding. Adding a 6–10 length PEG to the TLR7 ligand reduced its potency toward induction of interleukin (IL)-6 by murine macrophages in vitro and IL-6 and tumor necrosis factor (TNF) in vivo. However, PEGylation with 18 or longer chain restored, and even enhanced, the agonistic activity of the drug. In human peripheral blood mononuclear cells, similar effects of PEGylation were observed for secretion of proinflammatory cytokines, IL-6, IL-12, TNF-α, IL-1β and type 1 interferon, as well for B cell proliferation. In summary, these studies demonstrate that conjugation of PEG chains to a synthetic TLR ligand can impact its potency for cytokine induction depending on the size of the PEG moiety. Thus, PEGylation may be a feasible approach to regulate the pharmacological properties of TLR7 ligands. PMID:21338093
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Type I interferon dependence of plasmacytoid dendritic cell activation and migration
Asselin-Paturel, Carine; Brizard, Géraldine; Chemin, Karine; Boonstra, Andre; O'Garra, Anne; Vicari, Alain; Trinchieri, Giorgio
2005-01-01
Differential expression of Toll-like receptor (TLR) by conventional dendritic cells (cDCs) and plasmacytoid DC (pDCs) has been suggested to influence the type of immune response induced by microbial pathogens. In this study we show that, in vivo, cDCs and pDCs are equally activated by TLR4, -7, and -9 ligands. Type I interferon (IFN) was important for pDC activation in vivo in response to all three TLR ligands, whereas cDCs required type I IFN signaling only for TLR9- and partially for TLR7-mediated activation. Although TLR ligands induced in situ migration of spleen cDC into the T cell area, spleen pDCs formed clusters in the marginal zone and in the outer T cell area 6 h after injection of TLR9 and TLR7 ligands, respectively. In vivo treatment with TLR9 ligands decreased pDC ability to migrate ex vivo in response to IFN-induced CXCR3 ligands and increased their response to CCR7 ligands. Unlike cDCs, the migration pattern of pDCs required type I IFN for induction of CXCR3 ligands and responsiveness to CCR7 ligands. These data demonstrate that mouse pDCs differ from cDCs in the in vivo response to TLR ligands, in terms of pattern and type I IFN requirement for activation and migration. PMID:15795237
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Multiple ligand simultaneous docking: orchestrated dancing of ligands in binding sites of protein.
Li, Huameng; Li, Chenglong
2010-07-30
Present docking methodologies simulate only one single ligand at a time during docking process. In reality, the molecular recognition process always involves multiple molecular species. Typical protein-ligand interactions are, for example, substrate and cofactor in catalytic cycle; metal ion coordination together with ligand(s); and ligand binding with water molecules. To simulate the real molecular binding processes, we propose a novel multiple ligand simultaneous docking (MLSD) strategy, which can deal with all the above processes, vastly improving docking sampling and binding free energy scoring. The work also compares two search strategies: Lamarckian genetic algorithm and particle swarm optimization, which have respective advantages depending on the specific systems. The methodology proves robust through systematic testing against several diverse model systems: E. coli purine nucleoside phosphorylase (PNP) complex with two substrates, SHP2NSH2 complex with two peptides and Bcl-xL complex with ABT-737 fragments. In all cases, the final correct docking poses and relative binding free energies were obtained. In PNP case, the simulations also capture the binding intermediates and reveal the binding dynamics during the recognition processes, which are consistent with the proposed enzymatic mechanism. In the other two cases, conventional single-ligand docking fails due to energetic and dynamic coupling among ligands, whereas MLSD results in the correct binding modes. These three cases also represent potential applications in the areas of exploring enzymatic mechanism, interpreting noisy X-ray crystallographic maps, and aiding fragment-based drug design, respectively. 2010 Wiley Periodicals, Inc.
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A magnetic anti-cancer compound for magnet-guided delivery and magnetic resonance imaging
Eguchi, Haruki; Umemura, Masanari; Kurotani, Reiko; Fukumura, Hidenobu; Sato, Itaru; Kim, Jeong-Hwan; Hoshino, Yujiro; Lee, Jin; Amemiya, Naoyuki; Sato, Motohiko; Hirata, Kunio; Singh, David J.; Masuda, Takatsugu; Yamamoto, Masahiro; Urano, Tsutomu; Yoshida, Keiichiro; Tanigaki, Katsumi; Yamamoto, Masaki; Sato, Mamoru; Inoue, Seiichi; Aoki, Ichio; Ishikawa, Yoshihiro
2015-01-01
Research on controlled drug delivery for cancer chemotherapy has focused mainly on ways to deliver existing anti-cancer drug compounds to specified targets, e.g., by conjugating them with magnetic particles or encapsulating them in micelles. Here, we show that an iron-salen, i.e., μ-oxo N,N'- bis(salicylidene)ethylenediamine iron (Fe(Salen)), but not other metal salen derivatives, intrinsically exhibits both magnetic character and anti-cancer activity. X-Ray crystallographic analysis and first principles calculations based on the measured structure support this. It promoted apoptosis of various cancer cell lines, likely, via production of reactive oxygen species. In mouse leg tumor and tail melanoma models, Fe(Salen) delivery with magnet caused a robust decrease in tumor size, and the accumulation of Fe(Salen) was visualized by magnetic resonance imaging. Fe(Salen) is an anti-cancer compound with magnetic property, which is suitable for drug delivery and imaging. We believe such magnetic anti-cancer drugs have the potential to greatly advance cancer chemotherapy for new theranostics and drug-delivery strategies. PMID:25779357
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AFAL: a web service for profiling amino acids surrounding ligands in proteins
NASA Astrophysics Data System (ADS)
Arenas-Salinas, Mauricio; Ortega-Salazar, Samuel; Gonzales-Nilo, Fernando; Pohl, Ehmke; Holmes, David S.; Quatrini, Raquel
2014-11-01
With advancements in crystallographic technology and the increasing wealth of information populating structural databases, there is an increasing need for prediction tools based on spatial information that will support the characterization of proteins and protein-ligand interactions. Herein, a new web service is presented termed amino acid frequency around ligand (AFAL) for determining amino acids type and frequencies surrounding ligands within proteins deposited in the Protein Data Bank and for assessing the atoms and atom-ligand distances involved in each interaction (availability: http://structuralbio.utalca.cl/AFAL/index.html). AFAL allows the user to define a wide variety of filtering criteria (protein family, source organism, resolution, sequence redundancy and distance) in order to uncover trends and evolutionary differences in amino acid preferences that define interactions with particular ligands. Results obtained from AFAL provide valuable statistical information about amino acids that may be responsible for establishing particular ligand-protein interactions. The analysis will enable investigators to compare ligand-binding sites of different proteins and to uncover general as well as specific interaction patterns from existing data. Such patterns can be used subsequently to predict ligand binding in proteins that currently have no structural information and to refine the interpretation of existing protein models. The application of AFAL is illustrated by the analysis of proteins interacting with adenosine-5'-triphosphate.
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AFAL: a web service for profiling amino acids surrounding ligands in proteins.
Arenas-Salinas, Mauricio; Ortega-Salazar, Samuel; Gonzales-Nilo, Fernando; Pohl, Ehmke; Holmes, David S; Quatrini, Raquel
2014-11-01
With advancements in crystallographic technology and the increasing wealth of information populating structural databases, there is an increasing need for prediction tools based on spatial information that will support the characterization of proteins and protein-ligand interactions. Herein, a new web service is presented termed amino acid frequency around ligand (AFAL) for determining amino acids type and frequencies surrounding ligands within proteins deposited in the Protein Data Bank and for assessing the atoms and atom-ligand distances involved in each interaction (availability: http://structuralbio.utalca.cl/AFAL/index.html ). AFAL allows the user to define a wide variety of filtering criteria (protein family, source organism, resolution, sequence redundancy and distance) in order to uncover trends and evolutionary differences in amino acid preferences that define interactions with particular ligands. Results obtained from AFAL provide valuable statistical information about amino acids that may be responsible for establishing particular ligand-protein interactions. The analysis will enable investigators to compare ligand-binding sites of different proteins and to uncover general as well as specific interaction patterns from existing data. Such patterns can be used subsequently to predict ligand binding in proteins that currently have no structural information and to refine the interpretation of existing protein models. The application of AFAL is illustrated by the analysis of proteins interacting with adenosine-5'-triphosphate.
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Capping Ligand Vortices as “Atomic Orbitals” in Nanocrystal Self-Assembly
Waltmann, Curt; Horst, Nathan; Travesset, Alex
2017-10-27
In this work, we present a detailed analysis of the interaction between two nanocrystals capped with ligands consisting of hydrocarbon chains by united atom molecular dynamics simulations. We show that the bonding of two nanocrystals is characterized by ligand textures in the form of vortices. These results are generalized to nanocrystals of different types (differing core and ligand sizes) where the structure of the vortices depends on the softness asymmetry. We provide rigorous calculations for the binding free energy, show that these energies are independent of the chemical composition of the cores, and derive analytical formulas for the equilibrium separation.more » We discuss the implications of our results for the self-assembly of single-component and binary nanoparticle superlattices. Overall, our results show that the structure of the ligands completely determines the bonding of nanocrystals, fully supporting the predictions of the recently proposed Orbifold topological model.« less
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Cell Type-Specific Regulation of Immunological Synapse Dynamics by B7 Ligand Recognition
Brzostek, Joanna; Gascoigne, Nicholas R. J.; Rybakin, Vasily
2016-01-01
B7 proteins CD80 (B7-1) and CD86 (B7-2) are expressed on most antigen-presenting cells and provide critical co-stimulatory or inhibitory input to T cells via their T-cell-expressed receptors: CD28 and CTLA-4. CD28 is expressed on effector T cells and regulatory T cells (Tregs), and CD28-dependent signals are required for optimum activation of effector T cell functions. CD28 ligation on effector T cells leads to formation of distinct molecular patterns and induction of cytoskeletal rearrangements at the immunological synapse (IS). CD28 plays a critical role in recruitment of protein kinase C (PKC)-θ to the effector T cell IS. CTLA-4 is constitutively expressed on the surface of Tregs, but it is expressed on effector T cells only after activation. As CTLA-4 binds to B7 proteins with significantly higher affinity than CD28, B7 ligand recognition by cells expressing both receptors leads to displacement of CD28 and PKC-θ from the IS. In Tregs, B7 ligand recognition leads to recruitment of CTLA-4 and PKC-η to the IS. CTLA-4 plays a role in regulation of T effector and Treg IS stability and cell motility. Due to their important roles in regulating T-cell-mediated responses, B7 receptors are emerging as important drug targets in oncology. In this review, we present an integrated summary of current knowledge about the role of B7 family receptor–ligand interactions in the regulation of spatial and temporal IS dynamics in effector and Tregs. PMID:26870040
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Loukas, A; Doedens, A; Hintz, M; Maizels, R M
2000-11-01
Infective larvae of the dog roundworm Toxocara canis survive in the tissues of their hosts for extended periods in a state of developmental arrest, successfully evading immune destruction. This survival strategy is thought to be mediated by T. canis excretory/secretory (TES) products which downregulate or divert the immune response. We purified one of the major TES products, TES-70 and gained amino acid sequence from 4 tryptic peptides. These peptides were matched to a predicted protein from a cDNA that was isolated by expression screening a T. canis cDNA library with mouse anti-TES serum. The predicted protein (Tc-CTL-4) is similar to, but larger than, Tc-CTL-1, a 32-kDa C-type lectin secreted by T. canis larvae. Tc-CTL-4 has a signal peptide, 2 Cys-rich domains and a C-terminal calcium-dependent C-type lectin domain that shares sequence similarity with host immune cell receptors such as macrophage mannose receptor and CD23. The lectin domain was expressed in bacteria and antiserum to the purified recombinant protein was used to confirm that Tc-ctl-4 did encode the native TES-70 glycoprotein. TES-70 selectively bound to ligands on the surface of Madin-Darby Canine Kidney cells in vitro in a calcium-dependent manner, inhibitable by mammalian serum, indicating that a host glycan is the native ligand for this new parasite lectin.
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Importance of ligand reorganization free energy in protein-ligand binding-affinity prediction.
Yang, Chao-Yie; Sun, Haiying; Chen, Jianyong; Nikolovska-Coleska, Zaneta; Wang, Shaomeng
2009-09-30
Accurate prediction of the binding affinities of small-molecule ligands to their biological targets is fundamental for structure-based drug design but remains a very challenging task. In this paper, we have performed computational studies to predict the binding models of 31 small-molecule Smac (the second mitochondria-derived activator of caspase) mimetics to their target, the XIAP (X-linked inhibitor of apoptosis) protein, and their binding affinities. Our results showed that computational docking was able to reliably predict the binding models, as confirmed by experimentally determined crystal structures of some Smac mimetics complexed with XIAP. However, all the computational methods we have tested, including an empirical scoring function, two knowledge-based scoring functions, and MM-GBSA (molecular mechanics and generalized Born surface area), yield poor to modest prediction for binding affinities. The linear correlation coefficient (r(2)) value between the predicted affinities and the experimentally determined affinities was found to be between 0.21 and 0.36. Inclusion of ensemble protein-ligand conformations obtained from molecular dynamic simulations did not significantly improve the prediction. However, major improvement was achieved when the free-energy change for ligands between their free- and bound-states, or "ligand-reorganization free energy", was included in the MM-GBSA calculation, and the r(2) value increased from 0.36 to 0.66. The prediction was validated using 10 additional Smac mimetics designed and evaluated by an independent group. This study demonstrates that ligand reorganization free energy plays an important role in the overall binding free energy between Smac mimetics and XIAP. This term should be evaluated for other ligand-protein systems and included in the development of new scoring functions. To our best knowledge, this is the first computational study to demonstrate the importance of ligand reorganization free energy for the
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Enhanced Ligand Sampling for Relative Protein–Ligand Binding Free Energy Calculations
2016-01-01
Free energy calculations are used to study how strongly potential drug molecules interact with their target receptors. The accuracy of these calculations depends on the accuracy of the molecular dynamics (MD) force field as well as proper sampling of the major conformations of each molecule. However, proper sampling of ligand conformations can be difficult when there are large barriers separating the major ligand conformations. An example of this is for ligands with an asymmetrically substituted phenyl ring, where the presence of protein loops hinders the proper sampling of the different ring conformations. These ring conformations become more difficult to sample when the size of the functional groups attached to the ring increases. The Adaptive Integration Method (AIM) has been developed, which adaptively changes the alchemical coupling parameter λ during the MD simulation so that conformations sampled at one λ can aid sampling at the other λ values. The Accelerated Adaptive Integration Method (AcclAIM) builds on AIM by lowering potential barriers for specific degrees of freedom at intermediate λ values. However, these methods may not work when there are very large barriers separating the major ligand conformations. In this work, we describe a modification to AIM that improves sampling of the different ring conformations, even when there is a very large barrier between them. This method combines AIM with conformational Monte Carlo sampling, giving improved convergence of ring populations and the resulting free energy. This method, called AIM/MC, is applied to study the relative binding free energy for a pair of ligands that bind to thrombin and a different pair of ligands that bind to aspartyl protease β-APP cleaving enzyme 1 (BACE1). These protein–ligand binding free energy calculations illustrate the improvements in conformational sampling and the convergence of the free energy compared to both AIM and AcclAIM. PMID:25906170
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Andersen, Jacob Lauwring, E-mail: jla@mb.au.dk; Schrøder, Tenna Juul; Christensen, Søren
2014-02-01
The identification of the first small-molecule ligand of the neuronal receptor sortilin and structure determination of the receptor–ligand complex are reported. Sortilin is a type I membrane glycoprotein belonging to the vacuolar protein sorting 10 protein (Vps10p) family of sorting receptors and is most abundantly expressed in the central nervous system. Sortilin has emerged as a key player in the regulation of neuronal viability and has been implicated as a possible therapeutic target in a range of disorders. Here, the identification of AF40431, the first reported small-molecule ligand of sortilin, is reported. Crystals of the sortilin–AF40431 complex were obtained bymore » co-crystallization and the structure of the complex was solved to 2.7 Å resolution. AF40431 is bound in the neurotensin-binding site of sortilin, with the leucine moiety of AF40431 mimicking the binding mode of the C-terminal leucine of neurotensin and the 4-methylumbelliferone moiety of AF40431 forming π-stacking with a phenylalanine.« less
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Procházková, Jiřina; Strapáčová, Simona; Svržková, Lucie; Andrysík, Zdeněk; Hýžďalová, Martina; Hrubá, Eva; Pěnčíková, Kateřina; Líbalová, Helena; Topinka, Jan; Kléma, Jiří; Espinosa, Joaquín M; Vondráček, Jan; Machala, Miroslav
2018-08-01
Exposure to persistent ligands of aryl hydrocarbon receptor (AhR) has been found to cause lung cancer in experimental animals, and lung adenocarcinomas are often associated with enhanced AhR expression and aberrant AhR activation. In order to better understand the action of toxic AhR ligands in lung epithelial cells, we performed global gene expression profiling and analyze TCDD-induced changes in A549 transcriptome, both sensitive and non-sensitive to CH223191 co-treatment. Comparison of our data with results from previously reported microarray and ChIP-seq experiments enabled us to identify candidate genes, which expression status reflects exposure of lung cancer cells to TCDD, and to predict processes, pathways (e.g. ER stress, Wnt/β-cat, IFNɣ, EGFR/Erbb1), putative TFs (e.g. STAT, AP1, E2F1, TCF4), which may be implicated in adaptive response of lung cells to TCDD-induced AhR activation. Importantly, TCDD-like expression fingerprint of selected genes was observed also in A549 cells exposed acutely to both toxic (benzo[a]pyrene, benzo[k]fluoranthene) and endogenous AhR ligands (2-(1H-Indol-3-ylcarbonyl)-4-thiazolecarboxylic acid methyl ester and 6-formylindolo[3,2-b]carbazole). Overall, our results suggest novel cellular candidates, which could help to improve monitoring of AhR-dependent transcriptional activity during acute exposure of lung cells to distinct types of environmental pollutants. Copyright © 2018 Elsevier B.V. All rights reserved.
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NASA Astrophysics Data System (ADS)
Li, Long; Hu, Jinglei; Xu, Guangkui; Song, Fan
2018-01-01
Cell-cell adhesion and the adhesion of cells to tissues and extracellular matrix, which are pivotal for immune response, tissue development, and cell locomotion, depend sensitively on the binding constant of receptor and ligand molecules anchored on the apposing surfaces. An important question remains of whether the immobilization of ligands affects the affinity of binding with cell adhesion receptors. We have investigated the adhesion of multicomponent membranes to a flat substrate coated with immobile ligands using Monte Carlo simulations of a statistical mesoscopic model with biologically relevant parameters. We find that the binding of the adhesion receptors to ligands immobilized on the substrate is strongly affected by the ligand distribution. In the case of ligand clusters, the receptor-ligand binding constant can be significantly enhanced due to the less translational entropy loss of lipid-raft domains in the model cell membranes upon the formation of additional complexes. For ligands randomly or uniformly immobilized on the substrate, the binding constant is rather decreased since the receptors localized in lipid-raft domains have to pay an energetic penalty in order to bind ligands. Our findings help to understand why cell-substrate adhesion experiments for measuring the impact of lipid rafts on the receptor-ligand interactions led to contradictory results.
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EGF receptor ligands: recent advances.
Singh, Bhuminder; Carpenter, Graham; Coffey, Robert J
2016-01-01
Seven ligands bind to and activate the mammalian epidermal growth factor (EGF) receptor (EGFR/ERBB1/HER1): EGF, transforming growth factor-alpha (TGFA), heparin-binding EGF-like growth factor (HBEGF), betacellulin (BTC), amphiregulin (AREG), epiregulin (EREG), and epigen (EPGN). Of these, EGF, TGFA, HBEGF, and BTC are thought to be high-affinity ligands, whereas AREG, EREG, and EPGN constitute low-affinity ligands. This focused review is meant to highlight recent studies related to actions of the individual EGFR ligands, the interesting biology that has been uncovered, and relevant advances related to ligand interactions with the EGFR.
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EGF receptor ligands: recent advances
Singh, Bhuminder; Carpenter, Graham; Coffey, Robert J.
2016-01-01
Seven ligands bind to and activate the mammalian epidermal growth factor (EGF) receptor (EGFR/ERBB1/HER1): EGF, transforming growth factor-alpha (TGFA), heparin-binding EGF-like growth factor (HBEGF), betacellulin (BTC), amphiregulin (AREG), epiregulin (EREG), and epigen (EPGN). Of these, EGF, TGFA, HBEGF, and BTC are thought to be high-affinity ligands, whereas AREG, EREG, and EPGN constitute low-affinity ligands. This focused review is meant to highlight recent studies related to actions of the individual EGFR ligands, the interesting biology that has been uncovered, and relevant advances related to ligand interactions with the EGFR. PMID:27635238
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NASA Astrophysics Data System (ADS)
Wang, Fei; Gao, Lei; Zhao, Qing; Zhang, Yang; Dong, Wen-Kui; Ding, Yu-Jie
2018-02-01
The optical properties of a novel chemosensor for cyanide anions based on a symmetric bis(salamo)-type ligand (H3L) were investigated by UV-Vis and fluorescence spectroscopy in MeOH/H2O (1:1 v/v) solution. Sensor H3L can selectively sense CN- based on prominent color changes among other anions. The chemosensor exhibits an apparent fluorescence enhancement at 482 nm to CN- which because cyanide ions interact with Cdbnd N bonds. Combining the corrected Benesi-Hildebrand formula, the binding constant of the formed host-guest complex was calculated as 2.42 × 105 M- 1. Meanwhile, the detection limit of the sensor toward CN- was 8.91 × 10- 7 M. It is worth noting that the designed sensor can be used for rapid detection of cyanide anions in basic pH range, and has great practical value.
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Hovius, Ruud
2013-01-01
The application of fluorescent receptor ligands has become widespread, incited by two important reasons. "Seeing is believing"-it is possible to visualize in real time in live cells ligand-receptor interactions, and to locate the receptors with subcellular precision allowing one to follow, e.g., internalization of the ligand-receptor complex. The high sensitivity of photon detection permits observation of on the one hand receptor-ligand interactions on cells with low, native receptor abundance, and on the other of individual fluorophores unveiling the stochastic properties of single ligand-receptor complexes.The major bottlenecks that impede extensive use of fluorescent ligands are due to possible dramatic changes of the pharmacological properties of a ligand upon chemical modification and fluorophore conjugation, aggravated by the observation that different fluorophores can provoke very dissimilar effects. This makes it virtually impossible to predict beforehand which labelling strategy to use to produce a fluorescent ligand with the desired qualities.Here, we focus on the design, synthesis, and evaluation of a high-affinity fluorescent antagonist for the ionotropic serotonin type-3 receptor.
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Engle, Keary M.; Yu, Jin-Quan
2013-01-01
Homogeneous transition metal–catalyzed reactions are indispensable to all facets of modern chemical synthesis. It is thus difficult to imagine that for much of the early 20th century, the reactivity and selectivity of all known homogeneous metal catalysts paled in comparison to their heterogeneous and biological counterparts. In the intervening decades, advances in ligand design bridged this divide, such that today some of the most demanding bond-forming events are mediated by ligand-supported homogeneous metal species. While ligand design has propelled many areas of homogeneous catalysis, in the field of Pd(II)-catalyzed C–H functionalization, suitable ligand scaffolds are lacking, which has hampered the development of broadly practical transformations based on C–H functionalization logic. In this review, we offer an account of our research employing three ligand scaffolds, mono-N-protected amino acids, 2,6-disubstituted pyridines, and 2,2′-bipyridines, to address challenges posed by several synthetically versatile substrate classes. Drawing on this work, we discuss principles of ligand design, such as the need to match a ligand to a particular substrate class, and how ligand traits such as tunability and modularity can be advantageous in reaction discovery. PMID:23565982
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Sato, Itaru; Umemura, Masanari; Mitsudo, Kenji; Fukumura, Hidenobu; Kim, Jeong-Hwan; Hoshino, Yujiro; Nakashima, Hideyuki; Kioi, Mitomu; Nakakaji, Rina; Sato, Motohiko; Fujita, Takayuki; Yokoyama, Utako; Okumura, Satoshi; Oshiro, Hisashi; Eguchi, Haruki; Tohnai, Iwai; Ishikawa, Yoshihiro
2016-04-22
We previously investigated the utility of μ-oxo N,N'- bis(salicylidene)ethylenediamine iron (Fe(Salen)) nanoparticles as a new anti-cancer agent for magnet-guided delivery with anti-cancer activity. Fe(Salen) nanoparticles should rapidly heat up in an alternating magnetic field (AMF), and we hypothesized that these single-drug nanoparticles would be effective for combined hyperthermia-chemotherapy. Conventional hyperthermic particles are usually made of iron oxide, and thus cannot exhibit anti-cancer activity in the absence of an AMF. We found that Fe(Salen) nanoparticles induced apoptosis in cultured cancer cells, and that AMF exposure enhanced the apoptotic effect. Therefore, we evaluated the combined three-fold strategy, i.e., chemotherapy with Fe(Salen) nanoparticles, magnetically guided delivery of the nanoparticles to the tumor, and AMF-induced heating of the nanoparticles to induce local hyperthermia, in a rabbit model of tongue cancer. Intravenous administration of Fe(Salen) nanoparticles per se inhibited tumor growth before the other two modalities were applied. This inhibition was enhanced when a magnet was used to accumulate Fe(Salen) nanoparticles at the tongue. When an AMF was further applied (magnet-guided chemotherapy plus hyperthermia), the tumor masses were dramatically reduced. These results indicate that our strategy of combined hyperthermia-chemotherapy using Fe(Salen) nanoparticles specifically delivered with magnetic guidance represents a powerful new approach for cancer treatment.
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An intermetallic Au24Ag20 superatom nanocluster stabilized by labile ligands.
Wang, Yu; Su, Haifeng; Xu, Chaofa; Li, Gang; Gell, Lars; Lin, Shuichao; Tang, Zichao; Häkkinen, Hannu; Zheng, Nanfeng
2015-04-08
An intermetallic nanocluster containing 44 metal atoms, Au24Ag20(2-SPy)4(PhC≡C)20Cl2, was successfully synthesized and structurally characterized by single-crystal analysis and density funtional theory computations. The 44 metal atoms in the cluster are arranged as a concentric three-shell Au12@Ag20@Au12 Keplerate structure having a high symmetry. For the first time, the co-presence of three different types of anionic ligands (i.e., phenylalkynyl, 2-pyridylthiolate, and chloride) was revealed on the surface of metal nanoclusters. Similar to thiolates, alkynyls bind linearly to surface Au atoms using their σ-bonds, leading to the formation of two types of surface staple units (PhC≡C-Au-L, L = PhC≡C(-) or 2-pyridylthiolate) on the cluster. The co-presence of three different surface ligands allows the site-specific surface and functional modification of the cluster. The lability of PhC≡C(-) ligands on the cluster was demonstrated, making it possible to keep the metal core intact while removing partial surface capping. Moreover, it was found that ligand exchange on the cluster occurs easily to offer various derivatives with the same metal core but different surface functionality and thus different solubility.
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Why do receptor–ligand bonds in cell adhesion cluster into discrete focal-adhesion sites?
Gao, Zhiwen; Gao, Yanfei
2016-05-14
We report that cell adhesion often exhibits the clustering of the receptor–ligand bonds into discrete focal-adhesion sites near the contact edge, thus resembling a rosette shape or a contracting membrane anchored by a small number of peripheral forces. The ligands on the extracellular matrix are immobile, and the receptors in the cell plasma membrane consist of two types: high-affinity integrins (that bond to the substrate ligands and are immobile) and low-affinity integrins (that are mobile and not bonded to the ligands). Thus the adhesion energy density is proportional to the high-affinity integrin density. This paper provides a mechanistic explanation formore » the clustering/assembling of the receptor–ligand bonds from two main points: (1) the cellular contractile force leads to the density evolution of these two types of integrins, and results into a large high-affinity integrin density near the contact edge and (2) the front of a propagating crack into a decreasing toughness field will be unstable and wavy. From this fracture mechanics perspective, the chemomechanical equilibrium is reached when a small number of patches with large receptor–ligand bond density are anticipated to form at the cell periphery, as opposed to a uniform distribution of bonds on the entire interface. Finally, cohesive fracture simulations show that the de-adhesion force can be significantly enhanced by this nonuniform bond density field, but the de-adhesion force anisotropy due to the substrate elastic anisotropy is significantly reduced.« less
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Why do receptor–ligand bonds in cell adhesion cluster into discrete focal-adhesion sites?
DOE Office of Scientific and Technical Information (OSTI.GOV)
Gao, Zhiwen; Gao, Yanfei
We report that cell adhesion often exhibits the clustering of the receptor–ligand bonds into discrete focal-adhesion sites near the contact edge, thus resembling a rosette shape or a contracting membrane anchored by a small number of peripheral forces. The ligands on the extracellular matrix are immobile, and the receptors in the cell plasma membrane consist of two types: high-affinity integrins (that bond to the substrate ligands and are immobile) and low-affinity integrins (that are mobile and not bonded to the ligands). Thus the adhesion energy density is proportional to the high-affinity integrin density. This paper provides a mechanistic explanation formore » the clustering/assembling of the receptor–ligand bonds from two main points: (1) the cellular contractile force leads to the density evolution of these two types of integrins, and results into a large high-affinity integrin density near the contact edge and (2) the front of a propagating crack into a decreasing toughness field will be unstable and wavy. From this fracture mechanics perspective, the chemomechanical equilibrium is reached when a small number of patches with large receptor–ligand bond density are anticipated to form at the cell periphery, as opposed to a uniform distribution of bonds on the entire interface. Finally, cohesive fracture simulations show that the de-adhesion force can be significantly enhanced by this nonuniform bond density field, but the de-adhesion force anisotropy due to the substrate elastic anisotropy is significantly reduced.« less
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Grouleff, Julie; Schiøtt, Birgit
2013-01-01
The competitive inhibitor cocaine and the non-competitive inhibitor ibogaine induce different conformational states of the human serotonin transporter. It has been shown from accessibility experiments that cocaine mainly induces an outward-facing conformation, while the non-competitive inhibitor ibogaine, and its active metabolite noribogaine, have been proposed to induce an inward-facing conformation of the human serotonin transporter similar to what has been observed for the endogenous substrate, serotonin. The ligand induced conformational changes within the human serotonin transporter caused by these three different types of ligands, substrate, non-competitive and competitive inhibitors, are studied from multiple atomistic molecular dynamics simulations initiated from a homology model of the human serotonin transporter. The results reveal that diverse conformations of the human serotonin transporter are captured from the molecular dynamics simulations depending on the type of the ligand bound. The inward-facing conformation of the human serotonin transporter is reached with noribogaine bound, and this state resembles a previously identified inward-facing conformation of the human serotonin transporter obtained from molecular dynamics simulation with bound substrate, but also a recently published inward-facing conformation of a bacterial homolog, the leucine transporter from Aquifex Aoelicus. The differences observed in ligand induced behavior are found to originate from different interaction patterns between the ligands and the protein. Such atomic-level understanding of how an inhibitor can dictate the conformational response of a transporter by ligand binding may be of great importance for future drug design. PMID:23776432
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He, Yan; Estephan, Rima; Yang, Xiaomin; Vela, Adriana; Wang, Hsin; Bernard, Cédric; Stark, Ruth E.
2011-01-01
Liver fatty acid-binding protein (LFABP) is a 14-kDa cytosolic polypeptide, differing from other family members in number of ligand binding sites, diversity of bound ligands, and transfer of fatty acid(s) to membranes primarily via aqueous diffusion rather than direct collisional interactions. Distinct two-dimensional 1H-15N NMR signals indicative of slowly exchanging LFABP assemblies formed during stepwise ligand titration were exploited, without solving the protein-ligand complex structures, to yield the stoichiometries for the bound ligands, their locations within the protein binding cavity, the sequence of ligand occupation, and the corresponding protein structural accommodations. Chemical shifts were monitored for wild-type LFABP and a R122L/S124A mutant in which electrostatic interactions viewed as essential to fatty acid binding were removed. For wild-type LFABP the results compared favorably with previous tertiary structures of oleate-bound wild-type LFABP in crystals and in solution: there are two oleates, one U-shaped ligand that positions the long hydrophobic chain deep within the cavity and another extended structure with the hydrophobic chain facing the cavity and the carboxylate group lying close to the protein surface. The NMR titration validated a prior hypothesis that the first oleate to enter the cavity occupies the internal protein site. In contrast, 1H/15N chemical shift changes supported only one liganded oleate for R122L/S124A LFABP, at an intermediate location within the protein cavity. A rationale based on protein sequence and electrostatics was developed to explain the stoichiometry and binding site trends for LFABPs and to put these findings into context within the larger protein family. PMID:21226535
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Classification of ligand molecules in PDB with graph match-based structural superposition.
Shionyu-Mitsuyama, Clara; Hijikata, Atsushi; Tsuji, Toshiyuki; Shirai, Tsuyoshi
2016-12-01
The fast heuristic graph match algorithm for small molecules, COMPLIG, was improved by adding a structural superposition process to verify the atom-atom matching. The modified method was used to classify the small molecule ligands in the Protein Data Bank (PDB) by their three-dimensional structures, and 16,660 types of ligands in the PDB were classified into 7561 clusters. In contrast, a classification by a previous method (without structure superposition) generated 3371 clusters from the same ligand set. The characteristic feature in the current classification system is the increased number of singleton clusters, which contained only one ligand molecule in a cluster. Inspections of the singletons in the current classification system but not in the previous one implied that the major factors for the isolation were differences in chirality, cyclic conformations, separation of substructures, and bond length. Comparisons between current and previous classification systems revealed that the superposition-based classification was effective in clustering functionally related ligands, such as drugs targeted to specific biological processes, owing to the strictness of the atom-atom matching.
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Identification of Natural RORγ Ligands that Regulate the Development of Lymphoid Cells
Santori, Fabio R.; Huang, Pengxiang; van de Pavert, Serge A.; Douglass, Eugene F.; Leaver, David J.; Haubrich, Brad A.; Keber, Rok; Lorbek, Gregor; Konijn, Tanja; Rosales, Brittany N.; Horvat, Simon; Rozman, Damjana; Rahier, Alain; Mebius, Reina E.; Rastinejad, Fraydoon; Nes, W. David; Littman, Dan R.
2015-01-01
SUMMARY Mice deficient in the nuclear hormone receptor RORγt have defective development of thymocytes, lymphoid organs, Th17 cells and type 3 innate lymphoid cells. RORγt binds to oxysterols derived from cholesterol catabolism but it is not clear whether these are its natural ligands. Here, we show that sterol lipids are necessary and sufficient to drive RORγt-dependent transcription. We combined overexpression, RNA interference and genetic deletion of metabolic enzymes to study RORγ-dependent transcription. Our results are consistent with the RORγt ligand(s) being a cholesterol biosynthetic intermediate (CBI) downstream of lanosterol and upstream of zymosterol. Analysis of lipids bound to RORγ identified molecules with molecular weights consistent with CBIs. Furthermore, CBIs stabilized the RORγ ligand-binding domain and induced co-activator recruitment. Genetic deletion of metabolic enzymes upstream of the RORγt-ligand(s) affected the development of lymph nodes and Th17 cells. Our data suggest that CBIs play a role in lymphocyte development potentially through regulation of RORγt. PMID:25651181
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Rationalizing Tight Ligand Binding through Cooperative Interaction Networks
2011-01-01
Small modifications of the molecular structure of a ligand sometimes cause strong gains in binding affinity to a protein target, rendering a weakly active chemical series suddenly attractive for further optimization. Our goal in this study is to better rationalize and predict the occurrence of such interaction hot-spots in receptor binding sites. To this end, we introduce two new concepts into the computational description of molecular recognition. First, we take a broader view of noncovalent interactions and describe protein–ligand binding with a comprehensive set of favorable and unfavorable contact types, including for example halogen bonding and orthogonal multipolar interactions. Second, we go beyond the commonly used pairwise additive treatment of atomic interactions and use a small world network approach to describe how interactions are modulated by their environment. This approach allows us to capture local cooperativity effects and considerably improves the performance of a newly derived empirical scoring function, ScorpionScore. More importantly, however, we demonstrate how an intuitive visualization of key intermolecular interactions, interaction networks, and binding hot-spots supports the identification and rationalization of tight ligand binding. PMID:22087588
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Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach
NASA Astrophysics Data System (ADS)
Lam, Polo C.-H.; Abagyan, Ruben; Totrov, Maxim
2018-01-01
Ligand docking to flexible protein molecules can be efficiently carried out through ensemble docking to multiple protein conformations, either from experimental X-ray structures or from in silico simulations. The success of ensemble docking often requires the careful selection of complementary protein conformations, through docking and scoring of known co-crystallized ligands. False positives, in which a ligand in a wrong pose achieves a better docking score than that of native pose, arise as additional protein conformations are added. In the current study, we developed a new ligand-biased ensemble receptor docking method and composite scoring function which combine the use of ligand-based atomic property field (APF) method with receptor structure-based docking. This method helps us to correctly dock 30 out of 36 ligands presented by the D3R docking challenge. For the six mis-docked ligands, the cognate receptor structures prove to be too different from the 40 available experimental Pocketome conformations used for docking and could be identified only by receptor sampling beyond experimentally explored conformational subspace.
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Raman, E. Prabhu; Yu, Wenbo; Guvench, Olgun; MacKerell, Alexander D.
2011-01-01
The applicability of a computational method, Site Identification by Ligand Competitive Saturation (SILCS), to identify regions on a protein surface with which different types of functional groups on low-molecular weight inhibitors interact is demonstrated. The method involves molecular dynamics (MD) simulations of a protein in an aqueous solution of chemically diverse small molecules from which probability distributions of fragments types, termed FragMaps, are obtained. In the present application, SILCS simulations are performed with an aqueous solution of 1 M benzene and propane to map the affinity pattern of the protein for aromatic and aliphatic functional groups. In addition, water hydrogen and oxygen atoms serve as probes for hydrogen bond donor and acceptor affinity, respectively. The method is tested using a set of 7 proteins for which crystal structures of complexes with several high affinity inhibitors are known. Good agreement is obtained between FragMaps and the positions of chemically similar functional groups in inhibitors as observed in the X-ray crystallographic structures. Quantitative capabilities of the SILCS approach are demonstrated by converting FragMaps to free energies, termed Grid Free Energies (GFE), and showing correlation between the GFE values and experimental binding affinities. For proteins for which ligand decoy sets are available, GFE values are shown to typically score the crystal conformation and conformations similar to it more favorable than decoys. Additionally, SILCS is tested for its ability to capture the subtle differences in ligand affinity across homologous proteins, information which may be of utility towards specificity-guided drug design. Taken together, our results show that SILCS can recapitulate the known location of functional groups of bound inhibitors for a number of proteins, suggesting that the method may be of utility for rational drug design. PMID:21456594
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ProBiS-ligands: a web server for prediction of ligands by examination of protein binding sites.
Konc, Janez; Janežič, Dušanka
2014-07-01
The ProBiS-ligands web server predicts binding of ligands to a protein structure. Starting with a protein structure or binding site, ProBiS-ligands first identifies template proteins in the Protein Data Bank that share similar binding sites. Based on the superimpositions of the query protein and the similar binding sites found, the server then transposes the ligand structures from those sites to the query protein. Such ligand prediction supports many activities, e.g. drug repurposing. The ProBiS-ligands web server, an extension of the ProBiS web server, is open and free to all users at http://probis.cmm.ki.si/ligands. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.
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A novel computational approach "BP-STOCH" to study ligand binding to finite lattice.
Beshnova, Daria A; Bereznyak, Ekaterina G; Shestopalova, Anna V; Evstigneev, Maxim P
2011-03-01
We report a novel computational algorithm "BP-STOCH" to be used for studying single-type ligand binding with biopolymers of finite lengths, such as DNA oligonucleotides or oligopeptides. It is based on an idea to represent any type of ligand-biopolymer complex in a form of binary number, where "0" and "1" bits stand for vacant and engaged monomers of the biopolymer, respectively. Cycling over all binary numbers from the lowest 0 up to the highest 2(N) - 1 means a sequential generating of all possible configurations of vacant/engaged monomers, which, after proper filtering, results in a full set of possible types of complexes in solution between the ligand and the N-site lattice. The principal advantage of BP-STOCH algorithm is the possibility to incorporate into this cycle any conditions on computation of the concentrations and observed experimental parameters of the complexes in solution, and programmatic access to each monomer of the biopolymer within each binding site of every binding configuration. The latter is equivalent to unlimited extension of the basic reaction scheme and allows to use BP-STOCH algorithm as an alternative to conventional computational approaches.
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Introducing various ligands into superhalogen anions reduces their electronic stabilities
NASA Astrophysics Data System (ADS)
Smuczyńska, Sylwia; Skurski, Piotr
2008-02-01
The vertical electron detachment energies (VDE) of six NaX2- anions (where X = F, Cl, Br) were calculated at the OVGF level with the 6-311++G(3df) basis sets. In all the cases studied the VDE exceeds the electron affinity of chlorine atom and thus those species were classified as superhalogen anions. The largest vertical binding energy was found for the NaF2- system (6.644 eV). The strong VDE dependence on the ligand type, ligand-central atom distance, and the character of the highest occupied molecular orbital (HOMO) was observed and discussed.
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WY14,643, a PPARalpha ligand, attenuates expression of anti-glomerular basement membrane disease.
Archer, D C; Frkanec, J T; Cromwell, J; Clopton, P; Cunard, R
2007-11-01
Peroxisome proliferator-activated receptor alpha (PPARalpha) ligands are medications used to treat hyperlipidaemia and atherosclerosis. Increasing evidence suggests that these agents are immunosuppressive. In the following studies we demonstrate that WY14,643, a PPARalpha ligand, attenuates expression of anti-glomerular basement membrane disease (AGBMD). C57BL/6 mice were fed 0.05% WY14,643 or control food and immunized with the non-collagenous domain of the alpha3 chain of Type IV collagen [alpha3(IV) NC1] in complete Freund's adjuvant (CFA). WY14,643 reduced proteinuria and greatly improved glomerular and tubulo-interstitial lesions. However, the PPARalpha ligand did not alter the extent of IgG-binding to the GBM. Immunohistochemical studies revealed that the prominent tubulo-interstitial infiltrates in the control-fed mice consisted predominately of F4/80(+) macrophages and WY14,643-feeding decreased significantly the number of renal macrophages. The synthetic PPARalpha ligand also reduced significantly expression of the chemokine, monocyte chemoattractant protein (MCP)-1/CCL2. Sera from mice immunized with AGBMD were also evaluated for antigen-specific IgGs. There was a significant increase in the IgG1 : IgG2c ratio and a decline in the intrarenal and splenocyte interferon (IFN)-gamma mRNA expression in the WY14,643-fed mice, suggesting that the PPARalpha ligand could skew the immune response to a less inflammatory T helper 2-type of response. These studies suggest that PPARalpha ligands may be a novel treatment for inflammatory renal disease.
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WY14,643, a PPARα ligand, attenuates expression of anti-glomerular basement membrane disease
Archer, D C; Frkanec, J T; Cromwell, J; Clopton, P; Cunard, R
2007-01-01
Peroxisome proliferator-activated receptor alpha (PPARα) ligands are medications used to treat hyperlipidaemia and atherosclerosis. Increasing evidence suggests that these agents are immunosuppressive. In the following studies we demonstrate that WY14,643, a PPARα ligand, attenuates expression of anti-glomerular basement membrane disease (AGBMD). C57BL/6 mice were fed 0·05% WY14,643 or control food and immunized with the non-collagenous domain of the α3 chain of Type IV collagen [α3(IV) NC1] in complete Freund's adjuvant (CFA). WY14,643 reduced proteinuria and greatly improved glomerular and tubulo-interstitial lesions. However, the PPARα ligand did not alter the extent of IgG-binding to the GBM. Immunohistochemical studies revealed that the prominent tubulo-interstitial infiltrates in the control-fed mice consisted predominately of F4/80+ macrophages and WY14,643-feeding decreased significantly the number of renal macrophages. The synthetic PPARα ligand also reduced significantly expression of the chemokine, monocyte chemoattractant protein (MCP)-1/CCL2. Sera from mice immunized with AGBMD were also evaluated for antigen-specific IgGs. There was a significant increase in the IgG1 : IgG2c ratio and a decline in the intrarenal and splenocyte interferon (IFN)-γ mRNA expression in the WY14,643-fed mice, suggesting that the PPARα ligand could skew the immune response to a less inflammatory T helper 2-type of response. These studies suggest that PPARα ligands may be a novel treatment for inflammatory renal disease. PMID:17888025
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Gaden, Florence; Franqueville, Laure; Magnusson, Maria K.; Hong, Saw See; Merten, Marc D.; Lindholm, Leif; Boulanger, Pierre
2004-01-01
Monolayers of cystic fibrosis transmembrane conductance regulator (CFTR)-deficient human tracheal glandular cells (CF-KM4) were subjected to phage biopanning, and cell-internalized phages were isolated and sequenced, in order to identify CF-KM4-specific peptide ligands that would confer upon adenovirus type 5 (Ad5) vector a novel cell target specificity and/or higher efficiency of gene delivery into airway cells of patients with cystic fibrosis (CF). Three different ligands, corresponding to prototypes of the most represented families of phagotopes recovered from intracellular phages, were designed and individually inserted into Ad5-green fluorescent protein (GFP) (AdGFP) vectors at the extremities of short fiber shafts (seven repeats [R7]) terminated by scissile knobs. Only one vector, carrying the decapeptide GHPRQMSHVY (abbreviated as QM10), showed an enhanced gene transduction of CF-KM4 cells compared to control nonliganded vector with fibers of the same length (AdGFP-R7-knob). The enhancement in gene transfer efficiency was not specific to CF-KM4 cells but was observed in other mammalian cell lines tested. The QM10-liganded vector was referred to as AdGFP-QM10-knob in its knobbed version and as AdGFP-QM10 in its proteolytically deknobbed version. AdGFP-QM10 was found to transduce cells with a higher efficiency than its knob-bearing version, AdGFP-QM10-knob. Consistent with this, competition experiments indicated that the presence of knob domains was not an absolute requirement for cell attachment of the QM10-liganded vector and that the knobless AdGFP-QM10 used alternative cell-binding domains on its capsid, including penton base capsomer, via a site(s) different from its RGD motifs. The QM10-mediated effect on gene transduction seemed to take place at the step of endocytosis in both quantitative and qualitative manners. Virions of AdGFP-QM10 were endocytosed in higher numbers than virions of the control vector and were directed to a compartment different from
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NASA Astrophysics Data System (ADS)
Zhang, Yixuan; Deng, Lu; Kitova, Elena N.; Klassen, John S.
2013-10-01
The results of collision-induced dissociation (CID) experiments performed on gaseous protonated and deprotonated ions of complexes of cholera toxin B subunit homopentamer (CTB5) with the pentasaccharide (β-D-Gal p-(1→3)-β-D-Gal pNAc-(1→4)[α-D-Neu5Ac-(2→3)]-β-D-Gal p-(1→4)-β-D-Glc p (GM1)) and corresponding glycosphingolipid (β-D-Gal p-(1→3)-β-D-Gal pNAc-(1→4)[α-D-Neu5Ac-(2→3)]-β-D-Gal p-(1→4)-β-D-Glc p-Cer (GM1-Cer)) ligands, and the homotetramer streptavidin (S4) with biotin (B) and 1,2-dipalmitoyl- sn-glycero-3-phosphoethanolamine-N-(biotinyl) (Btl), are reported. The protonated (CTB5 + 5GM1)n+ ions dissociated predominantly by the loss of a single subunit, with the concomitant migration of ligand to another subunit. The simultaneous loss of ligand and subunit was observed as a minor pathway. In contrast, the deprotonated (CTB5 + 5GM1)n- ions dissociated preferentially by the loss of deprotonated ligand; the loss of ligand-bound and ligand-free subunit were minor pathways. The presence of ceramide (Cer) promoted ligand migration and the loss of subunit. The main dissociation pathway for the protonated and deprotonated (S4 + 4B)n+/- ions, as well as for deprotonated (S4 + 4Btl)n- ions, was loss of the ligand. However, subunit loss from the (S4 + 4B)n+ ions was observed as a minor pathway. The (S4 + 4Btl)n+ ions dissociated predominantly by the loss of free and ligand-bound subunit. The charge state of the complex and the collision energy were found to have little effect on the relative contribution of the different dissociation channels. Thermally-driven ligand migration between subunits was captured in the results of molecular dynamics simulations performed on protonated (CTB5 + 5GM1)15+ ions (with a range of charge configurations) at 800 K. Notably, the migration pathway was found to be highly dependent on the charge configuration of the ion. The main conclusion of this study is that the dissociation pathways of multisubunit protein-ligand
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Ligand-induced Epitope Masking
Mould, A. Paul; Askari, Janet A.; Byron, Adam; Takada, Yoshikazu; Jowitt, Thomas A.; Humphries, Martin J.
2016-01-01
We previously demonstrated that Arg-Gly-Asp (RGD)-containing ligand-mimetic inhibitors of integrins are unable to dissociate pre-formed integrin-fibronectin complexes (IFCs). These observations suggested that amino acid residues involved in integrin-fibronectin binding become obscured in the ligand-occupied state. Because the epitopes of some function-blocking anti-integrin monoclonal antibodies (mAbs) lie near the ligand-binding pocket, it follows that the epitopes of these mAbs may become shielded in the ligand-occupied state. Here, we tested whether function-blocking mAbs directed against α5β1 can interact with the integrin after it forms a complex with an RGD-containing fragment of fibronectin. We showed that the anti-α5 subunit mAbs JBS5, SNAKA52, 16, and P1D6 failed to disrupt IFCs and hence appeared unable to bind to the ligand-occupied state. In contrast, the allosteric anti-β1 subunit mAbs 13, 4B4, and AIIB2 could dissociate IFCs and therefore were able to interact with the ligand-bound state. However, another class of function-blocking anti-β1 mAbs, exemplified by Lia1/2, could not disrupt IFCs. This second class of mAbs was also distinguished from 13, 4B4, and AIIB2 by their ability to induce homotypic cell aggregation. Although the epitope of Lia1/2 was closely overlapping with those of 13, 4B4, and AIIB2, it appeared to lie closer to the ligand-binding pocket. A new model of the α5β1-fibronectin complex supports our hypothesis that the epitopes of mAbs that fail to bind to the ligand-occupied state lie within, or very close to, the integrin-fibronectin interface. Importantly, our findings imply that the efficacy of some therapeutic anti-integrin mAbs could be limited by epitope masking. PMID:27484800
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Quantum.Ligand.Dock: protein-ligand docking with quantum entanglement refinement on a GPU system.
Kantardjiev, Alexander A
2012-07-01
Quantum.Ligand.Dock (protein-ligand docking with graphic processing unit (GPU) quantum entanglement refinement on a GPU system) is an original modern method for in silico prediction of protein-ligand interactions via high-performance docking code. The main flavour of our approach is a combination of fast search with a special account for overlooked physical interactions. On the one hand, we take care of self-consistency and proton equilibria mutual effects of docking partners. On the other hand, Quantum.Ligand.Dock is the the only docking server offering such a subtle supplement to protein docking algorithms as quantum entanglement contributions. The motivation for development and proposition of the method to the community hinges upon two arguments-the fundamental importance of quantum entanglement contribution in molecular interaction and the realistic possibility to implement it by the availability of supercomputing power. The implementation of sophisticated quantum methods is made possible by parallelization at several bottlenecks on a GPU supercomputer. The high-performance implementation will be of use for large-scale virtual screening projects, structural bioinformatics, systems biology and fundamental research in understanding protein-ligand recognition. The design of the interface is focused on feasibility and ease of use. Protein and ligand molecule structures are supposed to be submitted as atomic coordinate files in PDB format. A customization section is offered for addition of user-specified charges, extra ionogenic groups with intrinsic pK(a) values or fixed ions. Final predicted complexes are ranked according to obtained scores and provided in PDB format as well as interactive visualization in a molecular viewer. Quantum.Ligand.Dock server can be accessed at http://87.116.85.141/LigandDock.html.
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Simple and fast screening of G-quadruplex ligands with electrochemical detection system.
Fan, Qiongxuan; Li, Chao; Tao, Yaqin; Mao, Xiaoxia; Li, Genxi
2016-11-01
Small molecules that may facilitate and stabilize the formation of G-quadruplexes can be used for cancer treatments, because the G-quadruplex structure can inhibit the activity of telomerase, an enzyme over-expressed in many cancer cells. Therefore, there is considerable interest in developing a simple and high-performance method for screening small molecules binding to G-quadruplex. Here, we have designed a simple electrochemical approach to screen such ligands based on the fact that the formation and stabilization of G-quadruplex by ligand may inhibit electron transfer of redox species to electrode surface. As a proof-of-concept study, two types of classical G-quadruplex ligands, TMPyP4 and BRACO-19, are studied in this work, which demonstrates that this method is fast and robust and it may be applied to screen G-quadruplex ligands for anticancer drugs testing and design in the future. Copyright © 2016 Elsevier B.V. All rights reserved.
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Rhenium complexes of bidentate, bis-bidentate and tridentate N-heterocyclic carbene ligands.
Chan, Chung Ying; Barnard, Peter J
2015-11-28
A series of eight Rhenium(I)-N-heterocyclic carbene (NHC) complexes of the general form [ReCl(CO)3(C^C)] (where C^C is a bis(NHC) bidentate ligand), [ReCl(CO)3(C^C)]2 (where C^C is a bis-bidentate tetra-NHC ligand) and [Re(CO)3(C^N^C)](+)[X](-) (where C^N^C is a bis(NHC)-amine ligand and the counter ion X is either the ReO4(-) or PF6(-)) have been synthesised using a Ag2O transmetallation protocol. The novel precursor imidazolium salts and Re(I) complexes were characterized by elemental analysis, (1)H and (13)C NMR spectroscopy and the molecular structures for two imidazolium salt and six Re(I) complexes were determined by single crystal X-ray diffraction. These NHC ligand systems are of interest for possible applications in the development of Tc-99m or Re-186/188 radiopharmaceuticals and as such the stability of two complexes of the form [ReCl(CO)3(C^C)] and [Re(CO)3(C^N^C)][ReO4] were evaluated in ligand challenge experiments using the metal binding amino acids L-histidine or L-cysteine. These studies showed that the former was unstable, with the chloride ligand being replaced by either cysteine or histidine, while no evidence for transchelation was observed for the latter suggesting that bis(NHC)-amine ligands of this type may be suitable for biological applications.
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Iron chelating ligand for iron overload diseases.
Ozbolat, G; Tuli, A
2018-01-01
Iron overloads are a serious clinical condition in the health of humans and are therefore a key target in drug development. In this study, iron(III) complex of 8-hydroxyquinoline-5 sulphonic acid was synthesized and structurally characterized in its solid state and solution state by FT-IR, UV-Vis, elemental analysis, magnetic susceptibility and 1H-NMR. The catalase activities of complex were investigated. It was showed that the complex has the catalase activity. It is suggested that this type of complex may constitute a new and interesting basis for the future search for new and more potential drugs. The electrochemical behaviour patterns of the ligand and complex were examined as supporting electrolyte and platinum electrode for cyclic voltammetry. The electrochemistry studies showed that the reductions in free ligand and complex take place differently.The cytotoxicity was evaluated by MTT assay. The complex exhibited a very high cytotoxic activity and showed a cytotoxic effect that was much better than that of the ligand.The observed cytotoxicity could be pursued to obtain a potential drug. These results indicate that using the 8-hydroxyquinoline-5 sulphonic acid for this aim in further studies is appropriate (Tab. 1, Fig. 4, Ref. 18). Text in PDF www.elis.sk.
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Highly stable biocompatible inorganic nanoparticles by self-assembly of triblock-copolymer ligands.
Pöselt, Elmar; Fischer, Steffen; Foerster, Stephan; Weller, Horst
2009-12-15
A novel type of ligand for biofunctionalization of nanoparticles is presented that comprises tailor-made triblock-copolymers consisting of a polyethylene imine binding block, a hydrophobic polycaprolactone and a terminal functionalized polyethelene oxide block. Phase transfer to water occurs simply by ligand and water addition and removal of the organic solvents. It is shown that the intermediate polycaprolacton block favors the attachment to the particle surface and shields the binding groups effectively from the solution. As a consequence, the particles exhibit an outstanding stability in various aqueous media for biological studies and give easy access to specific coupling reactions at the terminal end groups of the polyethylene oxide block. Controlling the ligand exchange parameters leads to self-assembly to either individual encapsulated nanoparticles or to multifunctional nanobeads.
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Prexl, Andrea; Münder, Sandra; Loy, Bernhard; Kremmer, Elisabeth; Tischer, Susanne; Böttger, Angelika
2011-09-07
The Notch signalling pathway is conserved in pre-bilaterian animals. In the Cnidarian Hydra it is involved in interstitial stem cell differentiation and in boundary formation during budding. Experimental evidence suggests that in Hydra Notch is activated by presenilin through proteolytic cleavage at the S3 site as in all animals. However, the endogenous ligand for HvNotch has not been described yet. We have cloned a cDNA from Hydra, which encodes a bona-fide Notch ligand with a conserved domain structure similar to that of Jagged-like Notch ligands from other animals. Hyjagged mRNA is undetectable in adult Hydra by in situ hybridisation but is strongly upregulated and easily visible at the border between bud and parent shortly before bud detachment. In contrast, HyJagged protein is found in all cell types of an adult hydra, where it localises to membranes and endosomes. Co-localisation experiments showed that it is present in the same cells as HvNotch, however not always in the same membrane structures. The putative Notch ligand HyJagged is conserved in Cnidarians. Together with HvNotch it may be involved in the formation of the parent-bud boundary in Hydra. Moreover, protein distribution of both, HvNotch receptor and HyJagged indicate a more widespread function for these two transmembrane proteins in the adult hydra, which may be regulated by additional factors, possibly involving endocytic pathways.
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2011-01-01
Background The Notch signalling pathway is conserved in pre-bilaterian animals. In the Cnidarian Hydra it is involved in interstitial stem cell differentiation and in boundary formation during budding. Experimental evidence suggests that in Hydra Notch is activated by presenilin through proteolytic cleavage at the S3 site as in all animals. However, the endogenous ligand for HvNotch has not been described yet. Results We have cloned a cDNA from Hydra, which encodes a bona-fide Notch ligand with a conserved domain structure similar to that of Jagged-like Notch ligands from other animals. Hyjagged mRNA is undetectable in adult Hydra by in situ hybridisation but is strongly upregulated and easily visible at the border between bud and parent shortly before bud detachment. In contrast, HyJagged protein is found in all cell types of an adult hydra, where it localises to membranes and endosomes. Co-localisation experiments showed that it is present in the same cells as HvNotch, however not always in the same membrane structures. Conclusions The putative Notch ligand HyJagged is conserved in Cnidarians. Together with HvNotch it may be involved in the formation of the parent-bud boundary in Hydra. Moreover, protein distribution of both, HvNotch receptor and HyJagged indicate a more widespread function for these two transmembrane proteins in the adult hydra, which may be regulated by additional factors, possibly involving endocytic pathways. PMID:21899759
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NASA Astrophysics Data System (ADS)
Anokhina, Ekaterina V.
Low-dimensional and open-framework materials containing transition metals have a wide range of applications in redox catalysis, solid-state batteries, and electronic and magnetic devices. This dissertation reports on research carried out with the goal to develop a strategy for the preparation of low-dimensional and open-framework materials using octahedral metal clusters as building blocks. Our approach takes its roots from crystal engineering principles where the desired framework topologies are achieved through building block design. The key idea of this work is to induce directional bonding preferences in the cluster units using a combination of ligands with a large difference in charge density. This investigation led to the preparation and characterization of a new family of niobium oxychloride cluster compounds with original structure types exhibiting 1ow-dimensional or open-framework character. Most of these materials have framework topologies unprecedented in compounds containing octahedral clusters. Comparative analysis of their structural features indicates that the novel cluster connectivity patterns in these systems are the result of complex interplay between the effects of anisotropic ligand arrangement in the cluster unit and optimization of ligand-counterion electrostatic interactions. The important role played by these factors sets niobium oxychloride systems apart from cluster compounds with one ligand type or statistical ligand distribution where the main structure-determining factor is the total number of ligands. These results provide a blueprint for expanding the ligand combination strategy to other transition metal cluster systems and for the future rational design of cluster-based materials.
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Speranskiy, Kirill; Kurnikova, Maria
2005-08-30
Ionotropic glutamate receptors (GluRs) are ligand-gated membrane channel proteins found in the central neural system that mediate a fast excitatory response of neurons. In this paper, we report theoretical analysis of the ligand-protein interactions in the binding pocket of the S1S2 (ligand binding) domain of the GluR2 receptor in the closed conformation. By utilizing several theoretical methods ranging from continuum electrostatics to all-atom molecular dynamics simulations and quantum chemical calculations, we were able to characterize in detail glutamate agonist binding to the wild-type and E705D mutant proteins. A theoretical model of the protein-ligand interactions is validated via direct comparison of theoretical and Fourier transform infrared spectroscopy (FTIR) measured frequency shifts of the ligand's carboxylate group vibrations [Jayaraman et al. (2000) Biochemistry 39, 8693-8697; Cheng et al. (2002) Biochemistry 41, 1602-1608]. A detailed picture of the interactions in the binding site is inferred by analyzing contributions to vibrational frequencies produced by protein residues forming the ligand-binding pocket. The role of mobility and hydrogen-bonding network of water in the ligand-binding pocket and the contribution of protein residues exposed in the binding pocket to the binding and selectivity of the ligand are discussed. It is demonstrated that the molecular surface of the protein in the ligand-free state has mainly positive electrostatic potential attractive to the negatively charged ligand, and the potential produced by the protein in the ligand-binding pocket in the closed state is complementary to the distribution of the electrostatic potential produced by the ligand itself. Such charge complementarity ensures specificity to the unique charge distribution of the ligand.
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Covalent modification of proteins by ligands of steroid hormone receptors.
Takahashi, N; Breitman, T R
1992-01-01
Retinoylation, acylation with retinoic acid (RA), is a covalent modification of proteins occurring in a variety of eukaryotic cell lines. In this study, we found that proteins in HL-60 cells were labeled by 17 beta-[3H]estradiol (E2), [3H]progesterone (Pg), 1 alpha,25-dihydroxy[3H]vitamin D3 [1,25(OH)2D3], [125I]triiodothyronine (T3), [125I]thyroxine (T4), and [3H]prostaglandin E2 (PGE2). All of these hormones, except PGE2, are ligands of the steroid hormone receptor family. Addition to the growth medium of 5 microM ketoconazole, an inhibitor of cytochrome P450-dependent enzymes, increased about 2-fold the labeling of proteins by T3, T4, 1,25(OH)2D3, and PGE2. In contrast, ketoconazole did not change markedly the extent of labeling by RA, E2, or Pg. Alkaline methanolysis, which cleaves ester bonds, released variable percentages of the radioactive ligands bound to protein. These values were about 80% for RA and PGE2; 50% for T3, T4, and Pg; and 20% for E2 and 1,25(OH)2D3. Treatment with thioether-cleavage reagents, iodomethane or Raney nickel catalyst, released < 2% of the covalently bound ligands. Two-dimensional polyacrylamide gel electrophoresis patterns of labeled proteins were unique for each ligand. Proteins of M(r) 47,000 and 51,000 were labeled by RA, E2, T3, and T4. These proteins had the same mobilities as RI and RII, the cAMP-binding regulatory subunits of type I and type II cAMP-dependent protein kinases. 1,25(OH)2D3 also bound to proteins of M(r) 47,000 and 51,000. However, these proteins had pI values different from those of RI or RII. These results suggest that some activities of ligands of the steroid hormone receptor family and of PGE2 may be mediated by their covalent modification of proteins. Images PMID:1438281
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Covalent modification of proteins by ligands of steroid hormone receptors.
Takahashi, N; Breitman, T R
1992-11-15
Retinoylation, acylation with retinoic acid (RA), is a covalent modification of proteins occurring in a variety of eukaryotic cell lines. In this study, we found that proteins in HL-60 cells were labeled by 17 beta-[3H]estradiol (E2), [3H]progesterone (Pg), 1 alpha,25-dihydroxy[3H]vitamin D3 [1,25(OH)2D3], [125I]triiodothyronine (T3), [125I]thyroxine (T4), and [3H]prostaglandin E2 (PGE2). All of these hormones, except PGE2, are ligands of the steroid hormone receptor family. Addition to the growth medium of 5 microM ketoconazole, an inhibitor of cytochrome P450-dependent enzymes, increased about 2-fold the labeling of proteins by T3, T4, 1,25(OH)2D3, and PGE2. In contrast, ketoconazole did not change markedly the extent of labeling by RA, E2, or Pg. Alkaline methanolysis, which cleaves ester bonds, released variable percentages of the radioactive ligands bound to protein. These values were about 80% for RA and PGE2; 50% for T3, T4, and Pg; and 20% for E2 and 1,25(OH)2D3. Treatment with thioether-cleavage reagents, iodomethane or Raney nickel catalyst, released < 2% of the covalently bound ligands. Two-dimensional polyacrylamide gel electrophoresis patterns of labeled proteins were unique for each ligand. Proteins of M(r) 47,000 and 51,000 were labeled by RA, E2, T3, and T4. These proteins had the same mobilities as RI and RII, the cAMP-binding regulatory subunits of type I and type II cAMP-dependent protein kinases. 1,25(OH)2D3 also bound to proteins of M(r) 47,000 and 51,000. However, these proteins had pI values different from those of RI or RII. These results suggest that some activities of ligands of the steroid hormone receptor family and of PGE2 may be mediated by their covalent modification of proteins.
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Rigas, Diamanda; Lewis, Gavin; Aron, Jennifer L; Wang, Bowen; Banie, Homayon; Sankaranarayanan, Ishwarya; Galle-Treger, Lauriane; Maazi, Hadi; Lo, Richard; Freeman, Gordon J; Sharpe, Arlene H; Soroosh, Pejman; Akbari, Omid
2017-05-01
Atopic diseases, including asthma, exacerbate type 2 immune responses and involve a number of immune cell types, including regulatory T (Treg) cells and the emerging type 2 innate lymphoid cells (ILC2s). Although ILC2s are potent producers of type 2 cytokines, the regulation of ILC2 activation and function is not well understood. In the present study, for the first time, we evaluate how Treg cells interact with pulmonary ILC2s and control their function. ILC2s and Treg cells were evaluated by using in vitro suppression assays, cell-contact assays, and gene expression panels. Also, human ILC2s and Treg cells were adoptively transferred into NOD SCID γC-deficient mice, which were given isotype or anti-inducible T-cell costimulator ligand (ICOSL) antibodies and then challenged with IL-33 and assessed for airway hyperreactivity. We show that induced Treg cells, but not natural Treg cells, effectively suppress the production of the ILC2-driven proinflammatory cytokines IL-5 and IL-13 both in vitro and in vivo. Mechanistically, our data reveal the necessity of inducible T-cell costimulator (ICOS)-ICOS ligand cell contact for Treg cell-mediated ILC2 suppression alongside the suppressive cytokines TGF-β and IL-10. Using a translational approach, we then demonstrate that human induced Treg cells suppress syngeneic human ILC2s through ICOSL to control airway inflammation in a humanized ILC2 mouse model. These findings suggest that peripheral expansion of induced Treg cells can serve as a promising therapeutic target against ILC2-dependent asthma. Copyright © 2016 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.
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NASA Astrophysics Data System (ADS)
Wang, Chao; Zhao, Jun; Xia, Liang; Wu, Xue-Qian; Wang, Jian-Fang; Dong, Wen-Wen; Wu, Ya-Pan
2016-06-01
Three new coordination polymers, namely, {[Ni(H2L)(bix)(H2O)2]·2h2O}n (1), {[Ni(HL)(Hdpa)(H2O)2]·H2O}n (2), {[Ni(L)0.5(bpp)(H2O)]·H2O}n (3) (H4L=terphenyl-2,2‧,4,4‧-tetracarboxylic acid; bix=1,4-bis(imidazol-1-ylmethyl)benzene; dpa =4,4‧-dipyridylamine; bpp=1,3-bis(4-pyridyl)propane), based on rigid H4L ligand and different N-donor co-ligands, have been synthesized under hydrothermal conditions. Compound 1 features a 3D 4-connected 66-dia-type framework with H4L ligand adopts a μ2-bridging mode with two symmetry-related carboxylate groups in μ1-η1:η0 monodentate mode. Compound 2 displays a 1D [Ni(HL)(Hdpa)]n ribbon chains motif, in which the H4L ligand adopts a μ2-bridging mode with two carboxylate groups in μ1-η1:η1 and μ1-η1:η0 monodentate modes, while 3 possesses a (4,4)-connected 3D frameworks with bbf topology, with H4L ligand displays a μ4-bridging coordination mode. The H4L ligand displays not only different deprotonated forms but also diverse coordination modes and conformations. The structural diversities among 1-3 have been carefully discussed, and the roles of N-donor co-ligands in the self-assembly of coordination polymers have been well documented.
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Lu, Zhengliang; Abbina, Srinivas; Sabin, Jared R; Nemykin, Victor N; Du, Guodong
2013-02-04
Reaction of lithiated chiral, unsymmetric β-diketimine type ligands HL(2a-e) containing oxazoline moiety (HL(2a-e) = 2-(2'-R(1)NH)-phenyl-4-R(2)-oxazoline) with trans-NiCl(Ph)(PPh(3))(2) afforded a series of new chiral CNN pincer type nickel complexes (3a-3e) via an unexpected cyclometalation at benzylic or aryl C-H positions. Single crystal X-ray diffraction analysis established the pincer coordination mode and the strained conformation. Chirality, and in one case, racemization of the target nickel complexes were confirmed by circular dichroism (CD) spectroscopy. Electronic structure and band assignments in experimental UV-vis and CD spectra were discussed on the basis of Density Functional Theory (DFT) and time-dependent (TD) DFT calculations.
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Exciton in a spherical core/shell nanostructure: Influence of surface ligand
NASA Astrophysics Data System (ADS)
Anitha, B.; Nithiananthi, P.
2018-04-01
Studies on exciton in an inverted type I spherical GaAs/Al0.3Ga0.7As core/shell nanostructure (CSN) are made using variational method. Dielectric constant and effective mass mismatches of the core and shell materials are considered. The effect of core and the shell dimensions on the exciton binding energy (BE) are analyzed for different shell (Rs) and core radii (Rc). It is observed that with the core and the shell inducement, significant change in BE can be achieved. In addition, the influence of ligand enclosureon the BE as a function of shell thickness (ST) is reviewed. The result exhibits that the presence of ligand considerably affects the BE. Further the transmission probability of exciton for various Rc and Rs are reported. The notable changes are compared and examined with and without ligand inclusion.
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PatchSurfers: Two methods for local molecular property-based binding ligand prediction.
Shin, Woong-Hee; Bures, Mark Gregory; Kihara, Daisuke
2016-01-15
Protein function prediction is an active area of research in computational biology. Function prediction can help biologists make hypotheses for characterization of genes and help interpret biological assays, and thus is a productive area for collaboration between experimental and computational biologists. Among various function prediction methods, predicting binding ligand molecules for a target protein is an important class because ligand binding events for a protein are usually closely intertwined with the proteins' biological function, and also because predicted binding ligands can often be directly tested by biochemical assays. Binding ligand prediction methods can be classified into two types: those which are based on protein-protein (or pocket-pocket) comparison, and those that compare a target pocket directly to ligands. Recently, our group proposed two computational binding ligand prediction methods, Patch-Surfer, which is a pocket-pocket comparison method, and PL-PatchSurfer, which compares a pocket to ligand molecules. The two programs apply surface patch-based descriptions to calculate similarity or complementarity between molecules. A surface patch is characterized by physicochemical properties such as shape, hydrophobicity, and electrostatic potentials. These properties on the surface are represented using three-dimensional Zernike descriptors (3DZD), which are based on a series expansion of a 3 dimensional function. Utilizing 3DZD for describing the physicochemical properties has two main advantages: (1) rotational invariance and (2) fast comparison. Here, we introduce Patch-Surfer and PL-PatchSurfer with an emphasis on PL-PatchSurfer, which is more recently developed. Illustrative examples of PL-PatchSurfer performance on binding ligand prediction as well as virtual drug screening are also provided. Copyright © 2015 Elsevier Inc. All rights reserved.
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Minireview: More Than Just a Hammer: Ligand “Bias” and Pharmaceutical Discovery
2014-01-01
Conventional orthosteric drug development programs targeting G protein-coupled receptors (GPCRs) have focused on the concepts of agonism and antagonism, in which receptor structure determines the nature of the downstream signal and ligand efficacy determines its intensity. Over the past decade, the emerging paradigms of “pluridimensional efficacy” and “functional selectivity” have revealed that GPCR signaling is not monolithic, and that ligand structure can “bias” signal output by stabilizing active receptor states in different proportions than the native ligand. Biased ligands are novel pharmacologic entities that possess the unique ability to qualitatively change GPCR signaling, in effect creating “new receptors” with distinct efficacy profiles driven by ligand structure. The promise of biased agonism lies in this ability to engender “mixed” effects not attainable using conventional agonists or antagonists, promoting therapeutically beneficial signals while antagonizing deleterious ones. Indeed, arrestin pathway-selective agonists for the type 1 parathyroid hormone and angiotensin AT1 receptors, and G protein pathway-selective agonists for the GPR109A nicotinic acid and μ-opioid receptors, have demonstrated unique, and potentially therapeutic, efficacy in cell-based assays and preclinical animal models. Conversely, activating GPCRs in “unnatural” ways may lead to downstream biological consequences that cannot be predicted from prior knowledge of the actions of the native ligand, especially in the case of ligands that selectively activate as-yet poorly characterized G protein-independent signaling networks mediated via arrestins. Although much needs to be done to realize the clinical potential of functional selectivity, biased GPCR ligands nonetheless appear to be important new additions to the pharmacologic toolbox. PMID:24433041
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Quantitative Assessment of the Interplay Between DNA Elasticity and Cooperative Binding of Ligands
NASA Astrophysics Data System (ADS)
Siman, L.; Carrasco, I. S. S.; da Silva, J. K. L.; de Oliveira, M. C.; Rocha, M. S.; Mesquita, O. N.
2012-12-01
Binding of ligands to DNA can be studied by measuring the change of the persistence length of the complex formed, in single-molecule assays. We propose a methodology for persistence length data analysis based on a quenched disorder statistical model and describing the binding isotherm by a Hill-type equation. We obtain an expression for the effective persistence length as a function of the total ligand concentration, which we apply to our data of the DNA-cationic β-cyclodextrin and to the DNA-HU protein data available in the literature, determining the values of the local persistence lengths, the dissociation constant, and the degree of cooperativity for each set of data. In both cases the persistence length behaves nonmonotonically as a function of ligand concentration and based on the results obtained we discuss some physical aspects of the interplay between DNA elasticity and cooperative binding of ligands.
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Koike, Kazuhide; Okoshi, Nobuaki; Hori, Hisao; Takeuchi, Koji; Ishitani, Osamu; Tsubaki, Hideaki; Clark, Ian P; George, Michael W; Johnson, Frank P A; Turner, James J
2002-09-25
We report herein the mechanism of the photochemical ligand substitution reactions of a series of fac-[Re(X(2)bpy)(CO)(3)(PR(3))](+) complexes (1) and the properties of their triplet ligand-field ((3)LF) excited states. The reason for the photostability of the rhenium complexes [Re(X(2)bpy)(CO)(3)(py)](+) (3) and [Re(X(2)bpy)(CO)(3)Cl] (4) was also investigated. Irradiation of an acetonitrile solution of 1 selectively gave the biscarbonyl complexes cis,trans-[Re(X(2)bpy)(CO)(2)(PR(3))(CH(3)CN)](+) (2). Isotope experiments clearly showed that the CO ligand trans to the PR(3) ligand was selectively substituted. The photochemical reactions proceeded via a dissociative mechanism from the (3)LF excited state. The thermodynamical data for the (3)LF excited states of complexes 1 and the corrective nonradiative decay rate constants for the triplet metal-to-ligand charge-transfer ((3)MLCT) states were obtained from temperature-dependence data for the emission lifetimes and for the quantum yields of the photochemical reactions and the emission. Comparison of 1 with [Re(X(2)bpy)(CO)(3)(py)](+) (3) and [Re(X(2)bpy)(CO)(3)Cl] (4) indicated that the (3)LF states of some 3- and 4-type complexes are probably accessible from the (3)MLCT state even at ambient temperature, but these complexes were stable to irradiation at 365 nm. The photostability of 3 and 4, in contrast to 1, can be explained by differences in the trans effects of the PR(3), py, and Cl(-) ligands.
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Durola, Fabien; Russo, Luca; Sauvage, Jean-Pierre; Rissanen, Kari; Wenger, Oliver S
2007-01-01
3,3'-biisoquinoline ligands (biiq) L, bearing aromatic substituents on their 8 and 8' positions, have been used to generate interwoven systems consisting of three crescent-shaped ligands disposed around an octahedral metal centre. Mono-ligand complexes of the type [ReL(CO)3py]+ (py: pyridine) have also been prepared, leading to sterically non-hindering complexes in spite of the endotopic nature of the chelate used. The three-component entanglements have been prepared by using either FeII or RuII as gathering metal centre. The synthetic procedure is simple and efficient, affording fully characterised complexes as their PF6 or SbCl6 salts. X-ray crystallography clearly shows that the crescent-shaped ligands do not repel each other in the tris-chelate complexes. In an analogous way, the ReI complexes show open structures with no steric repulsion between the L ligand and the ancillary CO or py groups. The FeL3 or RuL3 compounds are very unusual in the sense that, contrary to all the other tris-bidentate chelate complexes made till now, the three organic components are tangled up, in a situation which will be very favourable to the formation of new non trivial topologies of the catenane type.
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Synthesis and binding properties of new selective ligands for the nucleobase opposite the AP site.
Abe, Yukiko; Nakagawa, Osamu; Yamaguchi, Rie; Sasaki, Shigeki
2012-06-01
DNA is continuously damaged by endogenous and exogenous factors such as oxidative stress or DNA alkylating agents. These damaged nucleobases are removed by DNA N-glycosylase and form apurinic/apyrimidinic sites (AP sites) as intermediates in the base excision repair (BER) pathway. AP sites are also representative DNA damages formed by spontaneous hydrolysis. The AP sites block DNA polymerase and a mismatch nucleobase is inserted opposite the AP sites by polymerization to cause acute toxicities and mutations. Thus, AP site specific compounds have attracted much attention for therapeutic and diagnostic purposes. In this study, we have developed nucleobase-polyamine conjugates as the AP site binding ligand by expecting that the nucleobase part would play a role in the specific recognition of the nucleobase opposite the AP site by the Watson-Crick base pair formation and that the polyamine part should contribute to the access of the ligand to the AP site by a non-specific interaction to the DNA phosphate backbone. The nucleobase conjugated with 3,3'-diaminodipropylamine (A-ligand, G-ligand, C-ligand, T-ligand and U-ligand) showed a specific stabilization of the duplex containing the AP site depending on the complementary combination with the nucleobase opposite the AP site; that is A-ligand to T, G-ligand to C, C-ligand to G, T- and U-ligand to A. The thermodynamic binding parameters clearly indicated that the specific stabilization is due to specific binding of the ligands to the complementary AP site. These results have suggested that the complementary base pairs of the Watson-Crick type are formed at the AP site. Copyright © 2012 Elsevier Ltd. All rights reserved.
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Hayes, Thomas R; Bottorff, Shalina C; Slocumb, Winston S; Barnes, Charles L; Clark, Aurora E; Benny, Paul D
2017-01-24
In the last two decades, a number of chelate strategies have been proposed for the fac-[M I (CO) 3 ] + (M = Re, 99m Tc) core in radiopharmaceutical applications. However, the development of new ligands/complexes with improved function and in vivo performance has been limited in recent years. Expanding on our previous studies using the 2 + 1 labeling strategy, a series of bidentate ligands (neutral vs. anionic) containing an aromatic amine in combination with monodentate pyridine analogs or imidazole were explored to determine the influence of the bidentate and monodentate ligands on the formation and stability of the respective complexes. The 2 + 1 complexes with Re and 99m Tc were synthesized in two steps and characterized by standard radio/chemical methods. X-ray characterization and density functional theory analysis of the Re 2 + 1 complexes with the complete bidentate series with 4-dimethylaminopyridine were conducted, indicating enhanced ligand binding energies of the neutral over anionic ligands. In the 99m Tc studies, anionic bidentate ligands had significantly higher formation yields of the 2 + 1 product, but neutral ligands appear to have increased stability in an amino acid challenge assay. Both bidentate series exhibited improved stability by increasing the basicity of the pyridine ligands.
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Hayes, Thomas R.; Bottorff, Shalina C.; Slocumb, Winston S.; Barnes, Charles L.; Clark, Aurora E.; Benny, Paul D.
2017-01-01
In the last two decades, a number of chelate strategies have been proposed for the fac-[MI(CO)3]+ (M = Re, 99mTc) core in radiopharmaceutical applications. However, the development of new ligands/complexes with improved function and in vivo performance has been limited in recent years. Expanding on our previous studies using the 2+1 labeling strategy, a series of bidentate ligands (neutral vs. anionic) containing an aromatic amine in combination with monodentate pyridine analogs or imidazole were explored to determine the influence of the bidentate and monodentate ligands on the formation and stability of the respective complexes. The 2+1 complexes with Re and 99mTc were synthesized in two steps and characterized by standard radio/chemical methods. X-ray characterization and density functional theory analysis of the Re 2+1 complexes with the complete bidentate series with 4-dimethylaminopyridine were conducted, indicating enhanced ligand binding energies of the neutral over anionic ligands. In the 99mTc studies, anionic bidentate ligands had significantly higher formation yields of the 2+1 product, but neutral ligands appear to have increased stability in an amino acid challenge assay. Both bidentate series exhibited improved stability by increasing the basicity of the pyridine ligands. PMID:28045466
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Alborzian Deh Sheikh, Amin; Akatsu, Chizuru; Imamura, Akihiro; Abdu-Allah, Hajjaj H M; Takematsu, Hiromu; Ando, Hiromune; Ishida, Hideharu; Tsubata, Takeshi
2018-01-01
Lectins expressed on the cell surface are often bound and regulated by the membrane molecules containing the glycan ligands on the same cell (cis-ligands). However, molecular nature and function of cis-ligands are generally poorly understood partly because of weak interaction between lectins and glycan ligands. Cis-ligands are most extensively studied in CD22 (also known as Siglec-2), an inhibitory B lymphocyte receptor specifically recognizing α2,6 sialic acids. CD22, CD45 and IgM are suggested to be ligands of CD22. Here we labeled molecules in the proximity of CD22 in situ on B cell surface using biotin-tyramide. Molecules including CD22, CD45 and IgM were labeled in wild-type but not ST6GalI -/- B cells that lack α2,6 sialic acids, indicating that these molecules associate with CD22 by lectin-glycan interaction, and are therefore cis-ligands. In ST6GalI -/- B cells, these cis-ligands are located in a slightly more distance from CD22. Thus, the lectin-glycan interaction recruits cis-ligands already located in the relative proximity of CD22 through non-lectin-glycan interaction to the close proximity. Moreover, cis-ligands are labeled in Cmah -/- B cells that lack Neu5Gc preferred by mouse CD22 as efficiently as in wild-type B cells, indicating that very low affinity lectin-glycan interaction is sufficient for recruiting cis-ligands, and can be detected by proximity labeling. Thus, proximity labeling with tyramide appears to be a useful method to identify cis-ligands and to analyze their interaction with the lectins. Copyright © 2017 Elsevier Inc. All rights reserved.
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Gutiérrez Sánchez, Cristina; Su, Qiang; Schönherr, Holger; Grininger, Martin; Nöll, Gilbert
2015-01-01
In this paper the multiple (re)programming of protein-DNA nanostructures comprising generation, deletion, and reprogramming on the same flavin-DNA-modified surface is introduced. This work is based on a systematic study of the binding affinity of the multi-ligand-binding flavoprotein dodecin on flavin-terminated DNA monolayers by surface plasmon resonance and quartz crystal microbalance with dissipation (QCM-D) measurements, surface plasmon fluorescence spectroscopy (SPFS), and dynamic AFM force spectroscopy. Depending on the flavin surface coverage, a single apododecin is captured by one or more surface-immobilized flavins. The corresponding complex binding and unbinding rate constants kon(QCM) = 7.7 × 10(3) M(-1)·s(-1) and koff(QCM) = 4.5 × 10(-3) s(-1) (Kd(QCM) = 580 nM) were determined by QCM and were found to be in agreement with values for koff determined by SPFS and force spectroscopy. Even though a single apododecin-flavin bond is relatively weak, stable dodecin monolayers were formed on flavin-DNA-modified surfaces at high flavin surface coverage due to multivalent interactions between apododecin bearing six binding pockets and the surface-bound flavin-DNA ligands. If bi- or multivalent flavin ligands are adsorbed on dodecin monolayers, stable sandwich-type surface-DNA-flavin-apododecin-flavin ligand arrays are obtained. Nevertheless, the apododecin flavin complex is easily and quantitatively disassembled by flavin reduction. Binding and release of apododecin are reversible processes, which can be carried out alternatingly several times to release one type of ligand by an external redox trigger and subsequently replace it with a different ligand. Hence the versatile concept of reprogrammable functional biointerfaces with the multi-ligand-binding flavoprotein dodecin is demonstrated.
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Molecular Dynamics Methodologies for Probing Cannabinoid Ligand/Receptor Interaction
Lynch, Diane L.; Hurst, Dow P.; Shore, Derek M.; Pitman, Mike C.; Reggio, Patricia H.
2018-01-01
The cannabinoid type 1 and 2 G-protein-coupled receptors are currently important pharmacological targets with significant drug discovery potential. These receptors have been shown to display functional selectivity or biased agonism, a property currently thought to have substantial therapeutic potential. Although recent advances in crystallization techniques have provided a wealth of structural information about this important class of membrane-embedded proteins, these structures lack dynamical information. In order to fully understand the interplay of structure and function for this important class of proteins, complementary techniques that address the dynamical aspects of their function are required such as NMR as well as a variety of other spectroscopies. Complimentary to these experimental approaches is molecular dynamics, which has been effectively used to help unravel, at the atomic level, the dynamics of ligand binding and activation of these membrane-bound receptors. Here, we discuss and present several representative examples of the application of molecular dynamics simulations to the understanding of the signatures of ligand-binding and -biased signaling at the cannabinoid type 1 and 2 receptors. PMID:28750815
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Vempati, Sridhar; Reindl, Carola; Wolf, Ulla; Kern, Ruth; Petropoulos, Konstantin; Naidu, Vegi M; Buske, Christian; Hiddemann, Wolfgang; Kohl, Tobias M; Spiekermann, Karsten
2008-07-15
Mutations in the receptor tyrosine kinase FLT3 are found in up to 30% of acute myelogenous leukemia patients and are associated with an inferior prognosis. In this study, we characterized critical tyrosine residues responsible for the transforming potential of active FLT3-receptor mutants and ligand-dependent activation of FLT3-WT. We performed a detailed structure-function analysis of putative autophosphorylation tyrosine residues in the FLT3-D835Y tyrosine kinase domain (TKD) mutant. All tyrosine residues in the juxtamembrane domain (Y566, Y572, Y589, Y591, Y597, and Y599), interkinase domain (Y726 and Y768), and COOH-terminal domain (Y955 and Y969) of the FLT3-D835Y construct were successively mutated to phenylalanine and the transforming activity of these mutants was analyzed in interleukin-3-dependent Ba/F3 cells. Tyrosine residues critical for the transforming potential of FLT3-D835Y were also analyzed in FLT3 internal tandem duplication mutants (FLT3-ITD)and the FLT3 wild-type (FLT3-WT) receptor. The substitution of the tyrosine residues by phenylalanine in the juxtamembrane, interkinase, and COOH-terminal domains resulted in a complete loss of the transforming potential of FLT3-D835Y-expressing cells which can be attributed to a significant reduction of signal tranducer and activator of transcription 5 (STAT5) phosphorylation at the molecular level. Reintroduction of single tyrosine residues revealed the critical role of Y589 and Y591 in reconstituting interleukin-3-independent growth of FLT3-TKD-expressing cells. Combined mutation of Y589 and Y591 to phenylalanine also abrogated ligand-dependent proliferation of FLT3-WT and the transforming potential of FLT3-ITD-with a subsequent abrogation of STAT5 phosphorylation. We identified two tyrosine residues, Y589 and Y591, in the juxtamembrane domain that are critical for the ligand-dependent activation of FLT3-WT and the transforming potential of oncogenic FLT3 mutants.
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Dissection of the insulin-sensitizing effect of liver X receptor ligands.
Commerford, S Renee; Vargas, Leo; Dorfman, Suzanne E; Mitro, Nico; Rocheford, Erik C; Mak, Puiying A; Li, Xue; Kennedy, Patrick; Mullarkey, Tara L; Saez, Enrique
2007-12-01
The liver X receptors (LXRalpha and beta) are nuclear receptors that coordinate carbohydrate and lipid metabolism. Treatment of insulin-resistant mice with synthetic LXR ligands enhances glucose tolerance, inducing changes in gene expression expected to decrease hepatic gluconeogenesis (via indirect suppression of gluconeogenic enzymes) and increase peripheral glucose disposal (via direct up-regulation of glut4 in fat). To evaluate the relative contribution of each of these effects on whole-body insulin sensitivity, we performed hyperinsulinemic-euglycemic clamps in high-fat-fed insulin-resistant rats treated with an LXR agonist or a peroxisome proliferator-activated receptor gamma ligand. Both groups showed significant improvement in insulin action. Interestingly, rats treated with LXR ligand had lower body weight and smaller fat cells than controls. Insulin-stimulated suppression of the rate of glucose appearance (Ra) was pronounced in LXR-treated rats, but treatment failed to enhance peripheral glucose uptake (R'g), despite increased expression of glut4 in epididymal fat. To ascertain whether LXR ligands suppress hepatic gluconeogenesis directly, mice lacking LXRalpha (the primary isotype in liver) were treated with LXR ligand, and gluconeogenic gene expression was assessed. LXR activation decreased expression of gluconeogenic genes in wild-type and LXRbeta null mice, but failed to do so in animals lacking LXRalpha. Our observations indicate that despite inducing suggestive gene expression changes in adipose tissue in this model of diet-induced insulin resistance, the antidiabetic effect of LXR ligands is primarily due to effects in the liver that appear to require LXRalpha. These findings have important implications for clinical development of LXR agonists as insulin sensitizers.
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An alternate binding site for PPARγ ligands
Hughes, Travis S.; Giri, Pankaj Kumar; de Vera, Ian Mitchelle S.; Marciano, David P.; Kuruvilla, Dana S.; Shin, Youseung; Blayo, Anne-Laure; Kamenecka, Theodore M.; Burris, Thomas P.; Griffin, Patrick R.; Kojetin, Douglas J.
2014-01-01
PPARγ is a target for insulin sensitizing drugs such as glitazones, which improve plasma glucose maintenance in patients with diabetes. Synthetic ligands have been designed to mimic endogenous ligand binding to a canonical ligand-binding pocket to hyperactivate PPARγ. Here we reveal that synthetic PPARγ ligands also bind to an alternate site, leading to unique receptor conformational changes that impact coregulator binding, transactivation and target gene expression. Using structure-function studies we show that alternate site binding occurs at pharmacologically relevant ligand concentrations, and is neither blocked by covalently bound synthetic antagonists nor by endogenous ligands indicating non-overlapping binding with the canonical pocket. Alternate site binding likely contributes to PPARγ hyperactivation in vivo, perhaps explaining why PPARγ full and partial or weak agonists display similar adverse effects. These findings expand our understanding of PPARγ activation by ligands and suggest that allosteric modulators could be designed to fine tune PPARγ activity without competing with endogenous ligands. PMID:24705063
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Kadam, Kiran; Prabhakar, Prashant; Jayaraman, V K
2012-11-01
Bacterial lipoproteins play critical roles in various physiological processes including the maintenance of pathogenicity and numbers of them are being considered as potential candidates for generating novel vaccines. In this work, we put forth an algorithm to identify and predict ligand-binding sites in bacterial lipoproteins. The method uses three types of pocket descriptors, namely fpocket descriptors, 3D Zernike descriptors and shell descriptors, and combines them with Support Vector Machine (SVM) method for the classification. The three types of descriptors represent shape-based properties of the pocket as well as its local physio-chemical features. All three types of descriptors, along with their hybrid combinations are evaluated with SVM and to improve classification performance, WEKA-InfoGain feature selection is applied. Results obtained in the study show that the classifier successfully differentiates between ligand-binding and non-binding pockets. For the combination of three types of descriptors, 10 fold cross-validation accuracy of 86.83% is obtained for training while the selected model achieved test Matthews Correlation Coefficient (MCC) of 0.534. Individually or in combination with new and existing methods, our model can be a very useful tool for the prediction of potential ligand-binding sites in bacterial lipoproteins.
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Targeting B lymphoma with nanoparticles bearing glycan ligands of CD22.
Chen, Weihsu C; Sigal, Darren S; Saven, Alan; Paulson, James C
2012-02-01
CD22 is a member of the siglec (sialic acid-binding immunoglobulin-like lectin) family expressed on B cells that recognizes glycans of glycoproteins as ligands. Because siglecs exhibit restricted expression on one or a few leukocyte cell types, they have gained attention as attractive targets for cell-directed therapies. Several antibody-based therapies targeting CD22 (Siglec-2) are currently in clinical trials for the treatment of hairy cell leukemia and other B cell lymphomas. As an alternative to antibodies we have developed liposomal nanoparticles decorated with glycan ligands of CD22 that selectively target B cells. Because CD22 is an endocytic receptor, ligand-decorated liposomes are bound by CD22 and rapidly internalized by the cell. When loaded with a toxic cargo such as doxorubicin, they are efficacious in prolonging life in a Daudi B cell lymphoma model. These B cell targeted nanoparticles have been demonstrated to bind and kill malignant B cells from patients with hairy cell leukemia, marginal zone lymphoma and chronic lymphocytic leukemia. The results demonstrate the potential of using CD22 ligand-targeted liposomal nanoparticles as an alternative approach for the treatment of B cell malignancies.
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NASA Astrophysics Data System (ADS)
Ozrin, V. D.; Subbotin, M. V.; Nikitin, S. M.
2004-04-01
We have developed PLASS (Protein-Ligand Affinity Statistical Score), a pair-wise potential of mean-force for rapid estimation of the binding affinity of a ligand molecule to a protein active site. This scoring function is derived from the frequency of occurrence of atom-type pairs in crystallographic complexes taken from the Protein Data Bank (PDB). Statistical distributions are converted into distance-dependent contributions to the Gibbs free interaction energy for 10 atomic types using the Boltzmann hypothesis, with only one adjustable parameter. For a representative set of 72 protein-ligand structures, PLASS scores correlate well with the experimentally measured dissociation constants: a correlation coefficient R of 0.82 and RMS error of 2.0 kcal/mol. Such high accuracy results from our novel treatment of the volume correction term, which takes into account the inhomogeneous properties of the protein-ligand complexes. PLASS is able to rank reliably the affinity of complexes which have as much diversity as in the PDB.
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NASA Astrophysics Data System (ADS)
Hua, Xiu-Ni; Qin, Lan; Yan, Xiao-Zhi; Yu, Lei; Xie, Yi-Xin; Han, Lei
2015-12-01
Hydrothermal reactions of N-auxiliary flexible exo-bidentate ligand 1,3-bis(4-pyridyl)propane (bpp) and carboxylates ligands naphthalene-2,6-dicarboxylic acid (2,6-H2ndc) or 4,4‧-(hydroxymethylene)dibenzoic acid (H2hmdb), in the presence of cadmium(II) salts have given rise to two novel metal-organic frameworks based on flexible ligands (FL-MOFs), namely, [Cd2(2,6-ndc)2(bpp)(DMF)]·2DMF (1) and [Cd3(hmdb)3(bpp)]·2DMF·2EtOH (2) (DMF=N,N-Dimethylformamide). Single-crystal X-ray diffraction analyses revealed that compound 1 exhibits a three-dimensional self-penetrating 6-connected framework based on dinuclear cluster second building unit. Compound 2 displays an infinite three-dimensional 'Lucky Clover' shape (2,10)-connected network based on the trinuclear cluster and V-shaped organic linkers. The flexible bpp ligand displays different conformations in 1 and 2, which are successfully controlled by size-matching mixed ligands during the self-assembly process.
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Wang, Yanzhao; Wang, Zhixun; Li, Yuxue; Wu, Gongde; Cao, Zheng; Zhang, Liming
2014-04-07
Most homogenous gold catalyses demand ≥ 0.5 mol% catalyst loading. Owing to the high cost of gold, these reactions are unlikely to be applicable in medium- or large-scale applications. Here we disclose a novel ligand design based on the privileged (1,1'-biphenyl)-2-ylphosphine framework that offers a potentially general approach to dramatically lowering catalyst loading. In this design, an amide group at the 3'-position of the ligand framework directs and promotes nucleophilic attack at the ligand gold complex-activated alkyne, which is unprecedented in homogenous gold catalysis considering the spatial challenge of using ligand to reach anti-approaching nucleophile in a linear P-Au-alkyne centroid structure. With such a ligand, the gold(I) complex becomes highly efficient in catalysing acid addition to alkynes, with a turnover number up to 99,000. Density functional theory calculations support the role of the amide moiety in directing the attack of carboxylic acid via hydrogen bonding.
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Wang, Yanzhao; Wang, Zhixun; Li, Yuxue; Wu, Gongde; Cao, Zheng; Zhang, Liming
2014-01-01
Most homogenous gold catalyses demand ≥0.5 mol % catalyst loading. Due to the high cost of gold, these reactions are unlikely to be applicable in medium or large scale applications. Here we disclose a novel ligand design based on the privileged biphenyl-2-phosphine framework that offers a potentially general approach to dramatically lowering catalyst loading. In this design, an amide group at the 3’ position of the ligand framework directs and promotes nucleophilic attack at the ligand gold complex-activated alkyne, which is unprecedented in homogeneous gold catalysis considering the spatial challenge of using ligand to reach antiapproaching nucleophile in a linear P-Au-alkyne centroid structure. With such a ligand, the gold(I) complex becomes highly efficient in catalyzing acid addition to alkynes, with a turnover number up to 99,000. Density functional theory calculations support the role of the amide moiety in directing the attack of carboxylic acid via hydrogen bonding. PMID:24704803
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Findlay, James A; McAdam, C John; Sutton, Joshua J; Preston, Dan; Gordon, Keith C; Crowley, James D
2018-04-02
The self-assembly of ligands of different geometries with metal ions gives rise to metallosupramolecular architectures of differing structural types. The rotational flexibility of ferrocene allows for conformational diversity, and, as such, self-assembly processes with 1,1'-disubstituted ferrocene ligands could lead to a variety of interesting architectures. Herein, we report a small family of three bis-bidentate 1,1'-disubstituted ferrocene ligands, functionalized with either 2,2'-bipyridine or 2-pyridyl-1,2,3-triazole chelating units. The self-assembly of these ligands with the (usually) four-coordinate, diamagnetic metal ions Cu(I), Ag(I), and Pd(II) was examined using a range of techniques including 1 H and DOSY NMR spectroscopies, high-resolution electrospray ionization mass spectrometry, X-ray crystallography, and density functional theory calculations. Additionally, the electrochemical properties of these redox-active metallosupramolecular assemblies were examined using cyclic voltammetry and differential pulse voltammetry. The copper(I) complexes of the 1,1'-disubstituted ferrocene ligands were found to be coordination polymers, while the silver(I) and palladium(II) complexes formed discrete [1 + 1] or [2 + 2] metallomacrocyclic architectures.
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Mishra, Lallan; Yadaw, Ajay K; Bhattacharya, Subrato; Dubey, Santosh K
2005-05-01
The complexes of Ru(II)-2,2'-bipyridyl with substituted diazopentane-2,4-diones (L1H-L5H) were synthesized and characterized by elemental analyses, conductance, FAB (fast atom bombardment) mass and spectral (IR, UV/Vis (UV/visible), NMR) studies. Molecular geometry optimization of the complexes was also made. None of the complexes luminesce. However, facilitated oxidation of Ru(II) to Ru(III) was evidenced from their lower reduction potential data. The ligands and their complexes were tested for their antitumour activity against a variety of tumour cell lines. Though activity is found to vary with the type of tumour cell lines used, yet complex 5 with naphtyldiazopentane-2,4-dione as co-ligand was found to be a potential compound as it showed in general significant activity against all cell lines studied.
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AceDRG: a stereochemical description generator for ligands
Emsley, Paul; Gražulis, Saulius; Merkys, Andrius; Vaitkus, Antanas
2017-01-01
The program AceDRG is designed for the derivation of stereochemical information about small molecules. It uses local chemical and topological environment-based atom typing to derive and organize bond lengths and angles from a small-molecule database: the Crystallography Open Database (COD). Information about the hybridization states of atoms, whether they belong to small rings (up to seven-membered rings), ring aromaticity and nearest-neighbour information is encoded in the atom types. All atoms from the COD have been classified according to the generated atom types. All bonds and angles have also been classified according to the atom types and, in a certain sense, bond types. Derived data are tabulated in a machine-readable form that is freely available from CCP4. AceDRG can also generate stereochemical information, provided that the basic bonding pattern of a ligand is known. The basic bonding pattern is perceived from one of the computational chemistry file formats, including SMILES, mmCIF, SDF MOL and SYBYL MOL2 files. Using the bonding chemistry, atom types, and bond and angle tables generated from the COD, AceDRG derives the ‘ideal’ bond lengths, angles, plane groups, aromatic rings and chirality information, and writes them to an mmCIF file that can be used by the refinement program REFMAC5 and the model-building program Coot. Other refinement and model-building programs such as PHENIX and BUSTER can also use these files. AceDRG also generates one or more coordinate sets corresponding to the most favourable conformation(s) of a given ligand. AceDRG employs RDKit for chemistry perception and for initial conformation generation, as well as for the interpretation of SMILES strings, SDF MOL and SYBYL MOL2 files. PMID:28177307
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Brink, Alice; Visser, Hendrik G; Roodt, Andreas
2014-12-01
A range of N,O-donor atom salicylidene complexes of the type fac-[M(O,N-Bid)(CO)3(L)](n) (O,N-Bid = anionic N,O-bidentate ligands; L = neutral coordinated ligand) have been studied. The unique feature of the complexes which crystallize in a monoclinic isostructural space group for complexes containing methanol in the sixth position (L = MeOH) is highlighted. The reactivity and stability of the complexes were evaluated by rapid stopped-flow techniques, and the methanol substitution by a range of pyridine type ligands indicates significant activation by the N,O-salicylidene type of bidentate ligands as observed from the variation in the second-order rate constants. In particular, following the introduction of the sterically demanding and electron rich cyclohexyl salicylidene moiety on the bidentate ligand, novel limiting kinetic behavior is displayed by all entering ligands, thus enabling a systematic probe and manipulation of the limiting kinetic constants. Clear evidence of an interchange type of intimate mechanism for the methanol substitution is produced. The equilibrium and rate constants (25 °C) for the two steps in the dissociative interchange mechanism for methanol substitution in fac-[Re(Sal-Cy)(CO)3(MeOH)] (5) by the pyridine type ligands 3-chloropyridine, pyridine, 4-picoline, and DMAP are k3 (s(-1)), 40 ± 4, 13 ± 2, 10.4 ± 0.7, and 2.11 ± 0.09, and K2 (M(-1)), 0.13 ± 0.01, 0.21 ± 0.03, 0.26 ± 0.02, and 1.8 ± 0.1, respectively.
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Ru, Jing; Gao, Feng; Yao, Min-Xia; Wu, Tao; Zuo, Jing-Lin
2014-12-28
By the reaction of chiral Mn(III) Schiff-base complexes with the dicyanoruthenate building block, [Ru(salen)(CN)2](-) (salen(2-) = N,N'-ethylenebis(salicylideneimine) dianion), two couples of enantiomerically pure chiral cyano-bridged heterobimetallic one-dimensional (1D) chain complexes, [Mn((R,R)-salcy)Ru(salen)(CN)2]n (1-(RR)) and [Mn((S,S)-salcy)Ru(salen)(CN)2]n (1-(SS)) (Salcy = N,N'-(1,2-cyclohexanediylethylene)bis(salicylideneiminato) dianion), [Mn((R,R)-salphen)Ru(salen)(CN)2]n (2-(RR)) and [Mn((S,S)-salphen)Ru(salen)(CN)2]n (2-(SS)) (salphen = N,N'-(1,2-diphenylethylene)bis(salicylideneiminato) dianion), were synthesized and structurally characterized. Circular dichroism (CD) and vibrational circular dichroism (VCD) spectra confirm the enantiomeric nature of the optically active complexes. Structural analyses reveal the formation of neutral cyano-bridged zigzag single chains in 1-(RR) and 1-(SS), and double chains in 2-(RR) and 2-(SS). Magnetic studies show that antiferromagnetic coupling is operative between Ru(III) and Mn(III) centers bridged by cyanide. Compounds 1-(RR) and 1-(SS) show metamagnetic behavior with a critical field of about 7.2 kOe at 1.9 K resulting from the intermolecular π∙∙∙π interactions. Additionally, magnetostructural correlation for some typical cyano-bridged heterobimetallic Ru(III)-Mn(III) compounds is discussed.
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Kinetics and mechanism of vanadium catalysed asymmetric cyanohydrin synthesis in propylene carbonate
Omedes-Pujol, Marta
2010-01-01
Summary Propylene carbonate can be used as a green solvent for the asymmetric synthesis of cyanohydrin trimethylsilyl ethers from aldehydes and trimethylsilyl cyanide catalysed by VO(salen)NCS, though reactions are slower in this solvent than the corresponding reactions carried out in dichloromethane. A mechanistic study has been undertaken, comparing the catalytic activity of VO(salen)NCS in propylene carbonate and dichloromethane. Reactions in both solvents obey overall second-order kinetics, the rate of reaction being dependent on the concentration of both the aldehyde and trimethylsilyl cyanide. The order with respect to VO(salen)NCS was determined and found to decrease from 1.2 in dichloromethane to 1.0 in propylene carbonate, indicating that in propylene carbonate, VO(salen)NCS is present only as a mononuclear species, whereas in dichloromethane dinuclear species are present which have previously been shown to be responsible for most of the catalytic activity. Evidence from 51V NMR spectroscopy suggested that propylene carbonate coordinates to VO(salen)NCS, blocking the free coordination site, thus inhibiting its Lewis acidity and accounting for the reduction in catalytic activity. This explanation was further supported by a Hammett analysis study, which indicated that Lewis base catalysis made a much greater contribution to the overall catalytic activity of VO(salen)NCS in propylene carbonate than in dichloromethane. PMID:21085513
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Thioureas as ligands in the pd-catalyzed intramolecular Pauson-Khand reaction.
Tang, Yefeng; Deng, Lujiang; Zhang, Yangdong; Dong, Guangbin; Chen, Jiahua; Yang, Zhen
2005-04-14
[reaction: see text] The thiourea-Pd complex was established as a novel type of catalyst in the PKR of allylpropargylamine, and the demonstrated chemistry may prove to be valuable for developing thiuorea as a ligand for the Pd-catalyzed Pauson-Khand reaction.
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FES kinase participates in KIT-ligand induced chemotaxis
DOE Office of Scientific and Technical Information (OSTI.GOV)
Voisset, Edwige, E-mail: Edwige.Voisset@inserm.fr; Institut Paoli-Calmettes, Marseille; Universite de la Mediterranee, Aix-Marseille II
2010-02-26
FES is a cytoplasmic tyrosine kinase activated by several membrane receptors, originally identified as a viral oncogene product. We have recently identified FES as a crucial effector of oncogenic KIT mutant receptor. However, FES implication in wild-type KIT receptor function was not addressed. We report here that FES interacts with KIT and is phosphorylated following activation by its ligand SCF. Unlike in the context of oncogenic KIT mutant, FES is not involved in wild-type KIT proliferation signal, or in cell adhesion. Instead, FES is required for SCF-induced chemotaxis. In conclusion, FES kinase is a mediator of wild-type KIT signalling implicatedmore » in cell migration.« less
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Rojo, Isabel; Teixidor, Francesc; Viñas, Clara; Kivekäs, Raikko; Sillanpää, Reijo
2004-10-25
The anionic chelating ligand [1,1'-(PPh2)2-3,3'-Co(1,2-C2B9H10)2]- has been synthesized from [3,3'-Co(1,2-C2B9H11)2]- in very good yield in a one-pot process with an easy work-up procedure. The coordinating ability of this ligand has been studied with Group 11 metal ions (Ag, Au) and with transition-metal ions (Pd, Rh). The two dicarbollide halves of the [1,1'-(PPh2)2-3,3'-Co(1,2-C2B9H10)2]- ligand can swing about one axis in a manner analogous to the constituent parts of BINAP and ferrocenyl phosphine derivatives. All these ligands function as hinges, with the most important property in relation to the coordination requirements of the metal being the PP distance. [1,1'-(PPh2)2-3,3'-Co(1,2-C2B9H10)2]-, BINAP, ferrocenyl phosphine derivatives, and other hinge ligands present a range of different PP separations, and consequently different coordination spheres and dispositions around metal cations. To account for these differences, the equation Dphi2 = D02 + 4 R2cos2(90-phi/2) has been developed. It relates the PP distance (Dphi) in a complex with the minimum PP distance (D0) that is characteristic of the hinge-type ligand.
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Ligand cluster-based protein network and ePlatton, a multi-target ligand finder.
Du, Yu; Shi, Tieliu
2016-01-01
Small molecules are information carriers that make cells aware of external changes and couple internal metabolic and signalling pathway systems with each other. In some specific physiological status, natural or artificial molecules are used to interact with selective biological targets to activate or inhibit their functions to achieve expected biological and physiological output. Millions of years of evolution have optimized biological processes and pathways and now the endocrine and immune system cannot work properly without some key small molecules. In the past thousands of years, the human race has managed to find many medicines against diseases by trail-and-error experience. In the recent decades, with the deepening understanding of life and the progress of molecular biology, researchers spare no effort to design molecules targeting one or two key enzymes and receptors related to corresponding diseases. But recent studies in pharmacogenomics have shown that polypharmacology may be necessary for the effects of drugs, which challenge the paradigm, 'one drug, one target, one disease'. Nowadays, cheminformatics and structural biology can help us reasonably take advantage of the polypharmacology to design next-generation promiscuous drugs and drug combination therapies. 234,591 protein-ligand interactions were extracted from ChEMBL. By the 2D structure similarity, 13,769 ligand emerged from 156,151 distinct ligands which were recognized by 1477 proteins. Ligand cluster- and sequence-based protein networks (LCBN, SBN) were constructed, compared and analysed. For assisting compound designing, exploring polypharmacology and finding possible drug combination, we integrated the pathway, disease, drug adverse reaction and the relationship of targets and ligand clusters into the web platform, ePlatton, which is available at http://www.megabionet.org/eplatton. Although there were some disagreements between the LCBN and SBN, communities in both networks were largely the same
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Bai, Qifeng; Zhang, Yang; Ban, Yihe; Liu, Huanxiang; Yao, Xiaojun
2013-01-01
β2 adrenergic receptor (β2AR) regulated many key physiological processes by activation of a heterotrimeric GTP binding protein (Gs protein). This process could be modulated by different types of ligands. But the details about this modulation process were still not depicted. Here, we performed molecular dynamics (MD) simulations on the structures of β2AR-Gs protein in complex with different types of ligands. The simulation results demonstrated that the agonist BI-167107 could form hydrogen bonds with Ser2035.42, Ser2075.46 and Asn2936.55 more than the inverse agonist ICI 118,551. The different binding modes of ligands further affected the conformation of β2AR. The energy landscape profiled the energy contour map of the stable and dissociated conformation of Gαs and Gβγ when different types of ligands bound to β2AR. It also showed the minimum energy pathway about the conformational change of Gαs and Gβγ along the reaction coordinates. By using interactive essential dynamics analysis, we found that Gαs and Gβγ domain of Gs protein had the tendency to separate when the inverse agonist ICI 118,551 bound to β2AR. The α5-helix had a relatively quick movement with respect to transmembrane segments of β2AR when the inverse agonist ICI 118,551 bound to β2AR. Besides, the analysis of the centroid distance of Gαs and Gβγ showed that the Gαs was separated from Gβγ during the MD simulations. Our results not only could provide details about the different types of ligands that induced conformational change of β2AR and Gs protein, but also supplied more information for different efficacies of drug design of β2AR. PMID:23922653
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Chemistry of Marine Ligands and Siderophores
Vraspir, Julia M.; Butler, Alison
2011-01-01
Marine microorganisms are presented with unique challenges to obtain essential metal ions required to survive and thrive in the ocean. The production of organic ligands to complex transition metal ions is one strategy to both facilitate uptake of specific metals, such as iron, and to mitigate the potential toxic effects of other metal ions, such as copper. A number of important trace metal ions are complexed by organic ligands in seawater, including iron, cobalt, nickel, copper, zinc, and cadmium, thus defining the speciation of these metal ions in the ocean. In the case of iron, siderophores have been identified and structurally characterized. Siderophores are low molecular weight iron-binding ligands produced by marine bacteria. Although progress has been made toward the identity of in situ iron-binding ligands, few compounds have been identified that coordinate the other trace metals. Deciphering the chemical structures and production stimuli of naturally produced organic ligands and the organisms they come from is fundamental to understanding metal speciation and bioavailability. The current evidence for marine ligands, with an emphasis on siderophores, and discussion of the importance and implications of metal-binding ligands in controlling metal speciation and cycling within the world’s oceans are presented. PMID:21141029
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Srivastava, Ravi; Moneuse, Raphaël; Petit, Julien; Pavard, Paul-Alexis; Dardun, Vincent; Rivat, Madleen; Schiltz, Pauline; Solari, Marius; Jeanneau, Erwann; Veyre, Laurent; Thieuleux, Chloé; Quadrelli, Elsje Alessandra; Camp, Clément
2018-03-20
The straightforward synthesis of a new unsymmetrical hydroxy-tethered N-heterocyclic carbene (NHC) ligand, HL, is presented. The free ligand exhibits an unusual OH-carbene hydrogen-bonding interaction. This OH-carbene motif was used to yield 1) the first tantalum complex displaying both a Fischer- and Schrock-type carbene ligand and 2) a unique NHC-based early/late heterobimetallic complex. More specifically, the protonolysis chemistry between the ligand's hydroxy group and imido-alkyl or alkylidene-alkyl tantalum precursor complexes yielded the rare monometallic tantalum-NHC complexes [Ta(XtBu)(L)(CH 2 tBu) 2 ] (X=N, CH), in which the alkoxy-carbene ligand acts as a chelate. In contrast, HL only binds to rhodium through the NHC unit in [Rh(HL)(cod)Cl] (cod=cycloocta-1,5-diene), the hydroxy pendant arm remaining unbound. This bifunctional ligand scaffold successfully promoted the assembly of rhodium/tantalum heterobimetallic complexes upon either 1) the insertion of [Rh(cod)Cl] 2 into the Ta-NHC bond in [Ta(NtBu)(L)(CH 2 tBu) 2 ] or 2) protonolysis between the free hydroxy group in [Rh(HL)(cod)Cl] and one alkyl group in [Ta(NtBu)(CH 2 tBu) 3 ]. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
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NASA Astrophysics Data System (ADS)
Regupathy, Sthanumoorthy; Nair, Madhavan Sivasankaran
2010-02-01
Equilibrium studies on the ternary complex systems involving ampicillin (amp) as ligand (A) and imidazole containing ligands viz., imidazole (Him), benzimidazole (Hbim), histamine (Hist) and histidine (His) as ligands (B) at 37 °C and I = 0.15 mol dm -3 (NaClO 4) show the presence of CuABH, CuAB and CuAB 2. The proton in the CuABH species is attached to ligand A. In the ternary complexes the ligand, amp(A) binds the metal ion via amino nitrogen and carbonyl oxygen atom. The CuAB (B = Hist/His)/CuAB 2 (B = Him/Hbim) species have also been isolated and the analytical data confirmed its formation. Non-electrolytic behavior and monomeric type of chelates have been assessed from their low conductance and magnetic susceptibility values. The electronic and vibrational spectral results were interpreted to find the mode of binding of ligands to metal and geometry of the complexes. This is also supported by the g tensor values calculated from ESR spectra. The thermal behaviour of complexes were studied by TGA/DTA. The redox behavior of the complexes has been studied by cyclic voltammetry. The antimicrobial activity and CT DNA cleavage study of the complexes show higher activity for ternary complexes.
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Perfluorinated Ligands in Organometallic Chemistry
1989-12-12
C49t00ooVER ,or C M’ AD"OV’~mDecember 12) 199IFinal 1/1/86 to 8/31/89C smuS. FUNOING NUMgIERS cJ Perfluorinated Ligands in Organometallic Chemistry 612...compounds, stabilized by tridentate perfluorinated ligands. Dinuclear rhodium complexes of OFCOT undergo a selective C-F bond activation reaction...hexafluorocyclooctatrieneyne ligand. Stereospecific cleavage of a fluorinated C-C bond,#-bond in perfluorocyclopropene by platinum and iridium complexes has been achieved
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Coordination- and Redox-Noninnocent Behavior of Ambiphilic Ligands Containing Antimony.
Jones, J Stuart; Gabbaï, François P
2016-05-17
Stimulated by applications in catalysis, the chemistry of ambiphilic ligands featuring both donor and acceptor functionalities has experienced substantial growth in the past several years. The unique opportunities in catalysis offered by ambiphilic ligands stem from the ability of their acceptor functionalities to play key roles via metal-ligand cooperation or modulation of the reactivity of the metal center. Ligands featuring group 13 centers, most notably boranes, as their acceptor functionalities have undoubtedly spearheaded these developments, with remarkable results having been achieved in catalytic hydrogenation and hydrosilylation. Motivated by these developments as well as by our fundamental interest in the chemistry of heavy group 15 elements, we became fascinated by the possibility of employing antimony centers as Lewis acids within ambiphilic ligands. The chemistry of antimony-based ligands, most often encountered as trivalent stibines, has historically been considered to mirror that of their lighter phosphorus-based congeners. There is growing evidence, however, that antimony-based ligands may display unique coordination behavior and reactivity. Additionally, despite the diverse Lewis acid and redox chemistry that antimony exhibits, there have been only limited efforts to explore this chemistry within the coordination sphere of a transition metal. By incorporation of antimony into the framework of polydentate ligands in order to enforce the main group metal-transition metal interaction, the effect of redox and coordination events at the antimony center on the structure, electronics, and reactivity of the metal complex may be investigated. This Account describes our group's continuing efforts to probe the coordination behavior, reactivity, and application of ambiphilic ligands incorporating antimony centers. Structural and theoretical studies have established that both Sb(III) and Sb(V) centers in polydentate ligands may act as Z-type ligands toward late
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Structural Analysis of Chemokine Receptor–Ligand Interactions
2017-01-01
This review focuses on the construction and application of structural chemokine receptor models for the elucidation of molecular determinants of chemokine receptor modulation and the structure-based discovery and design of chemokine receptor ligands. A comparative analysis of ligand binding pockets in chemokine receptors is presented, including a detailed description of the CXCR4, CCR2, CCR5, CCR9, and US28 X-ray structures, and their implication for modeling molecular interactions of chemokine receptors with small-molecule ligands, peptide ligands, and large antibodies and chemokines. These studies demonstrate how the integration of new structural information on chemokine receptors with extensive structure–activity relationship and site-directed mutagenesis data facilitates the prediction of the structure of chemokine receptor–ligand complexes that have not been crystallized. Finally, a review of structure-based ligand discovery and design studies based on chemokine receptor crystal structures and homology models illustrates the possibilities and challenges to find novel ligands for chemokine receptors. PMID:28165741
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Farnesoid X Receptor and Liver X Receptor Ligands Initiate Formation of Coated Platelets
Unsworth, Amanda J.; Bye, Alexander P.; Tannetta, Dionne S.; Desborough, Michael J.R.; Kriek, Neline; Sage, Tanya; Allan, Harriet E.; Crescente, Marilena; Yaqoob, Parveen; Warner, Timothy D.; Jones, Chris I.
2017-01-01
Objectives— The liver X receptors (LXRs) and farnesoid X receptor (FXR) have been identified in human platelets. Ligands of these receptors have been shown to have nongenomic inhibitory effects on platelet activation by platelet agonists. This, however, seems contradictory with the platelet hyper-reactivity that is associated with several pathological conditions that are associated with increased circulating levels of molecules that are LXR and FXR ligands, such as hyperlipidemia, type 2 diabetes mellitus, and obesity. Approach and Results— We, therefore, investigated whether ligands for the LXR and FXR receptors were capable of priming platelets to the activated state without stimulation by platelet agonists. Treatment of platelets with ligands for LXR and FXR converted platelets to the procoagulant state, with increases in phosphatidylserine exposure, platelet swelling, reduced membrane integrity, depolarization of the mitochondrial membrane, and microparticle release observed. Additionally, platelets also displayed features associated with coated platelets such as P-selectin exposure, fibrinogen binding, fibrin generation that is supported by increased serine protease activity, and inhibition of integrin αIIbβ3. LXR and FXR ligand-induced formation of coated platelets was found to be dependent on both reactive oxygen species and intracellular calcium mobilization, and for FXR ligands, this process was found to be dependent on cyclophilin D. Conclusions— We conclude that treatment with LXR and FXR ligands initiates coated platelet formation, which is thought to support coagulation but results in desensitization to platelet stimuli through inhibition of αIIbβ3 consistent with their ability to inhibit platelet function and stable thrombus formation in vivo. PMID:28619996
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Abdullah, Hani'ah; Brankin, Brenda; Brady, Clare; Cosby, Sara Louise
2013-07-01
Small numbers of brain endothelial cells (BECs) are infected in children with neurologic complications of measles virus (MV) infection. This may provide a mechanism for virus entry into the central nervous system, but the mechanisms are unclear. Both in vitro culture systems and animal models are required to elucidate events in the endothelium. We compared the ability of wild-type (WT), vaccine, and rodent-adapted MV strains to infect, replicate, and induce apoptosis in human and murine brain endothelial cells (HBECs and MBECs, respectively). Mice also were infected intracerebrally. All MV stains productively infected HBECs and induced the MV receptor PVRL4. Efficient WT MV production also occurred in MBECs. Extensive monolayer destruction associated with activated caspase 3 staining was observed in HBECs and MBECs, most markedly with WT MV. Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL), but not Fas ligand, was induced by MV infection. Treatment of MBECs with supernatants from MV-infected MBEC cultures with an anti-TRAIL antibody blocked caspase 3 expression and monolayer destruction. TRAIL was also expressed in the endothelium and other cell types in infected murine brains. This is the first demonstration that infection of low numbers of BECs with WT MV allows efficient virus production, induction of TRAIL, and subsequent widespread apoptosis.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Cao, Ke-Li; Zhang, Yi-Ping; Cai, Yi-Ni
2014-07-01
To investigate the influence of hydrogen bonds and secondary ligands on the structures and properties of the resulting frameworks, five new Co(II) compounds have been synthesized by the reactions of Co(II) salts and 3,5-bis(pyridin-4-ylmethoxy)benzoic acid (HL) with four rationally selected dicarboxylic acid ligands. Without secondary ligand, we got one compound [CoL{sub 2}(H{sub 2}O){sub 2}]{sub n}·2nH{sub 2}O (1), which possesses a 1D chain structure. In the presence of ancillary ligands, namely, 1,3-adamantanedicarboxylic acid (H{sub 2}adbc), terephthalic acid (H{sub 2}tpa), thiophene-2,5-dicarboxylic acid (H{sub 2}tdc) and 1,4-benzenedithioacetic acid (H{sub 2}bdtc), four 3D structures [Co{sub 2}L{sub 2}(adbc)]{sub n}·nH{sub 2}O (2), [Co{sub 2}L{sub 2}(tpa)]{sub n}more » (3), [Co{sub 2}L{sub 2}(tdc)]{sub n} (4), [Co{sub 2}L{sub 2}(bdtc)(H{sub 2}O)]{sub n} (5) were obtained, respectively. It can be observed from the architectures of 1–5 that hydrogen bonds and secondary ligands both have great effects on the spatial connective fashions, resulting in the formation of various dimensional compounds. The XRPD, TGA data of title polymers and the magnetic properties for 2 and 5 have also been investigated. - Graphical abstract: The structural differences show that the ancillary ligands have great effects on the spatial connective fashions, resulting in the formation of various dimensional compounds. - Highlights: • Five new Co(II) coordination polymers have been synthesized by solvothermal reactions based on 3,5-bis(pyridin-4-ylmethoxy)benzoic acid (HL). • The long-flexible ligand (HL) is a good candidate to produce interpenetrating architectures. • The secondary dicarboxylic acid ligands play important roles in the spatial connective fashions and the formation of various dimensional compounds. • The magnetism studies show that both 2 and 5 exhibit antiferromagnetic interactions.« less
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Liu, Haoliang; Feng, Juan; Chen, Liuping
2015-01-01
A novel dynamic covalent gel strategy is reported to immobilize an asymmetric catalyst within the channels of a microfluidic flow reactor. A layer of a catalytically active Mn–salen dynamic covalent imine gel matrix was coated onto a functionalized capillary. Mn–salen active moiety was incorporated into dynamic covalent imine gel matrix via the reaction of a chiral Mn–salen dialdehyde unit with a tetraamine linker. The catalytic activity of the capillary reactor has been demonstrated in enantioselective kinetic resolution of secondary alcohols. PMID:28706652
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NASA Astrophysics Data System (ADS)
Sun, Gui-Fang; Zhang, Cong-Ming; Guo, Jian-Ni; Yang, Meng; Li, Li-Cun
2017-05-01
Two binuclear lanthanide complexes [Ln2(hfac)6(HL)2] (LnIII = Dy(1), Tb(2); hfac = hexafluoroacetylacetonate, HL = (R)-2-amino-2-phenylethanol) have been successfully obtained by using amino alcoholate ligand. In two complexes, the Ln(III) ions are bridged by two alkoxido groups from HL ligands, resulting in binuclear complexes. The variable-temperature magnetic susceptibility studies indicate that there exists ferromagnetic interaction between two Ln(III) ions. Frequency dependent out-of-phase signals are observed for complex 1, suggesting SMM type behavior. Complexes 1 and 2 display intensely characteristic luminescent properties.
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Designing ligands to bind proteins
Whitesides, George M.; Krishnamurthy, Vijay M.
2009-01-01
The ability to design drugs (so-called ‘rational drug design’) has been one of the long-term objectives of chemistry for 50 years. It is an exceptionally difficult problem, and many of its parts lie outside the expertise of chemistry. The much more limited problem – how to design tight-binding ligands (rational ligand design) – would seem to be one that chemistry could solve, but has also proved remarkably recalcitrant. The question is ‘Why is it so difficult?’ and the answer is ‘We still don't entirely know’. This perspective discusses some of the technical issues – potential functions, protein plasticity, enthalpy/entropy compensation, and others – that contribute, and suggests areas where fundamental understanding of protein–ligand interactions falls short of what is needed. It surveys recent technological developments (in particular, isothermal titration calorimetry) that will, hopefully, make now the time for serious progress in this area. It concludes with the calorimetric examination of the association of a series of systematically varied ligands with a model protein. The counterintuitive thermodynamic results observed serve to illustrate that, even in relatively simple systems, understanding protein–ligand association is challenging. PMID:16817982
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Structural Analysis on the Pathologic Mutant Glucocorticoid Receptor Ligand-Binding Domains.
Hurt, Darrell E; Suzuki, Shigeru; Mayama, Takafumi; Charmandari, Evangelia; Kino, Tomoshige
2016-02-01
Glucocorticoid receptor (GR) gene mutations may cause familial or sporadic generalized glucocorticoid resistance syndrome. Most of the missense forms distribute in the ligand-binding domain and impair its ligand-binding activity and formation of the activation function (AF)-2 that binds LXXLL motif-containing coactivators. We performed molecular dynamics simulations to ligand-binding domain of pathologic GR mutants to reveal their structural defects. Several calculated parameters including interaction energy for dexamethasone or the LXXLL peptide indicate that destruction of ligand-binding pocket (LBP) is a primary character. Their LBP defects are driven primarily by loss/reduction of the electrostatic interaction formed by R611 and T739 of the receptor to dexamethasone and a subsequent conformational mismatch, which deacylcortivazol resolves with its large phenylpyrazole moiety and efficiently stimulates transcriptional activity of the mutant receptors with LBP defect. Reduced affinity of the LXXLL peptide to AF-2 is caused mainly by disruption of the electrostatic bonds to the noncore leucine residues of this peptide that determine the peptide's specificity to GR, as well as by reduced noncovalent interaction against core leucines and subsequent exposure of the AF-2 surface to solvent. The results reveal molecular defects of pathologic mutant receptors and provide important insights to the actions of wild-type GR.
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Yang, Guang; Hallinan, Daniel T.
2016-01-01
Using a three-phase system, centimeter-scale monolayer gold nanoparticle (Au NP) films have been prepared that have long-range order and hydrophobic ligands. The system contains an interface between an aqueous phase containing Au NPs and an oil phase containing one of various types of amine ligands, and a water/air interface. As the Au NPs diffuse to the water/oil interface, ligand exchange takes place which temporarily traps them at the water/oil interface. The ligand-exchanged particles then spontaneously migrate to the air/water interface, where they self-assemble, forming a monolayer under certain conditions. The spontaneous formation of the NP film at the air/water interface was due to the minimization of the system Helmholtz free energy. However, the extent of surface functionalization was dictated by kinetics. This decouples interfacial ligand exchange from interfacial self-assembly, while maintaining the simplicity of a single system. The interparticle center-to-center distance was dictated by the amine ligand length. The Au NP monolayers exhibit tunable surface plasma resonance and excellent spatial homogeneity, which is useful for surface-enhanced Raman scattering. The “air/water/oil” self-assembly method developed here not only benefits the fundamental understanding of NP ligand conformations, but is also applicable to the manufacture of plasmonic nanoparticle devices with precisely designed optical properties. PMID:27762394
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Crystallization of bi-functional ligand protein complexes.
Antoni, Claudia; Vera, Laura; Devel, Laurent; Catalani, Maria Pia; Czarny, Bertrand; Cassar-Lajeunesse, Evelyn; Nuti, Elisa; Rossello, Armando; Dive, Vincent; Stura, Enrico Adriano
2013-06-01
Homodimerization is important in signal transduction and can play a crucial role in many other biological systems. To obtaining structural information for the design of molecules able to control the signalization pathways, the proteins involved will have to be crystallized in complex with ligands that induce dimerization. Bi-functional drugs have been generated by linking two ligands together chemically and the relative crystallizability of complexes with mono-functional and bi-functional ligands has been evaluated. There are problems associated with crystallization with such ligands, but overall, the advantages appear to be greater than the drawbacks. The study involves two matrix metalloproteinases, MMP-12 and MMP-9. Using flexible and rigid linkers we show that it is possible to control the crystal packing and that by changing the ligand-enzyme stoichiometric ratio, one can toggle between having one bi-functional ligand binding to two enzymes and having the same ligand bound to each enzyme. The nature of linker and its point of attachment on the ligand can be varied to aid crystallization, and such variations can also provide valuable structural information about the interactions made by the linker with the protein. We report here the crystallization and structure determination of seven ligand-dimerized complexes. These results suggest that the use of bi-functional drugs can be extended beyond the realm of protein dimerization to include all drug design projects. Copyright © 2013 Elsevier Inc. All rights reserved.
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Autocrine signal transmission with extracellular ligand degradation
NASA Astrophysics Data System (ADS)
Muratov, C B; Posta, F; Shvartsman, S Y
2009-03-01
Traveling waves of cell signaling in epithelial layers orchestrate a number of important processes in developing and adult tissues. These waves can be mediated by positive feedback autocrine loops, a mode of cell signaling where binding of a diffusible extracellular ligand to a cell surface receptor can lead to further ligand release. We formulate and analyze a biophysical model that accounts for ligand-induced ligand release, extracellular ligand diffusion and ligand-receptor interaction. We focus on the case when the main mode for ligand degradation is extracellular and analyze the problem with the sharp threshold positive feedback nonlinearity. We derive expressions that link the speed of propagation and other characteristics of traveling waves to the parameters of the biophysical processes, such as diffusion rates, receptor expression level, etc. Analyzing the derived expressions we found that traveling waves in such systems can exhibit a number of unusual properties, e.g. non-monotonic dependence of the speed of propagation on ligand diffusivity. Our results for the fully developed traveling fronts can be used to analyze wave initiation from localized perturbations, a scenario that frequently arises in the in vitro models of epithelial wound healing, and guide future modeling studies of cell communication in epithelial layers.
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NASA Astrophysics Data System (ADS)
Costanzi, Stefano; Tikhonova, Irina G.; Harden, T. Kendall; Jacobson, Kenneth A.
2009-11-01
Accurate in silico models for the quantitative prediction of the activity of G protein-coupled receptor (GPCR) ligands would greatly facilitate the process of drug discovery and development. Several methodologies have been developed based on the properties of the ligands, the direct study of the receptor-ligand interactions, or a combination of both approaches. Ligand-based three-dimensional quantitative structure-activity relationships (3D-QSAR) techniques, not requiring knowledge of the receptor structure, have been historically the first to be applied to the prediction of the activity of GPCR ligands. They are generally endowed with robustness and good ranking ability; however they are highly dependent on training sets. Structure-based techniques generally do not provide the level of accuracy necessary to yield meaningful rankings when applied to GPCR homology models. However, they are essentially independent from training sets and have a sufficient level of accuracy to allow an effective discrimination between binders and nonbinders, thus qualifying as viable lead discovery tools. The combination of ligand and structure-based methodologies in the form of receptor-based 3D-QSAR and ligand and structure-based consensus models results in robust and accurate quantitative predictions. The contribution of the structure-based component to these combined approaches is expected to become more substantial and effective in the future, as more sophisticated scoring functions are developed and more detailed structural information on GPCRs is gathered.
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NASA Astrophysics Data System (ADS)
Kurnikova, Maria
2009-03-01
Understanding of protein motion and energetics of conformational transitions is crucial to understanding protein function. The glutamate receptor ligand binding domain (GluR2 S1S2) is a two lobe protein, which binds ligand at the interface of two lobes and undergoes conformational transition. The cleft closure conformational transition of S1S2 has been implicated in gating of the ion channel formed by the transmembrane domain of the receptor. In this study we present a composite multi-faceted theoretical analysis of the detailed mechanism of this conformational transition based on rigid cluster decomposition of the protein structure [1] and identifying hydrogen bonds that are responsible for stabilizing the closed conformation [2]. Free energy of the protein reorganization upon ligand binding was calculated using combined Thermodynamic Integration (TI) and Umbrella Sampling (US) simulations [3]. Ligand -- protein interactions in the binding cleft were analyzed using Molecular Dynamics, continuum electrostatics and QM/MM models [4]. All model calculations compare well with corresponding experimental measurements. [4pt] [1] Protein Flexibility using Constraints from Molecular Dynamics Simulations T. Mamonova, B. Hespenheide, R. Straub, M. F. Thorpe, M. G. Kurnikova , Phys. Biol., 2, S137 (2005)[0pt] [2] Theoretical Study of the Glutamate Receptor Ligand Binding Domain Flexibility and Conformational Reorganization T. Mamonova, K. Speranskiy, and M. Kurnikova , Prot.: Struct., Func., Bioinf., 73,656 (2008)[0pt] [3] Energetics of the cleft closing transition and glutamate binding in the Glutamate Receptor ligand Binding Domain T. Mamonova, M. Yonkunas, and M. Kurnikova Biochemistry 47, 11077 (2008)[0pt] [4] On the Binding Determinants of the Glutamate Agonist with the Glutamate Receptor Ligand Binding Domain K. Speranskiy and M. Kurnikova Biochemistry 44, 11208 (2005)
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Bergmann, Larissa; Braun, Carolin; Nieger, Martin; Bräse, Stefan
2018-01-02
The prediction of coordination modes is of high importance when structure-property relationships are discussed. Herein, the coordination chemistry of copper(i) with pyridine-amines with a varying number of coordinating N-atoms, namely pyridine-benzimidazole, -triazole and -tetrazole, or their deprotonated analogues, and different phosphines was systematically studied and the photoluminescence properties of all synthesized complexes examined and related to DFT data. Each complex was characterized by single-crystal X-ray analysis and elemental analysis, and a set of prediction rules derived for the coordination chemistry of copper(i) with these ligands. A mononuclear cationic coordination motif was found for PPh 3 or DPEPhos with all N^N ligands, which exhibits blue to green luminescence of MLCT character d(Cu) → π*(pyridine-amine ligand) with quantum yields up to 46%. With the deprotonated N^N ligands, mononuclear neutral complexes were only expected with DPEPhos. The emission's nature of this complex type is strongly dependent on the electronic effects of the N^N ligand and was characterized as (ML + IL)CT transition. In contrast to the high quantum yields up to 78% for the tetrazolate complexes (as reported before), the triazolate and imidazolate based complexes show much lower emission efficiencies below 10%. Besides the mononuclear copper(i) complexes, cluster-type complexes were obtained, which show moderate luminescence in the blue to green region of the visible spectrum (469-505 nm).
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Eu3+ complex of ligand4’-(4-carboxyphenyl)-2,2’:6’,2″-terpyridine as fluorosensor of heavy metals
NASA Astrophysics Data System (ADS)
Zulys, A.; Rachmawati, N.
2017-04-01
Ligand 4’-(4-carboxyphenyl)-2,2’:6’,2″-terpyridine (2-Hcptpy) has been synthesized by modification of Kröhnke method. The synthesize was performed using aldol condensation reaction. The white precipitate was collected and produced 62% yield (1.062 gr). Ligand 2-Hcptpy has been characterized by FTIR, Elemental analyzer, H-NMR, UV-vis, and UV-DRS spectrometer. It was then reacted with lanthanide group (Eu3+) to form a complex by hydrothermal process. The result of Eu3+ complex was 0.352 gr. of white yellowish precipitate. The application of this research is for the fluorosensor of heavy metals (Pb2+dan Cd2+). The data of fluorescence showed two types of fluorescence, either turn on or turn off fluorosensor. Ligand 2-Hcptpy has an on-off type with the addition of Pb2+ and Cd2+, while complex Eu3+ has two types of fluorosensor. The complex showed turn on-off and turn on-off by addition of Pb2+ and type of turn off by addition of Cd2+. Either ligand or complex, showed fluorescence intensity by adding heavy metals up to concentration 5×10-8 M.
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Espa, Davide; Pilia, Luca; Marchiò, Luciano; Artizzu, Flavia; Serpe, Angela; Mercuri, Maria Laura; Simão, Dulce; Almeida, Manuel; Pizzotti, Maddalena; Tessore, Francesca; Deplano, Paola
2012-03-28
The mixed-ligand dithiolene complex [Pt(Bz(2)pipdt)(dcbdt)] (1) bearing the two ligands Bz(2)pipdt = 1,4-dibenzyl-piperazine-3,2-dithione and dcbdt = dicyanobenzodithiolato, has been synthesized, characterized and studied to evaluate its second-order optical nonlinearity. The dithione/dithiolato character of the two ligands gives rise to an asymmetric distribution of the charge in the molecule. This is reflected by structural data showing that in the C(2)S(2)PtS(2)C(2) dithiolene core the four sulfur atoms define a square-planar coordination environment of the metal where the Pt-S bond distances involving the two ligands are similar, while the C-S bond distances in the C(2)S(2) units exhibit a significant difference in Bz(2)pipdt (dithione) and dcbdt (dithiolato). 1 shows a moderately strong absorption peak in the visible region, which can be related to a HOMO-LUMO transition, where the dcbdt ligand (dithiolato) contributes mostly to the HOMO, and the Bz(2)pipdt one (dithione) mostly to the LUMO. Thus this transition has ligand-to-ligand charge transfer (CT) character with some contribution of the metal and undergoes negative solvatochromism and molecular quadratic optical nonlinearity (μβ(0) = -1296 × 10(-48) esu), which was determined by the EFISH (electric-field-induced second-harmonic generation) technique and compared with the values of similar complexes on varying the dithiolato ligand (mnt = maleonitriledithiolato, dmit = 2-thioxo-1,3-dithiole-4,5-dithiolato). Theoretical calculations help to elucidate the role of the dithiolato ligands in affecting the molecular quadratic optical nonlinearity of these complexes.
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Pertwee, R G; Howlett, A C; Abood, M E; Alexander, S P H; Di Marzo, V; Elphick, M R; Greasley, P J; Hansen, H S; Kunos, G; Mackie, K; Mechoulam, R; Ross, R A
2010-12-01
There are at least two types of cannabinoid receptors (CB(1) and CB(2)). Ligands activating these G protein-coupled receptors (GPCRs) include the phytocannabinoid Δ(9)-tetrahydrocannabinol, numerous synthetic compounds, and endogenous compounds known as endocannabinoids. Cannabinoid receptor antagonists have also been developed. Some of these ligands activate or block one type of cannabinoid receptor more potently than the other type. This review summarizes current data indicating the extent to which cannabinoid receptor ligands undergo orthosteric or allosteric interactions with non-CB(1), non-CB(2) established GPCRs, deorphanized receptors such as GPR55, ligand-gated ion channels, transient receptor potential (TRP) channels, and other ion channels or peroxisome proliferator-activated nuclear receptors. From these data, it is clear that some ligands that interact similarly with CB(1) and/or CB(2) receptors are likely to display significantly different pharmacological profiles. The review also lists some criteria that any novel "CB(3)" cannabinoid receptor or channel should fulfil and concludes that these criteria are not currently met by any non-CB(1), non-CB(2) pharmacological receptor or channel. However, it does identify certain pharmacological targets that should be investigated further as potential CB(3) receptors or channels. These include TRP vanilloid 1, which possibly functions as an ionotropic cannabinoid receptor under physiological and/or pathological conditions, and some deorphanized GPCRs. Also discussed are 1) the ability of CB(1) receptors to form heteromeric complexes with certain other GPCRs, 2) phylogenetic relationships that exist between CB(1)/CB(2) receptors and other GPCRs, 3) evidence for the existence of several as-yet-uncharacterized non-CB(1), non-CB(2) cannabinoid receptors; and 4) current cannabinoid receptor nomenclature.
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Role of ligands in permanganate oxidation of organics.
Jiang, Jin; Pang, Su-Yan; Ma, Jun
2010-06-01
We previously demonstrated that several ligands such as phosphate, pyrophosphate, EDTA, and humic acid could significantly enhance permanganate oxidation of triclosan (one phenolic biocide), which was explained by the contribution of ligand-stabilized reactive manganese intermediates in situ formed upon permanganate reduction. To further understand the underlying mechanism, we comparatively investigated the influence of ligands on permanganate oxidation of bisphenol A (BPA, one phenolic endocrine-disrupting chemical), carbamazepine (CBZ, a pharmaceutical containing the olefinic group), and methyl p-tolyl sulfoxide (TMSO, a typical oxygen-atom acceptor). Selected ligands exerted oxidation enhancement for BPA but had negligible influence for CBZ and TMSO. This was mainly attributed to the effects of identified Mn(III) complexes, which would otherwise disproportionate spontaneously in the absence of ligands. The one-electron oxidant Mn(III) species exhibited no reactivity toward CBZ and TMSO for which the two-electron oxygen donation may be the primary oxidation mechanism but readily oxidized BPA. The latter case was a function of pH, the complexing ligand, and the molar [Mn(III)]:[ligand] ratio, generally consistent with the patterns of ligand-affected permanganate oxidation. Moreover, the combination of the one-electron reduction of Mn(III) (Mn(III) + e(-) -->Mn(II)) and the Mn(VII)/Mn(II) reaction in excess ligands (Mn(VII) + 4Mn(II) ----> (ligands) 5Mn(III)) suggested a catalytic role of the Mn(III)/Mn(II) pair in permanganate oxidation of some phenolics in the presence of ligands.
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Vařeková, Radka Svobodová; Jaiswal, Deepti; Sehnal, David; Ionescu, Crina-Maria; Geidl, Stanislav; Pravda, Lukáš; Horský, Vladimír; Wimmerová, Michaela; Koča, Jaroslav
2014-07-01
Structure validation has become a major issue in the structural biology community, and an essential step is checking the ligand structure. This paper introduces MotiveValidator, a web-based application for the validation of ligands and residues in PDB or PDBx/mmCIF format files provided by the user. Specifically, MotiveValidator is able to evaluate in a straightforward manner whether the ligand or residue being studied has a correct annotation (3-letter code), i.e. if it has the same topology and stereochemistry as the model ligand or residue with this annotation. If not, MotiveValidator explicitly describes the differences. MotiveValidator offers a user-friendly, interactive and platform-independent environment for validating structures obtained by any type of experiment. The results of the validation are presented in both tabular and graphical form, facilitating their interpretation. MotiveValidator can process thousands of ligands or residues in a single validation run that takes no more than a few minutes. MotiveValidator can be used for testing single structures, or the analysis of large sets of ligands or fragments prepared for binding site analysis, docking or virtual screening. MotiveValidator is freely available via the Internet at http://ncbr.muni.cz/MotiveValidator. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.
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Rational and Modular Design of Potent Ligands Targeting the RNA that Causes Myotonic Dystrophy 2
Lee, Melissa M.; Pushechnikov, Alexei; Disney, Matthew D.
2009-01-01
Most ligands targeting RNA are identified through screening a therapeutic target for binding members of a ligand library. A potential alternative way to construct RNA binders is through rational design using information about the RNA motifs ligands prefer to bind. Herein, we describe such an approach to design modularly assembled ligands targeting the RNA that causes myotonic dystrophy type 2 (DM2), a currently untreatable disease. A previous study identified that 6′-N-5-hexynoate kanamycin A (1) prefers to bind 2×2 nucleotide, pyrimidine-rich RNA internal loops. Multiple copies of such loops were found in the RNA hairpin that causes DM2. The 1 ligand was then modularly displayed on a peptoid scaffold with varied number and spacing to target several internal loops simultaneously. Modularly assembled ligands were tested for binding to a series of RNAs and for inhibiting the formation of the toxic DM2 RNA-muscleblind protein (MBNL-1) interaction. The most potent ligand displays three 1 modules, each separated by four spacing submonomers, and inhibits the formation of the RNA-protein complex with an IC50 of 25 nM. This ligand is higher affinity and more specific for binding DM2 RNA than MBNL-1. It binds the DM2 RNA at least 20-times more tightly than related RNAs and 15-fold more tightly than MBNL-1. A related control peptoid displaying 6′-N-5-hexynoate neamine (2) is >100-fold less potent at inhibiting the RNA-protein interaction and binds to DM2 RNA >125-fold more weakly. Uptake studies into a mouse myoblast cell line also show that the most potent ligand is cell permeable. PMID:19348464
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Zell, Thomas; Milstein, David
2015-07-21
The substitution of expensive and potentially toxic noble-metal catalysts by cheap, abundant, environmentally benign, and less toxic metals is highly desirable and in line with green chemistry guidelines. We have recently discovered a new type of metal-ligand cooperation, which is based on the reversible dearomatization/aromatization of different heteroaromatic ligand cores caused by deprotonation/protonation of the ligand. More specifically, we have studied complexes of various transition metals (Ru, Fe, Co, Rh, Ir, Ni, Pd, Pt, and Re) bearing pyridine- and bipyridine-based PNP and PNN pincer ligands, which have slightly acidic methylene protons. In addition, we have discovered long-range metal-ligand cooperation in acridine-based pincer ligands, where the cooperation takes place at the electrophilic C-9 position of the acridine moiety leading to dearomatization of its middle ring. This type of metal-ligand cooperation was used for the activation of chemical bonds, including H-H, C-H (sp(2) and sp(3)), O-H, N-H, and B-H bonds. This unusual reactivity likely takes place in various catalytic hydrogenation, dehydrogenation, and related reactions. In this Account, we summarize our studies on novel bifunctional iron PNP and PNN pincer complexes, which were designed on the basis of their ruthenium congeners. Iron PNP pincer complexes serve as efficient (pre)catalysts for hydrogenation and dehydrogenation reactions under remarkably mild conditions. Their catalytic applications include atom-efficient and industrially important hydrogenation reactions of ketones, aldehydes, and esters to the corresponding alcohols. Moreover, they catalyze the hydrogenation of carbon dioxide to sodium formate in the presence of sodium hydroxide, the selective decomposition of formic acid to carbon dioxide and hydrogen, and the E-selective semihydrogenation of alkynes to give E-alkenes. These catalysts feature, compared to other iron-based catalysts, very high catalytic activities which in
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Walter, Markus; Philotheou, Areti; Bonnici, François; Ziegler, Anette-G; Jimenez, Roland
2009-11-01
This randomized, four-arm, placebo-controlled, dose-ranging phase 2 trial was conducted to determine whether repeated subcutaneous injections of the altered peptide ligand, NBI-6024, designed to inhibit autoreactive T-cells, improves beta-cell function in patients with recently diagnosed type 1 diabetes. A total of 188 patients, aged 10-35 years, with recently diagnosed type 1 diabetes were randomly assigned for a treatment consisting of the subcutaneous administration of placebo or 1, 0.5, or 0.1 mg NBI-6024 at baseline, weeks 2 and 4, and then monthly until month 24. Fasting, peak, and area under the curve (AUC) C-peptide concentrations during a 2-h mixed-meal tolerance test were measured at 3-month intervals during treatment. Immune function parameters (islet antibodies and CD4 and CD8 T-cells) were also studied. The mean peak C-peptide concentration at 24 months after study entry showed no significant difference between the groups treated with 0.1 mg (0.59 pmol/ml), 0.5 mg (0.57 pmol/ml), and 1.0 mg NBI-6024 (0.48 pmol/ml) and the placebo group (0.54 pmol/ml). Fasting, stimulated peak, and AUC C-peptide concentrations declined linearly in all groups by approximately 60% over the 24-month treatment period. The average daily insulin needs at month 24 were also comparable between the four groups. No treatment-related changes in islet antibodies and T cell numbers were observed. Treatment with altered peptide ligand NBI-6024 at repeated doses of 0.1, 0.5, or 1.0 mg did not improve or maintain beta-cell function.
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Transition-metal phosphors with cyclometalating ligands: fundamentals and applications.
Chi, Yun; Chou, Pi-Tai
2010-02-01
One goal of this critical review is to provide advanced methodologies for systematic preparation of transition-metal based phosphors that show latent applications in the field of organic light emitting diodes (OLEDs). We are therefore reviewing various types of cyclometalating chelates for which the favorable metal-chelate bonding interaction, on the one hand, makes the resulting phosphorescent complexes highly emissive in both fluid and solid states at room temperature. On the other hand, fine adjustment of ligand-centered pi-pi* electronic transitions allows tuning of emission wavelength across the whole visible spectrum. The cyclometalating chelates are then classified according to types of cyclometalating groups, i.e. either aromatic C-H or azolic N-H fragment, and the adjacent donor fragment involved in the formation of metallacycles; the latter is an N-containing heterocycle, N-heterocyclic (NHC) carbene fragment or even diphenylphosphino group. These cyclometalating ligands are capable to react with heavy transition-metal elements, namely: Ru(II), Os(II), Ir(III) and Pt(II), to afford a variety of highly emissive phosphors, for which the photophysical properties as a function of chelate or metal characteristics are systematically discussed. Using Ir(III) complexes as examples, the C--N chelates possessing both C-H site and N-heterocyclic donor group are essential for obtaining phosphors with emission ranging from sky-blue to saturated red, while the N--N chelates such as 2-pyridyl-C-linked azolates are found useful for serving as true-blue chromophores due to their increased ligand-centered pi-pi* energy gap. Lastly, the remaining NHC carbene and benzyl phosphine chelates are highly desirable to serve as ancillary chelates in localizing the electronic transition between the metal and remaining lower energy chromophoric chelates. As for the potential opto-electronic applications, many of them exhibit remarkable performance data, which are convincing to pave a
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Flexible ligand docking using a genetic algorithm
NASA Astrophysics Data System (ADS)
Oshiro, C. M.; Kuntz, I. D.; Dixon, J. Scott
1995-04-01
Two computational techniques have been developed to explore the orientational and conformational space of a flexible ligand within an enzyme. Both methods use the Genetic Algorithm (GA) to generate conformationally flexible ligands in conjunction with algorithms from the DOCK suite of programs to characterize the receptor site. The methods are applied to three enzyme-ligand complexes: dihydrofolate reductase-methotrexate, thymidylate synthase-phenolpthalein and HIV protease-thioketal haloperidol. Conformations and orientations close to the crystallographically determined structures are obtained, as well as alternative structures with low energy. The potential for the GA method to screen a database of compounds is also examined. A collection of ligands is evaluated simultaneously, rather than docking the ligands individually into the enzyme.
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Identifying Marine Copper-Binding Ligands in Seawater
NASA Astrophysics Data System (ADS)
Whitby, H.; Hollibaugh, J. T.; Maldonado, M. T.; Ouchi, S.; van den Berg, S. M.
2016-02-01
Complexation reactions are important because they affect the bioavailability of trace metals such as copper and iron. For example, organic complexation can determine whether copper is a limiting or a toxic micronutrient at natural levels. Copper competes with iron for complexing ligands, and when iron is limiting, copper can also substitute for iron in some metabolic pathways. The speciation of copper can be measured using complexing capacity titrations, which provide the concentration of individual ligand classes (L1, L2 etc.) and the complex stabilities (log K). Using methods recently developed in our laboratory, we show that the ligands within these classes can be measured independently of titrations, thus confirming the titration method and simultaneously identifying the ligands within each class. Thiols were identified as the L1 ligand class and humic compounds as the weaker L2 class in samples from coastal Georgia, USA, collected monthly from April to December. Log K values of the ligand complexes were consistent with values expected for thiols and humic substances. Recent results from culture studies and from samples collected along Line P, a coastal - oceanic transect in the HNLC region of the NE subarctic Pacific, will be presented in comparison to the estuarine results. This comparison will help to broaden our perspective on copper complexation and the ligands responsible, furthering our understanding of ligand sources and life cycles.
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Structures of undecagold clusters: Ligand effect
NASA Astrophysics Data System (ADS)
Spivey, Kasi; Williams, Joseph I.; Wang, Lichang
2006-12-01
The most stable structure of undecagold, or Au 11, clusters was predicted from our DFT calculations to be planar [L. Xiao, L. Wang, Chem. Phys. Lett. 392 (2004) 452; L. Xiao, B. Tollberg, X. Hu, L. Wang, J. Chem. Phys. 124 (2005) 114309.]. The structures of ligand protected undecagold clusters were shown to be three-dimensional experimentally. In this work, we used DFT calculations to study the ligand effect on the structures of Au 11 clusters. Our results show that the most stable structure of Au 11 is in fact three-dimensional when SCH 3 ligands are attached. This indicates that the structures of small gold clusters are altered substantially in the presence of ligands.
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Mullen, Douglas G; Banaszak Holl, Mark M
2011-11-15
Nanoparticles conjugated with functional ligands are expected to have a major impact in medicine, photonics, sensing, and nanoarchitecture design. One major obstacle to realizing the promise of these materials, however, is the difficulty in controlling the ligand/nanoparticle ratio. This obstacle can be segmented into three key areas: First, many designs of these systems have failed to account for the true heterogeneity of ligand/nanoparticle ratios that compose each material. Second, studies in the field often use the mean ligand/nanoparticle ratio as the accepted level of characterization of these materials. This measure is insufficient because it does not provide information about the distribution of ligand/nanoparticle species within a sample or the number and relative amount of the different species that compose a material. Without these data, researchers do not have an accurate definition of material composition necessary both to understand the material-property relationships and to monitor the consistency of the material. Third, some synthetic approaches now in use may not produce consistent materials because of their sensitivity to reaction kinetics and to the synthetic history of the nanoparticle. In this Account, we describe recent advances that we have made in under standing the material composition of ligand-nanoparticle systems. Our work has been enabled by a model system using poly(amidoamine) dendrimers and two small molecule ligands. Using reverse phase high-pressure liquid chromatography (HPLC), we have successfully resolved and quantified the relative amounts and ratios of each ligand/dendrimer combination. This type of information is rare within the field of ligand-nanoparticle materials because most analytical techniques have been unable to identify the components in the distribution. Our experimental data indicate that the actual distribution of ligand-nanoparticle components is much more heterogeneous than is commonly assumed. The mean ligand
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Gill, Samuel C; Lim, Nathan M; Grinaway, Patrick B; Rustenburg, Ariën S; Fass, Josh; Ross, Gregory A; Chodera, John D; Mobley, David L
2018-05-31
Accurately predicting protein-ligand binding affinities and binding modes is a major goal in computational chemistry, but even the prediction of ligand binding modes in proteins poses major challenges. Here, we focus on solving the binding mode prediction problem for rigid fragments. That is, we focus on computing the dominant placement, conformation, and orientations of a relatively rigid, fragment-like ligand in a receptor, and the populations of the multiple binding modes which may be relevant. This problem is important in its own right, but is even more timely given the recent success of alchemical free energy calculations. Alchemical calculations are increasingly used to predict binding free energies of ligands to receptors. However, the accuracy of these calculations is dependent on proper sampling of the relevant ligand binding modes. Unfortunately, ligand binding modes may often be uncertain, hard to predict, and/or slow to interconvert on simulation time scales, so proper sampling with current techniques can require prohibitively long simulations. We need new methods which dramatically improve sampling of ligand binding modes. Here, we develop and apply a nonequilibrium candidate Monte Carlo (NCMC) method to improve sampling of ligand binding modes. In this technique, the ligand is rotated and subsequently allowed to relax in its new position through alchemical perturbation before accepting or rejecting the rotation and relaxation as a nonequilibrium Monte Carlo move. When applied to a T4 lysozyme model binding system, this NCMC method shows over 2 orders of magnitude improvement in binding mode sampling efficiency compared to a brute force molecular dynamics simulation. This is a first step toward applying this methodology to pharmaceutically relevant binding of fragments and, eventually, drug-like molecules. We are making this approach available via our new Binding modes of ligands using enhanced sampling (BLUES) package which is freely available on GitHub.
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Assessment of automatic ligand building in ARP/wARP.
Evrard, Guillaume X; Langer, Gerrit G; Perrakis, Anastassis; Lamzin, Victor S
2007-01-01
The efficiency of the ligand-building module of ARP/wARP version 6.1 has been assessed through extensive tests on a large variety of protein-ligand complexes from the PDB, as available from the Uppsala Electron Density Server. Ligand building in ARP/wARP involves two main steps: automatic identification of the location of the ligand and the actual construction of its atomic model. The first step is most successful for large ligands. The second step, ligand construction, is more powerful with X-ray data at high resolution and ligands of small to medium size. Both steps are successful for ligands with low to moderate atomic displacement parameters. The results highlight the strengths and weaknesses of both the method of ligand building and the large-scale validation procedure and help to identify means of further improvement.
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Allosteric ligands for the pharmacologically dark receptors GPR68 and GPR65
Huang, Xi-Ping; Karpiak, Joel; Kroeze, Wesley K.; Zhu, Hu; Chen, Xin; Moy, Sheryl S.; Saddoris, Kara A.; Nikolova, Viktoriya; Farrell, Martilias S.; Wang, Sheng; Mangano, Thomas J.; Deshpande, Deepak A.; Jiang, Alice; Penn, Raymond B.; Jin, Jian; Koller, Beverly H.; Kenakin, Terry; Shoichet, Brian K.; Roth, Bryan L.
2016-01-01
At least 120 non-olfactory G protein-coupled receptors in the human genome are ”orphans” for which endogenous ligands are unknown, and many have no selective ligands, hindering elucidation of their biological functions and clinical relevance. Among these is GPR68, a proton receptor that lacks small molecule modulators for probing its biology. Yeast-based screens against GPR68 identified the benzodiazepine drug lorazepam as a non-selective GPR68 positive allosteric modulator. Over 3000 GPR68 homology models were refined to recognize lorazepam in a putative allosteric site. Docking 3.1 million molecules predicted new GPR68 modulators many of which were confirmed in functional assays. One potent GPR68 modulator—ogerin– suppressed recall in fear conditioning in wild-type, but not in GPR68 knockout mice. The same approach led to the discovery of allosteric agonists and negative allosteric modulators for GPR65. Combining physical and structure-based screening may be broadly useful for ligand discovery for understudied and orphan GPCRs. PMID:26550826
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Bilder, David; Fischer, Janice A.
2011-01-01
Notch signaling requires ligand internalization by the signal sending cells. Two endocytic proteins, epsin and auxilin, are essential for ligand internalization and signaling. Epsin promotes clathrin-coated vesicle formation, and auxilin uncoats clathrin from newly internalized vesicles. Two hypotheses have been advanced to explain the requirement for ligand endocytosis. One idea is that after ligand/receptor binding, ligand endocytosis leads to receptor activation by pulling on the receptor, which either exposes a cleavage site on the extracellular domain, or dissociates two receptor subunits. Alternatively, ligand internalization prior to receptor binding, followed by trafficking through an endosomal pathway and recycling to the plasma membrane may enable ligand activation. Activation could mean ligand modification or ligand transcytosis to a membrane environment conducive to signaling. A key piece of evidence supporting the recycling model is the requirement in signaling cells for Rab11, which encodes a GTPase critical for endosomal recycling. Here, we use Drosophila Rab11 and auxilin mutants to test the ligand recycling hypothesis. First, we find that Rab11 is dispensable for several Notch signaling events in the eye disc. Second, we find that Drosophila female germline cells, the one cell type known to signal without clathrin, also do not require auxilin to signal. Third, we find that much of the requirement for auxilin in Notch signaling was bypassed by overexpression of both clathrin heavy chain and epsin. Thus, the main role of auxilin in Notch signaling is not to produce uncoated ligand-containing vesicles, but to maintain the pool of free clathrin. Taken together, these results argue strongly that at least in some cell types, the primary function of Notch ligand endocytosis is not for ligand recycling. PMID:21448287
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Ligand structure and mechanical properties of single-nanoparticle-thick membranes.
Salerno, K Michael; Bolintineanu, Dan S; Lane, J Matthew D; Grest, Gary S
2015-06-01
The high mechanical stiffness of single-nanoparticle-thick membranes is believed to result from the local structure of ligand coatings that mediate interactions between nanoparticles. These ligand structures are not directly observable experimentally. We use molecular dynamics simulations to observe variations in ligand structure and simultaneously measure variations in membrane mechanical properties. We have shown previously that ligand end group has a large impact on ligand structure and membrane mechanical properties. Here we introduce and apply quantitative molecular structure measures to these membranes and extend analysis to multiple nanoparticle core sizes and ligand lengths. Simulations of nanoparticle membranes with a nanoparticle core diameter of 4 or 6 nm, a ligand length of 11 or 17 methylenes, and either carboxyl (COOH) or methyl (CH(3)) ligand end groups are presented. In carboxyl-terminated ligand systems, structure and interactions are dominated by an end-to-end orientation of ligands. In methyl-terminated ligand systems large ordered ligand structures form, but nanoparticle interactions are dominated by disordered, partially interdigitated ligands. Core size and ligand length also affect both ligand arrangement within the membrane and the membrane's macroscopic mechanical response, but are secondary to the role of the ligand end group. Moreover, the particular end group (COOH or CH(3)) alters the nature of how ligand length, in turn, affects the membrane properties. The effect of core size does not depend on the ligand end group, with larger cores always leading to stiffer membranes. Asymmetry in the stress and ligand density is observed in membranes during preparation at a water-vapor interface, with the stress asymmetry persisting in all membranes after drying.
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Ligand structure and mechanical properties of single-nanoparticle thick membranes
Salerno, Kenneth Michael; Bolintineanu, Dan S.; Lane, J. Matthew D.; ...
2015-06-16
We believe that the high mechanical stiffness of single-nanoparticle-thick membranes is the result of the local structure of ligand coatings that mediate interactions between nanoparticles. These ligand structures are not directly observable experimentally. We use molecular dynamics simulations to observe variations in ligand structure and simultaneously measure variations in membrane mechanical properties. We have shown previously that ligand end group has a large impact on ligand structure and membrane mechanical properties. Here we introduce and apply quantitative molecular structure measures to these membranes and extend analysis to multiple nanoparticle core sizes and ligand lengths. Simulations of nanoparticle membranes with amore » nanoparticle core diameter of 4 or 6 nm, a ligand length of 11 or 17 methylenes, and either carboxyl (COOH) or methyl (CH 3) ligand end groups are presented. In carboxyl-terminated ligand systems, structure and interactions are dominated by an end-to-end orientation of ligands. In methyl-terminated ligand systems large ordered ligand structures form, but nanoparticle interactions are dominated by disordered, partially interdigitated ligands. Core size and ligand length also affect both ligand arrangement within the membrane and the membrane's macroscopic mechanical response, but are secondary to the role of the ligand end group. Additionally, the particular end group (COOH or CH 3) alters the nature of how ligand length, in turn, affects the membrane properties. The effect of core size does not depend on the ligand end group, with larger cores always leading to stiffer membranes. Asymmetry in the stress and ligand density is observed in membranes during preparation at a water-vapor interface, with the stress asymmetry persisting in all membranes after drying.« less
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Ramsay, Douglas; Bevan, Nicola; Rees, Stephen; Milligan, Graeme
2001-01-01
The wild-type β2-adrenoceptor and a constitutively active mutant of this receptor were C-terminally tagged with luciferase from the sea pansy Renilla reniformis. C-terminal addition of Renilla luciferase did not substantially alter the levels of expression of either form of the receptor, the elevated constitutive activity of the mutant β2-adrenoceptor nor the capacity of isoprenaline to elevate cyclic AMP levels in intact cells expressing these constructs. Treatment of cells expressing constitutively active mutant β2-adrenoceptor-Renilla luciferase with antagonist/inverse agonist ligands resulted in upregulation of levels of this polypeptide which could be monitored by the elevated luciferase activity. The pEC50 for ligand-induced luciferase upregulation and ligand affinity to bind the receptor were highly correlated. Similar upregulation could be observed following sustained treatment with agonist ligands. These effects were only observed at a constitutively active mutant of the β2-adrenoceptor. Co-expression of the wild-type β2-adrenoceptor C-terminally tagged with the luciferase from Photinus pyralis did not result in ligand-induced upregulation of the levels of activity of this luciferase. Co-expression of the constitutively active mutant β2-adrenoceptor-Renilla luciferase and an equivalent mutant of the α1b-adrenoceptor C-terminally tagged with green fluorescent protein allowed pharmacological selectivity of adrenoceptor antagonists to be demonstrated. This approach offers a sensitive and convenient means, which is amenable to high throughput analysis, to monitor ligand binding to a constitutively active mutant receptor. As no prior knowledge of receptor ligands is required this approach may be suitable to identify ligands at orphan G protein-coupled receptors. PMID:11350868
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Effect of Ligand Exchange on the Photoluminescence Properties of Cu-Doped Zn-In-Se Quantum Dots
NASA Astrophysics Data System (ADS)
Dong, Xiaofei; Xu, Jianping; Yang, Hui; Zhang, Xiaosong; Mo, Zhaojun; Shi, Shaobo; Li, Lan; Yin, Shougen
2018-04-01
The surface-bound ligands of a semiconductor nanocrystal can affect its electron transition behavior. We investigate the photoluminescence (PL) properties of Cu-doped Zn-In-Se quantum dots (QDs) through the exchange of oleylamine with 6-mercaptohexanol (MCH). Fourier transform infrared and 1H nuclear magnetic resonance spectroscopies, and mass spectrometry reveal that the short-chain MCH molecules are bound to the QD surface. The emission peaks remain unchanged after ligand exchange, and the PL quantum yield is reduced from 49% to 38%. The effects of particle size and defect type on the change in PL behavior upon ligand substitution are excluded through high-resolution transmission electron microscopy, UV-Vis absorption, and PL spectroscopies. The origin of the decreased PL intensity is associated with increased ligand density and the stronger ligand electron-donating abilities of MCH-capped QDs that induce an increase in the nonradiative transition probability. A lower PL quenching transition temperature is observed for MCH-capped QDs and is associated with increasing electron-acoustic phonon coupling due to the lower melting temperature of MCH.
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Synthesis and characterization of Pd(II)-methyl complexes with N-heterocyclic carbene-amine ligands.
Warsink, Stefan; de Boer, Sandra Y; Jongens, Lianne M; Fu, Ching-Feng; Liu, Shiuh-Tzung; Chen, Jwu-Ting; Lutz, Martin; Spek, Anthony L; Elsevier, Cornelis J
2009-09-21
A number of palladium(ii) complexes with a heteroditopic NHC-amine ligand and their precursor silver(i) carbene complexes have been efficiently prepared and their structural features have been investigated. The heteroditopic coordination of this ligand class was unequivocally shown by NMR-spectroscopy and X-ray crystallographic analysis. The neutral and cationic cis-methyl-palladium(NHC) complexes are not prone to reductive elimination, which is normally a major degenerative pathway for this type of complex. In contrast, under carbon monoxide atmosphere rapid reductive elimination of the acyl-imidazolium salt was observed.
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High-throughput screening of dye-ligands for chromatography.
Kumar, Sunil; Punekar, Narayan S
2014-01-01
Dye-ligand-based chromatography has become popular after Cibacron Blue, the first reactive textile dye, found application for protein purification. Many other textile dyes have since been successfully used to purify a number of proteins and enzymes. While the exact nature of their interaction with target proteins is often unclear, dye-ligands are thought to mimic the structural features of their corresponding substrates, cofactors, etc. The dye-ligand affinity matrices are therefore considered pseudo-affinity matrices. In addition, dye-ligands may simply bind with proteins due to electrostatic, hydrophobic, and hydrogen-bonding interactions. Because of their low cost, ready availability, and structural stability, dye-ligand affinity matrices have gained much popularity. Choice of a large number of dye structures offers a range of matrices to be prepared and tested. When presented in the high-throughput screening mode, these dye-ligand matrices provide a formidable tool for protein purification. One could pick from the list of dye-ligands already available or build a systematic library of such structures for use. A high-throughput screen may be set up to choose best dye-ligand matrix as well as ideal conditions for binding and elution, for a given protein. The mode of operation could be either manual or automated. The technology is available to test the performance of dye-ligand matrices in small volumes in an automated liquid-handling workstation. Screening a systematic library of dye-ligand structures can help establish a structure-activity relationship. While the origins of dye-ligand chromatography lay in exploiting pseudo-affinity, it is now possible to design very specific biomimetic dye structures. High-throughput screening will be of value in this endeavor as well.
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Zhao, Xiang-Yu; Luo, Xue-Yi; Yu, Xing-Xing; Zhao, Xiao-Su; Han, Ting-Ting; Chang, Ying-Jun; Huo, Ming-Rui; Xu, Lan-Ping; Zhang, Xiao-Hui; Liu, Kai-Yan; Li, Dan; Jiang, Zheng-Fan; Huang, Xiao-Jun
2017-06-01
Licensed natural killer (NK) cells have been demonstrated to have anti-cytomegalovirus (CMV) activity. We prospectively analysed the human leucocyte antigen typing of donor-recipient pairs and the killer cell immunoglobulin-like receptor (KIR) typing of donors for 180 leukaemia patients to assess the predictive roles of licensed NK cells on CMV reactivation post-T-cell-replete haploidentical stem cell transplantation. Multivariate analysis showed that donor-recipient KIR ligand graft-versus-host or host-versus-graft direction mismatch was associated with increased refractory CMV infection (Hazard ratio = 2·556, 95% confidence interval, 1·377-4·744, P = 0·003) post-transplantation. Donor-recipient KIR ligand matching decreased CMV reactivation [51·65% (46·67, 56·62%) vs. 75·28% (70·87, 79·69%), P = 0·012], refractory CMV infection [17·58% (13·77, 21·40%) vs. 35·96% (31·09, 40·82%), P = 0·004] and CMV disease [3·30% (1·51, 5·08%) vs. 11·24% (8·04, 14·43%), P = 0·024] by day 100 post-transplantation. In addition, the percentage of γ-interferon expression on donor-derived NK cells was significantly higher in the recipients among the recipient-donor pairs with a KIR ligand match compared with that in the recipients among the pairs with a KIR ligand graft-versus-host or host-versus-graft direction mismatch on days 30 and 100 post-transplantation (P = 0·036 and 0·047, respectively). These findings have suggested that donor-recipient KIR ligand matching might promote the NK cell licensing process, thereby increasing NK cell-mediated protection against CMV reactivation. © 2017 John Wiley & Sons Ltd.
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Use of natural AhR ligands as potential therapeutic modalities against inflammatory disorders
Busbee, Philip B; Rouse, Michael; Nagarkatti, Mitzi; Nagarkatti, Prakash S
2014-01-01
The aim of this review is to discuss research involving ligands for the aryl hydrocarbon receptor (AhR) and their role in immunomodulation. While activation of the AhR is well known for its ability to regulate the biochemical and toxic effects of environmental chemicals, more recently an exciting discovery has been made indicating that AhR ligation can also regulate T-cell differentiation, specifically through activation of Foxp3+ regulatory T cells (Tregs) and downregulation of the proinflammatory Th17 cells. Such findings have opened new avenues of research on the possibility of targeting the AhR to treat inflammatory and autoimmune diseases. Specifically, this review will discuss the current research involving natural and dietary AhR ligands. In addition, evidence indicating the potential use of these ligands in regulating inflammation in various diseases will be highlighted. The importance of the AhR in immunological processes can be illustrated by expression of this receptor on a majority of immune cell types. In addition, AhR signaling pathways have been reported to influence a number of genes responsible for mediating inflammation and other immune responses. As interest in the AhR and its ligands increases, it seems prudent to consolidate current research on the contributions of these ligands to immune regulation during the course of inflammatory diseases. PMID:23731446
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NASA Astrophysics Data System (ADS)
Abd El-Halim, Hanan F.; Mohamed, Gehad G.; Khalil, Eman A. M.
2017-10-01
A series of mixed ligand complexes were prepared from the Schiff base (L1) as a primary ligand, prepared by condensation of oxamide and furan-2-carbaldehyde, and 1,10-phenanthroline (1,10-phen) as a secondary ligand. The Schiff base ligand and its mixed ligand chelates were characterized based on elemental analysis, IR, 1H NMR, thermal analysis, UV-Visible, mass, molar conductance, magnetic moment. X-ray diffraction, solid reflectance and ESR also have been studied. The mixed ligand complexes were found to have the formulae of [M(L1) (1,10-phen)]Clm.nH2O (M = Cr(III) and Fe(III) (m = 3) (n = 0); M = Mn(II), Cu(II) and Cd(II) (m = 2) (n = 0); and M = Co(II) (m = 2) (n = 1), Ni(II) (m = 2) (n = 2) and Zn(II) (m = 2) (n = 3)) and that the geometrical structure of the complexes were octahedral. The parameters of thermodynamic using Coats-Redfern and Horowitz-Metzger equations were calculated. The synthesized Schiff base ligand, 1,10-phenanthroline ligand and Their mixed ligand complexes were also investigated for their antibacterial and antifungal activity against bacterial species (Gram-Ve bacteria: Pseudomonas aeruginosa and Escherichia coli) and (Gram + Ve bacteria: Bacillus subtilis and Streptococcus pneumonia) and fungi (Aspergillus fumigates and Candida albicans). The anticancer activity of the new compounds had been tested against breast (MFC7) and colon (HCT-116) cell lines. The results showed high activity for the synthesized compounds.
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Vezzi, Vanessa; Onaran, H Ongun; Molinari, Paola; Guerrini, Remo; Balboni, Gianfranco; Calò, Girolamo; Costa, Tommaso
2013-08-16
Using a cell-free bioluminescence resonance energy transfer strategy we compared the levels of spontaneous and ligand-induced receptor-G protein coupling in δ (DOP) and μ (MOP) opioid receptors. In this assay GDP can suppress spontaneous coupling, thus allowing its quantification. The level of constitutive activity was 4-5 times greater at the DOP than at the MOP receptor. A series of opioid analogues with a common peptidomimetic scaffold displayed remarkable inversions of efficacy in the two receptors. Agonists that enhanced coupling above the low intrinsic level of the MOP receptor were inverse agonists in reducing the greater level of constitutive coupling of the DOP receptor. Yet the intrinsic activities of such ligands are identical when scaled over the GDP base line of both receptors. This pattern is in conflict with the predictions of the ternary complex model and the "two state" extensions. According to this theory, the order of spontaneous and ligand-induced coupling cannot be reversed if a shift of the equilibrium between active and inactive forms raises constitutive activation in one receptor type. We propose that constitutive activation results from a lessened intrinsic barrier that restrains spontaneous coupling. Any ligand, regardless of its efficacy, must enhance this constraint to stabilize the ligand-bound complexed form.
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Ligand-Induced Conformational Change in the α7 Nicotinic Receptor Ligand Binding Domain
Henchman, Richard H.; Wang, Hai-Long; Sine, Steven M.; Taylor, Palmer; McCammon, J. Andrew
2005-01-01
Molecular dynamics simulations of a homology model of the ligand binding domain of the α7 nicotinic receptor are conducted with a range of bound ligands to induce different conformational states. Four simulations of 15 ns each are run with no ligand, antagonist d-tubocurarine (dTC), agonist acetylcholine (ACh), and agonist ACh with potentiator Ca2+, to give insight into the conformations of the active and inactive states of the receptor and suggest the mechanism for conformational change. The main structural factor distinguishing the active and inactive states is that a more open, symmetric arrangement of the five subunits arises for the two agonist simulations, whereas a more closed and asymmetric arrangement results for the apo and dTC cases. Most of the difference arises in the lower portion of the ligand binding domain near its connection to the adjacent transmembrane domain. The transfer of the more open state to the transmembrane domain could then promote ion flow through the channel. Variation in how subunits pack together with no ligand bound appears to give rise to asymmetry in the apo case. The presence of dTC expands the receptor but induces rotations in alternate directions in adjacent subunits that lead to an asymmetric arrangement as in the apo case. Ca2+ appears to promote a slightly greater expansion in the subunits than ACh alone by stabilizing the C-loop and ACh positions. Although the simulations are unlikely to be long enough to view the full conformational changes between open and closed states, a collection of different motions at a range of length scales are observed that are likely to participate in the conformational change. PMID:15665135
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PDBToSDF: Create ligand structure files from PDB file.
Muppalaneni, Naresh Babu; Rao, Allam Appa
2011-01-01
Protein Data Bank (PDB) file contains atomic data for protein and ligand in protein-ligand complexes. Structure data file (SDF) contains data for atoms, bonds, connectivity and coordinates of molecule for ligands. We describe PDBToSDF as a tool to separate the ligand data from pdb file for the calculation of ligand properties like molecular weight, number of hydrogen bond acceptors, hydrogen bond receptors easily.
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Predicting Monoamine Oxidase Inhibitory Activity through Ligand-Based Models
Vilar, Santiago; Ferino, Giulio; Quezada, Elias; Santana, Lourdes; Friedman, Carol
2013-01-01
The evolution of bio- and cheminformatics associated with the development of specialized software and increasing computer power has produced a great interest in theoretical in silico methods applied in drug rational design. These techniques apply the concept that “similar molecules have similar biological properties” that has been exploited in Medicinal Chemistry for years to design new molecules with desirable pharmacological profiles. Ligand-based methods are not dependent on receptor structural data and take into account two and three-dimensional molecular properties to assess similarity of new compounds in regards to the set of molecules with the biological property under study. Depending on the complexity of the calculation, there are different types of ligand-based methods, such as QSAR (Quantitative Structure-Activity Relationship) with 2D and 3D descriptors, CoMFA (Comparative Molecular Field Analysis) or pharmacophoric approaches. This work provides a description of a series of ligand-based models applied in the prediction of the inhibitory activity of monoamine oxidase (MAO) enzymes. The controlled regulation of the enzymes’ function through the use of MAO inhibitors is used as a treatment in many psychiatric and neurological disorders, such as depression, anxiety, Alzheimer’s and Parkinson’s disease. For this reason, multiple scaffolds, such as substituted coumarins, indolylmethylamine or pyridazine derivatives were synthesized and assayed toward MAO-A and MAO-B inhibition. Our intention is to focus on the description of ligand-based models to provide new insights in the relationship between the MAO inhibitory activity and the molecular structure of the different inhibitors, and further study enzyme selectivity and possible mechanisms of action. PMID:23231398
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Sahasrabudhe, Neha M; Lenos, Kristiaan; van der Horst, Joost C; Rodríguez, Ernesto; van Vliet, Sandra J
2018-06-27
Colorectal cancer is the third most common cancer type worldwide. It is characterized by a high expression of aberrantly glycosylated ligands, such as the Tn antigen (GalNAcα1-Ser/Thr), which is a major ligand for the C-type lectin macrophage galactose-type lectin (MGL). We have previously determined that a high level of MGL ligands in colorectal tumors is associated with lower disease-free survival in patients with late stage disease, which we could attribute to the presence of oncogenic BRAFV600E mutations. Here we aimed to elucidate the downstream pathway of BRAFV600E governing high MGL ligand and Tn antigen expression. We focused on glycosylation-related enzymes involved in the synthesis or elongation of Tn antigen, N-acetylgalactosamine-transferases (GALNTs) and C1GalT1/COSMC, respectively. Both the activity and expression of C1GalT1 and COSMC were unrelated to the BRAF mutational status. In contrast, GALNT3, GALNT7 and GALNT12 were increased in colorectal cancer cells harboring the BRAFV600E mutation. Through CRISPR-Cas9 gene knockouts we could establish that GALNT3 increased MGL ligand synthesis in the HT29 cell line, while GALNT7 and GALNT12 appeared to have redundant roles. Together our results highlight a novel mechanistic pathway connecting BRAFV600E to aberrant glycosylation in colorectal cancer through GALNT3.
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Minimum Free Energy Path of Ligand-Induced Transition in Adenylate Kinase
Matsunaga, Yasuhiro; Fujisaki, Hiroshi; Terada, Tohru; Furuta, Tadaomi; Moritsugu, Kei; Kidera, Akinori
2012-01-01
Large-scale conformational changes in proteins involve barrier-crossing transitions on the complex free energy surfaces of high-dimensional space. Such rare events cannot be efficiently captured by conventional molecular dynamics simulations. Here we show that, by combining the on-the-fly string method and the multi-state Bennett acceptance ratio (MBAR) method, the free energy profile of a conformational transition pathway in Escherichia coli adenylate kinase can be characterized in a high-dimensional space. The minimum free energy paths of the conformational transitions in adenylate kinase were explored by the on-the-fly string method in 20-dimensional space spanned by the 20 largest-amplitude principal modes, and the free energy and various kinds of average physical quantities along the pathways were successfully evaluated by the MBAR method. The influence of ligand binding on the pathways was characterized in terms of rigid-body motions of the lid-shaped ATP-binding domain (LID) and the AMP-binding (AMPbd) domains. It was found that the LID domain was able to partially close without the ligand, while the closure of the AMPbd domain required the ligand binding. The transition state ensemble of the ligand bound form was identified as those structures characterized by highly specific binding of the ligand to the AMPbd domain, and was validated by unrestrained MD simulations. It was also found that complete closure of the LID domain required the dehydration of solvents around the P-loop. These findings suggest that the interplay of the two different types of domain motion is an essential feature in the conformational transition of the enzyme. PMID:22685395
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Ligand-induced dependence of charge transfer in nanotube–quantum dot heterostructures
Wang, Lei; Han, Jinkyu; Sundahl, Bryan; ...
2016-07-01
As a model system to probe ligand-dependent charge transfer in complex composite heterostructures, we fabricated double-walled carbon nanotube (DWNT) – CdSe quantum dot (QD) composites. Whereas the average diameter of the QDs probed was kept fixed at ~4.1 nm and the nanotubes analyzed were similarly oxidatively processed, by contrast, the ligands used to mediate the covalent attachment between the QDs and DWNTs were systematically varied to include p-phenylenediamine (PPD), 2-aminoethanethiol (AET), and 4-aminothiophenol (ATP). Herein, we have put forth a unique compilation of complementary data from experiment and theory, including results from transmission electron microscopy (TEM), near-edge X-ray absorption finemore » structure (NEXAFS) spectroscopy, Raman spectroscopy, electrical transport measurements, and theoretical modeling studies, in order to fundamentally assess the nature of the charge transfer between CdSe QDs and DWNTs, as a function of the structure of various, intervening bridging ligand molecules. Specifically, we correlated evidence of charge transfer as manifested by changes and shifts associated with NEXAFS intensities, Raman peak positions, and threshold voltages both before and after CdSe QD deposition onto the underlying DWNT surface. Importantly, for the first time ever in these types of nanoscale composite systems, we have sought to use theoretical modeling to justify and account for our experimental results. Finally, our overall data suggest that (i) QD coverage density on the DWNTs varies, based upon the different ligand pendant groups used and that (ii) the presence of a π-conjugated carbon framework within the ligands themselves and the electron affinity of the pendant groups collectively play important roles in the resulting charge transfer from QDs to the underlying CNTs.« less
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Tisato, Francesco; Porchia, Marina; Shegani, Antoni; Maina, Theodosia; Papadopoulos, Minas S; Seraglia, Roberta; Traldi, Pietro
2018-05-08
fac-[Re(CO) 3 (PO)(X)]-type complexes (PO = chelated bidentate tertiary phosphine(1-), X = various neutral, mono-dentate ligands) represent a class of compounds that meets the synthetic criteria for the preparation of potential carbon monoxide (CO) release molecules (CORMs) for medicinal application. The aim of our investigation was to achieve qualitative information whether the nature of the ancillary X ligand might influence the release of CO. The release of CO has been investigated by means of product ion spectrometry of electrospray ionization-generated [M + H] + species, produced by multiple collisional experiments, using an ion trap mass spectrometer. Tandem mass spectrometry applied to the protonated species [Re(CO) 3 (PO)(X) + H] + of seven complexes (those including X = OH 2 (1), isonitrile (2, 3), imidazole (4), pyridine (5) and phosphine (6, 7) show initial loss of coordinated water (1) or pyridine (5), whereas the majority of investigated entries display initial, sequential release of CO groups. The energetics of CO release have been investigated by breakdown curves for selected collisionally-activated decomposition processes involving CO, and compared with those involving X groups. The nature of the co-ligand X drives the primary loss in the MS n processes of [Re(CO) 3 (PO)(X) + H] + compounds. When X = solvent, the energetics of these decompositions follow the trend H 2 O < MeOH < CO. In each case, loss of CO is a favored fragmentation route with associated energies following the trend: N-py ≤ P-phosphine < C-isonitrile. Overall, MS n pathways indicate that [Re(PO)] (Re with chelated PO phosphine) constitutes the residual moiety. This behavior indicates that the presence of a functionalized phosphine is essential for a sequential, controlled release of CO. This article is protected by copyright. All rights reserved.
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All-inorganic Germanium nanocrystal films by cationic ligand exchange
Wheeler, Lance M.; Nichols, Asa W.; Chernomordik, Boris D.; ...
2016-01-21
In this study, we introduce a new paradigm for group IV nanocrystal surface chemistry based on room temperature surface activation that enables ionic ligand exchange. Germanium nanocrystals synthesized in a gas-phase plasma reactor are functionalized with labile, cationic alkylammonium ligands rather than with traditional covalently bound groups. We employ Fourier transform infrared and 1H nuclear magnetic resonance spectroscopies to demonstrate the alkylammonium ligands are freely exchanged on the germanium nanocrystal surface with a variety of cationic ligands, including short inorganic ligands such as ammonium and alkali metal cations. This ionic ligand exchange chemistry is used to demonstrate enhanced transport inmore » germanium nanocrystal films following ligand exchange as well as the first photovoltaic device based on an all-inorganic germanium nanocrystal absorber layer cast from solution. This new ligand chemistry should accelerate progress in utilizing germanium and other group IV nanocrystals for optoelectronic applications.« less
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Enhanced stability of Janus nanoparticles by covalent cross-linking of surface ligands.
Song, Yang; Klivansky, Liana M; Liu, Yi; Chen, Shaowei
2011-12-06
A mercapto derivative of diacetylene was used as the hydrophilic ligand to prepare Janus nanoparticles by using hydrophobic hexanethiolate-protected gold (AuC6, diameter 5 nm) nanoparticles as the starting materials. The amphiphilic surface characters of the Janus nanoparticles were verified by contact angle measurements, as compared to those of the bulk-exchange counterparts where the two types of ligands were distributed rather homogeneously on the nanoparticle surface. Dynamic light scattering studies showed that the Janus nanoparticles formed stable superstructures in various solvent media that were significantly larger than those by the bulk-exchange counterparts. This was ascribed to the amphiphilic characters of the Janus nanoparticles that rendered the particles to behave analogously to conventional surfactant molecules. Notably, because of the close proximity of the diacetylene moieties on the Janus nanoparticle surface, exposure to UV irradiation led to effective covalent cross-linking between the diacetylene moieties of neighboring ligands, as manifested in UV-vis and fluorescence measurements where the emission characteristics of dimers and trimers of diacetylene were rather well-defined, in addition to the monomeric emission. In contrast, for bulk-exchange nanoparticles, no trimer emission could be identified, and the intensity of dimer emission was markedly lower (though the intensity increased with increasing diacetylene coverage on the particle surface) under the otherwise identical experimental conditions. This is largely because the diacetylene ligands were distributed on the entire particle surface, and it was difficult to find a large number of ligands situated closely so that the stringent topochemical principles for the polymerization of diacetylene derivatives could be met. Importantly, the cross-linked Janus nanoparticles were found to exhibit marked enhancement of the structural integrity, which was attributable to the impeded surface
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Liao, Bei-Sih; Liu, Yi-Hung; Peng, Shie-Ming; Reddy, K Rajender; Liu, Shin-Hung; Chou, Pi-Tai; Liu, Shiuh-Tzung
2014-03-07
Thermal reaction of 2,7-bis(2-pyridinyl)-l,8-naphthyridine () with Ru3(CO)12 in the presence of moisture resulted in the formation of a formate-bridged diruthenium complex [(-H3)Ru2(μ-HCOO)(CO)4] (), in which the ligand was partially hydrogenated. Complex was fully characterized by spectroscopic analyses and X-ray single crystal determination. Regarding the partially reduced ligand in , it occurs through a water-gas shift type reduction. The bridging formate ligand can be substituted by other carboxylate ligands. Physical and chemical properties of the newly prepared complexes were investigated.
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Ohashi, Nami; Nomura, Wataru; Narumi, Tetsuo; Lewin, Nancy E; Itotani, Kyoko; Blumberg, Peter M; Tamamura, Hirokazu
2011-01-19
Protein kinase C (PKC) is a critical cell signaling pathway involved in many disorders such as cancer and Alzheimer-type dementia. To date, evaluation of PKC ligand binding affinity has been performed by competitive studies against radiolabeled probes that are problematic for high-throughput screening. In the present study, we have developed a fluorescent-based binding assay system for identifying ligands that target the PKC ligand binding domain (C1 domain). An environmentally sensitive fluorescent dye (solvatochromic fluorophore), which has been used in multiple applications to assess protein-binding interactions, was inserted in proximity to the binding pocket of a novel PKCδ C1b domain. These resultant fluorescent-labeled δC1b domain analogues underwent a significant change in fluorescent intensity upon ligand binding, and we further demonstrate that the fluorescent δC1b domain analogues can be used to evaluate ligand binding affinity.
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2011-01-01
Abstract Background The combinatorial library strategy of using multiple candidate ligands in mixtures as library members is ideal in terms of cost and efficiency, but needs special screening methods to estimate the affinities of candidate ligands in such mixtures. Herein, a new method to screen candidate ligands present in unknown molar quantities in mixtures was investigated. Results The proposed method involves preparing a processed-mixture-for-screening (PMFS) with each mixture sample and an exogenous reference ligand, initiating competitive binding among ligands from the PMFS to a target immobilized on magnetic particles, recovering target-ligand complexes in equilibrium by magnetic force, extracting and concentrating bound ligands, and analyzing ligands in the PMFS and the concentrated extract by chromatography. The relative affinity of each candidate ligand to its reference ligand is estimated via an approximation equation assuming (a) the candidate ligand and its reference ligand bind to the same site(s) on the target, (b) their chromatographic peak areas are over five times their intercepts of linear response but within their linear ranges, (c) their binding ratios are below 10%. These prerequisites are met by optimizing primarily the quantity of the target used and the PMFS composition ratio. The new method was tested using the competitive binding of biotin derivatives from mixtures to streptavidin immobilized on magnetic particles as a model. Each mixture sample containing a limited number of candidate biotin derivatives with moderate differences in their molar quantities were prepared via parallel-combinatorial-synthesis (PCS) without purification, or via the pooling of individual compounds. Some purified biotin derivatives were used as reference ligands. This method showed resistance to variations in chromatographic quantification sensitivity and concentration ratios; optimized conditions to validate the approximation equation could be applied to
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Fomitchev, Dmitry V; McLauchlan, Craig C; Holm, R H
2002-02-25
A series of heterometal cubane-type clusters containing [VFe(3)S(4)](2+) and [MoFe(3)S(4)](3+,2+) cores has been prepared. Ligand substitution of [(DMF)(3)VFe(3)S(4)Cl(3)](-) affords [(Tpms)VFe(3)S(4)L(3)](2)(-) (L = Cl(-) (8), EtS(-) (9), p-MeC(6)H(4)S(-), p-MeC(6)H(4)O(-)). A new procedure for the preparation of molybdenum single cubanes is introduced by the reaction of recently reported [(Tp)MoS(S(4))](-) with FeCl(2)/NaSEt to afford [(Tp)MoFe(3)S(4)Cl(3)](-) (1, 75% yield). This procedure is more efficient that the existing multistep synthesis of single cubanes, which generally affords clusters of mirror symmetry. Also prepared were [(Tp)MoFe(3)S(4)L(3)](-) (L = EtS(-) (2), p-MeC(6)H(4)S(-)). Reduction of 1 with borohydride gives [(Tp)MoFe(3)S(4)Cl(3)](2-) (5, 67%). Owing to the nature of the heterometal ligand, all clusters have idealized trigonal symmetry, reflected in their (1)H NMR spectra. Trigonal structures are demonstrated by crystallography of (Bu(4)N)[1,2], (Bu(4)N)(2)[5] x MeCN, and (Me(4)N)(2)[8,9]. The availability of 1 and 5 allows the first comparison of structures and (57)Fe isomer shifts of [MoFe(3)S(4)](3+,2+) in a constant ligand environment. Small increases in most bond distances indicate that an antibonding electron is added in the reduction of 1. Collective synthetic and electrochemical results from this and other studies demonstrate the existence of the series of oxidation states [VFe(3)S(4)](3+,2+,1+) and [MoFe(3)S(4)](4+,3+,2+) whose relative stabilities within a given series are strongly ligand dependent. Isomer shifts indicate that the reduction of 1 largely affects the Fe(3) subcluster and are consistent with the formal descriptions [MoFe(3+)(2)Fe(2+)S(4)](3+) (1) and [MoFe(3+)Fe(2+)(2)S(4)](2+) (5). Reaction of 1 with excess Li(2)S in acetonitrile affords the double cubane [[(Tp)MoFe(3)S(4)Cl(2)](2)(mu(2)(-)S)](2)(-), whose sulfide-bridged structure is supported by two sequential reductions separated by 290 mV, in analogy with
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Genet, Jean-Pierre
2003-12-01
This Account covers the design of Ru catalysts and ligands. Two classes of chiral phosphine ligands are prepared: the electron-rich trans-2,4-substituted phosphetanes, readily available from optically pure 1,3-diol cyclic sulfates, and atropoisomeric ligands (SYNPHOS, MeO-NAPhePHOS, bearing heterotopic biaryl moieties, and a chiral water-soluble diguanidinium binaphthyl diphosphine, Digm-BINAP). Applications of these ligands to rhodium- and ruthenium-mediated hydrogenation of ketones and olefins have been reported with high enantioselectivities. The recognition abilities of Ru-SYNPHOS for a wide range of ketones is superior to those observed with BINAP, MeO-NAPhePHOS, and MeO-BIPHEP. Several biologically active compounds have been prepared through dynamic kinetic resolution. This work gives access to a number of highly active catalysts of the type [Ru(biphosphane)(H)(eta(6)-cot)]BF(4). These catalysts have demonstrated their utility in the enantioselective hydrogenation of the tetrasubstituted cyclopentenone "dehydrodione", which leads to the commercially important perfume component Paradisone (Firmenich).
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A semisynthetic strategy leads to alteration of the backbone amidate ligand in the NiSOD active site
Campeciño, Julius O.; Dudycz, Lech W.; Tumelty, David; ...
2015-07-01
Computational investigations have implicated the amidate ligand in nickel superoxide dismutase (NiSOD) in stabilizing Ni-centered redox catalysis and in preventing cysteine thiolate ligand oxidation. To test these predictions, we have used an experimental approach utilizing a semisynthetic scheme that employs native chemical ligation of a pentapeptide (HCDLP) to recombinant S. coelicolor NiSOD lacking these N-terminal residues, NΔ5-NiSOD. Wild-type enzyme produced in this manner exhibits the characteristic spectral properties of recombinant WT-NiSOD and is as catalytically active. The semisynthetic scheme was also employed to construct a variant where the amidate ligand was converted to a secondary amine, H1*-NiSOD, a novel strategymore » that retains a backbone N-donor atom. The H1*-NiSOD variant was found to have only ~1% of the catalytic activity of the recombinant wild-type enzyme, and had altered spectroscopic properties. X-ray absorption spectroscopy reveals a four-coordinate planar site with N 2S 2-donor ligands, consistent with electronic absorption spectroscopic results indicating that the Ni center in H1*-NiSOD is mostly reduced in the as-isolated sample, as opposed to 50:50 Ni(II)/Ni(III) mixture that is typical for the recombinant wild-type enzyme. The EPR spectrum of as-isolated H1*-NiSOD accounts for ~11% of the Ni in the sample and is similar to WT-NiSOD, but more axial, with g z < g x,y. 14N-hyperfine is observed on g z« less
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NASA Astrophysics Data System (ADS)
Kalinovskaya, I. V.
2014-09-01
The luminescence spectral characteristics of mixed-ligand compounds of ytterbium(III) with cinnamic acid and neutral phosphorus-containing ligands were studied by luminescence spectroscopy. The intensity of luminescence of the compounds was determined. The highest intensity of luminescence was found for the ytterbium(III) compound with triphenylphosphine oxide.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Liu Guocheng; Chen Yongqiang; Wang Xiuli
Three novel Cd(II) coordination polymers, namely, [Cd(Dpq)(1,8-NDC)(H{sub 2}O){sub 2}][Cd(Dpq)(1,8-NDC)].2H{sub 2}O (1), [Cd(Dpq)(1,4-NDC)(H{sub 2}O)] (2), and [Cd(Dpq)(2,6-NDC)] (3) have been obtained from hydrothermal reactions of cadmium(II) nitrate with the mixed ligands dipyrido [3,2-d:2',3'-f]quinoxaline (Dpq) and three structurally related naphthalene-dicarboxylate ligands [1,8-naphthalene-dicarboxylic acid (1,8-H{sub 2}NDC), 1,4-naphthalene-dicarboxylic acid (1,4-H{sub 2}NDC), and 2,6-naphthalene-dicarboxylic acid (2,6-H{sub 2}NDC)]. Single-crystal X-ray diffraction analysis reveals that the three polymers exhibit novel structures due to different naphthalene-dicarboxylic acid. Compound 1 is a novel cocrystal of left- and right-handed helical chains and binuclear complexes and ultimately packed into a 3D supramolecular structure through hydrogen bonds and {pi}-{pi} stacking interactions. Compoundmore » 2 shows a 2D rectangular network (4,4) bridged by 1,4-NDC with two kinds of coordination modes and ultimately packed into a 3D supramolecular structure through inter-layer {pi}-{pi} stacking interactions. Compound 3 is a new 3D coordination polymer with distorted PtS-type network. In addition, the title compounds exhibit blue/green emission in solid state at room temperature. - Graphical abstract: Three novel Cd(II) compounds have been synthesized under hydrothermal conditions exhibiting a systematic variation of architecture by the employment of three structurally related naphthalene-dicarboxylate ligands.« less
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Ligand-Induced Dynamics of Neurotrophin Receptors Investigated by Single-Molecule Imaging Approaches
Marchetti, Laura; Luin, Stefano; Bonsignore, Fulvio; de Nadai, Teresa; Beltram, Fabio; Cattaneo, Antonino
2015-01-01
Neurotrophins are secreted proteins that regulate neuronal development and survival, as well as maintenance and plasticity of the adult nervous system. The biological activity of neurotrophins stems from their binding to two membrane receptor types, the tropomyosin receptor kinase and the p75 neurotrophin receptors (NRs). The intracellular signalling cascades thereby activated have been extensively investigated. Nevertheless, a comprehensive description of the ligand-induced nanoscale details of NRs dynamics and interactions spanning from the initial lateral movements triggered at the plasma membrane to the internalization and transport processes is still missing. Recent advances in high spatio-temporal resolution imaging techniques have yielded new insight on the dynamics of NRs upon ligand binding. Here we discuss requirements, potential and practical implementation of these novel approaches for the study of neurotrophin trafficking and signalling, in the framework of current knowledge available also for other ligand-receptor systems. We shall especially highlight the correlation between the receptor dynamics activated by different neurotrophins and the respective signalling outcome, as recently revealed by single-molecule tracking of NRs in living neuronal cells. PMID:25603178
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The Notch Ligand Jagged1 as a Target for Anti-Tumor Therapy
Li, Demin; Masiero, Massimo; Banham, Alison H.; Harris, Adrian L.
2014-01-01
The Notch pathway is increasingly attracting attention as a source of therapeutic targets for cancer. Ligand-induced Notch signaling has been implicated in various aspects of cancer biology; as a consequence, pan-Notch inhibitors and therapeutic antibodies targeting one or more of the Notch receptors have been investigated for cancer therapy. Alternatively, Notch ligands provide attractive options for therapy in cancer treatment due to their more restricted expression and better-defined functions, as well as their low rate of mutations in cancer. One of the Notch ligands, Jagged1 (JAG1), is overexpressed in many cancer types, and plays an important role in several aspects of tumor biology. In fact, JAG1-stimulated Notch activation is directly implicated in tumor growth through maintaining cancer stem cell populations, promoting cell survival, inhibiting apoptosis, and driving cell proliferation and metastasis. In addition, JAG1 can indirectly affect cancer by influencing tumor microenvironment components such as tumor vasculature and immune cell infiltration. This article gives an overview of JAG1 and its role in tumor biology, and its potential as a therapeutic target. PMID:25309874
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Monaco, Serena; Tailford, Louise E; Juge, Nathalie; Angulo, Jesus
2017-11-27
Saturation transfer difference (STD) NMR spectroscopy is extensively used to obtain epitope maps of ligands binding to protein receptors, thereby revealing structural details of the interaction, which is key to direct lead optimization efforts in drug discovery. However, it does not give information about the nature of the amino acids surrounding the ligand in the binding pocket. Herein, we report the development of the novel method differential epitope mapping by STD NMR (DEEP-STD NMR) for identifying the type of protein residues contacting the ligand. The method produces differential epitope maps through 1) differential frequency STD NMR and/or 2) differential solvent (D 2 O/H 2 O) STD NMR experiments. The two approaches provide different complementary information on the binding pocket. We demonstrate that DEEP-STD NMR can be used to readily obtain pharmacophore information on the protein. Furthermore, if the 3D structure of the protein is known, this information also helps in orienting the ligand in the binding pocket. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.
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In silico identification of novel ligands for G-quadruplex in the c- MYC promoter
NASA Astrophysics Data System (ADS)
Kang, Hyun-Jin; Park, Hyun-Ju
2015-04-01
G-quadruplex DNA formed in NHEIII1 region of oncogene promoter inhibits transcription of the genes. In this study, virtual screening combining pharmacophore-based search and structure-based docking screening was conducted to discover ligands binding to G-quadruplex in promoter region of c- MYC. Several hit ligands showed the selective PCR-arresting effects for oligonucleotide containing c- MYC G-quadruplex forming sequence. Among them, three hits selectively inhibited cell proliferation and decreased c- MYC mRNA level in Ramos cells, where NHEIII1 is included in translocated c- MYC gene for overexpression. Promoter assay using two kinds of constructs with wild-type and mutant sequences showed that interaction of these ligands with the G-quadruplex resulted in turning-off of the reporter gene. In conclusion, combined virtual screening methods were successfully used for discovery of selective c- MYC promoter G-quadruplex binders with anticancer activity.
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Semiconductor Quantum Dots with Photoresponsive Ligands.
Sansalone, Lorenzo; Tang, Sicheng; Zhang, Yang; Thapaliya, Ek Raj; Raymo, Françisco M; Garcia-Amorós, Jaume
2016-10-01
Photochromic or photocaged ligands can be anchored to the outer shell of semiconductor quantum dots in order to control the photophysical properties of these inorganic nanocrystals with optical stimulations. One of the two interconvertible states of the photoresponsive ligands can be designed to accept either an electron or energy from the excited quantum dots and quench their luminescence. Under these conditions, the reversible transformations of photochromic ligands or the irreversible cleavage of photocaged counterparts translates into the possibility to switch luminescence with external control. As an alternative to regulating the photophysics of a quantum dot via the photochemistry of its ligands, the photochemistry of the latter can be controlled by relying on the photophysics of the former. The transfer of excitation energy from a quantum dot to a photocaged ligand populates the excited state of the species adsorbed on the nanocrystal to induce a photochemical reaction. This mechanism, in conjunction with the large two-photon absorption cross section of quantum dots, can be exploited to release nitric oxide or to generate singlet oxygen under near-infrared irradiation. Thus, the combination of semiconductor quantum dots and photoresponsive ligands offers the opportunity to assemble nanostructured constructs with specific functions on the basis of electron or energy transfer processes. The photoswitchable luminescence and ability to photoinduce the release of reactive chemicals, associated with the resulting systems, can be particularly valuable in biomedical research and can, ultimately, lead to the realization of imaging probes for diagnostic applications as well as to therapeutic agents for the treatment of cancer.
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Good, Sara; Yegorov, Sergey; Martijn, Joran; Franck, Jens; Bogerd, Jan
2012-01-01
Relaxin-like peptides (RLN/INSL) play diverse roles in reproductive and neuroendocrine processes in placental mammals and are functionally associated with two distinct types of receptors (RXFP) for each respective function. The diversification of RLN/INSL and RXFP gene families in vertebrates was predominantly driven by whole genome duplications (2R and 3R). Teleosts preferentially retained duplicates of genes putatively involved in neuroendocrine regulation, harboring a total of 10-11 receptors and 6 ligand genes, while most mammals have equal numbers of ligands and receptors. To date, the ligand-receptor relationships of teleost Rln/Insl peptides and their receptors have largely remained unexplored. Here, we use selection analyses based on sequence data from 5 teleosts and qPCR expression data from zebrafish to explore possible ligand-receptor pairings in teleosts. We find support for the hypothesis that, with the exception of RLN, which has undergone strong positive selection in mammalian lineages, the ligand and receptor genes shared between mammals and teleosts appear to have similar pairings. On the other hand, the teleost-specific receptors show evidence of subfunctionalization. Overall, this study underscores the complexity of RLN/INSL and RXFP ligand-receptor interactions in teleosts and establishes theoretical background for further experimental work in nonmammals. PMID:23008798
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Quantification of Ligand Binding to G-Protein Coupled Receptors on Cell Membranes by Ellipsometry
Kriechbaumer, Verena; Nabok, Alexei; Widdowson, Robert; Smith, David P.; Abell, Ben M.
2012-01-01
G-protein-coupled receptors (GPCRs) are prime drug targets and targeted by approximately 60% of current therapeutic drugs such as β-blockers, antipsychotics and analgesics. However, no biophysical methods are available to quantify their interactions with ligand binding in a native environment. Here, we use ellipsometry to quantify specific interactions of receptors within native cell membranes. As a model system, the GPCR-ligand CXCL12α and its receptor CXCR4 are used. Human-derived Ishikawa cells were deposited onto gold coated slides via Langmuir-Schaefer film deposition and interactions between the receptor CXCR4 on these cells and its ligand CXCL12α were detected via total internal reflection ellipsometry (TIRE). This interaction could be inhibited by application of the CXCR4-binding drug AMD3100. Advantages of this approach are that it allows measurement of interactions in a lipid environment without the need for labelling, protein purification or reconstitution of membrane proteins. This technique is potentially applicable to a wide variety of cell types and their membrane receptors, providing a novel method to determine ligand or drug interactions targeting GPCRs and other membrane proteins. PMID:23049983
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NASA Astrophysics Data System (ADS)
Yang, Guang; Nanda, Jagjit; Wang, Boya; Chen, Gang; Hallinan, Daniel T., Jr.
An effective self-assembly technique was developed to prepare centimeter-scale monolayer gold nanoparticle (Au NP) films of long-range order with hydrophobic ligands. Aqueous Au NPs were entrapped in the organic/aqueous interface where the Au NP surface was in situ modified with different types of amine ligands, including amine-terminated polystyrene. The Au NPs then spontaneously relocated to the air/water interface to form an NP monolayer. The spontaneous formation of an Au NP film at the organic/water interface was due to the minimization of the system Helmholtz free energy. Self-assembled Au NP films has a hexagonal close packed structure. The interparticle spacing was dictated by the amine ligand length. Thus-assembled Au NP monolayers exhibit tunable surface plasma resonance and excellent spacial homogeneity of surface-enhanced Raman-scattering. The ``air/water/oil'' self-assembly method developed in this study not only benefits the fundamental understanding of NP ligand conformations, but is also promising to scale up the manufacture of plasmonic nanoparticle devices with precisely designed optical properties. This study was financially supported by start-up funding supplied by the Florida State University and the FAMU-FSU College of Engineering.
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Ancillary ligand effects upon dithiolene redox noninnocence in tungsten bis(dithiolene) complexes.
Yan, Yong; Keating, Christopher; Chandrasekaran, Perumalreddy; Jayarathne, Upul; Mague, Joel T; DeBeer, Serena; Lancaster, Kyle M; Sproules, Stephen; Rubtsov, Igor V; Donahue, James P
2013-06-03
An expanded set of compounds of the type [W(S2C2Me2)2L1L2](n) (n = 0: L1 = L2 = CO, 1; L1 = L2 = CN(t)Bu, 2; L1 = CO, L2 = carbene, 3; L1 = CO, L2 = phosphine, 4; L1 = L2 = phosphine, 5. n = 2-: L1 = L2 = CN(-), [6](2-)) has been synthesized and characterized. Despite isoelectronic formulations, the compound set reveals gradations in the dithiolene ligand redox level as revealed by intraligand bond lengths, υ(CCchelate), and rising edge energies in the sulfur K-edge X-ray absorption spectra (XAS). Differences among the terminal series members, 1 and [6](2-), are comparable to differences seen in homoleptic dithiolene complexes related by full electron transfer to/from a dithiolene-based MO. The key feature governing these differences is the favorable energy of the CO π* orbitals, which are suitably positioned to overlap with tungsten d orbitals and exert an oxidizing effect on both metal and dithiolene ligand via π-backbonding. The CN(-) π* orbitals are too high in energy to mix effectively with tungsten and thus leave the filled dithiolene π* orbitals unperturbed. This work shows how, and the degree to which, the redox level of a noninnocent ligand can be modulated by the choice of ancillary ligands(s).
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Kumar, Ashish; Singh, Roop Shikha; Kumar, Amit; Ali, Afsar; Biswas, Arnab; Pandey, Daya Shankar
2016-09-19
A pioneering approach towards controlling the efficiency of saponification assisted gelation in ethyl ester based Zn II -complexes have been described. Using four new ester containing bis-salen Zn II complexes (C1-C4) involving different para-azo phenyl substituted ligands it has been clearly shown that gelation efficiency is greatly influenced by the electronic effects of the substituents (-H (C1), -CH 3 (C2), -NO 2 (C3), and -OCH 3 (C4)). Morphological, photophysical, and rheological investigations corroborated the experimental observations well and established that gelation efficiency was enhanced with electron-withdrawing characteristics of substituents (C4
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Shedding Light on Anesthetic Mechanisms: Application of Photoaffinity Ligands
Woll, Kellie A.; Dailey, William P.; Brannigan, Grace; Eckenhoff, Roderic G.
2016-01-01
Anesthetic photoaffinity ligands have had an increasing presence within anesthesiology research. These ligands mimic parent general anesthetics, and allow investigators to study anesthetic interactions with receptors and enzymes; identify novel targets; and determine distribution within biological systems. To date nearly all general anesthetics used in medicine have a corresponding photoaffinity ligand represented in the literature. In this review we examine all aspects of the current methodologies, including ligand design, characterization and deployment. Finally we offer points of consideration and highlight the future outlook as more photoaffinity ligands emerge within the field. PMID:27464974
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Shedding Light on Anesthetic Mechanisms: Application of Photoaffinity Ligands.
Woll, Kellie A; Dailey, William P; Brannigan, Grace; Eckenhoff, Roderic G
2016-11-01
Anesthetic photoaffinity ligands have had an increasing presence within anesthesiology research. These ligands mimic parent general anesthetics and allow investigators to study anesthetic interactions with receptors and enzymes; identify novel targets; and determine distribution within biological systems. To date, nearly all general anesthetics used in medicine have a corresponding photoaffinity ligand represented in the literature. In this review, we examine all aspects of the current methodologies, including ligand design, characterization, and deployment. Finally we offer points of consideration and highlight the future outlook as more photoaffinity ligands emerge within the field.
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Nimczick, Martin; Pemp, Daniela; Darras, Fouad H; Chen, Xinyu; Heilmann, Jörg; Decker, Michael
2014-08-01
The design of bivalent ligands targeting G protein-coupled receptors (GPCRs) often leads to the development of new, highly selective and potent compounds. To date, no bivalent ligands for the human cannabinoid receptor type 2 (hCB₂R) of the endocannabinoid system (ECS) are described. Therefore, two sets of homobivalent ligands containing as parent structure the hCB2R selective agonist 13a and coupled at different attachment positions were synthesized. Changes of the parent structure at these positions have a crucial effect on the potency and efficacy of the ligands. However, we discovered that bivalency has an influence on the effect at both cannabinoid receptors. Moreover, we found out that the spacer length and the attachment position altered the efficacy of the bivalent ligands at the receptors by turning agonists into antagonists and inverse agonists. Copyright © 2014 Elsevier Ltd. All rights reserved.
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Sensing multiple ligands with single receptor
NASA Astrophysics Data System (ADS)
Singh, Vijay; Nemenman, Ilya
2015-03-01
Cells use surface receptors to measure concentrations of external ligand molecules. Limits on the accuracy of such sensing are well-known for the scenario where concentration of one molecular species is being determined by one receptor [Endres]. However, in more realistic scenarios, a cognate (high-affinity) ligand competes with many non-cognate (low-affinity) ligands for binding to the receptor. We analyze effects of this competition on the accuracy of sensing. We show that maximum-likelihood statistical inference allows determination of concentrations of multiple ligands, cognate and non-cognate, by the same receptor concurrently. While it is unclear if traditional biochemical circuitry downstream of the receptor can implement such inference exactly, we show that an approximate inference can be performed by coupling the receptor to a kinetic proofreading cascade. We characterize the accuracy of such kinetic proofreading sensing in comparison to the exact maximum-likelihood approach. We acknowledge the support from the James S. McDonnell Foundation and the Human Frontier Science Program.
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Lin, Ying-Ting
2013-04-30
A tandem technique of hard equipment is often used for the chemical analysis of a single cell to first isolate and then detect the wanted identities. The first part is the separation of wanted chemicals from the bulk of a cell; the second part is the actual detection of the important identities. To identify the key structural modifications around ligand binding, the present study aims to develop a counterpart of tandem technique for cheminformatics. A statistical regression and its outliers act as a computational technique for separation. A PPARγ (peroxisome proliferator-activated receptor gamma) agonist cellular system was subjected to such an investigation. Results show that this tandem regression-outlier analysis, or the prioritization of the context equations tagged with features of the outliers, is an effective regression technique of cheminformatics to detect key structural modifications, as well as their tendency of impact to ligand binding. The key structural modifications around ligand binding are effectively extracted or characterized out of cellular reactions. This is because molecular binding is the paramount factor in such ligand cellular system and key structural modifications around ligand binding are expected to create outliers. Therefore, such outliers can be captured by this tandem regression-outlier analysis.
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Ligand-controlled Fe mobilization catalyzed by adsorbed Fe(II) on Fe(hydr)oxides
NASA Astrophysics Data System (ADS)
Kang, Kyounglim; Biswakarma, Jagannath; Borowski, Susan C.; Hug, Stephan J.; Hering, Janet G.; Schenkeveld, Walter D. C.; Kraemer, Stephan M.
2017-04-01
Dissolution of Fe(hydr)oxides is a key process in biological iron acquisition. Due to the low solubility of iron oxides in environments with a circumneutral pH, organisms may exude organic compounds catalyzing iron mobilization by reductive and ligand controlled dissolution mechanisms. Recently, we have shown synergistic effects between reductive dissolution and ligand-controlled dissolution that may operate in biological iron acquisition. The synergistic effects were observed in Fe mobilization from single goethite suspensions as well as in suspensions containing calcareous soil[1],[2]. However, how the redox reaction accelerates Fe(hydr)oxide dissolution by ligands is not studied intensively. In our study, we hypothesized that electron transfer to structural Fe(III) labilizes the Fe(hydr)oxide structure, and that this can accelerate ligand controlled dissolution. Systematical batch dissolution experiments were carried out under anoxic conditions at environmentally relevant pH values in which various Fe(hydr)oxides (goethite, hematite, lepidocrocite) interacted with two different types of ligand (desferrioxamine B (DFOB) and N,N'-Di(2-hydroxybenzyl)ethylenediamine-N,N'-diacetic acid monohydrochloride (HBED)). Electron transfer to the structure was induced by adsorbing Fe(II) to the mineral surface at various Fe(II) concentrations. Our results show a distinct catalytic effect of adsorbed Fe(II) on ligand controlled dissolution, even at submicromolar Fe(II) concentrations. We observed the effect for a range of iron oxides, but it was strongest in lepidocrocite, most likely due to anisotropy in conductivity leading to higher near-surface concentration of reduced iron. Our results demonstrate that the catalytic effect of reductive processes on ligand controlled dissolution require a very low degree of reduction making this an efficient process for biological iron acquisition and a potentially important effect in natural iron cycling. References 1. Wang, Z. M
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Virtual screening using the ligand ZINC database for novel lipoxygenase-3 inhibitors.
Monika; Kour, Janmeet; Singh, Kulwinder
2013-01-01
The leukotrienes constitute a group of arachidonic acid-derived compounds with biologic activities suggesting important roles in inflammation and immediate hypersensitivity. Epidermis-type lipoxygenase-3 (ALOXE3), a distinct subclass within the multigene family of mammalian lipoxygenases, is a novel isoenzyme involved in the metabolism of leukotrienes and plays a very important role in skin barrier functions. Lipoxygenase selective inhibitors such as azelastine and zileuton are currently used to reduce inflammatory response. Nausea, pharyngolaryngeal pain, headache, nasal burning and somnolence are the most frequently reported adverse effects of these drugs. Therefore, there is still a need to develop more potent lipoxygenase inhibitors. In this paper, we report the screening of various compounds from the ZINC database (contains over 21 million compounds) using the Molegro Virtual Docker software against the ALOXE3 protein. Screening was performed using molecular constraints tool to filter compounds with physico-chemical properties similar to the 1N8Q bound ligand protocatechuic acid. The analysis resulted in 4319 Lipinski compliant hits which are docked and scored to identify structurally novel ligands that make similar interactions to those of known ligands or may have different interactions with other parts of the binding site. Our screening approach identified four molecules ZINC84299674; ZINC76643455; ZINC84299122 & ZINC75626957 with MolDock score of -128.901, -120.22, -116.873 & - 102.116 kcal/mol, respectively. Their energy scores were better than the 1N8Q bound co-crystallized ligand protocatechuic acid (with MolDock score of -77.225 kcal/mol). All the ligands were docked within the binding pocket forming interactions with amino acid residues.
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ɣδ T cell receptor ligands and modes of antigen recognition
Champagne, Eric
2011-01-01
T lymphocytes expressing the γδ-type of T cell receptors for antigens contribute to all aspects of immune responses, including defenses against viruses, bacteria, parasites and tumors, allergy and autoimmunity. Multiple subsets have been individualized in humans as well as in mice and they appear to recognize in a TCR-dependent manner antigens as diverse as small non-peptidic molecules, soluble or membrane-anchored polypeptides and molecules related to MHC antigens on cell surfaces, implying diverse modes of antigen recognition. We review here the γδ TCR ligands which have been identified along the years and their characteristics, with emphasis on a few systems which have been extensively studied such as human γδ T cells responding to phosphoantigens or murine γδ T cells activated by allogeneic MHC antigens. We discuss a speculative model of antigen recognition involving simultaneous TCR recognition of MHC-like and non-MHC ligands which could fit with most available data and shares many similarities with the classical model of MHC-restricted antigen recognition for peptides or lipids by T cells subsets with αβ-type TCRs. PMID:21298486
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γδ T cell receptor ligands and modes of antigen recognition.
Champagne, Eric
2011-04-01
T lymphocytes expressing the γδ-type of T cell receptors (TCRs) for antigens contribute to all aspects of immune responses, including defenses against viruses, bacteria, parasites and tumors, allergy and autoimmunity. Multiple subsets have been individualized in humans as well as in mice and they appear to recognize in a TCR-dependent manner antigens as diverse as small non-peptidic molecules, soluble or membrane-anchored polypeptides and molecules related to MHC antigens on cell surfaces, implying diverse modes of antigen recognition. We review here the γδ TCR ligands which have been identified along the years and their characteristics, with emphasis on a few systems which have been extensively studied such as human γδ T cells responding to phosphoantigens or murine γδ T cells activated by allogeneic MHC antigens. We discuss a speculative model of antigen recognition involving simultaneous TCR recognition of MHC-like and non-MHC ligands which could fit with most available data and shares many similarities with the classical model of MHC-restricted antigen recognition for peptides or lipids by T cells subsets with αβ-type TCRs.
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Howlett, A. C.; Abood, M. E.; Alexander, S. P. H.; Di Marzo, V.; Elphick, M. R.; Greasley, P. J.; Hansen, H. S.; Kunos, G.; Mackie, K.; Mechoulam, R.; Ross, R. A.
2010-01-01
There are at least two types of cannabinoid receptors (CB1 and CB2). Ligands activating these G protein-coupled receptors (GPCRs) include the phytocannabinoid Δ9-tetrahydrocannabinol, numerous synthetic compounds, and endogenous compounds known as endocannabinoids. Cannabinoid receptor antagonists have also been developed. Some of these ligands activate or block one type of cannabinoid receptor more potently than the other type. This review summarizes current data indicating the extent to which cannabinoid receptor ligands undergo orthosteric or allosteric interactions with non-CB1, non-CB2 established GPCRs, deorphanized receptors such as GPR55, ligand-gated ion channels, transient receptor potential (TRP) channels, and other ion channels or peroxisome proliferator-activated nuclear receptors. From these data, it is clear that some ligands that interact similarly with CB1 and/or CB2 receptors are likely to display significantly different pharmacological profiles. The review also lists some criteria that any novel “CB3” cannabinoid receptor or channel should fulfil and concludes that these criteria are not currently met by any non-CB1, non-CB2 pharmacological receptor or channel. However, it does identify certain pharmacological targets that should be investigated further as potential CB3 receptors or channels. These include TRP vanilloid 1, which possibly functions as an ionotropic cannabinoid receptor under physiological and/or pathological conditions, and some deorphanized GPCRs. Also discussed are 1) the ability of CB1 receptors to form heteromeric complexes with certain other GPCRs, 2) phylogenetic relationships that exist between CB1/CB2 receptors and other GPCRs, 3) evidence for the existence of several as-yet-uncharacterized non-CB1, non-CB2 cannabinoid receptors; and 4) current cannabinoid receptor nomenclature. PMID:21079038
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Visualizing ligand molecules in Twilight electron density.
Weichenberger, Christian X; Pozharski, Edwin; Rupp, Bernhard
2013-02-01
Three-dimensional models of protein structures determined by X-ray crystallography are based on the interpretation of experimentally derived electron-density maps. The real-space correlation coefficient (RSCC) provides an easily comprehensible, objective measure of the residue-based fit of atom coordinates to electron density. Among protein structure models, protein-ligand complexes are of special interest, given their contribution to understanding the molecular underpinnings of biological activity and to drug design. For consumers of such models, it is not trivial to determine the degree to which ligand-structure modelling is biased by subjective electron-density interpretation. A standalone script, Twilight, is presented for the analysis, visualization and annotation of a pre-filtered set of 2815 protein-ligand complexes deposited with the PDB as of 15 January 2012 with ligand RSCC values that are below a threshold of 0.6. It also provides simplified access to the visualization of any protein-ligand complex available from the PDB and annotated by the Uppsala Electron Density Server. The script runs on various platforms and is available for download at http://www.ruppweb.org/twilight/.
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Engineering death receptor ligands for cancer therapy.
Wajant, Harald; Gerspach, Jeannette; Pfizenmaier, Klaus
2013-05-28
CD95, TNFR1, TRAILR1 and TRAILR2 belong to a subgroup of TNF receptors which is characterized by a conserved cell death-inducing protein domain that connects these receptors to the apoptotic machinery of the cell. Activation of death receptors in malignant cells attracts increasing attention as a principle to fight cancer. Besides agonistic antibodies the major way to stimulate death receptors is the use of their naturally occurring "death ligands" CD95L, TNF and TRAIL. However, dependent from the concept followed to develop a death ligand-based therapy various limiting aspects have to be taken into consideration on the way to a "bedside" usable drug. Problems arise in particular from the cell associated transmembrane nature of the death ligands, the poor serum half life of the soluble fragments derived from the transmembrane ligands, the ubiquitous expression of the death receptors and the existence of additional non-death receptors of the death ligands. Here, we summarize strategies how these limitations can be overcome by genetic engineering. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.
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Receptor-ligand binding sites and virtual screening.
Hattotuwagama, Channa K; Davies, Matthew N; Flower, Darren R
2006-01-01
Within the pharmaceutical industry, the ultimate source of continuing profitability is the unremitting process of drug discovery. To be profitable, drugs must be marketable: legally novel, safe and relatively free of side effects, efficacious, and ideally inexpensive to produce. While drug discovery was once typified by a haphazard and empirical process, it is now increasingly driven by both knowledge of the receptor-mediated basis of disease and how drug molecules interact with receptors and the wider physiome. Medicinal chemistry postulates that to understand a congeneric ligand series, or set thereof, is to understand the nature and requirements of a ligand binding site. Likewise, structural molecular biology posits that to understand a binding site is to understand the nature of ligands bound therein. Reality sits somewhere between these extremes, yet subsumes them both. Complementary to rules of ligand design, arising through decades of medicinal chemistry, structural biology and computational chemistry are able to elucidate the nature of binding site-ligand interactions, facilitating, at both pragmatic and conceptual levels, the drug discovery process.
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Thermometric titration studies of mixed ligand complexes of thorium.
Kugler, G C; Carey, G H
1970-10-01
Mixed-ligand chelates consisting of two different multidentate ligands linked to a central thorium(IV) ion have been prepared in aqueous solution and their heats of formation studied thermo metrically. Pyrocatechol, tiron, chromotropic acid, potassium hydrogen phthalate, 8-hydroxyquinoline-S-sulphonic acid, iminodiacetic acid, 5-sulphosalicylic acid and salicylic acid were used as the secondary ligands, while ethylenediaminetetra-acetate and 1, 2-diaminocyclohexane-N,N,N',N'-tetra-acetate were used as primary ligands. DeltaH values for the overall reactions are given, and where possible, the DeltaH and DeltaS values for the specific secondary ligand addition were calculated. The overall stability of the mixed-ligand chelates and the enhanced stability of EDTA mixed chelates relative to the analogous DCTA chelates were found to be due to entropy rather than enthalpy effects.
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Shen, Lu; Decker, Caitlin G; Maynard, Heather D; Levine, Alex J
2016-09-01
We present here the calculation of the mean time to capture of a tethered ligand to the receptor. This calculation is then used to determine the shift in the partitioning between (1) free, (2) singly bound, and (3) doubly bound ligands in chemical equilibrium as a function of the length of the tether. These calculations are used in the research article Fibroblast Growth Factor 2 Dimer with Superagonist in vitro Activity Improves Granulation Tissue Formation During Wound Healing (Decker et al., in press [1]) to explain quantitatively how changes in polymeric linker length in the ligand dimers modifies the efficacy of these molecules relative to that of free ligands.
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Predicting receptor-ligand pairs through kernel learning
2011-01-01
Background Regulation of cellular events is, often, initiated via extracellular signaling. Extracellular signaling occurs when a circulating ligand interacts with one or more membrane-bound receptors. Identification of receptor-ligand pairs is thus an important and specific form of PPI prediction. Results Given a set of disparate data sources (expression data, domain content, and phylogenetic profile) we seek to predict new receptor-ligand pairs. We create a combined kernel classifier and assess its performance with respect to the Database of Ligand-Receptor Partners (DLRP) 'golden standard' as well as the method proposed by Gertz et al. Among our findings, we discover that our predictions for the tgfβ family accurately reconstruct over 76% of the supported edges (0.76 recall and 0.67 precision) of the receptor-ligand bipartite graph defined by the DLRP "golden standard". In addition, for the tgfβ family, the combined kernel classifier is able to relatively improve upon the Gertz et al. work by a factor of approximately 1.5 when considering that our method has an F-measure of 0.71 while that of Gertz et al. has a value of 0.48. Conclusions The prediction of receptor-ligand pairings is a difficult and complex task. We have demonstrated that using kernel learning on multiple data sources provides a stronger alternative to the existing method in solving this task. PMID:21834994
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Lagarde, Nathalie; Zagury, Jean-François; Montes, Matthieu
2014-10-27
The evaluation of virtual ligand screening methods is of major importance to ensure their reliability. Taking into account the agonist/antagonist pharmacological profile should improve the quality of the benchmarking data sets since ligand binding can induce conformational changes in the nuclear receptor structure and such changes may vary according to the agonist/antagonist ligand profile. We indeed found that splitting the agonist and antagonist ligands into two separate data sets for a given nuclear receptor target significantly enhances the quality of the evaluation. The pharmacological profile of the ligand bound in the binding site of the target structure was also found to be an additional critical parameter. We also illustrate that active compound data sets for a given pharmacological activity can be used as a set of experimentally validated decoy ligands for another pharmacological activity to ensure a reliable and challenging evaluation of virtual screening methods.
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Ligand-independent activation of the oestrogen receptor by mutation of a conserved tyrosine.
White, R; Sjöberg, M; Kalkhoven, E; Parker, M G
1997-01-01
The oestrogen receptor is a member of the nuclear receptor family of transcription factors which, on binding the steroid hormone 17beta-oestradiol, interacts with co-activator proteins and stimulates gene expression. Replacement of a single tyrosine in the hormone-binding domain generated activated forms of the receptor which stimulated transcription in the absence of hormone. This increased activation is related to a decrease in hydrophobicity and a reduction in size of the side chain of the amino acid with which the tyrosine is replaced. Ligand-independent, in common with ligand-dependent transcriptional activation, requires an amphipathic alpha-helix at the C-terminus of the ligand-binding domain which is essential for the interaction of the receptor with a number of potential co-activator proteins. In contrast to the wild-type protein, constitutively active receptors were able to bind both the receptor-interacting protein RIP-140 and the steroid receptor co-activator SRC-1 in a ligand-independent manner, although in the case of SRC-1 this was only evident when the receptors were prebound to DNA. We propose, therefore, that this tyrosine is required to maintain the receptor in a transcriptionally inactive state in the absence of hormone. Modification of this residue may generate a conformational change in the ligand-binding domain of the receptor to form an interacting surface which allows the recruitment of co-activators independent of hormone binding. This suggests that this tyrosine may be a target for a different signalling pathway which forms an alternative mechanism of activating oestrogen receptor-mediated transcription. PMID:9135157
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Zarkesh, Ryan A.; Ichimura, Andrew S.; Monson, Todd C.; ...
2016-02-01
We used the redox-active bis(imino)acenapthene (BIAN) ligand to synthesize homoleptic aluminum, chromium, and gallium complexes of the general formula (BIAN) 3M. The resulting compounds were characterized using X-ray crystallography, NMR, EPR, magnetic susceptibility and cyclic voltammetry measurements and modeled using both DFT and ab initio wavefunction calculations to compare the orbital contributions of main group elements and transition metals in ligand-based redox events. Ultimately, complexes of this type have the potential to improve the energy density and electrolyte stability of grid-scale energy storage technologies, such as redox flow batteries, through thermodynamically-clustered redox events.
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Design of a Hole Trapping Ligand
La Croix, Andrew D.; O’Hara, Andrew; Reid, Kemar R.; ...
2017-01-18
A new ligand that covalently attaches to the surface of colloidal CdSe/ CdS nanorods and can simultaneously chelate a molecular metal center is described. The dithiocarbamate$-$bipyridine ligand system facilitates hole transfer through energetic overlap at the inorganic$-$organic interface and conjugation through the organic ligand to a chelated metal center. Density functional theory calculations show that the coordination of the free ligand to a CdS surface causes the formation of two hybridized molecular states that lie in the band gap of CdS. The further chelation of Fe(II) to the bipyridine moiety causes the presence of seven midgap states. Hole transfer frommore » the CdS valence band to the midgap states is dipole allowed and occurs at a faster rate than what is experimentally known for the CdSe/CdS band-edge radiative recombination. In the case of the ligand bound with iron, a two-step process emerges that places the hole on the iron, again at rates much faster than band gap recombination. The system was experimentally assembled and characterized via UV$-$vis absorbance spectroscopy, fluorescence spectroscopy, time-resolved photoluminescence spectroscopy, and energy dispersive X-ray spectroscopy. Lastly, theoretically predicted red shifts in absorbance were observed experimentally, as well as the expected quench in photoluminescence and lifetimes in time-resolved photoluminescence« less
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Design of a Hole Trapping Ligand
DOE Office of Scientific and Technical Information (OSTI.GOV)
La Croix, Andrew D.; O’Hara, Andrew; Reid, Kemar R.
A new ligand that covalently attaches to the surface of colloidal CdSe/ CdS nanorods and can simultaneously chelate a molecular metal center is described. The dithiocarbamate$-$bipyridine ligand system facilitates hole transfer through energetic overlap at the inorganic$-$organic interface and conjugation through the organic ligand to a chelated metal center. Density functional theory calculations show that the coordination of the free ligand to a CdS surface causes the formation of two hybridized molecular states that lie in the band gap of CdS. The further chelation of Fe(II) to the bipyridine moiety causes the presence of seven midgap states. Hole transfer frommore » the CdS valence band to the midgap states is dipole allowed and occurs at a faster rate than what is experimentally known for the CdSe/CdS band-edge radiative recombination. In the case of the ligand bound with iron, a two-step process emerges that places the hole on the iron, again at rates much faster than band gap recombination. The system was experimentally assembled and characterized via UV$-$vis absorbance spectroscopy, fluorescence spectroscopy, time-resolved photoluminescence spectroscopy, and energy dispersive X-ray spectroscopy. Lastly, theoretically predicted red shifts in absorbance were observed experimentally, as well as the expected quench in photoluminescence and lifetimes in time-resolved photoluminescence« less
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Expression of nociceptive ligands in canine osteosarcoma.
Shor, S; Fadl-Alla, B A; Pondenis, H C; Zhang, X; Wycislo, K L; Lezmi, S; Fan, T M
2015-01-01
Canine osteosarcoma (OS) is associated with localized pain as a result of tissue injury from tumor infiltration and peritumoral inflammation. Malignant bone pain is caused by stimulation of peripheral pain receptors, termed nociceptors, which reside in the localized tumor microenvironment, including the periosteal and intramedullary bone cavities. Several nociceptive ligands have been determined to participate directly or indirectly in generating bone pain associated with diverse skeletal abnormalities. Canine OS cells actively produce nociceptive ligands with the capacity to directly or indirectly activate peripheral pain receptors residing in the bone tumor microenvironment. Ten dogs with appendicular OS. Expression of nerve growth factor, endothelin-1, and microsomal prostaglandin E synthase-1 was characterized in OS cell lines and naturally occurring OS samples. In 10 dogs with OS, circulating concentrations of nociceptive ligands were quantified and correlated with subjective pain scores and tumor volume in patients treated with standardized palliative therapies. Canine OS cells express and secrete nerve growth factor, endothelin-1, and prostaglandin E2. Naturally occurring OS samples uniformly express nociceptive ligands. In a subset of OS-bearing dogs, circulating nociceptive ligand concentrations were detectable but failed to correlate with pain status. Localized foci of nerve terminal proliferation were identified in a minority of primary bone tumor samples. Canine OS cells express nociceptive ligands, potentially permitting active participation of OS cells in the generation of malignant bone pain. Specific inhibitors of nociceptive ligand signaling pathways might improve pain control in dogs with OS. Copyright © 2015 The Authors. Journal of Veterinary Internal Medicine published by Wiley Periodicals, Inc. on behalf of American College of Veterinary Internal Medicine.
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Implicit ligand theory for relative binding free energies
NASA Astrophysics Data System (ADS)
Nguyen, Trung Hai; Minh, David D. L.
2018-03-01
Implicit ligand theory enables noncovalent binding free energies to be calculated based on an exponential average of the binding potential of mean force (BPMF)—the binding free energy between a flexible ligand and rigid receptor—over a precomputed ensemble of receptor configurations. In the original formalism, receptor configurations were drawn from or reweighted to the apo ensemble. Here we show that BPMFs averaged over a holo ensemble yield binding free energies relative to the reference ligand that specifies the ensemble. When using receptor snapshots from an alchemical simulation with a single ligand, the new statistical estimator outperforms the original.
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Hu, Guodong; Xu, Shicai; Wang, Jihua
2015-12-01
Inhibition of p53-MDM2 interaction by small molecules is considered to be a promising approach to re-activate wild-type p53 for tumor suppression. Several inhibitors of the MDM2-p53 interaction were designed and studied by the experimental methods and the molecular dynamics simulation. However, the unbinding mechanism was still unclear. The steered molecular dynamics simulations combined with Brownian dynamics fluctuation-dissipation theorem were employed to obtain the free-energy landscape of unbinding between MDM2 and their four ligands. It was shown that compounds 4 and 8 dissociate faster than compounds 5 and 7. The absolute binding free energies for these four ligands are in close agreement with experimental results. The open movement of helix II and helix IV in the MDM2 protein-binding pocket upon unbinding is also consistent with experimental MDM2-unbound conformation. We further found that different binding mechanisms among different ligands are associated with H-bond with Lys51 and Glu25. These mechanistic results may be useful for improving ligand design. © 2015 John Wiley & Sons A/S.
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NASA Astrophysics Data System (ADS)
Kumar Naik, K. H.; Ashok, B.; Naik, Nagaraja; Mulla, Jameel Ahmed S.; Prakasha, Avinash
2015-04-01
Transition metal complexes containing tri-dentate NSN donor ligands i.e., 5-((1(aminomethyl)cyclohexyl)methyl)-1,3,4-thiadiazol-2-amine (AMTA) (2) and 5-(2-aminophenyl)-1,3,4-thiadiazol-2-amine (ATA) (4i-ii) have been synthesized. The newly synthesized ligands and their respective complexes were characterized by elemental analysis, molar conductance measurement and various spectral studies [infrared (IR), electronic, and NMR (for ligands only)]. Metal complexes are like [M(AMTA)2], [M(ATA)2] type, where M = Mn(II), Co(II) and Cu(II). The proposed geometries of the complexes are octahedral in nature. The synthesized ligands and their complexes were exhibits effective anti-inflammatory, analgesic and DNA binding activities. All the tested compounds exhibited significant analgesic activity, whereas the compound 4i, 4(ia) and 4(iib) is equipotent with Diclofenac sodium.
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Arcon, Juan Pablo; Defelipe, Lucas A; Modenutti, Carlos P; López, Elias D; Alvarez-Garcia, Daniel; Barril, Xavier; Turjanski, Adrián G; Martí, Marcelo A
2017-04-24
One of the most important biological processes at the molecular level is the formation of protein-ligand complexes. Therefore, determining their structure and underlying key interactions is of paramount relevance and has direct applications in drug development. Because of its low cost relative to its experimental sibling, molecular dynamics (MD) simulations in the presence of different solvent probes mimicking specific types of interactions have been increasingly used to analyze protein binding sites and reveal protein-ligand interaction hot spots. However, a systematic comparison of different probes and their real predictive power from a quantitative and thermodynamic point of view is still missing. In the present work, we have performed MD simulations of 18 different proteins in pure water as well as water mixtures of ethanol, acetamide, acetonitrile and methylammonium acetate, leading to a total of 5.4 μs simulation time. For each system, we determined the corresponding solvent sites, defined as space regions adjacent to the protein surface where the probability of finding a probe atom is higher than that in the bulk solvent. Finally, we compared the identified solvent sites with 121 different protein-ligand complexes and used them to perform molecular docking and ligand binding free energy estimates. Our results show that combining solely water and ethanol sites allows sampling over 70% of all possible protein-ligand interactions, especially those that coincide with ligand-based pharmacophoric points. Most important, we also show how the solvent sites can be used to significantly improve ligand docking in terms of both accuracy and precision, and that accurate predictions of ligand binding free energies, along with relative ranking of ligand affinity, can be performed.
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Lazennec, Gwendal; Canaple, Laurence; Saugy, Damien; Wahli, Walter
2000-01-01
The nuclear peroxisome proliferator-activated receptors (PPARs) α, β and γ activate the transcription of multiple genes involved in lipid metabolism. Several natural and synthetic ligands have been identified for each PPAR isotype but little is known about the phosphorylation state of these receptors. We show here that activators of protein kinase A (PKA) can enhance mouse PPAR activity in the absence and the presence of exogenous ligands in transient transfection experiments. The activation function 1 (AF-1) of PPARs was dispensable for transcriptional enhancement, whereas the activation function 2 (AF-2) was required for this effect. We also show that several domains of PPAR can be phosphorylated by PKA in vitro. Moreover, gel experiments suggest that PKA stabilizes binding of the liganded PPAR to DNA. PKA inhibitors decreased not only the kinase dependent induction of PPARs but also their ligand-dependent induction, suggesting that the ligands may also mobilize the PKA pathway to lead to maximal transcriptional induction by PPARs. Moreover, comparing PPARα KO with PPARα wild-type mice, we show that the expression of the ACO gene can be regulated by PKA-activated PPARα in liver. These data demonstrate that the PKA pathway is an important modulator of PPAR activity and we propose a model associating this pathway in the control of fatty acid β-oxidation under conditions of fasting, stress and exercise. PMID:11117527
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Superior serum half life of albumin tagged TNF ligands
DOE Office of Scientific and Technical Information (OSTI.GOV)
Mueller, Nicole; Schneider, Britta; Pfizenmaier, Klaus
2010-06-11
Due to their immune stimulating and apoptosis inducing properties, ligands of the TNF family attract increasing interest as therapeutic proteins. A general limitation of in vivo applications of recombinant soluble TNF ligands is their notoriously rapid clearance from circulation. To improve the serum half life of the TNF family members TNF, TWEAK and TRAIL, we genetically fused soluble variants of these molecules to human serum albumin (HSA). The serum albumin-TNF ligand fusion proteins were found to be of similar bioactivity as the corresponding HSA-less counterparts. Upon intravenous injection (i.v.), serum half life of HSA-TNF ligand fusion proteins, as determined bymore » ELISA, was around 15 h as compared to approximately 1 h for all of the recombinant control TNF ligands without HSA domain. Moreover, serum samples collected 6 or 24 h after i.v. injection still contained high TNF ligand bioactivity, demonstrating that there is only limited degradation/inactivation of circulating HSA-TNF ligand fusion proteins in vivo. In a xenotransplantation model, significantly less of the HSA-TRAIL fusion protein compared to the respective control TRAIL protein was required to achieve inhibition of tumor growth indicating that the increased half life of HSA-TNF ligand fusion proteins translates into better therapeutic action in vivo. In conclusion, our data suggest that genetic fusion to serum albumin is a powerful and generally applicable mean to improve bioavailability and in vivo activity of TNF ligands.« less
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Stabilization of peroxisome proliferator-activated receptor alpha by the ligand.
Hirotani, M; Tsukamoto, T; Bourdeaux, J; Sadano, H; Osumi, T
2001-10-19
Peroxisome proliferator-activated receptor (PPAR) constitutes a subfamily among a large group of ligand-activated transcription factors, the nuclear receptor superfamily. We studied the effects of ligand on the intracellular behaviors of PPARalpha. Although nuclear localization of PPARalpha was not affected by a selective ligand, Wy14643, we observed that exogenously expressed PPARalpha was rapidly degraded in HeLa cells, and the ligand significantly stabilized the protein. The stability of PPARalpha was also improved by coexpression of the heterodimer partner retinoid X receptor (RXR) alpha, and further stabilization was not observed with the ligand. These results indicate that PPARalpha is stabilized through heterodimerization with RXR, and the excess protein unpaired with RXR is rapidly turned over, if not bound by an appropriate ligand. These observations on PPARalpha are in sharp contrast to the ligand-stimulated degradation reported on PPARgamma. The ligand-dependent stabilization would have physiological significance when the synthesis of PPARalpha is elevated exceeding the available level of RXR. Copyright 2001 Academic Press.
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[Supercomputer investigation of the protein-ligand system low-energy minima].
Oferkin, I V; Sulimov, A V; Katkova, E V; Kutov, D K; Grigoriev, F V; Kondakova, O A; Sulimov, V B
2015-01-01
The accuracy of the protein-ligand binding energy calculations and ligand positioning is strongly influenced by the choice of the docking target function. This work demonstrates the evaluation of the five different target functions used in docking: functions based on MMFF94 force field and functions based on PM7 quantum-chemical method accounting or without accounting the implicit solvent model (PCM, COSMO or SGB). For these purposes the ligand positions corresponding to the minima of the target function and the experimentally known ligand positions in the protein active site (crystal ligand positions) were compared. Each function was examined on the same test-set of 16 protein-ligand complexes. The new parallelized docking program FLM based on Monte Carlo search algorithm was developed to perform the comprehensive low-energy minima search and to calculate the protein-ligand binding energy. This study demonstrates that the docking target function based on the MMFF94 force field can be used to detect the crystal or near crystal positions of the ligand by the finding the low-energy local minima spectrum of the target function. The importance of solvent accounting in the docking process for the accurate ligand positioning is also shown. The accuracy of the ligand positioning as well as the correlation between the calculated and experimentally determined protein-ligand binding energies are improved when the MMFF94 force field is substituted by the new PM7 method with implicit solvent accounting.
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Critical ligand binding reagent preparation/selection: when specificity depends on reagents.
Rup, Bonita; O'Hara, Denise
2007-05-11
Throughout the life cycle of biopharmaceutical products, bioanalytical support is provided using ligand binding assays to measure the drug product for pharmacokinetic, pharmacodynamic, and immunogenicity studies. The specificity and selectivity of these ligand binding assays are highly dependent on the ligand binding reagents. Thus the selection, characterization, and management processes for ligand binding reagents are crucial to successful assay development and application. This report describes process considerations for selection and characterization of ligand binding reagents that are integral parts of the different phases of assay development. Changes in expression, purification, modification, and storage of the ligand binding reagents may have a profound effect on the ligand binding assay performance. Thus long-term management of the critical ligand binding assay reagents is addressed including suggested characterization criteria that allow ligand binding reagents to be used in as consistent a manner as possible. Examples of challenges related to the selection, modification, and characterization of ligand binding reagents are included.
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Garcia-Vallvé, Santiago; Guasch, Laura; Tomas-Hernández, Sarah; del Bas, Josep Maria; Ollendorff, Vincent; Arola, Lluís; Pujadas, Gerard; Mulero, Miquel
2015-07-23
Thiazolidinediones (TZDs), such as rosiglitazone and pioglitazone, are peroxisome proliferator-activated receptor γ (PPARγ) full agonists that have been widely used in the treatment of type 2 diabetes mellitus. Despite the demonstrated beneficial effect of reducing glucose levels in the plasma, TZDs also induce several adverse effects. Consequently, the search for new compounds with potent antidiabetic effects but fewer undesired effects is an active field of research. Interestingly, the novel proposed mechanisms for the antidiabetic activity of PPARγ agonists, consisting of PPARγ Ser273 phosphorylation inhibition, ligand and receptor mutual dynamics, and the presence of an alternate binding site, have recently changed the view regarding the optimal characteristics for the screening of novel PPARγ ligands. Furthermore, transcriptional genomics could bring essential information about the genome-wide effects of PPARγ ligands. Consequently, facing the new mechanistic scenario proposed for these compounds is essential for resolving the paradoxes among their agonistic function, antidiabetic activities, and side effects and should allow the rational development of better and safer PPARγ-mediated antidiabetic drugs.
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Ligand.Info small-molecule Meta-Database.
von Grotthuss, Marcin; Koczyk, Grzegorz; Pas, Jakub; Wyrwicz, Lucjan S; Rychlewski, Leszek
2004-12-01
Ligand.Info is a compilation of various publicly available databases of small molecules. The total size of the Meta-Database is over 1 million entries. The compound records contain calculated three-dimensional coordinates and sometimes information about biological activity. Some molecules have information about FDA drug approving status or about anti-HIV activity. Meta-Database can be downloaded from the http://Ligand.Info web page. The database can also be screened using a Java-based tool. The tool can interactively cluster sets of molecules on the user side and automatically download similar molecules from the server. The application requires the Java Runtime Environment 1.4 or higher, which can be automatically downloaded from Sun Microsystems or Apple Computer and installed during the first use of Ligand.Info on desktop systems, which support Java (Ms Windows, Mac OS, Solaris, and Linux). The Ligand.Info Meta-Database can be used for virtual high-throughput screening of new potential drugs. Presented examples showed that using a known antiviral drug as query the system was able to find others antiviral drugs and inhibitors.
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[Functional selectivity of opioid receptors ligands].
Audet, Nicolas; Archer-Lahlou, Elodie; Richard-Lalonde, Mélissa; Piñeyro-Filpo, Graciela
2010-01-01
Opiates are the most effective analgesics available for the treatment of severe pain. However, their clinical use is restricted by unwanted side effects such as tolerance, physical dependence and respiratory depression. The strategy to develop new opiates with reduced side effects has mainly focused on the study and production of ligands that specifically bind to different opiate receptors subtypes. However, this strategy has not allowed the production of novel therapeutic ligands with a better side effects profile. Thus, other research strategies need to be explored. One which is receiving increasing attention is the possibility of exploiting ligand ability to stabilize different receptor conformations with distinct signalling profiles. This newly described property, termed functional selectivity, provides a potential means of directing the stimulus generated by an activated receptor towards a specific cellular response. Here we summarize evidence supporting the existence of ligand-specific active conformations for two opioid receptors subtypes (delta and mu), and analyze how functional selectivity may contribute in the production of longer lasting, better tolerated opiate analgesics. double dagger.
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Kim, Jae Il; Kwak, Hyun Young; Yoon, Jung Hee; Ryu, Dae Won; Yoo, In Young; Yang, Namgeun; Cho, Beong Ki; Park, Je-Geun; Lee, Hyosug; Hong, Chang Seop
2009-04-06
Four cyanide-linked Fe(III)-Mn(III) complexes were prepared by reacting Mn Schiff bases with a new molecular precursor (PPh(4))[Fe(qcq)(CN)(3)] [1; qcq = 8-(2-quinolinecarboxamido)quinoline anion]. They include a dimeric molecule, [Fe(qcq)(CN)(3)][Mn(3-MeOsalen)(H(2)O)] x 2 H(2)O [2 x 2 H(2)O; 3-MeOsalen = N,N'-ethylenebis(3-methoxysalicylideneiminato) dianion], and three 1D zigzag chains, [Fe(qcq)(CN)(3)][Mn(5-Clsalen)] x 3 H(2)O [3 x 2 MeOH; 5-Clsalen = N,N'-ethylenebis(5-chlorosalicylideneiminato) dianion], [Fe(qcq)(CN)(3)][Mn(5-Brsalen)] x 2 MeOH [4 x 2 MeOH; 5-Brsalen = N,N'-ethylenebis(5-bromosalicylideneiminato) dianion], and Fe(qcq)(CN)(3)][Mn(salen)].MeCN x H(2)O [5 x MeCN; salen = N,N'-ethylenebis(salicylideneiminato) dianion]. The complexes consist of extensive hydrogen bonding and pi-pi stacking interactions, generating multidimensional structures. Magnetic studies demonstrate that antiferromagnetic couplings are operative between Fe(III) and Mn(III) centers bridged by cyanide ligands. On the basis of an infinite chain model, magnetic coupling parameters of 2-5 range from -9.3 to -14.1 cm(-1). A long-range order is observed at 2.3 K for 3 and 2.2 K for 4, while compound 5 shows spin glass behavior possibly coupled with magnetic ordering.
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Synthesis and binding studies of Alzheimer ligands on solid support.
Rzepecki, Petra; Geib, Nina; Peifer, Manuel; Biesemeier, Frank; Schrader, Thomas
2007-05-11
Aminopyrazole derivatives constitute the first class of nonpeptidic rationally designed beta-sheet ligands. Here we describe a double solid-phase protocol for both synthesis and affinity testing. The presented solid-phase synthesis of four types of hybrid compounds relies on the Fmoc strategy and circumvents subsequent HPLC purification by precipitating the final product from organic solution in pure form. Hexa- and octapeptide pendants with internal di- and tetrapeptide bridges are now amenable in high yields to combinatorial synthesis of compound libraries for high-throughput screening purposes. Solid-phase peptide synthesis (SPPS) on an acid-resistant PAM allows us, after PMB deprotection, to subject the free aminopyrazole binding sites in an immobilized state to on-bead assays with fluorescence-labeled peptides. From the fluorescence emission intensity decrease, individual binding constants can be calculated via reference curves by simple application of the law of mass action. Gratifyingly, host/guest complexation can be monitored quantitatively even for those ligands, which are almost insoluble in water.
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Zinc complex chemistry of N,N,O ligands providing a hydrophobic cavity.
Gross, Florian; Vahrenkamp, Heinrich
2005-05-02
Three new highly substituted bis(2-picolyl)(2-hydroxybenzyl)amine ligands were synthesized, and their biomimetic zinc complex chemistry was explored. They have tert-butyl substituents at the 3-and 5-positions of their phenyl rings, and they bear one phenyl group (HL2), two methyl groups (HL3), or two phenyl groups (HL4) at the 6-positions of their pyridyl rings. Their reactions with hydrated zinc perchlorate yield three distinctively different complex types. L2 forms a trigonal-bipyramidal aqua complex, and L3, a square-pyramidal aqua complex. The substituents on L4 leave no room for a water ligand, and the resulting zinc complex is trigonal-monopyramidal with a vacant coordination site. The water ligands on the L2Zn and L3Zn units can be replaced by anionic halide, thiocyanate, p-nitrophenolate, benzoate, and organophosphate as well as uncharged pyridine ligands. The L4Zn unit forms labile halide, p-nitrophenolate, and pyridine complexes. Triethylamine converts the aqua complexes to the labile hydroxides L2Zn-OH and L3Zn-OH, and in polar media [L3Zn-OH2]+ seems to be in equilibrium with L3Zn-OH. The hydroxides, but not the water complexes, effect the hydrolytic cleavage of tris(p-nitrophenyl) phosphate to bis(p-nitrophenyl) phosphate. The kinetic investigation of the cleavage reactions has shown them to be second-order reactions, thereby supporting the proposed four-center mechanism.
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Rational Ligand Design for U(VI) and Pu(IV)
DOE Office of Scientific and Technical Information (OSTI.GOV)
Szigethy, Geza
2009-08-12
Nuclear power is an attractive alternative to hydrocarbon-based energy production at a time when moving away from carbon-producing processes is widely accepted as a significant developmental need. Hence, the radioactive actinide power sources for this industry are necessarily becoming more widespread, which is accompanied by the increased risk of exposure to both biological and environmental systems. This, in turn, requires the development of technology designed to remove such radioactive threats efficiently and selectively from contaminated material, whether that be contained nuclear waste streams or the human body. Raymond and coworkers (University of California, Berkeley) have for decades investigated the interactionmore » of biologically-inspired, hard Lewis-base ligands with high-valent, early-actinide cations. It has been established that such ligands bind strongly to the hard Lewis-acidic early actinides, and many poly-bidentate ligands have been developed and shown to be effective chelators of actinide contaminants in vivo. Work reported herein explores the effect of ligand geometry on the linear U(IV) dioxo dication (uranyl, UO 2 2+). The goal is to utilize rational ligand design to develop ligands that exhibit shape selectivity towards linear dioxo cations and provides thermodynamically favorable binding interactions. The uranyl complexes with a series of tetradentate 3-hydroxy-pyridin-2-one (3,2-HOPO) ligands were studied in both the crystalline state as well as in solution. Despite significant geometric differences, the uranyl affinities of these ligands vary only slightly but are better than DTPA, the only FDA-approved chelation therapy for actinide contamination. The terepthalamide (TAM) moiety was combined into tris-beidentate ligands with 1,2- and 3,2-HOPO moieties were combined into hexadentate ligands whose structural preferences and solution thermodynamics were measured with the uranyl cation. In addition to achieving coordinative saturation
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Ligand- and receptor-based docking with LiBELa
NASA Astrophysics Data System (ADS)
dos Santos Muniz, Heloisa; Nascimento, Alessandro S.
2015-08-01
Methodologies on molecular docking are constantly improving. The problem consists on finding an optimal interplay between the computational cost and a satisfactory physical description of ligand-receptor interaction. In pursuit of an advance in current methods we developed a mixed docking approach combining ligand- and receptor-based strategies in a docking engine, where tridimensional descriptors for shape and charge distribution of a reference ligand guide the initial placement of the docking molecule and an interaction energy-based global minimization follows. This hybrid docking was evaluated with soft-core and force field potentials taking into account ligand pose and scoring. Our approach was found to be competitive to a purely receptor-based dock resulting in improved logAUC values when evaluated with DUD and DUD-E. Furthermore, the smoothed potential as evaluated here, was not advantageous when ligand binding poses were compared to experimentally determined conformations. In conclusion we show that a combination of ligand- and receptor-based strategy docking with a force field energy model results in good reproduction of binding poses and enrichment of active molecules against decoys. This strategy is implemented in our tool, LiBELa, available to the scientific community.
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NASA Astrophysics Data System (ADS)
Ammar, Reda A.; Alaghaz, Abdel-Nasser M. A.; Zayed, Mohamed E.; Al-Bedair, Lamia A.
2017-08-01
Tridentate Schiff's base (HL) ligand was synthesized via condensation of salicylaldehyde and 3-hydroxypyridin-2-yliminomethyl-4H-chromen-4-one and their corresponding Mn(II), Co(II), Ni(II), Cu(II) and Zn(II) complexes have been synthesized. The isolated solid complexes were characterized by elemental analyses, molar conductance, spectral (IR, UV-Vis, 1H NMR), magnetic moment, EPR, and thermal measurements. The IR spectra showed that HL was coordinated to the metal ions in tridentate manner with O2N donor sites of the azomethine N, deprotonated phenolic-OH and carbonyl-O. The activation of thermodynamic parameters are calculated using Coast-Redfern and Horowitz-Metzger (HM). The octahedral geometry of the complexes is confirmed using DFT method from DMOL3 calculations, UV-Vis and magnetic moment measurements, ESR and ligand field parameters. Antioxidant activities have also been performed for all the compounds. The investigated ligand and metal complexes were screened for their in-vitro antimicrobial activities against different types of fungal and bacterial strains. The resulting data assert on the inspected compounds as a highly promising bactericides and fungicides. The antitumor activities of all inspected compounds were evaluated towards human liver Carcinoma (HepG2) cell line.
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Natural-product-derived fragments for fragment-based ligand discovery
NASA Astrophysics Data System (ADS)
Over, Björn; Wetzel, Stefan; Grütter, Christian; Nakai, Yasushi; Renner, Steffen; Rauh, Daniel; Waldmann, Herbert
2013-01-01
Fragment-based ligand and drug discovery predominantly employs sp2-rich compounds covering well-explored regions of chemical space. Despite the ease with which such fragments can be coupled, this focus on flat compounds is widely cited as contributing to the attrition rate of the drug discovery process. In contrast, biologically validated natural products are rich in stereogenic centres and populate areas of chemical space not occupied by average synthetic molecules. Here, we have analysed more than 180,000 natural product structures to arrive at 2,000 clusters of natural-product-derived fragments with high structural diversity, which resemble natural scaffolds and are rich in sp3-configured centres. The structures of the cluster centres differ from previously explored fragment libraries, but for nearly half of the clusters representative members are commercially available. We validate their usefulness for the discovery of novel ligand and inhibitor types by means of protein X-ray crystallography and the identification of novel stabilizers of inactive conformations of p38α MAP kinase and of inhibitors of several phosphatases.
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AsteriX: a Web server to automatically extract ligand coordinates from figures in PDF articles.
Lounnas, V; Vriend, G
2012-02-27
Coordinates describing the chemical structures of small molecules that are potential ligands for pharmaceutical targets are used at many stages of the drug design process. The coordinates of the vast majority of ligands can be obtained from either publicly accessible or commercial databases. However, interesting ligands sometimes are only available from the scientific literature, in which case their coordinates need to be reconstructed manually--a process that consists of a series of time-consuming steps. We present a Web server that helps reconstruct the three-dimensional (3D) coordinates of ligands for which a two-dimensional (2D) picture is available in a PDF file. The software, called AsteriX, analyses every picture contained in the PDF file and attempts to determine automatically whether or not it contains ligands. Areas in pictures that may contain molecular structures are processed to extract connectivity and atom type information that allow coordinates to be subsequently reconstructed. The AsteriX Web server was tested on a series of articles containing a large diversity in graphical representations. In total, 88% of 3249 ligand structures present in the test set were identified as chemical diagrams. Of these, about half were interpreted correctly as 3D structures, and a further one-third required only minor manual corrections. It is principally impossible to always correctly reconstruct 3D coordinates from pictures because there are many different protocols for drawing a 2D image of a ligand, but more importantly a wide variety of semantic annotations are possible. The AsteriX Web server therefore includes facilities that allow the users to augment partial or partially correct 3D reconstructions. All 3D reconstructions are submitted, checked, and corrected by the users domain at the server and are freely available for everybody. The coordinates of the reconstructed ligands are made available in a series of formats commonly used in drug design research. The
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Mapping of ligand-binding cavities in proteins.
Andersson, C David; Chen, Brian Y; Linusson, Anna
2010-05-01
The complex interactions between proteins and small organic molecules (ligands) are intensively studied because they play key roles in biological processes and drug activities. Here, we present a novel approach to characterize and map the ligand-binding cavities of proteins without direct geometric comparison of structures, based on Principal Component Analysis of cavity properties (related mainly to size, polarity, and charge). This approach can provide valuable information on the similarities and dissimilarities, of binding cavities due to mutations, between-species differences and flexibility upon ligand-binding. The presented results show that information on ligand-binding cavity variations can complement information on protein similarity obtained from sequence comparisons. The predictive aspect of the method is exemplified by successful predictions of serine proteases that were not included in the model construction. The presented strategy to compare ligand-binding cavities of related and unrelated proteins has many potential applications within protein and medicinal chemistry, for example in the characterization and mapping of "orphan structures", selection of protein structures for docking studies in structure-based design, and identification of proteins for selectivity screens in drug design programs. 2009 Wiley-Liss, Inc.
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Mapping of Ligand-Binding Cavities in Proteins
Andersson, C. David; Chen, Brian Y.; Linusson, Anna
2010-01-01
The complex interactions between proteins and small organic molecules (ligands) are intensively studied because they play key roles in biological processes and drug activities. Here, we present a novel approach to characterise and map the ligand-binding cavities of proteins without direct geometric comparison of structures, based on Principal Component Analysis of cavity properties (related mainly to size, polarity and charge). This approach can provide valuable information on the similarities, and dissimilarities, of binding cavities due to mutations, between-species differences and flexibility upon ligand-binding. The presented results show that information on ligand-binding cavity variations can complement information on protein similarity obtained from sequence comparisons. The predictive aspect of the method is exemplified by successful predictions of serine proteases that were not included in the model construction. The presented strategy to compare ligand-binding cavities of related and unrelated proteins has many potential applications within protein and medicinal chemistry, for example in the characterisation and mapping of “orphan structures”, selection of protein structures for docking studies in structure-based design and identification of proteins for selectivity screens in drug design programs. PMID:20034113
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Visualizing ligand molecules in twilight electron density
Weichenberger, Christian X.; Pozharski, Edwin; Rupp, Bernhard
2013-01-01
Three-dimensional models of protein structures determined by X-ray crystallography are based on the interpretation of experimentally derived electron-density maps. The real-space correlation coefficient (RSCC) provides an easily comprehensible, objective measure of the residue-based fit of atom coordinates to electron density. Among protein structure models, protein–ligand complexes are of special interest, given their contribution to understanding the molecular underpinnings of biological activity and to drug design. For consumers of such models, it is not trivial to determine the degree to which ligand-structure modelling is biased by subjective electron-density interpretation. A standalone script, Twilight, is presented for the analysis, visualization and annotation of a pre-filtered set of 2815 protein–ligand complexes deposited with the PDB as of 15 January 2012 with ligand RSCC values that are below a threshold of 0.6. It also provides simplified access to the visualization of any protein–ligand complex available from the PDB and annotated by the Uppsala Electron Density Server. The script runs on various platforms and is available for download at http://www.ruppweb.org/twilight/. PMID:23385767
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Modification of the 5' terminus of oligodeoxyribonucleotides for conjugation with ligands.
Asseline, U; Thuong, N T
2001-08-01
Ligands can be introduced at the 5' terminus of an oligonucleotide by adding a linker to the ligand and modifying the 5' terminus of the oligonucleotide. These are then reacted to give the ligand-oligonucleotide conjugate. This unit describes the addition of carboxylated and aminoalkylated linkers, and phosphorothioate, phosphate, and masked thiol groups to the 5' terminus of an oligonucleotide. The addition of linkers to ligands and the final reaction that produces the ligand-conjugated oligonucleotide are described elsewhere in the series. This approach is particularly useful when there is a limited amount of ligand available, when the ligand is sensitive to chemical conditions required for oligonucleotide deprotection, or when the ligand is weakly soluble in solvents required for phosphoramidite- or H-phosphonate-mediated oligonucleotide synthesis.
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Staehle, Robert; Tong, Lianpeng; Wang, Lei; Duan, Lele; Fischer, Andreas; Ahlquist, Mårten S G; Sun, Licheng; Rau, Sven
2014-02-03
A new water oxidation catalyst [Ru(III)(bda)(mmi)(OH2)](CF3SO3) (2, H2bda = 2,2'-bipyridine-6,6'-dicarboxylic acid; mmi = 1,3-dimethylimidazolium-2-ylidene) containing an axial N-heterocyclic carbene ligand and one aqua ligand was synthesized and fully characterized. The kinetics of catalytic water oxidation by 2 were measured using stopped-flow technique, and key intermediates in the catalytic cycle were probed by density functional theory calculations. While analogous Ru-bda water oxidation catalysts [Ru(bda)L2] (L = pyridyl ligands) are supposed to catalyze water oxidation through a bimolecular coupling pathway, our study points out that 2, surprisingly, undergoes a single-site water nucleophilic attack (acid-base) pathway. The diversion of catalytic mechanisms is mainly ascribed to the different ligand environments, from nonaqua ligands to an aqua ligand. Findings in this work provide some critical proof for our previous hypothesis about how alternation of ancillary ligands of water oxidation catalysts influences their catalytic efficiency.
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Transient Ligand Docking Sites in Cerebratulus lacteus Mini-Hemoglobin
Deng, Pengchi; Nienhaus, Karin; Palladino, Pasquale; Olson, John S.; Blouin, George; Moens, Luc; Dewilde, Sylvia; Geuens, Eva; Nienhaus, G. Ulrich
2007-01-01
The monomeric hemoglobin of the nemertean worm Cerebratulus lacteus functions as an oxygen storage protein to maintain neural activity under hypoxic conditions. It shares a large, apolar matrix tunnel with other small hemoglobins, which has been implicated as a potential ligand migration pathway. Here we explore ligand migration and binding within the distal heme pocket, to which the tunnel provides access to ligands from the outside. FTIR/TDS experiments performed at cryogenic temperatures reveal the presence of three transient ligand docking sites within the distal pocket, the primary docking site B on top of pyrrole C and secondary sites C and D. Site C is assigned to a cavity adjacent to the distal portion of the heme pocket, surrounded by the B and E helices. It has an opening to the apolar tunnel and is expected to be on the pathway for ligand entry and exit, whereas site D, circumscribed by TyrB10, GlnE7, and the CD corner, most likely is located on a side pathway of ligand migration. Flash photolysis experiments at ambient temperatures indicate that the rate-limiting step for ligand binding to CerHb is migration through the apolar channel to site C. Movement from C to B and iron-ligand bond formation involve low energy barriers and thus are very rapid processes in the wt protein. PMID:17531406
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NASA Astrophysics Data System (ADS)
Shankarwar, Sunil G.; Nagolkar, Bhagwat B.; Shelke, Vinod A.; Chondhekar, Trimbak K.
2015-06-01
A series of metal complexes of Mn(II), Co(II), Ni(II), Cu(II), have been synthesized with newly synthesized biologically active macrocyclic ligand. The ligand was synthesized by condensation of β-diketone 1-(4-chlorophenyl)-3-(2-hydroxyphenyl)propane-1,3-dione and o-phenylene diamine. All the complexes were characterized by elemental analysis, molar conductivity, magnetic susceptibility, thermal analysis, X-ray diffraction, IR, 1H-NMR, UV-Vis spectroscopy and mass spectroscopy. From the analytical data, stoichiometry of the complexes was found to be 1:2 (metal:ligand). Thermal behavior (TG/DTA) and kinetic parameters suggest more ordered activated state in complex formation. All the complexes are of high spin type and six coordinated. On the basis of IR, electronic spectral studies and magnetic behavior, an octahedral geometry has been assigned to these complexes. The antibacterial and antifungal activities of the ligand and its metal complexes, has been screened in vitro against Staphylococcus aureus, Escherichia coli and Aspergillus niger, Trichoderma respectively.
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Yaacobi-Gross, Nir; Garphunkin, Natalia; Solomeshch, Olga; Vaneski, Aleksandar; Susha, Andrei S; Rogach, Andrey L; Tessler, Nir
2012-04-24
We show that it is possible to combine several charge generation strategies in a single device structure, the performance of which benefits from all methods used. Exploiting the inherent type II heterojunction between layered structures of CdSe and CdTe colloidal quantum dots, we systematically study different ways of combining such nanocrystals of different size and surface chemistry and with different linking agents in a bilayer solar cell configuration. We demonstrate the beneficial use of two distinctly different sizes of NCs not only to improve the solar spectrum matching but also to reduce exciton binding energy, allowing their efficient dissociation at the interface. We further make use of the ligand-induced quantum-confined Stark effect in order to enhance charge generation and, hence, overall efficiency of nanocrystal-based solar cells.
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Janero, David R; Korde, Anisha; Makriyannis, Alexandros
2017-01-01
Detailed characterization of the ligand-binding motifs and structure-function correlates of the principal GPCRs of the endocannabinoid-signaling system, the cannabinoid 1 (CB1R) and cannabinoid 2 (CB2R) receptors, is essential to inform the rational design of drugs that modulate CB1R- and CB2R-dependent biosignaling for therapeutic gain. We discuss herein an experimental paradigm termed "ligand-assisted protein structure" (LAPS) that affords a means of characterizing, at the amino acid level, CB1R and CB2R structural features key to ligand engagement and receptor-dependent information transmission. For this purpose, LAPS integrates three key disciplines and methodologies: (a) medicinal chemistry: design and synthesis of high-affinity, pharmacologically active probes as reporters capable of reacting irreversibly with particular amino acids at (or in the immediate vicinity of) the ligand-binding domain of the functionally active receptor; (b) molecular and cellular biology: introduction of discrete, conservative point mutations into the target GPCR and determination of their effect on probe binding and pharmacological activity; (c) analytical chemistry: identification of the site(s) of probe-GPCR interaction through focused, bottom-up, amino acid-level proteomic identification of the probe-receptor complex using liquid chromatography tandem mass spectrometry. Subsequent in silico methods including ligand docking and computational modeling provide supplementary data on the probe-receptor interaction as defined by LAPS. Examples of LAPS as applied to human CB2R orthosteric binding site characterization for a biarylpyrazole antagonist/inverse agonist and a classical cannabinoid agonist belonging to distinct chemical classes of cannabinergic compounds are given as paradigms for further application of this methodology to other therapeutic protein targets. LAPS is well positioned to complement other experimental and in silico methods in contemporary structural biology such
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Cash, Jennifer N; Angerman, Elizabeth B; Kattamuri, Chandramohan; Nolan, Kristof; Zhao, Huaying; Sidis, Yisrael; Keutmann, Henry T; Thompson, Thomas B
2012-01-06
TGF-β family ligands are involved in a variety of critical physiological processes. For instance, the TGF-β ligand myostatin is a staunch negative regulator of muscle growth and a therapeutic target for muscle-wasting disorders. Therefore, it is important to understand the molecular mechanisms of TGF-β family regulation. One form of regulation is through inhibition by extracellular antagonists such as the follistatin (Fst)-type proteins. Myostatin is tightly controlled by Fst-like 3 (Fstl3), which is the only Fst-type molecule that has been identified in the serum bound to myostatin. Here, we present the crystal structure of myostatin in complex with Fstl3. The structure reveals that the N-terminal domain (ND) of Fstl3 interacts uniquely with myostatin as compared with activin A, because it utilizes different surfaces on the ligand. This results in conformational differences in the ND of Fstl3 that alter its position in the type I receptor-binding site of the ligand. We also show that single point mutations in the ND of Fstl3 are detrimental to ligand binding, whereas corresponding mutations in Fst have little effect. Overall, we have shown that the NDs of Fst-type molecules exhibit distinctive modes of ligand binding, which may affect overall affinity of ligand·Fst-type protein complexes.
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Pedziwiatr, Jakub; Ghiviriga, Ion; Abboud, Khalil A; Veige, Adam S
2017-02-01
This report describes a synthetic protocols and the crystal structures involving a novel pincer-type H 3 [NNN] ligand, namely di-μ-bromido-μ-{2-(2,2-di-methylpropanimido-yl)- N -[2-(2,2-di-methyl-propanimido-yl)-4-methyl-phen-yl]-4-methylaniline}-bis-[(diethyl ether)lithium], [Li 2 Br 2 (C 24 H 33 N 3 )(C 4 H 10 O) 2 ] ( 1 ) and a dinuclear metal complex, namely di-μ-bromido-2:3κ 4 Br : Br -bis-{2-(2,2-di-methylpropanimido-yl)- N -[2-(2,2-di-methyl-propanimido-yl)-4-methyl-phen-yl]-4-methylaniline}-1κ 3 N , N ', N '';4κ 3 N , N ', N ''-tetra-μ-iso-propano-lato-1:2κ 4 O : O ;3:4κ 4 O : O -diiso-propano-lato-1κ O ,4κ O -2,3-dilithium-1,4-dititanium, [Li 2 Ti 2 Br 2 (C 24 H 32 N 3 ) 2 (C 3 H 7 O) 6 ] or {[NHNNH]Ti(O i Pr) 3 (LiBr) 2 } 2 ( 2 ). Complex 1 , which sits on a twofold rotation axis, is a rare example of a pincer-type ligand which bears ketimine side arms. A unique feature of complex 1 is that the ketimine N atoms have an LiBr(Et 2 O) fragment bonded to them, with the Li atom adopting a distorted tetra-hedral geometry. This particular fragment creates an LiBr bridge between the two ketimine sidearms, which leads to a cage-type appearance of the ligand. Complex 2 consists of the previously described ligand and a Ti IV metal atom in an octa-hedral environment, and is located on an inversion center. Complex 2 crystallizes as a dinuclear species with the metal atoms being bridged by an LiBr entity [the Br atoms are disordered and refined in two positions with their site occupation factors refining to 0.674 (12)/0.372 (12)], and the Li cation being bonded to the isopropoxide O atoms (Li having a tetra-hedral coordination as in 1 ). The organic ligand of compound 2 exhibits disorder in its periphery groups; isopropyl and tert -butyl groups (occupation factors fixed at 0.6/0.4). The novel [NNN]H 3 pincer-type ligand was characterized by multinuclear and multidimensional NMR, HRMS and X-ray crystallography. The dinuclear metal complex 2 was
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Optical Absorbance Enhancement in PbS QD/Cinnamate Ligand Complexes.
Kroupa, Daniel M; Vörös, Márton; Brawand, Nicholas P; Bronstein, Noah; McNichols, Brett W; Castaneda, Chloe V; Nozik, Arthur J; Sellinger, Alan; Galli, Giulia; Beard, Matthew C
2018-06-08
We studied the optical absorption enhancement in colloidal suspensions of PbS quantum dots (QD) upon ligand exchange from oleate to a series of cinnamate ligands. By combining experiments and ab initio simulations, we elucidate physical parameters that govern the optical absorption enhancement. We find that, within the cinnamate/PbS QD system, the optical absorption enhancement scales linearly with the electronic gap of the ligand, indicating that the ligand/QD coupling occurs equally efficient between the QD and ligand HOMO and their respective LUMO levels. Disruption of the conjugation that connects the aromatic ring and its substituents to the QD core causes a reduction of the electronic coupling. Our results further support the notion that the ligand/QD complex should be considered as a distinct chemical system with emergent behavior rather than a QD core with ligands whose sole purpose is to passivate surface dangling bonds and prevent agglomeration.
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New synthetic routes toward enantiopure nitrogen donor ligands.
Sala, Xavier; Rodríguez, Anna M; Rodríguez, Montserrat; Romero, Isabel; Parella, Teodor; von Zelewsky, Alexander; Llobet, Antoni; Benet-Buchholz, Jordi
2006-12-08
New polypyridylic chiral ligands, having either C3 or lower symmetry, have been prepared via a de novo construction of the pyridine nucleus by means of Kröhnke methodology in the key step. The chiral moieties of these ligands originate from the monoterpen chiral pool, namely (-)-alpha-pinene ((-)-14, (-)-15) and (-)-myrtenal ((-)-9, (-)-10). Extension of the above-mentioned asymmetric synthesis procedure to the preparation of enantiopure derivatives of some commonly used polypyridylic ligands has been achieved through a new aldehyde building block ((-)-16). As an example, the synthesis of a chiral derivative of N,N-bis(2-pyridylmethyl)ethylamine (bpea) ligand, (-)-19, has been performed to illustrate the viability of the method. The coordinative ability of the ligands has been tested through the synthesis and characterization of complexes [Mn((-)-19)Br2], (-)-20, and [RuCl((-)-10)(bpy)](BF4), (-)-21. Some preliminary results related to the enantioselective catalytic epoxidation of styrene with the ruthenium complex are also presented.
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Thiophene-Core Estrogen Receptor Ligands Having Superagonist Activity
Min, Jian; Wang, Pengcheng; Srinivasan, Sathish; Nwachukwu, Jerome C.; Guo, Pu; Huang, Minjian; Carlson, Kathryn E.; Katzenellenbogen, John A.; Nettles, Kendall W.; Zhou, Hai-Bing
2013-01-01
To probe the importance of the heterocyclic core of estrogen receptor (ER) ligands, we prepared a series of thiophene-core ligands by Suzuki cross-coupling of aryl boronic acids with bromo-thiophenes, and we assessed their receptor binding and cell biological activities. The disposition of the phenol substituents on the thiophene core, at alternate or adjacent sites, and the nature of substituents on these phenols all contribute to binding affinity and subtype selectivity. Most of the bis(hydroxyphenyl)-thiophenes were ERβ selective, whereas the tris(hydroxyphenyl)-thiophenes were ERα selective; analogous furan-core compounds generally have lower affinity and less selectivity. Some diarylthiophenes show distinct superagonist activity in reporter gene assays, giving maximal activities 2–3 times that of estradiol, and modeling suggests that these ligands have a different interaction with a hydrogen-bonding residue in helix-11. Ligand-core modification may be a new strategy for developing ER ligands whose selectivity is based on having transcriptional activity greater than that of estradiol. PMID:23586645
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Cloud computing for protein-ligand binding site comparison.
Hung, Che-Lun; Hua, Guan-Jie
2013-01-01
The proteome-wide analysis of protein-ligand binding sites and their interactions with ligands is important in structure-based drug design and in understanding ligand cross reactivity and toxicity. The well-known and commonly used software, SMAP, has been designed for 3D ligand binding site comparison and similarity searching of a structural proteome. SMAP can also predict drug side effects and reassign existing drugs to new indications. However, the computing scale of SMAP is limited. We have developed a high availability, high performance system that expands the comparison scale of SMAP. This cloud computing service, called Cloud-PLBS, combines the SMAP and Hadoop frameworks and is deployed on a virtual cloud computing platform. To handle the vast amount of experimental data on protein-ligand binding site pairs, Cloud-PLBS exploits the MapReduce paradigm as a management and parallelizing tool. Cloud-PLBS provides a web portal and scalability through which biologists can address a wide range of computer-intensive questions in biology and drug discovery.
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Ligand binding by repeat proteins: natural and designed
Grove, Tijana Z; Cortajarena, Aitziber L; Regan, Lynne
2012-01-01
Repeat proteins contain tandem arrays of small structural motifs. As a consequence of this architecture, they adopt non-globular, extended structures that present large, highly specific surfaces for ligand binding. Here we discuss recent advances toward understanding the functional role of this unique modular architecture. We showcase specific examples of natural repeat proteins interacting with diverse ligands and also present examples of designed repeat protein–ligand interactions. PMID:18602006
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How to Compute Labile Metal-Ligand Equilibria
ERIC Educational Resources Information Center
de Levie, Robert
2007-01-01
The different methods used for computing labile metal-ligand complexes, which are suitable for an iterative computer solution, are illustrated. The ligand function has allowed students to relegate otherwise tedious iterations to a computer, while retaining complete control over what is calculated.
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Yu, Xian-Yong; Deng, Lin; Zheng, Baishu; Zeng, Bi-Rong; Yi, Pinggui; Xu, Xin
2014-01-28
In order to understand the substitution effects of pyrazolylpyridine (pzpy) on the coordination reaction equilibria, the interactions between a series of pzpy-like ligands and biperoxidovanadate ([OV(O2)2(D2O)](-)/[OV(O2)2(HOD)](-), abbrv. bpV) have been explored using a combination of multinuclear ((1)H, (13)C, and (51)V) magnetic resonance, heteronuclear single quantum coherence (HSQC), and variable temperature NMR in a 0.15 mol L(-1) NaCl D2O solution that mimics the physiological conditions. Both the direct NMR data and the equilibrium constants are reported for the first time. A series of new hepta-coordinated peroxidovanadate species [OV(O2)2L](-) (L = pzpy-like chelating ligands) are formed due to several competitive coordination interactions. According to the equilibrium constants for products between bpV and the pzpy-like ligands, the relative affinity of the ligands is found to be pzpy > 2-Ester-pzpy ≈ 2-Me-pzpy ≈ 2-Amide-pzpy > 2-Et-pzpy. In the interaction system between bpV and pzpy, a pair of isomers (Isomers A and B) are observed in aqueous solution, which are attributed to different types of coordination modes between the metal center and the ligands, while the crystal structure of NH4[OV(O2)2(pzpy)]·6H2O (CCDC 898554) has the same coordination structure as Isomer A (the main product for pzpy). For the N-substituted ligands, however, Isomer A or B type complexes can also be observed in solution but the molar ratios of the isomer are reversed (i.e., Isomer B type is the main product). These results demonstrate that when the N atom in the pyrazole ring has a substitution group, hydrogen bonding (from the H atom in the pyrazole ring), the steric effect (from alkyl) and the solvation effect (from the ester or amide group) can jointly affect the coordination reaction equilibrium.
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Ligand binding was acquired during evolution of nuclear receptors
Escriva, Hector; Safi, Rachid; Hänni, Catherine; Langlois, Marie-Claire; Saumitou-Laprade, Pierre; Stehelin, Dominique; Capron, André; Pierce, Raymond; Laudet, Vincent
1997-01-01
The nuclear receptor (NR) superfamily comprises, in addition to ligand-activated transcription factors, members for which no ligand has been identified to date. We demonstrate that orphan receptors are randomly distributed in the evolutionary tree and that there is no relationship between the position of a given liganded receptor in the tree and the chemical nature of its ligand. NRs are specific to metazoans, as revealed by a screen of NR-related sequences in early- and non-metazoan organisms. The analysis of the NR gene duplication pattern during the evolution of metazoans shows that the present NR diversity arose from two waves of gene duplications. Strikingly, our results suggest that the ancestral NR was an orphan receptor that acquired ligand-binding ability during subsequent evolution. PMID:9192646
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High cell surface death receptor expression determines type I versus type II signaling.
Meng, Xue Wei; Peterson, Kevin L; Dai, Haiming; Schneider, Paula; Lee, Sun-Hee; Zhang, Jin-San; Koenig, Alexander; Bronk, Steve; Billadeau, Daniel D; Gores, Gregory J; Kaufmann, Scott H
2011-10-14
Previous studies have suggested that there are two signaling pathways leading from ligation of the Fas receptor to induction of apoptosis. Type I signaling involves Fas ligand-induced recruitment of large amounts of FADD (FAS-associated death domain protein) and procaspase 8, leading to direct activation of caspase 3, whereas type II signaling involves Bid-mediated mitochondrial perturbation to amplify a more modest death receptor-initiated signal. The biochemical basis for this dichotomy has previously been unclear. Here we show that type I cells have a longer half-life for Fas message and express higher amounts of cell surface Fas, explaining the increased recruitment of FADD and subsequent signaling. Moreover, we demonstrate that cells with type II Fas signaling (Jurkat or HCT-15) can signal through a type I pathway upon forced receptor overexpression and that shRNA-mediated Fas down-regulation converts cells with type I signaling (A498) to type II signaling. Importantly, the same cells can exhibit type I signaling for Fas and type II signaling for TRAIL (TNF-α-related apoptosis-inducing ligand), indicating that the choice of signaling pathway is related to the specific receptor, not some other cellular feature. Additional experiments revealed that up-regulation of cell surface death receptor 5 levels by treatment with 7-ethyl-10-hydroxy-camptothecin converted TRAIL signaling in HCT116 cells from type II to type I. Collectively, these results suggest that the type I/type II dichotomy reflects differences in cell surface death receptor expression.
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Conformational Transitions upon Ligand Binding: Holo-Structure Prediction from Apo Conformations
Seeliger, Daniel; de Groot, Bert L.
2010-01-01
Biological function of proteins is frequently associated with the formation of complexes with small-molecule ligands. Experimental structure determination of such complexes at atomic resolution, however, can be time-consuming and costly. Computational methods for structure prediction of protein/ligand complexes, particularly docking, are as yet restricted by their limited consideration of receptor flexibility, rendering them not applicable for predicting protein/ligand complexes if large conformational changes of the receptor upon ligand binding are involved. Accurate receptor models in the ligand-bound state (holo structures), however, are a prerequisite for successful structure-based drug design. Hence, if only an unbound (apo) structure is available distinct from the ligand-bound conformation, structure-based drug design is severely limited. We present a method to predict the structure of protein/ligand complexes based solely on the apo structure, the ligand and the radius of gyration of the holo structure. The method is applied to ten cases in which proteins undergo structural rearrangements of up to 7.1 Å backbone RMSD upon ligand binding. In all cases, receptor models within 1.6 Å backbone RMSD to the target were predicted and close-to-native ligand binding poses were obtained for 8 of 10 cases in the top-ranked complex models. A protocol is presented that is expected to enable structure modeling of protein/ligand complexes and structure-based drug design for cases where crystal structures of ligand-bound conformations are not available. PMID:20066034
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A label-free approach to detect ligand binding to cell surface proteins in real time.
Burtscher, Verena; Hotka, Matej; Li, Yang; Freissmuth, Michael; Sandtner, Walter
2018-04-26
Electrophysiological recordings allow for monitoring the operation of proteins with high temporal resolution down to the single molecule level. This technique has been exploited to track either ion flow arising from channel opening or the synchronized movement of charged residues and/or ions within the membrane electric field. Here, we describe a novel type of current by using the serotonin transporter (SERT) as a model. We examined transient currents elicited on rapid application of specific SERT inhibitors. Our analysis shows that these currents originate from ligand binding and not from a long-range conformational change. The Gouy-Chapman model predicts that adsorption of charged ligands to surface proteins must produce displacement currents and related apparent changes in membrane capacitance. Here we verified these predictions with SERT. Our observations demonstrate that ligand binding to a protein can be monitored in real time and in a label-free manner by recording the membrane capacitance. © 2018, Burtscher et al.
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Patil, Sunil S.; Thakur, Ganesh A.; Shaikh, Manzoor M.
2011-01-01
Mixed ligand complexes of dioxouranium (VI) of the type [UO2(Q)(L)·2H2O] have been synthesized using 8-hydroxyquinoline (HQ) as a primary ligand and amino acids (HL) such as L-threonine, L-tryptophan, and L-isoleucine as secondary ligands. The metal complexes have been characterized by elemental analysis, electrical conductance, magnetic susceptibility measurements, and spectral and thermal studies. The electrical conductance studies of the complexes indicate their nonelectrolytic nature. Magnetic susceptibility measurements revealed diamagnetic nature of the complexes. Electronic absorption spectra of the complexes show intraligand and charge transfer transitions, respectively. Bonding of the metal ion through N- and O-donor atoms of the ligands is revealed by IR studies, and the chemical environment of the protons is confirmed by NMR studies. The thermal analysis data of the complexes indicate the presence of coordinated water molecules. The agar cup and tube dilution methods have been used to study the antibacterial activity of the complexes against the pathogenic bacteria S. aureus, C. diphtheriae, S. typhi, and E. coli. PMID:22389843
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Proteome-wide covalent ligand discovery in native biological systems
Backus, Keriann M.; Correia, Bruno E.; Lum, Kenneth M.; Forli, Stefano; Horning, Benjamin D.; González-Páez, Gonzalo E.; Chatterjee, Sandip; Lanning, Bryan R.; Teijaro, John R.; Olson, Arthur J.; Wolan, Dennis W.; Cravatt, Benjamin F.
2016-01-01
Small molecules are powerful tools for investigating protein function and can serve as leads for new therapeutics. Most human proteins, however, lack small-molecule ligands, and entire protein classes are considered “undruggable” 1,2. Fragment-based ligand discovery (FBLD) can identify small-molecule probes for proteins that have proven difficult to target using high-throughput screening of complex compound libraries 1,3. Although reversibly binding ligands are commonly pursued, covalent fragments provide an alternative route to small-molecule probes 4–10, including those that can access regions of proteins that are difficult to access through binding affinity alone 5,10,11. In this manuscript, we report a quantitative analysis of cysteine-reactive small-molecule fragments screened against thousands of proteins. Covalent ligands were identified for >700 cysteines found in both druggable proteins and proteins deficient in chemical probes, including transcription factors, adaptor/scaffolding proteins, and uncharacterized proteins. Among the atypical ligand-protein interactions discovered were compounds that react preferentially with pro- (inactive) caspases. We used these ligands to distinguish extrinsic apoptosis pathways in human cell lines versus primary human T-cells, showing that the former is largely mediated by caspase-8 while the latter depends on both caspase-8 and −10. Fragment-based covalent ligand discovery provides a greatly expanded portrait of the ligandable proteome and furnishes compounds that can illuminate protein functions in native biological systems. PMID:27309814
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Models of protein–ligand crystal structures: trust, but verify
Deller, Marc C.
2015-01-01
X-ray crystallography provides the most accurate models of protein–ligand structures. These models serve as the foundation of many computational methods including structure prediction, molecular modelling, and structure-based drug design. The success of these computational methods ultimately depends on the quality of the underlying protein–ligand models. X-ray crystallography offers the unparalleled advantage of a clear mathematical formalism relating the experimental data to the protein–ligand model. In the case of X-ray crystallography, the primary experimental evidence is the electron density of the molecules forming the crystal. The first step in the generation of an accurate and precise crystallographic model is the interpretation of the electron density of the crystal, typically carried out by construction of an atomic model. The atomic model must then be validated for fit to the experimental electron density and also for agreement with prior expectations of stereochemistry. Stringent validation of protein–ligand models has become possible as a result of the mandatory deposition of primary diffraction data, and many computational tools are now available to aid in the validation process. Validation of protein–ligand complexes has revealed some instances of overenthusiastic interpretation of ligand density. Fundamental concepts and metrics of protein–ligand quality validation are discussed and we highlight software tools to assist in this process. It is essential that end users select high quality protein–ligand models for their computational and biological studies, and we provide an overview of how this can be achieved. PMID:25665575
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Models of protein-ligand crystal structures: trust, but verify.
Deller, Marc C; Rupp, Bernhard
2015-09-01
X-ray crystallography provides the most accurate models of protein-ligand structures. These models serve as the foundation of many computational methods including structure prediction, molecular modelling, and structure-based drug design. The success of these computational methods ultimately depends on the quality of the underlying protein-ligand models. X-ray crystallography offers the unparalleled advantage of a clear mathematical formalism relating the experimental data to the protein-ligand model. In the case of X-ray crystallography, the primary experimental evidence is the electron density of the molecules forming the crystal. The first step in the generation of an accurate and precise crystallographic model is the interpretation of the electron density of the crystal, typically carried out by construction of an atomic model. The atomic model must then be validated for fit to the experimental electron density and also for agreement with prior expectations of stereochemistry. Stringent validation of protein-ligand models has become possible as a result of the mandatory deposition of primary diffraction data, and many computational tools are now available to aid in the validation process. Validation of protein-ligand complexes has revealed some instances of overenthusiastic interpretation of ligand density. Fundamental concepts and metrics of protein-ligand quality validation are discussed and we highlight software tools to assist in this process. It is essential that end users select high quality protein-ligand models for their computational and biological studies, and we provide an overview of how this can be achieved.
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Ligand-protected gold clusters: the structure, synthesis and applications
NASA Astrophysics Data System (ADS)
Pichugina, D. A.; Kuz'menko, N. E.; Shestakov, A. F.
2015-11-01
Modern concepts of the structure and properties of atomic gold clusters protected by thiolate, selenolate, phosphine and phenylacetylene ligands are analyzed. Within the framework of the superatom theory, the 'divide and protect' approach and the structure rule, the stability and composition of a cluster are determined by the structure of the cluster core, the type of ligands and the total number of valence electrons. Methods of selective synthesis of gold clusters in solution and on the surface of inorganic composites based, in particular, on the reaction of Aun with RS, RSe, PhC≡C, Hal ligands or functional groups of proteins, on stabilization of clusters in cavities of the α-, β and γ-cyclodextrin molecules (Au15 and Au25) and on anchorage to a support surface (Au25/SiO2, Au20/C, Au10/FeOx) are reviewed. Problems in this field are also discussed. Among the methods for cluster structure prediction, particular attention is given to the theoretical approaches based on the density functional theory (DFT). The structures of a number of synthesized clusters are described using the results obtained by X-ray diffraction analysis and DFT calculations. A possible mechanism of formation of the SR(AuSR)n 'staple' units in the cluster shell is proposed. The structure and properties of bimetallic clusters MxAunLm (M=Pd, Pt, Ag, Cu) are discussed. The Pd or Pt atom is located at the centre of the cluster, whereas Ag and Cu atoms form bimetallic compounds in which the heteroatom is located on the surface of the cluster core or in the 'staple' units. The optical properties, fluorescence and luminescence of ligand-protected gold clusters originate from the quantum effects of the Au atoms in the cluster core and in the oligomeric SR(AuSR)x units in the cluster shell. Homogeneous and heterogeneous reactions catalyzed by atomic gold clusters are discussed in the context of the reaction mechanism and the nature of the active sites. The bibliography includes 345 references.
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Kaulage, Mangesh H; Maji, Basudeb; Pasadi, Sanjeev; Ali, Asfa; Bhattacharya, Santanu; Muniyappa, K
2018-03-25
Recent studies support the idea that G-quadruplex structures in the promoter regions of oncogenes and telomere DNA can serve as potential therapeutic targets in the treatment of cancer. Accordingly, several different types of organic small molecules that stabilize G-quadruplex structures and inhibit telomerase activity have been discerned. Here, we describe the binding of benzimidazole-carbazole ligands to G-quadruplex structures formed in G-rich DNA sequences containing the promoter regions of human c-MYC, c-KIT1, c-KIT2, VEGF and BCL2 proto-oncogenes. The fluorescence spectroscopic data indicate that benzimidazole-carbazole ligands bind and stabilize the G-quadruplexes in the promoter region of oncogenes. The molecular docking studies provide insights into the mode and extent of binding of this class of ligands to the G-quadruplexes formed in oncogene promoters. The high stability of these G-quadruplex structures was validated by thermal denaturation and telomerase-catalyzed extension of the 3' end. Notably, benzimidazole-carbazole ligands suppress the expression of oncogenes in cancer cells in a dose-dependent manner. We anticipate that benzimidazole-carbazole ligands, by virtue of their ability to stabilize G-quadruplex structures in the promoter regions of oncogenes, might reduce the risk of cancer through the loss of function in the proteins encoded by these genes. Copyright © 2018 Elsevier Masson SAS. All rights reserved.
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Ligand-based virtual screening under partial shape constraints.
von Behren, Mathias M; Rarey, Matthias
2017-04-01
Ligand-based virtual screening has proven to be a viable technology during the search for new lead structures in drug discovery. Despite the rapidly increasing number of published methods, meaningful shape matching as well as ligand and target flexibility still remain open challenges. In this work, we analyze the influence of knowledge-based sterical constraints on the performance of the recently published ligand-based virtual screening method mRAISE. We introduce the concept of partial shape matching enabling a more differentiated view on chemical structure. The new method is integrated into the LBVS tool mRAISE providing multiple options for such constraints. The applied constraints can either be derived automatically from a protein-ligand complex structure or by manual selection of ligand atoms. In this way, the descriptor directly encodes the fit of a ligand into the binding site. Furthermore, the conservation of close contacts between the binding site surface and the query ligand can be enforced. We validated our new method on the DUD and DUD-E datasets. Although the statistical performance remains on the same level, detailed analysis reveal that for certain and especially very flexible targets a significant improvement can be achieved. This is further highlighted looking at the quality of calculated molecular alignments using the recently introduced mRAISE dataset. The new partial shape constraints improved the overall quality of molecular alignments especially for difficult targets with highly flexible or different sized molecules. The software tool mRAISE is freely available on Linux operating systems for evaluation purposes and academic use (see http://www.zbh.uni-hamburg.de/raise ).
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Ligand-based virtual screening under partial shape constraints
NASA Astrophysics Data System (ADS)
von Behren, Mathias M.; Rarey, Matthias
2017-04-01
Ligand-based virtual screening has proven to be a viable technology during the search for new lead structures in drug discovery. Despite the rapidly increasing number of published methods, meaningful shape matching as well as ligand and target flexibility still remain open challenges. In this work, we analyze the influence of knowledge-based sterical constraints on the performance of the recently published ligand-based virtual screening method mRAISE. We introduce the concept of partial shape matching enabling a more differentiated view on chemical structure. The new method is integrated into the LBVS tool mRAISE providing multiple options for such constraints. The applied constraints can either be derived automatically from a protein-ligand complex structure or by manual selection of ligand atoms. In this way, the descriptor directly encodes the fit of a ligand into the binding site. Furthermore, the conservation of close contacts between the binding site surface and the query ligand can be enforced. We validated our new method on the DUD and DUD-E datasets. Although the statistical performance remains on the same level, detailed analysis reveal that for certain and especially very flexible targets a significant improvement can be achieved. This is further highlighted looking at the quality of calculated molecular alignments using the recently introduced mRAISE dataset. The new partial shape constraints improved the overall quality of molecular alignments especially for difficult targets with highly flexible or different sized molecules. The software tool mRAISE is freely available on Linux operating systems for evaluation purposes and academic use (see http://www.zbh.uni-hamburg.de/raise).
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Ligand diffusion in proteins via enhanced sampling in molecular dynamics.
Rydzewski, J; Nowak, W
2017-12-01
Computational simulations in biophysics describe the dynamics and functions of biological macromolecules at the atomic level. Among motions particularly important for life are the transport processes in heterogeneous media. The process of ligand diffusion inside proteins is an example of a complex rare event that can be modeled using molecular dynamics simulations. The study of physical interactions between a ligand and its biological target is of paramount importance for the design of novel drugs and enzymes. Unfortunately, the process of ligand diffusion is difficult to study experimentally. The need for identifying the ligand egress pathways and understanding how ligands migrate through protein tunnels has spurred the development of several methodological approaches to this problem. The complex topology of protein channels and the transient nature of the ligand passage pose difficulties in the modeling of the ligand entry/escape pathways by canonical molecular dynamics simulations. In this review, we report a methodology involving a reconstruction of the ligand diffusion reaction coordinates and the free-energy profiles along these reaction coordinates using enhanced sampling of conformational space. We illustrate the above methods on several ligand-protein systems, including cytochromes and G-protein-coupled receptors. The methods are general and may be adopted to other transport processes in living matter. Copyright © 2017 Elsevier B.V. All rights reserved.
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Rydzak, Joanna; Kaczmarek, Radoslaw; Czerwinski, Marcin; Lukasiewicz, Jolanta; Tyborowska, Jolanta; Szewczyk, Boguslaw; Jaskiewicz, Ewa
2015-01-01
The erythrocyte binding ligand 140 (EBA-140) is a member of the Plasmodium falciparum DBL family of erythrocyte binding proteins, which are considered as prospective candidates for malaria vaccine development. The EBA-140 ligand is a paralogue of the well-characterized P. falciparum EBA-175 protein. They share homology of domain structure, including Region II, which consists of two homologous F1 and F2 domains and is responsible for ligand-erythrocyte receptor interaction during invasion. In this report we describe, for the first time, the glycophorin C specificity of the recombinant, baculovirus-expressed binding region (Region II) of P. falciparum EBA-140 ligand. It was found that the recombinant EBA-140 Region II binds to the endogenous and recombinant glycophorin C, but does not bind to Gerbich-type glycophorin C, neither normal nor recombinant, which lacks amino acid residues 36–63 of its polypeptide chain. Our results emphasize the crucial role of this glycophorin C region in EBA-140 ligand binding. Moreover, the EBA-140 Region II did not bind either to glycophorin D, the truncated form of glycophorin C lacking the N-glycan or to desialylated GPC. These results draw attention to the role of glycophorin C glycans in EBA-140 binding. The full identification of the EBA-140 binding site on glycophorin C molecule, consisting most likely of its glycans and peptide backbone, may help to design therapeutics or vaccines that target the erythrocyte binding merozoite ligands. PMID:25588042
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Lineage-specific co-evolution of the Egf receptor/ligand signaling system.
Laisney, Juliette A G C; Braasch, Ingo; Walter, Ronald B; Meierjohann, Svenja; Schartl, Manfred
2010-01-27
The epidermal growth factor receptor (Egfr) with its numerous ligands has fundamental roles in development, cell differentiation and physiology. Dysfunction of the receptor-ligand system contributes to many human malignancies. Consistent with such various tasks, the Egfr gene family has expanded during vertebrate evolution as a consequence of several rounds of whole genome duplication. Of particular interest is the effect of the fish-specific whole genome duplication (FSGD) on the ligand-receptor system, as it has supplied this largest group of vertebrates with additional opportunities for sub- and/or neofunctionalization in this signaling system. We identified the predicted components of the Egf receptor-ligand signaling system in teleost fishes (medaka, platyfish, stickleback, pufferfishes and zebrafish). We found two duplicated egfr genes, egfra and egfrb, in all available teleost genomes. Surprisingly only one copy for each of the seven Egfr ligands could be identified in most fishes, with zebrafish hbegf being the only exception. Special focus was put on medaka, for which we more closely investigated all Egf receptors and Egfr ligands. The different expression patterns of egfra, egfrb and their ligands in medaka tissues and embryo stages suggest differences in role and function. Preferential co-expression of different subsets of Egfr ligands corroborates the possible subfunctionalization and specialization of the two receptors in adult tissues. Bioinformatic analyses of the ligand-receptor interface between Egfr and its ligands show a very weak evolutionary conservation within this region. Using in vitro analyses of medaka Egfra, we could show that this receptor is only activated by medaka ligands, but not by human EGF. Altogether, our data suggest a lineage-specific Egfr/Egfr ligand co-evolution. Our data indicate that medaka Egfr signaling occurs via its two copies, Egfra and Egfrb, each of them being preferentially coexpressed with different subsets of Egfr
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Lineage-specific co-evolution of the Egf receptor/ligand signaling system
2010-01-01
Background The epidermal growth factor receptor (Egfr) with its numerous ligands has fundamental roles in development, cell differentiation and physiology. Dysfunction of the receptor-ligand system contributes to many human malignancies. Consistent with such various tasks, the Egfr gene family has expanded during vertebrate evolution as a consequence of several rounds of whole genome duplication. Of particular interest is the effect of the fish-specific whole genome duplication (FSGD) on the ligand-receptor system, as it has supplied this largest group of vertebrates with additional opportunities for sub- and/or neofunctionalization in this signaling system. Results We identified the predicted components of the Egf receptor-ligand signaling system in teleost fishes (medaka, platyfish, stickleback, pufferfishes and zebrafish). We found two duplicated egfr genes, egfra and egfrb, in all available teleost genomes. Surprisingly only one copy for each of the seven Egfr ligands could be identified in most fishes, with zebrafish hbegf being the only exception. Special focus was put on medaka, for which we more closely investigated all Egf receptors and Egfr ligands. The different expression patterns of egfra, egfrb and their ligands in medaka tissues and embryo stages suggest differences in role and function. Preferential co-expression of different subsets of Egfr ligands corroborates the possible subfunctionalization and specialization of the two receptors in adult tissues. Bioinformatic analyses of the ligand-receptor interface between Egfr and its ligands show a very weak evolutionary conservation within this region. Using in vitro analyses of medaka Egfra, we could show that this receptor is only activated by medaka ligands, but not by human EGF. Altogether, our data suggest a lineage-specific Egfr/Egfr ligand co-evolution. Conclusions Our data indicate that medaka Egfr signaling occurs via its two copies, Egfra and Egfrb, each of them being preferentially coexpressed
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NASA Astrophysics Data System (ADS)
Kajita, Masashi K.; Aihara, Kazuyuki; Kobayashi, Tetsuya J.
2017-07-01
Specific interactions between receptors and their target ligands in the presence of nontarget ligands are crucial for biological processes such as T cell ligand discrimination. To discriminate between the target and nontarget ligands, cells have to increase specificity to the target ligands by amplifying the small differences in affinity among ligands. In addition, sensitivity to the ligand concentration and quick discrimination are also important to detect low amounts of target ligands and facilitate fast cellular decision making after ligand recognition. In this work we propose a mechanism for nonlinear specificity amplification (ultraspecificity) based on zero-order saturating reactions, which was originally proposed to explain nonlinear sensitivity amplification (ultrasensitivity) to the ligand concentration. In contrast to the previously proposed proofreading mechanisms that amplify the specificity by a multistep reaction, our model can produce an optimal balance of specificity, sensitivity, and quick discrimination. Furthermore, we show that a model for insensitivity to a large number of nontarget ligands can be naturally derived from a model with the zero-order ultraspecificity. The zero-order ultraspecificity, therefore, may provide an alternative way to understand ligand discrimination from the viewpoint of nonlinear properties in biochemical reactions.
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Gavia, Diego J.
2015-01-01
This Minireview summarizes a variety of intriguing catalytic studies accomplished by employing unsupported, either solubilized or freely mobilized, and small organic ligand-capped palladium nanoparticles as catalysts. Small organic ligands are gaining more attention as nanoparticle stabilizers and alternates to larger organic supports, such as polymers and dendrimers, owing to their tremendous potential for a well-defined system with spatial control in surrounding environments of reactive surfaces. The nanoparticle catalysts are grouped depending on the type of surface stabilizers with reactive head groups, which include thiolate, phosphine, amine, and alkyl azide. Applications for the reactions such as hydrogenation, alkene isomerization, oxidation, and carbon-carbon cross coupling reactions are extensively discussed. The systems defined as “ligandless” Pd nanoparticle catalysts and solvent (e.g. ionic liquid)-stabilized Pd nanoparticle catalysts are not discussed in this review. PMID:25937846
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Reversibly Switchable, pH-Dependent Peptide Ligand Binding via 3,5-Diiodotyrosine Substitutions.
Ngambenjawong, Chayanon; Sylvestre, Meilyn; Gustafson, Heather H; Pineda, Julio Marco B; Pun, Suzie H
2018-04-20
Cell type-specific targeting ligands utilized in drug delivery applications typically recognize receptors that are overexpressed on the cells of interest. Nonetheless, these receptors may also be expressed, to varying extents, on off-target cells, contributing to unintended side effects. For the selectivity profile of targeting ligands in cancer therapy to be improved, stimuli-responsive masking of these ligands with acid-, redox-, or enzyme-cleavable molecules has been reported, whereby the targeting ligands are exposed in specific environments, e.g., acidic tumor hypoxia. One possible drawback of these systems lies in their one-time, permanent trigger, which enables the "demasked" ligands to bind off-target cells if released back into the systemic circulation. A promising strategy to address the aforementioned problem is to design ligands that show selective binding based on ionization state, which may be microenvironment-dependent. In this study, we report a systematic strategy to engineer low pH-selective targeting peptides using an M2 macrophage-targeting peptide (M2pep) as an example. 3,5-Diiodotyrosine mutagenesis into native tyrosine residues of M2pep confers pH-dependent binding behavior specific to acidic environment (pH 6) when the amino acid is protonated into the native tyrosine-like state. At physiological pH of 7.4, the hydroxyl group of 3,5-diiodotyrosine on the peptide is deprotonated leading to interruption of the peptide native binding property. Our engineered pH-responsive M2pep (Ac-Y-Î-Î) binds target M2 macrophages more selectively at pH 6 than at pH 7.4. In addition, 3,5-diiodotyrosine substitutions also improve serum stability of the peptide. Finally, we demonstrate pH-dependent reversibility in target binding via a postbinding peptide elution study. The strategy presented here should be applicable for engineering pH-dependent functionality of other targeting peptides with potential applications in physiology-dependent in vivo targeting
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The Retinoid X Receptors and Their Ligands
Dawson, Marcia I.; Xia, Zebin
2014-01-01
This chapter presents an overview of the current status of studies on the structural and molecular biology of the retinoid X receptor subtypes α, β, and γ (RXRs, NR2B1–3), their nuclear and cytoplasmic functions, post-transcriptional processing, and recently reported ligands. Points of interest are the different changes in the ligand-binding pocket induced by variously shaped agonists, the communication of the ligand–bound pocket with the coactivator binding surface and the heterodimerization interface, and recently identified ligands that are natural products, those that function as environmental toxins or drugs that had been originally designed to interact with other targets, as well as those that were deliberately designed as RXR-selective transcriptional agonists, synergists, or antagonists. Of these synthetic ligands, the general trend in design appears to be away from fully aromatic rigid structures to those containing partial elements of the flexible tetraene side chain of 9-cis-retinoic acid. PMID:22020178
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NASA Astrophysics Data System (ADS)
Skrabal, Stephen A.; Donat, John R.; Burdige, David J.
2000-06-01
differences in the type of Cu-complexing organic matter. Total ligand concentrations ( L1 S + L2 S) are 15 to >100 times higher in the upper intervals of the pore waters relative to ligand concentrations in the bottom waters of the Chesapeake Bay (30-60 nM), consistent with previous observations of fluxes of these ligands from the sediments to overlying waters. These results suggest that sediments are potentially significant sources of Cu-complexing ligands to the overlying waters of the Chesapeake Bay, and perhaps, other shallow water estuarine and coastal environments. Copper-complexing ligands released from sediment pore waters may play an important role in influencing Cu speciation in overlying waters.
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Benny, Paul D; Fugate, Glenn A; Barden, Adam O; Morley, Jennifer E; Silva-Lopez, Elsa; Twamley, Brendan
2008-04-07
Reaction of [NEt4]2[ReBr3(CO)3] with 2,4-pentanedione (acac) yields a complex of the type fac-Re(acac)(OH2)(CO)3 (1) under aqueous conditions. 1 was further reacted with a monodentate ligand (pyridine) to yield a fac-Re(acac)(pyridine)(CO)3 complex (2). Complex 1 was found to react with primary amines to generate a Schiff base (imine) in aqueous solutions. When a mixed-nitrogen donor bidentate ligand, 2-(2-aminoethyl)pyridine, that has different coordination affinities for fac-Re(acac)(OH2)(CO)3 was utilized, a unique tridentate ligand was formed in situ utilizing a metal-assisted Schiff base formation to yield a complex fac-Re(CO)3(3[(2-phenylethyl)imino]-2-pentanone) (3). Tridentate ligand formation was found to occur only with the Re-coordinated acac ligand. Reactions of acac with fac-Re(CO)3Br(2-(2-aminoethyl)pyridine) (4) or a mixture of [NEt4]2[ReBr3(CO)3], acac, and 2-(2-aminoethyl)pyridine did not yield the formation of complex 3 in water.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Kroupa, Daniel M.; Arias, Dylan H.; Blackburn, Jeffrey L.
We have prepared a series of samples with the ligand 6,13-bistri(iso-propyl)silylethynyl tetracene 2-carboxylic acid (TIPS-Tc-COOH) attached to PbS quantum dot (QD) samples of three different sizes in order to monitor and control the extent and time scales of energy flow after photoexcitation. Fast energy transfer (~1 ps) to the PbS QD occurs upon direct excitation of the ligand for all samples. The largest size QD maintains the microsecond exciton lifetime characteristic of the as-prepared oleate terminated PbS QDs. However, two smaller QD sizes with lowest exciton energies similar to or larger than the TIPS-Tc-COO- triplet energy undergo energy transfer betweenmore » QD core and ligand triplet on nanosecond to microsecond timescales. For the intermediate size QDs in particular, energy can be recycled many times between ligand and core, but the triplet remains the dominant excited species at long times, living for ~3 us for fully exchanged QDs and up to 30 us for partial ligand exchange, which is revealed as a method for controlling the triplet lifetime. A unique upconverted luminescence spectrum is observed that results from annihilation of triplets after exclusive excitation of the QD core.« less
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Kroupa, Daniel M.; Arias, Dylan H.; Blackburn, Jeffrey L.; ...
2018-01-24
We have prepared a series of samples with the ligand 6,13-bistri(iso-propyl)silylethynyl tetracene 2-carboxylic acid (TIPS-Tc-COOH) attached to PbS quantum dot (QD) samples of three different sizes in order to monitor and control the extent and time scales of energy flow after photoexcitation. Fast energy transfer (~1 ps) to the PbS QD occurs upon direct excitation of the ligand for all samples. The largest size QD maintains the microsecond exciton lifetime characteristic of the as-prepared oleate terminated PbS QDs. However, two smaller QD sizes with lowest exciton energies similar to or larger than the TIPS-Tc-COO- triplet energy undergo energy transfer betweenmore » QD core and ligand triplet on nanosecond to microsecond timescales. For the intermediate size QDs in particular, energy can be recycled many times between ligand and core, but the triplet remains the dominant excited species at long times, living for ~3 us for fully exchanged QDs and up to 30 us for partial ligand exchange, which is revealed as a method for controlling the triplet lifetime. A unique upconverted luminescence spectrum is observed that results from annihilation of triplets after exclusive excitation of the QD core.« less
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de Bellefeuille, David; Askari, Mohammad S; Lassalle-Kaiser, Benedikt; Journaux, Yves; Aukauloo, Ally; Orio, Maylis; Thomas, Fabrice; Ottenwaelder, Xavier
2012-12-03
Substitution on the aromatic bridge of a nickel(II) salophen complex with electron-donating dimethylamino substituents creates a ligand with three stable, easily and reversibly accessible oxidation states. The one-electron-oxidized product is characterized as a nickel(II) radical complex with the radical bore by the central substituted aromatic ring, in contrast to other nickel(II) salen or salophen complexes that oxidize on the phenolate moieties. The doubly oxidized product, a singlet species, is best described as having an iminobenzoquinone bridge with a vinylogous distribution of bond lengths between the dimethylamino substituents. Protonation of the dimethylamino substituents inhibits these redox processes on the time scale of cyclovoltammetry, but electrolysis and chemical oxidation are consistent with deprotonation occurring concomitantly with electron transfer to yield the mono- and dioxidized species described above.
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NASA Astrophysics Data System (ADS)
Luo, Yi-Ming; Chen, Zhe; Tang, Rui-Ren; Xiao, Lin-Xiang; Peng, Hong-Jian
2008-02-01
A novel bis- β-diketon ligand, 1,1'-(2,6-bispyridyl)bis-3-phenyl-1,3-propane-dione (L), was designed and synthesized and its complexes with Eu(III), Tb(III), Sm(III) and Gd(III) ions were successfully prepared. The ligand and the corresponding metal complexes were characterized by elemental analysis, and infrared, mass and proton nuclear magnetic resonance spectroscopy. Analysis of the IR spectra suggested that each of the lanthanide metal ions coordinated to the ligand via the carbonyl oxygen atoms and the nitrogen atom of the pyridine ring. The fluorescence properties of these complexes in solid state were investigated and it was discovered that all of the lanthanide ions could be sensitized by the ligand (L) to some extent. In particular, the Tb(III) complex was an excellent green-emitter and would be a potential candidate material for applications in organic light-emitting devices (OLEDs) and medical diagnosis.
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A grand unified model for liganded gold clusters
NASA Astrophysics Data System (ADS)
Xu, Wen Wu; Zhu, Beien; Zeng, Xiao Cheng; Gao, Yi
2016-12-01
A grand unified model (GUM) is developed to achieve fundamental understanding of rich structures of all 71 liganded gold clusters reported to date. Inspired by the quark model by which composite particles (for example, protons and neutrons) are formed by combining three quarks (or flavours), here gold atoms are assigned three `flavours' (namely, bottom, middle and top) to represent three possible valence states. The `composite particles' in GUM are categorized into two groups: variants of triangular elementary block Au3(2e) and tetrahedral elementary block Au4(2e), all satisfying the duet rule (2e) of the valence shell, akin to the octet rule in general chemistry. The elementary blocks, when packed together, form the cores of liganded gold clusters. With the GUM, structures of 71 liganded gold clusters and their growth mechanism can be deciphered altogether. Although GUM is a predictive heuristic and may not be necessarily reflective of the actual electronic structure, several highly stable liganded gold clusters are predicted, thereby offering GUM-guided synthesis of liganded gold clusters by design.
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Cloud Computing for Protein-Ligand Binding Site Comparison
2013-01-01
The proteome-wide analysis of protein-ligand binding sites and their interactions with ligands is important in structure-based drug design and in understanding ligand cross reactivity and toxicity. The well-known and commonly used software, SMAP, has been designed for 3D ligand binding site comparison and similarity searching of a structural proteome. SMAP can also predict drug side effects and reassign existing drugs to new indications. However, the computing scale of SMAP is limited. We have developed a high availability, high performance system that expands the comparison scale of SMAP. This cloud computing service, called Cloud-PLBS, combines the SMAP and Hadoop frameworks and is deployed on a virtual cloud computing platform. To handle the vast amount of experimental data on protein-ligand binding site pairs, Cloud-PLBS exploits the MapReduce paradigm as a management and parallelizing tool. Cloud-PLBS provides a web portal and scalability through which biologists can address a wide range of computer-intensive questions in biology and drug discovery. PMID:23762824
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A grand unified model for liganded gold clusters
Xu, Wen Wu; Zhu, Beien; Zeng, Xiao Cheng; Gao, Yi
2016-01-01
A grand unified model (GUM) is developed to achieve fundamental understanding of rich structures of all 71 liganded gold clusters reported to date. Inspired by the quark model by which composite particles (for example, protons and neutrons) are formed by combining three quarks (or flavours), here gold atoms are assigned three ‘flavours' (namely, bottom, middle and top) to represent three possible valence states. The ‘composite particles' in GUM are categorized into two groups: variants of triangular elementary block Au3(2e) and tetrahedral elementary block Au4(2e), all satisfying the duet rule (2e) of the valence shell, akin to the octet rule in general chemistry. The elementary blocks, when packed together, form the cores of liganded gold clusters. With the GUM, structures of 71 liganded gold clusters and their growth mechanism can be deciphered altogether. Although GUM is a predictive heuristic and may not be necessarily reflective of the actual electronic structure, several highly stable liganded gold clusters are predicted, thereby offering GUM-guided synthesis of liganded gold clusters by design. PMID:27910848
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The energy and work of a ligand-gated ion channel
Auerbach, Anthony
2015-01-01
Ligand-gated ion channels are allosteric membrane proteins that isomerize between C(losed) and O(pen) conformations. A difference in affinity for ligands in the two shapes influences the C↔O ‘gating’ equilibrium constant. The energies associated with adult-type mouse neuromuscular nicotinic acetylcholine receptor-channel (AChR) gating have been measured by using single-channel electrophysiology. Without ligands the free energy, enthalpy and entropy of gating are ΔG0=+8.4, ΔH0=+10.9 and ΔS0=+2.4 kcal/mol (−100 mV, 23 °C). Many mutations throughout the protein change ΔG0, including natural ones that cause disease. Agonists and most mutations change approximately independently the ground state energy difference, so it is possible to forecast and engineer AChR responses simply by combining perturbations. The free energy of the low↔high affinity change for the neurotransmitter at each of two functionally-equivalent binding sites is ΔGBACh=−5.1 kcal/mol. ΔGBACh is set mainly by interactions of ACh with just three binding site aromatic groups. For a series of structurally-related agonists there is a correlation between the energies of low- and high-affinity binding, which implies that gating commences with the formation of the low affinity complex. Brief, intermediate states in binding and gating have been detected. Several proposals for the nature of the gating transition state energy landscape and the isomerization mechanism are discussed. PMID:23357172
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2012-01-01
Background Research interest in phosphonates metal organic frameworks (MOF) has increased extremely in the last two decades, because of theirs fascinating and complex topology and structural flexibility. In this paper we present a mathematical model for ligand/metal ion ratio of an octahedral (Oh) network of cobalt vinylphosphonate (Co(vP)·H2O). Results A recurrent relationship of the ratio between the number of ligands and the number of metal ions in a lamellar octahedral (Oh) network Co(vP)·H2O, has been deducted by building the 3D network step by step using HyperChem 7.52 package. The mathematical relationship has been validated using X ray analysis, experimental thermogravimetric and elemental analysis data. Conclusions Based on deducted recurrence relationship, we can conclude prior to perform X ray analysis, that in the case of a thermogravimetric analysis pointing a ratio between the number of metal ions and ligands number around 1, the 3D network will have a central metal ion that corresponds to a single ligand. This relation is valid for every type of supramolecular network with divalent metal central ion Oh coordinated and bring valuable information with low effort and cost. PMID:22932493
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Dual genetically encoded phage-displayed ligands.
Mohan, Kritika; Weiss, Gregory A
2014-05-15
M13 bacteriophage display presents polypeptides as fusions to phage coat proteins. Such phage-displayed ligands offer useful reagents for biosensors. Here, we report a modified phage propagation protocol for the consistent and robust display of two different genetically encoded ligands on the major coat protein, P8. The results demonstrate that the phage surface reaches a saturation point for maximum peptide display. Copyright © 2014 Elsevier Inc. All rights reserved.
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Wang, Yan; Liang, Wei-Cheng; Pan, Wen-Liang; Law, Wai-Kit; Hu, Jian-Shu; Ip, Denis Tsz-Ming; Waye, Mary Miu-Yee; Ng, Tzi-Bun; Wan, David Chi-Cheong
2014-09-25
C-X-C chemokine receptor type 4 (CXCR4) signaling has been demonstrated to be involved in cancer invasion and migration; therefore, CXCR4 antagonist can serve as an anti-cancer drug by preventing tumor metastasis. This study aimed to identify the CXCR4 antagonists that could reduce and/or inhibit tumor metastasis from natural products. According to the molecular docking screening, we reported here silibinin as a novel CXCR4 antagonist. Biochemical characterization showed that silibinin blocked chemokine ligand 12 (CXCL12)-induced CXCR4 internalization by competitive binding to CXCR4, therefore inhibiting downstream intracellular signaling. In human breast cancer cells MDA-MB-231, which expresses high levels of CXCR4, inhibition of CXCL12-induced chemomigration can be found under silibinin treatment. Overexpression of CXCL12 sensitized MDA-MB-231 cells to the inhibition of silibinin, which was abolished by CXCR4 knockdown. The inhibition of silibinin was also observed in MCF-7/CXCR4 cells rather than MCF-7 cells that express low level of CXCR4. Our work demonstrated that silibinin is a novel CXCR4 antagonist that may have potential therapeutic use for prevention of tumor metastasis. Copyright © 2014 Elsevier GmbH. All rights reserved.
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Muñoz-García, Juan C; Inacio Dos Reis, Rosana; Taylor, Richard J; Henry, Alistair J; Watts, Anthony
2018-05-18
Saturation transfer difference (STD) NMR spectroscopy is one of the most popular ligand-based NMR techniques for the study of protein-ligand interactions. This is due to its robustness and the fact that it is focused on the signals of the ligand, without any need for NMR information on the macromolecular target. This technique is most commonly applied to systems involving different types of ligands (e.g., small organic molecules, carbohydrates or lipids) and a protein as the target, in which the latter is selectively saturated. However, only a few examples have been reported where membrane mimetics are the macromolecular binding partners. Here, we have employed STD NMR spectroscopy to investigate the interactions of the neurotransmitter dopamine with mimetics of lipid bilayers, such as nanodiscs, by saturation of the latter. In particular, the interactions between dopamine and model lipid nanodiscs formed either from charged or zwitterionic lipids have been resolved at the atomic level. The results, in agreement with previous isothermal titration calorimetry studies, show that dopamine preferentially binds to negatively charged model membranes, but also provide detailed atomic insights into the mode of interaction of dopamine with membrane mimetics. Our findings provide relevant structural information for the design of lipid-based drug carriers of dopamine and its structural analogues and are of general applicability to other systems. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Spatiotemporal Targeting of a Dual-Ligand Nanoparticle to Cancer Metastasis.
Doolittle, Elizabeth; Peiris, Pubudu M; Doron, Gilad; Goldberg, Amy; Tucci, Samantha; Rao, Swetha; Shah, Shruti; Sylvestre, Meilyn; Govender, Priya; Turan, Oguz; Lee, Zhenghong; Schiemann, William P; Karathanasis, Efstathios
2015-08-25
Various targeting strategies and ligands have been employed to direct nanoparticles to tumors that upregulate specific cell-surface molecules. However, tumors display a dynamic, heterogeneous microenvironment, which undergoes spatiotemporal changes including the expression of targetable cell-surface biomarkers. Here, we investigated a dual-ligand nanoparticle to effectively target two receptors overexpressed in aggressive tumors. By using two different chemical specificities, the dual-ligand strategy considered the spatiotemporal alterations in the expression patterns of the receptors in cancer sites. As a case study, we used two mouse models of metastasis of triple-negative breast cancer using the MDA-MB-231 and 4T1 cells. The dual-ligand system utilized two peptides targeting P-selectin and αvβ3 integrin, which are functionally linked to different stages of the development of metastatic disease at a distal site. Using in vivo multimodal imaging and post mortem histological analyses, this study shows that the dual-ligand nanoparticle effectively targeted metastatic disease that was otherwise missed by single-ligand strategies. The dual-ligand nanoparticle was capable of capturing different metastatic sites within the same animal that overexpressed either receptor or both of them. Furthermore, the highly efficient targeting resulted in 22% of the injected dual-ligand nanoparticles being deposited in early-stage metastases within 2 h after injection.
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Podocalyxin Is a Glycoprotein Ligand of the Human Pluripotent Stem Cell-Specific Probe rBC2LCN
Tateno, Hiroaki; Matsushima, Asako; Hiemori, Keiko; Onuma, Yasuko; Ito, Yuzuru; Hasehira, Kayo; Nishimura, Ken; Ohtaka, Manami; Takayasu, Satoko; Nakanishi, Mahito; Ikehara, Yuzuru; Nakanishi, Mio; Ohnuma, Kiyoshi; Chan, Techuan; Toyoda, Masashi; Akutsu, Hidenori; Umezawa, Akihiro; Asashima, Makoto
2013-01-01
In comprehensive glycome analysis with a high-density lectin microarray, we have previously shown that the recombinant N-terminal domain of the lectin BC2L-C from Burkholderia cenocepacia (rBC2LCN) binds exclusively to undifferentiated human induced pluripotent stem (iPS) cells and embryonic stem (ES) cells but not to differentiated somatic cells. Here we demonstrate that podocalyxin, a heavily glycosylated type 1 transmembrane protein, is a glycoprotein ligand of rBC2LCN on human iPS cells and ES cells. When analyzed by DNA microarray, podocalyxin was found to be highly expressed in both iPS cells and ES cells. Western and lectin blotting revealed that rBC2LCN binds to podocalyxin with a high molecular weight of more than 240 kDa in undifferentiated iPS cells of six different origins and four ES cell lines, but no binding was observed in either differentiated mouse feeder cells or somatic cells. The specific binding of rBC2LCN to podocalyxin prepared from a large set of iPS cells (138 types) and ES cells (15 types) was also confirmed using a high-throughput antibody-overlay lectin microarray. Alkaline digestion greatly reduced the binding of rBC2LCN to podocalyxin, indicating that the major glycan ligands of rBC2LCN are presented on O-glycans. Furthermore, rBC2LCN was found to exhibit significant affinity to a branched O-glycan comprising an H type 3 structure (Ka, 2.5 × 104 M−1) prepared from human 201B7 iPS cells, indicating that H type 3 is a most probable potential pluripotency marker. We conclude that podocalyxin is a glycoprotein ligand of rBC2LCN on human iPS cells and ES cells. PMID:23526252
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The role of ligands in coinage-metal nanoparticles for electronics
Kanelidis, Ioannis
2017-01-01
Coinage-metal nanoparticles are key components of many printable electronic inks. They can be combined with polymers to form conductive composites and have been used as the basis of molecular electronic devices. This review summarizes the multidimensional role of surface ligands that cover their metal cores. Ligands not only passivate crystal facets and determine growth rates and shapes; they also affect size and colloidal stability. Particle shapes can be tuned via the ligand choice while ligand length, size, ω-functionalities, and chemical nature influence shelf-life and stability of nanoparticles in dispersions. When particles are deposited, ligands affect the electrical properties of the resulting film, the morphology of particle films, and the nature of the interfaces. The effects of the ligands on sintering, cross-linking, and self-assembly of particles in electronic materials are discussed. PMID:29259877
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Polymerization catalysts containing electron-withdrawing amide ligands
Watkin, John G.; Click, Damon R.
2002-01-01
The present invention describes methods of making a series of amine-containing organic compounds which are used as ligands for group 3-10 and lanthanide metal compounds. The ligands have electron-withdrawing groups bonded to them. The metal compounds, when combined with a cocatalyst, are catalysts for the polymerization of olefins.
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Selectivity in ligand recognition of G-quadruplex loops.
Campbell, Nancy H; Patel, Manisha; Tofa, Amina B; Ghosh, Ragina; Parkinson, Gary N; Neidle, Stephen
2009-03-03
A series of disubstituted acridine ligands have been cocrystallized with a bimolecular DNA G-quadruplex. The ligands have a range of cyclic amino end groups of varying size. The crystal structures show that the diagonal loop in this quadruplex results in a large cavity for these groups, in contrast to the steric constraints imposed by propeller loops in human telomeric quadruplexes. We conclude that the nature of the loop has a significant influence on ligand selectivity for particular quadruplex folds.
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Sigma Receptor (σR) Ligands with Antiproliferative and Anticancer Activity.
Georgiadis, Markos-Orestis; Karoutzou, Olga; Foscolos, Angeliki-Sofia; Papanastasiou, Ioannis
2017-08-25
Sigma receptor (σR) ligands have proven to be useful as cancer diagnostics and anticancer therapeutics and their ligands have been developed as molecular probes in oncology. Moreover, various σR ligands generate cancer cell death in vitro and in vivo. These σR ligands have exhibited promising results against numerous human and rodent cancers and are investigated under preclinical and clinical study trials, indicating a new category of drugs in cancer therapy.
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Synthesis, structures and properties of three copper complexes with dibutyldithiocarbamate ligand
NASA Astrophysics Data System (ADS)
Wang, Chen; Niu, Jiao; Li, Jun; Ma, Xiaoxun
2017-05-01
Three copper complexes constructed with sulfur-containing dibutyldithiocarbamate ligand (DDTC), [(Et2NCS2)4Cu2] (1), [(Et2NCS2)(EtO)Cu]2 (2) and [(Et2NCS2)6Cu13I10]n (3) have been synthesized through the reaction of CuI with different mole ratios of DDTC under solution-diffusion conditions. The single crystal X-ray diffraction revealed that divalent Cu cations in complexes 1 and 2 imply that the reactant, Cu(I), was involved in the redox process. They formed binuclear complexes according to bridging S from DDTC ligands and O atoms from ethanol molecules respectively. The mixed valence Cu cations had two types of coordination environments in complex 3 and formed a two-dimensional layered coordination polymer by bridging the five-core Cu(I) clusters and Cu(II). The powder X-ray diffraction, luminescent, thermogravimetric analysis, etc. were also studied in this paper.
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Charfi, Iness; Nagi, Karim; Mnie-Filali, Ouissame; Thibault, Dominic; Balboni, Gianfranco; Schiller, Peter W.; Trudeau, Louis-Eric
2014-01-01
Signaling bias refers to G protein-coupled receptor ligand ability to preferentially activate one type of signal over another. Bias to evoke signaling as opposed to sequestration has been proposed as a predictor of opioid ligand potential for generating tolerance. Here we measured whether delta opioid receptor agonists preferentially inhibited cyclase activity over internalization in HEK cells. Efficacy (τ) and affinity (KA) values were estimated from functional data and bias was calculated from efficiency coefficients (log τ/KA). This approach better represented the data as compared to alternative methods that estimate bias exclusively from τ values. Log (τ/KA) coefficients indicated that SNC-80 and UFP-512 promoted cyclase inhibition more efficiently than DOR internalization as compared to DPDPE (bias factor for SNC-80: 50 and for UFP-512: 132). Molecular determinants of internalization were different in HEK293 cells and neurons with βarrs contributing to internalization in both cell types, while PKC and GRK2 activities were only involved in neurons. Rank orders of ligand ability to engage different internalization mechanisms in neurons were compared to rank order of Emax values for cyclase assays in HEK cells. Comparison revealed a significant reversal in rank order for cyclase Emax values and βarr-dependent internalization in neurons, indicating that these responses were ligand-specific. Despite this evidence, and because kinases involved in internalization were not the same across cellular backgrounds, it is not possible to assert if the magnitude and nature of bias revealed by rank orders of maximal responses is the same as the one measured in HEK cells. PMID:24022593
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Ligand Entry and Exit Pathways in the β2-adrenergic Receptor
Wang, Ting; Duan, Yong
2009-01-01
The recently determined crystal structure of the human β2-adrenergic (β2AR) G-protein coupled receptor provides an excellent structural basis for exploring β2AR -ligand binding and dissociation process. Based on this crystal structure, we simulated ligand exit from the β2AR receptor by applying the random acceleration molecular dynamics (RAMD) simulation method. The simulation results showed that the extracellular opening on the receptor surface was the most frequently observed egress point (referred to as pathway A) and a few other pathways through inter-helical clefts were also observed with significantly lower frequencies. In the egress trajectories along pathway A, the D192-K305 salt bridge between the extracellular loop 2 (ECL2) and the apex of the transmembrane helix 7 (TM7) was exclusively broken. The spatial occupancy maps of the ligand computed from the 100 RAMD simulation trajectories indicated that the receptor-ligand interactions that restrained the ligand in the binding pocket were the major resistance encountered by the ligand during exit and no second barrier was notable. We next performed RAMD simulations by using a putative ligand-free conformation of the receptor as input structure. This conformation was obtained in a standard MD simulation in the absence of the ligand and it differed from the ligand-bound conformation in a hydrophobic patch bridging ECL2 and TM7 due to the rotation of F193 of ECL2. Results from the RAMD simulations with this putative ligand-free conformation suggest that the cleft formed by the hydrophobic bridge, TM2, TM3 and TM7 on the extracellular surface likely serves as a more specific ligand-entry site and the ECL2-TM7 hydrophobic junction can be partially interrupted upon the entry of ligand that pushes F193 to rotate, resulting in a conformation as observed in the ligand-bound crystal structure. These results may help design β2AR-targeting drugs with improved efficacy as well as understand the receptor subtype
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New ligands for melanocortin receptors.
Kaelin, C B; Candille, S I; Yu, B; Jackson, P; Thompson, D A; Nix, M A; Binkley, J; Millhauser, G L; Barsh, G S
2008-12-01
Named originally for their effects on peripheral end organs, the melanocortin system controls a diverse set of physiological processes through a series of five G-protein-coupled receptors and several sets of small peptide ligands. The central melanocortin system plays an essential role in homeostatic regulation of body weight, in which two alternative ligands, alpha-melanocyte-stimulating hormone and agouti-related protein, stimulate and inhibit receptor signaling in several key brain regions that ultimately affect food intake and energy expenditure. Much of what we know about the relationship between central melanocortin signaling and body weight regulation stems from genetic studies. Comparative genomic studies indicate that melanocortin receptors used for controlling pigmentation and body weight regulation existed more than 500 million years ago in primitive vertebrates, but that fine-grained control of melanocortin receptors through neuropeptides and endogenous antagonists developed more recently. Recent studies based on dog coat-color genetics revealed a new class of melanocortin ligands, the beta-defensins, which reveal the potential for cross talk between the melanocortin and the immune systems.
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Mote, Nilesh R; Patel, Ketan; Shinde, Dinesh R; Gaikwad, Shahaji R; Koshti, Vijay S; Gonnade, Rajesh G; Chikkali, Samir H
2017-10-16
Self-assembly of two neutral ligands on a metal to mimic bidentate ligand coordination has been frequently encountered in the recent past, but self-assembly of an anionic ligand on a metal template alongside a neutral ligand remains an elusive target. Such a self-assembly is hampered by additional complexity, wherein a highly negatively charged anion can form intermolecular hydrogen bonding with the supramolecular motif, leaving no scope for self-assembly with neutral ligand. Presented here is the self-association of anionic ligand 3-ureidobenzoic acid (2a) and neutral ligand 1-(3-(diphenylphosphanyl)phenyl)urea (1a) on a metal template to yield metal complex [{COOC 6 H 4 NH(CO)NH 2 }{Ph 2 PC 6 H 4 NH(CO)NH 2 }PdMeDMSO] (4a). The identity of 4a was established by NMR and mass spectroscopy. Along the same lines, 3-(3-phenylureido)benzoic acid (2b) and 1-(3-(diphenylphosphanyl)phenyl)-3-phenylurea (1b) self-assemble on a metal template to produce palladium complex [{COOC 6 H 4 NH(CO)NHPh}{Ph 2 PC 6 H 4 NH(CO)NHPh}PdMePy] (5c). The existence of 5c was confirmed by Job plot, 1-2D NMR spectroscopy, deuterium labeling, IR spectroscopy, UV-vis spectroscopy, model complex synthesis, and DFT calculations. These solution and gas phase investigations authenticated the presence of intramolecular hydrogen bonding between hydrogen's of 1b and carbonyl oxygen of 2b. The generality of the supramolecular approach has been validated by preparing six complexes from four monodentate ligands, and their synthetic utility was demonstrated in ethylene polymerization. Complex 4a was found to be the most active, leading to the production of highly branched polyethylene with a molecular weight of 55700 g/mol and melting temperature of 112 °C.
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Atomic resolution mechanism of ligand binding to a solvent inaccessible cavity in T4 lysozyme
Ahalawat, Navjeet; Pandit, Subhendu; Kay, Lewis E.
2018-01-01
Ligand binding sites in proteins are often localized to deeply buried cavities, inaccessible to bulk solvent. Yet, in many cases binding of cognate ligands occurs rapidly. An intriguing system is presented by the L99A cavity mutant of T4 Lysozyme (T4L L99A) that rapidly binds benzene (~106 M-1s-1). Although the protein has long served as a model system for protein thermodynamics and crystal structures of both free and benzene-bound T4L L99A are available, the kinetic pathways by which benzene reaches its solvent-inaccessible binding cavity remain elusive. The current work, using extensive molecular dynamics simulation, achieves this by capturing the complete process of spontaneous recognition of benzene by T4L L99A at atomistic resolution. A series of multi-microsecond unbiased molecular dynamics simulation trajectories unequivocally reveal how benzene, starting in bulk solvent, diffuses to the protein and spontaneously reaches the solvent inaccessible cavity of T4L L99A. The simulated and high-resolution X-ray derived bound structures are in excellent agreement. A robust four-state Markov model, developed using cumulative 60 μs trajectories, identifies and quantifies multiple ligand binding pathways with low activation barriers. Interestingly, none of these identified binding pathways required large conformational changes for ligand access to the buried cavity. Rather, these involve transient but crucial opening of a channel to the cavity via subtle displacements in the positions of key helices (helix4/helix6, helix7/helix9) leading to rapid binding. Free energy simulations further elucidate that these channel-opening events would have been unfavorable in wild type T4L. Taken together and via integrating with results from experiments, these simulations provide unprecedented mechanistic insights into the complete ligand recognition process in a buried cavity. By illustrating the power of subtle helix movements in opening up multiple pathways for ligand access
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Free-energy relationships in ion channels activated by voltage and ligand
Chowdhury, Sandipan
2013-01-01
Many ion channels are modulated by multiple stimuli, which allow them to integrate a variety of cellular signals and precisely respond to physiological needs. Understanding how these different signaling pathways interact has been a challenge in part because of the complexity of underlying models. In this study, we analyzed the energetic relationships in polymodal ion channels using linkage principles. We first show that in proteins dually modulated by voltage and ligand, the net free-energy change can be obtained by measuring the charge-voltage (Q-V) relationship in zero ligand condition and the ligand binding curve at highly depolarizing membrane voltages. Next, we show that the voltage-dependent changes in ligand occupancy of the protein can be directly obtained by measuring the Q-V curves at multiple ligand concentrations. When a single reference ligand binding curve is available, this relationship allows us to reconstruct ligand binding curves at different voltages. More significantly, we establish that the shift of the Q-V curve between zero and saturating ligand concentration is a direct estimate of the interaction energy between the ligand- and voltage-dependent pathway. These free-energy relationships were tested by numerical simulations of a detailed gating model of the BK channel. Furthermore, as a proof of principle, we estimate the interaction energy between the ligand binding and voltage-dependent pathways for HCN2 channels whose ligand binding curves at various voltages are available. These emerging principles will be useful for high-throughput mutagenesis studies aimed at identifying interaction pathways between various regulatory domains in a polymodal ion channel. PMID:23250866
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Probing interaction of a fluorescent ligand with HIV TAR RNA
NASA Astrophysics Data System (ADS)
Qi, Liang; Zhang, Jing; He, Tian; Huo, Yuan; Zhang, Zhi-Qi
2017-02-01
Trans-activator of Transcription (Tat) antagonists could block the interaction between Tat protein and its target, trans-activation responsive region (TAR) RNA, to inhibit Tat function and prevent human immunodeficiency virus type 1 (HIV-1) replication. For the first time, a small fluorescence ligand, ICR 191, was found to interact with TAR RNA at the Tat binding site and compete with Tat. It was also observed that the fluorescence of ICR 191 could be quenched when binding to TAR RNA and recovered when discharged via competition with Tat peptide or a well-known Tat inhibitor, neomycin B. The binding parameters of ICR 191 to TAR RNA were determined through theoretical calculations. Mass spectrometry, circular dichroism and molecular docking were used to further confirm the interaction of ICR 191 with TAR RNA. Inspired by these discoveries, a primary fluorescence model for the discovery of Tat antagonists was built using ICR 191 as a fluorescence indicator and the feasibility of this model was evaluated. This ligand-RNA interaction could provide a new strategy for research aimed at discovering Tat antagonists.
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Identification and characterization of PPARα ligands in the hippocampus
Roy, Avik; Kundu, Madhuchhanda; Jana, Malabendu; Mishra, Rama K.; Yung, Yeni; Luan, Chi-Hao; Gonzalez, Frank J.; Pahan, Kalipada
2016-01-01
Peroxisome proliferator-activated receptor alpha (PPARα) regulates hepatic fatty acid catabolism and mediates the metabolic response to starvation. Recently, we have found that PPARα is constitutively activated in nuclei of hippocampal neurons and controls plasticity via direct transcriptional activation of CREB. Here, three endogenous ligands of PPARα, 3-hydroxy-(2,2)-dimethyl butyrate, hexadecanamide, and 9-octadecenamide were discovered in mouse brain hippocampus. Mass spectrometric detection of these compounds in mouse hippocampal nuclear extracts, in silico interaction studies, time-resolved FRET analyses, and thermal shift assay clearly indicated that these three compounds served as ligands of PPARα. Site-directed mutagenesis studies further revealed that PPARα Tyr 464 and Tyr 314 were involved in binding these hippocampal ligands. Moreover, these ligands activated PPARα and upregulated synaptic function of hippocampal neurons. These results highlight the discovery of hippocampal ligands of PPARα capable of modulating synaptic functions. PMID:27748752
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Identification and characterization of PPARα ligands in the hippocampus.
Roy, Avik; Kundu, Madhuchhanda; Jana, Malabendu; Mishra, Rama K; Yung, Yeni; Luan, Chi-Hao; Gonzalez, Frank J; Pahan, Kalipada
2016-12-01
Peroxisome proliferator-activated receptor-α (PPARα) regulates hepatic fatty acid catabolism and mediates the metabolic response to starvation. Recently we found that PPARα is constitutively activated in nuclei of hippocampal neurons and controls plasticity via direct transcriptional activation of CREB. Here we report the discovery of three endogenous PPARα ligands-3-hydroxy-(2,2)-dimethyl butyrate, hexadecanamide, and 9-octadecenamide-in mouse brain hippocampus. Mass spectrometric detection of these compounds in mouse hippocampal nuclear extracts, in silico interaction studies, time-resolved FRET analyses, and thermal shift assay results clearly indicated that these three compounds served as ligands of PPARα. Site-directed mutagenesis studies further revealed that PPARα Y464 and Y314 are involved in binding these hippocampal ligands. Moreover, these ligands activated PPARα and upregulated the synaptic function of hippocampal neurons. These results highlight the discovery of hippocampal ligands of PPARα capable of modulating synaptic functions.
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NASA Astrophysics Data System (ADS)
Vlasenko, Valery G.; Vasilchenko, Igor S.; Pirog, Irina V.; Shestakova, Tatiana E.; Uraev, Ali I.; Burlov, Anatolii S.; Garnovskii, Alexander D.
2007-02-01
Binuclear copper complexes are known to be models for metalloenzymes containing copper active sites, and some of them are of considerable interest due to their magnetic and charge transfer properties. The reactions of the complex formation of bibasic tridentate heterocyclic imines with copper acetate leads to two types of chelates with mono deprotonated ligands and with totally deprotonated ligands. Cu K-edge EXAFS has been applied to determine the local structure around the metal center in copper(II) azomethine complexes with five tridentate ligands: 1-(salycilideneimino)- or 1-(2-tosylaminobenzilideneimino)-2-amino(oxo, thio)benzimidazoles. It has been found that some of the chelates studied are bridged binuclear copper complexes, and others are mononuclear complexes. The copper-copper interatomic distances in the bridged binuclear copper complexes were found to be 2.85-3.01 Å. Variable temperature magnetic susceptibility data indicate the presence of both ferromagnetic and antiferromagnetic interactions within the dimer, the former is dominating at low temperatures and the latter at high temperatures.
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Ligand-protein docking using a quantum stochastic tunneling optimization method.
Mancera, Ricardo L; Källblad, Per; Todorov, Nikolay P
2004-04-30
A novel hybrid optimization method called quantum stochastic tunneling has been recently introduced. Here, we report its implementation within a new docking program called EasyDock and a validation with the CCDC/Astex data set of ligand-protein complexes using the PLP score to represent the ligand-protein potential energy surface and ScreenScore to score the ligand-protein binding energies. When taking the top energy-ranked ligand binding mode pose, we were able to predict the correct crystallographic ligand binding mode in up to 75% of the cases. By using this novel optimization method run times for typical docking simulations are significantly shortened. Copyright 2004 Wiley Periodicals, Inc. J Comput Chem 25: 858-864, 2004
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Use of microelectrodes for electrochemical measurement of nitric oxide in natural seawater
NASA Astrophysics Data System (ADS)
Zhang, Zhengbin; Xing, Lei; Cai, Weijun; Ren, Chunyan; Jiang, Liqing
2004-12-01
In this paper, the application of a homemade Nafion and Co(Salen) modified platinum microelectrode and an ISO-NOPMC microsensor (World Precision Instruments, USA) to measure nitric oxide in natural seawater is reported. These two microelectrodes are suitable for the measurement. In natural seawater, the sensitivity and stability of the ISO-NOPMC microsensor are higher than that of the homemade Nafion and Co(Salen) modified platinum microelectrode.
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Spatiotemporal Targeting of a Dual-Ligand Nanoparticle to Cancer Metastasis
Doolittle, Elizabeth; Peiris, Pubudu M.; Doron, Gilad; Goldberg, Amy; Tucci, Samantha; Rao, Swetha; Shah, Shruti; Sylvestre, Meilyn; Govender, Priya; Turan, Oguz; Lee, Zhenghong; Schiemann, William P.; Karathanasis, Efstathios
2015-01-01
Various targeting strategies and ligands have been employed to direct nanoparticles to tumors that upregulate specific cell-surface molecules. However, tumors display a dynamic, heterogeneous microenvironment, which undergoes spatiotemporal changes including the expression of targetable cell-surface biomarkers. Here, we investigated a dual-ligand nanoparticle to effectively target two receptors overexpressed in aggressive tumors. By using two different chemical specificities, the dual-ligand strategy considered the spatiotemporal alterations in the expression patterns of the receptors in cancer sites. As a case study, we used two mouse models of metastasis of triple-negative breast cancer using the MDA-MB-231 and 4T1 cells. The dual-ligand system utilized two peptides targeting P-selectin and αvβ3 integrin, which are functionally linked to different stages of the development of metastatic disease at a distal site. Using in vivo multimodal imaging and post mortem histological analyses, this study shows that the dual-ligand nanoparticle effectively targeted metastatic disease that was otherwise missed by single-ligand strategies. The dual-ligand nanoparticle was capable of capturing different metastatic sites within the same animal that overexpressed either receptor or both of them. Furthermore, the highly efficient targeting resulted in 22% of the injected dual-ligand nanoparticles being deposited in early-stage metastases within 2 h after injection. PMID:26203676
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Improved ligand geometries in crystallographic refinement using AFITT in PHENIX
Janowski, Pawel A.; Moriarty, Nigel W.; Kelley, Brian P.; ...
2016-08-31
Modern crystal structure refinement programs rely on geometry restraints to overcome the challenge of a low data-to-parameter ratio. While the classical Engh and Huber restraints work well for standard amino-acid residues, the chemical complexity of small-molecule ligands presents a particular challenge. Most current approaches either limit ligand restraints to those that can be readily described in the Crystallographic Information File (CIF) format, thus sacrificing chemical flexibility and energetic accuracy, or they employ protocols that substantially lengthen the refinement time, potentially hindering rapid automated refinement workflows.PHENIX–AFITTrefinement uses a full molecular-mechanics force field for user-selected small-molecule ligands during refinement, eliminating the potentiallymore » difficult problem of finding or generating high-quality geometry restraints. It is fully integrated with a standard refinement protocol and requires practically no additional steps from the user, making it ideal for high-throughput workflows.PHENIX–AFITTrefinements also handle multiple ligands in a single model, alternate conformations and covalently bound ligands. Here, the results of combiningAFITTand thePHENIXsoftware suite on a data set of 189 protein–ligand PDB structures are presented. Refinements usingPHENIX–AFITTsignificantly reduce ligand conformational energy and lead to improved geometries without detriment to the fit to the experimental data. Finally, for the data presented,PHENIX–AFITTrefinements result in more chemically accurate models for small-molecule ligands.« less
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Deciphering CD30 ligand biology and its role in humoral immunity
Kennedy, Mary K; Willis, Cynthia R; Armitage, Richard J
2006-01-01
Ligands and receptors in the tumour necrosis factor (TNF) and tumour necrosis factor receptor (TNFR) superfamilies have been the subject of extensive investigation over the past 10–15 years. For certain TNFR family members, such as Fas and CD40, some of the consequences of receptor ligation were predicted before the identification and cloning of their corresponding ligands through in vitro functional studies using agonistic receptor-specific antibodies. For other members of the TNFR family, including CD30, cross-linking the receptor with specific antibodies failed to yield many clues about the functional significance of the relevant ligand–receptor interactions. In many instances, the subsequent availability of TNF family ligands in the form of recombinant protein facilitated the determination of biological consequences of interactions with their relevant receptor in both in vitro and in vivo settings. In the case of CD30 ligand (CD30L; CD153), definition of its biological role remained frustratingly elusive. Early functional studies using CD30L+ cells or agonistic CD30-specific antibodies logically focused attention on cell types that had been shown to express CD30, namely certain lymphoid malignancies and subsets of activated T cells. However, it was not immediately clear how the reported activities from these in vitro studies relate to the biological activity of CD30L in the more complex whole animal setting. Recently, results from in vivo models involving CD30 or CD30L gene disruption, CD30L overexpression, or pharmacological blockade of CD30/CD30L interactions have begun to provide clues about the role played by CD30L in immunological processes. In this review we consider the reported biology of CD30L and focus on results from several recent studies that point to an important role for CD30/CD30L interactions in humoral immune responses. PMID:16771849
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Myint, Kyaw Z.; Xie, Xiang-Qun
2015-01-01
This chapter focuses on the fingerprint-based artificial neural networks QSAR (FANN-QSAR) approach to predict biological activities of structurally diverse compounds. Three types of fingerprints, namely ECFP6, FP2, and MACCS, were used as inputs to train the FANN-QSAR models. The results were benchmarked against known 2D and 3D QSAR methods, and the derived models were used to predict cannabinoid (CB) ligand binding activities as a case study. In addition, the FANN-QSAR model was used as a virtual screening tool to search a large NCI compound database for lead cannabinoid compounds. We discovered several compounds with good CB2 binding affinities ranging from 6.70 nM to 3.75 μM. The studies proved that the FANN-QSAR method is a useful approach to predict bioactivities or properties of ligands and to find novel lead compounds for drug discovery research. PMID:25502380
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Wu, Xue; Xiu, Zhilong; Li, Guohui; Luo, Bing-Hao
2013-01-01
The Asp of the RGD motif of the ligand coordinates with the β I domain metal ion dependent adhesion site (MIDAS) divalent cation, emphasizing the importance of the MIDAS in ligand binding. There appears to be two distinct groups of integrins that differ in their ligand binding affinity and adhesion ability. These differences may be due to a specific residue associated with the MIDAS, particularly the β3 residue Ala252 and corresponding Ala in the β1 integrin compared to the analogous Asp residue in the β2 and β7 integrins. Interestingly, mutations in the adjacent to MIDAS (ADMIDAS) of integrins α4β7 and αLβ2 increased the binding and adhesion abilities compared to the wild-type, while the same mutations in the α2β1, α5β1, αVβ3, and αIIbβ3 integrins demonstrated decreased ligand binding and adhesion. We introduced a mutation in the αIIbβ3 to convert this MIDAS associated Ala252 to Asp. By combination of this mutant with mutations of one or two ADMIDAS residues, we studied the effects of this residue on ligand binding and adhesion. Then, we performed molecular dynamics simulations on the wild-type and mutant αIIbβ3 integrin β I domains, and investigated the dynamics of metal ion binding sites in different integrin-RGD complexes. We found that the tendency of calculated binding free energies was in excellent agreement with the experimental results, suggesting that the variation in this MIDAS associated residue accounts for the differences in ligand binding and adhesion among different integrins, and it accounts for the conflicting results of ADMIDAS mutations within different integrins. This study sheds more light on the role of the MIDAS associated residue pertaining to ligand binding and adhesion and suggests that this residue may play a pivotal role in integrin-mediated cell rolling and firm adhesion. PMID:24116162
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Aza-macrocyclic Triphenylamine Ligands for G-Quadruplex Recognition.
García-España, Enrique Victor; Pont, Isabel; González-García, Jorge; Inclán, Mario; Reynolds, Matthew; Delgado-Pinar, Estefanía; Albelda, M Teresa; Vilar, Ramon
2018-05-16
A new series of triphenylamine-based ligands with one (TPA1PY), two (TPA2PY) or three pending aza-macrocycle(s) (TPA3PY) have been synthesised and studied by means of pH-metric titrations, UV/Vis spectroscopy and fluorescence experiments. The affinity of these ligands for G-quadruplex (G4) DNA and its selectivity over duplex DNA were investigated by FRET melting assays, fluorimetric titrations and circular dichroism (CD) spectroscopy. Interestingly, the interaction of the bi- and specially the tri-branched ligand with G4 leads to a very intense red-shifted fluorescence emission band which may be associated with intermolecular aggregation between the molecule and the DNA. This light-up effect allows the application of the ligands as fluorescence probes to selectivity detect G4. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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In vitro evaluation of biodegradable microspheres with surface-bound ligands.
Keegan, Mark E; Royce, Sara M; Fahmy, Tarek; Saltzman, W Mark
2006-02-21
Protein ligands were conjugated to the surface of biodegradable microspheres. These microsphere-ligand conjugates were then used in two in vitro model systems to evaluate the effect of conjugated ligands on microsphere behavior. Microsphere retention in agarose columns was increased by ligands on the microsphere surface specific for receptors on the agarose matrix. In another experiment, conjugating the lectin Ulex europaeus agglutinin 1 to the microsphere surface increased microsphere adhesion to Caco-2 monolayers compared to control microspheres. This increase in microsphere adhesion was negated by co-administration of l-fucose, indicating that the increase in adhesion is due to specific interaction of the ligand with carbohydrate receptors on the cell surface. These results demonstrate that the ligands conjugated to the microspheres maintain their receptor binding activity and are present on the microsphere surface at a density sufficient to target the microspheres to both monolayers and three-dimensional matrices bearing complementary receptors.
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Schrevel, Marlies; Osse, E Michelle; Prins, Frans A; Trimbos, J Baptist M Z; Fleuren, Gert Jan; Gorter, Arko; Jordanova, Ekaterina S
2017-06-01
In cervical cancer, the epidermal growth factor receptor (EGFR) is overexpressed in 70-90% of the cases and has been associated with poor prognosis. EGFR-based therapy is currently being explored in cervical cancer. We investigated which EGFR ligand is primarily expressed in cervical cancer and which cell type functions as the major source of this ligand. We hypothesized that macrophages are the main source of EGFR ligands and that a paracrine loop between tumor cells and macrophages is responsible for ligand expression. mRNA expression analysis was performed on 32 cervical cancer cases to determine the expression of the EGFR ligands amphiregulin, β-cellulin, epidermal growth factor (EGF), epiregulin, heparin-binding EGF-like growth factor (HB‑EGF) and transforming growth factor α (TGFα). Subsequently, protein expression was determined immunohistochemically on 36 additional cases. To assess whether macrophages are the major source of EGFR ligands, immunohistochemical double staining was performed on four representative tissue slides. Expression of the chemokines granulocyte-macrophage colony-stimulating factor (GM-CSF) and C-C motif ligand 2 (CCL2) was determined by mRNA in situ hybridization. Of the known EGFR ligands, HB‑EGF had the highest mRNA expression and HB‑EGF and EGFR protein expression were highly correlated. Tumor specimens with high EGFR expression showed higher numbers of macrophages, and higher expression of GM-CSF and CCL2, but only a small subset (9%) of macrophages was found to be HB‑EGF-positive. Strikingly, 78% of cervical cancer specimens were found to express HB‑EGF. Standardized assessment of staining intensity, using spectral imaging analysis, showed that HB‑EGF expression was higher in the tumor compartment than in the stromal compartment. These results suggest that HB‑EGF is an important EGFR ligand in cervical cancer and that cervical cancer cells are the predominant source of HB‑EGF. Therefore, we propose an autocrine
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Distinct Iron-binding Ligands in the Upper Water Column at Station ALOHA
NASA Astrophysics Data System (ADS)
Bundy, R.; Boiteau, R.; Repeta, D.
2016-02-01
The distribution and chemical properties of iron-binding organic ligands at station ALOHA were examined using a combination of solid phase extraction (SPE) followed by high pressure liquid chromatography-inductively coupled plasma mass spectrometry (HPLC-ICPMS). HPLC-ICPMS ligand measurements were complemented by competitive ligand exchange adsorptive cathodic stripping voltammetry (CLE-ACSV) analysis using salicylaldoxime as the added ligand. By HPLC-ICPMS, we find enhanced concentrations of distinct naturally-occurring polar iron-binding ligands present at the surface and in the chlorophyll maximum. Lower concentrations were found in the subsurface, where a suite of non-polar ligands was detected. Siderophores were present at the deepest depths sampled at station ALOHA, down to 400m. Incubation studies provided evidence for the production of iron-binding ligands associated with nutrient amended phytoplankton growth in surface waters, and as a result of microbial particle remineralization in the subsurface water column. Ligands classes identified via SPE were then compared to CLE-ACSV ligand measurements, as well as the conditional stability constants measured from model polar and non-polar siderophores, yielding insight to the sources of iron-binding ligands throughout the water column at station ALOHA.
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Resolving DNA-ligand intercalation in the entropic stretching regime
NASA Astrophysics Data System (ADS)
Almaqwashi, Ali A.
Single molecule studies of DNA intercalation are typically conducted by applying stretching forces to obtain force-dependent DNA elongation measurements. The zero-force properties of DNA intercalation are determined by equilibrium and kinetic force-analysis. However, the applied stretching forces that are above the entropic regime (>5 pN) prevent DNA-DNA contact which may eliminate competitive DNA-ligand interactions. In particular, it is noted that cationic mono-intercalators investigated by single molecule force spectroscopy are mostly found to intercalate DNA with single rate, while bulk studies reported additional slower rates. Here, a proposed framework quantifies DNA intercalation by cationic ligands in competition with relatively rapid kinetic DNA-ligand aggregation. At a constant applied force in the entropic stretching regime, the analysis illustrates that DNA intercalation would be measurably optimized only within a narrow range of low ligand concentrations. As DNA intercalators are considered for potential DNA-targeted therapeutics, this analysis provides insights in tuning ligand concertation to maximize therapeutics efficiency.
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NASA Astrophysics Data System (ADS)
Xu, Wen Wu; Zeng, Xiao Cheng; Gao, Yi
2017-05-01
A grand unified model (GUM) has been proposed recently to understand structure anatomy and evolution of liganded gold clusters. In this work, besides the two types of elementary blocks (triangular Au3(2e) and tetrahedral Au4(2e)), we introduce a secondary block, namely, the icosahedral Au13 with 8e valence electrons, noted as Au13(8e). Using this secondary block, structural anatomy and evolution of a special group of liganded gold nanoclusters containing icosahedral Au13 motifs can be conveniently analyzed. In addition, a new ligand-protected cluster Au49(PR3)10(SR)15Cl2 is predicted to exhibit high chemical and thermal stability, suggesting likelihood of its synthesis in the laboratory.
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Lipinski, Christopher A
2016-06-01
The rule of five (Ro5), based on physicochemical profiles of phase II drugs, is consistent with structural limitations in protein targets and the drug target ligands. Three of four parameters in Ro5 are fundamental to the structure of both target and drug binding sites. The chemical structure of the drug ligand depends on the ligand chemistry and design philosophy. Two extremes of chemical structure and design philosophy exist; ligands constructed in the medicinal chemistry synthesis laboratory without input from natural selection and natural product (NP) metabolites biosynthesized based on evolutionary selection. Exceptions to Ro5 are found mostly among NPs. Chemistry chameleon-like behavior of some NPs due to intra-molecular hydrogen bonding as exemplified by cyclosporine A is a strong contributor to NP Ro5 outliers. The fragment derived, drug Navitoclax is an example of the extensive expertise, resources, time and key decisions required for the rare discovery of a non-NP Ro5 outlier. Copyright © 2016 Elsevier B.V. All rights reserved.
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NASA Astrophysics Data System (ADS)
Smirnova, T. D.; Shtykov, S. N.; Kochubei, V. I.; Khryachkova, E. S.
2011-01-01
The complexation of Eu3+ with doxycycline (DC) antibiotic in the presence of several second ligands and surfactant micelles of different types is studied by the spectrophotometric and luminescence methods. It is found that the efficiency of excitation energy transfer in Eu3+-DC chelate depends on the nature of the second ligand and surfactant micelles. Using thenoyltrifluoroacetone (TTA) as an example, it is shown that the second ligand additionally sensitizes the europium fluorescence, and the possibility of intermediate sensitization of DC and then of europium is shown by the example of 1,10-phenanthroline. In all cases, the excitation energy transfer efficiency was increased due to the so-called antenna effect. The decay kinetics of the sensitized fluorescence of the binary and mixed-ligand chelates in aqueous and micellar solutions of nonionic surfactants is studied and the relative quantum yields and lifetimes of fluorescence are determined.
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Gas adsorption and gas mixture separations using mixed-ligand MOF material
Hupp, Joseph T [Northfield, IL; Mulfort, Karen L [Chicago, IL; Snurr, Randall Q [Evanston, IL; Bae, Youn-Sang [Evanston, IL
2011-01-04
A method of separating a mixture of carbon dioxiode and hydrocarbon gas using a mixed-ligand, metal-organic framework (MOF) material having metal ions coordinated to carboxylate ligands and pyridyl ligands.
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Dissecting Orthosteric Contacts for a Reverse-Fragment-Based Ligand Design.
Chandramohan, Arun; Tulsian, Nikhil K; Anand, Ganesh S
2017-08-01
Orthosteric sites on proteins are formed typically from noncontiguous interacting sites in three-dimensional space where the composite binding interaction of a biological ligand is mediated by multiple synergistic interactions of its constituent functional groups. Through these multiple interactions, ligands stabilize both the ligand binding site and the local secondary structure. However, relative energetic contributions of the individual contacts in these protein-ligand interactions are difficult to resolve. Deconvolution of the contributions of these various functional groups in natural inhibitors/ligand would greatly aid in iterative fragment-based drug discovery (FBDD). In this study, we describe an approach of progressive unfolding of a target protein using a gradient of denaturant urea to reveal the individual energetic contributions of various ligand-functional groups to the affinity of the entire ligand. Through calibrated unfolding of two protein-ligand systems: cAMP-bound regulatory subunit of Protein Kinase A (RIα) and IBMX-bound phosphodiesterase8 (PDE8), monitored by amide hydrogen-deuterium exchange mass spectrometry, we show progressive disruption of individual orthosteric contacts in the ligand binding sites, allowing us to rank the energetic contributions of these individual interactions. In the two cAMP-binding sites of RIα, exocyclic phosphate oxygens of cAMP were identified to mediate stronger interactions than ribose 2'-OH in both the RIα-cAMP binding interfaces. Further, we have also ranked the relative contributions of the different functional groups of IBMX based on their interactions with the orthosteric residues of PDE8. This strategy for deconstruction of individual binding sites and identification of the strongest functional group interaction in enzyme orthosteric sites offers a rational starting point for FBDD.
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In Vivo Ligands of MDA5 and RIG-I in Measles Virus-Infected Cells
Hembach, Katharina; Baum, Alina; García-Sastre, Adolfo; Söding, Johannes; Conzelmann, Karl-Klaus
2014-01-01
RIG-I-like receptors (RLRs: RIG-I, MDA5 and LGP2) play a major role in the innate immune response against viral infections and detect patterns on viral RNA molecules that are typically absent from host RNA. Upon RNA binding, RLRs trigger a complex downstream signaling cascade resulting in the expression of type I interferons and proinflammatory cytokines. In the past decade extensive efforts were made to elucidate the nature of putative RLR ligands. In vitro and transfection studies identified 5′-triphosphate containing blunt-ended double-strand RNAs as potent RIG-I inducers and these findings were confirmed by next-generation sequencing of RIG-I associated RNAs from virus-infected cells. The nature of RNA ligands of MDA5 is less clear. Several studies suggest that double-stranded RNAs are the preferred agonists for the protein. However, the exact nature of physiological MDA5 ligands from virus-infected cells needs to be elucidated. In this work, we combine a crosslinking technique with next-generation sequencing in order to shed light on MDA5-associated RNAs from human cells infected with measles virus. Our findings suggest that RIG-I and MDA5 associate with AU-rich RNA species originating from the mRNA of the measles virus L gene. Corresponding sequences are poorer activators of ATP-hydrolysis by MDA5 in vitro, suggesting that they result in more stable MDA5 filaments. These data provide a possible model of how AU-rich sequences could activate type I interferon signaling. PMID:24743923
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Synthesis and studies on Cu(II), Co(II), Ni(II) complexes of Knoevenagel β-diketone ligands.
Sumathi, S; Tharmaraj, P; Sheela, C D; Anitha, C
2012-11-01
Transition metal complexes of various acetylacetone based ligands of the type ML [where M=Cu(II), Ni(II), Co(II); L=3-(aryl)-pentane-2,4-dione] have been synthesized. The structural features have been derived from their elemental analysis, magnetic susceptibility, molar conductance, IR, UV-Vis, (1)H NMR, Mass and ESR spectral studies. Conductivity measurements reveal that all the complexes are non-electrolytic in nature. Spectroscopic and other analytical data of the complexes suggest octahedral geometry for other metal(II) complexes. The redox behavior of the copper(II) complexes have been studied by cyclic voltammetry. The free ligands and their metal complexes have been screened for their in vitro biological activities against the bacteria Pseudomonas aeruginosa, Escherichia coli and Staphylococcus aureus as well as the fungus Candida albicans by well diffusion method. The zone of inhibition value indicates that the most of the metal(II) complexes are found to possess increased activities compared to those of the free ligands. All synthesized compounds may serve as potential photoactive materials as indicated from their characteristic fluorescence properties. The second harmonic generation (SHG) efficiency of the ligands (L1-L3) was found to be considerable effect than that of urea and KDP (potassium dihydrogen phosphate). Copyright © 2012 Elsevier B.V. All rights reserved.
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Synthesis and studies on Cu(II), Co(II), Ni(II) complexes of Knoevenagel β-diketone ligands
NASA Astrophysics Data System (ADS)
Sumathi, S.; Tharmaraj, P.; Sheela, C. D.; Anitha, C.
2012-11-01
Transition metal complexes of various acetylacetone based ligands of the type ML [where M = Cu(II), Ni(II), Co(II); L = 3-(aryl)-pentane-2,4-dione] have been synthesized. The structural features have been derived from their elemental analysis, magnetic susceptibility, molar conductance, IR, UV-Vis, 1H NMR, Mass and ESR spectral studies. Conductivity measurements reveal that all the complexes are non-electrolytic in nature. Spectroscopic and other analytical data of the complexes suggest octahedral geometry for other metal(II) complexes. The redox behavior of the copper(II) complexes have been studied by cyclic voltammetry. The free ligands and their metal complexes have been screened for their in vitro biological activities against the bacteria Pseudomonas aeruginosa, Escherichia coli and Staphylococcus aureus as well as the fungus Candida albicans by well diffusion method. The zone of inhibition value indicates that the most of the metal(II) complexes are found to possess increased activities compared to those of the free ligands. All synthesized compounds may serve as potential photoactive materials as indicated from their characteristic fluorescence properties. The second harmonic generation (SHG) efficiency of the ligands (L1-L3) was found to be considerable effect than that of urea and KDP (potassium dihydrogen phosphate).
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Boujday, Souhir; Lambert, Jean-François; Che, Michel
2004-07-19
Selective adsorption of Ni(II) amine complexes used as precursors for supported catalysts was studied on amorphous silica surfaces. The nature of the adsorption sites was probed by [Ni(en)(dien) (H2O)]2+, [Ni(en)2(H2O)2]2+, and [Ni(dien)(H2O)3]2+ (en = ethylenediamine, dien = diethylenetriamine), which respectively contain one, two, and three labile aqua ligands. The silica surface acts as a mono- or polydentate ligand that can substitute the aqua ligands of the Ni(II) complexes in an inner-sphere adsorption mechanism. Room-temperature adsorption isotherms indicate that each nickel complex selects a limited number of adsorption sites; different sites are recognised by the three complexes, even though they have the same charge and comparable sizes. Several spectroscopic techniques (UV/Vis/NIR, EXAFS, and 29Si NMR) were used to confirm the selective character of the interaction of Ni(II) amine complexes with the silica surface. The specific sites include both silanol/silanolate groups in the same number as the original labile ligands and other surface groups that probably act as hydrogen-bond acceptors. These two types of groups cooperate to result in interfacial molecular-recognition phenomena with interactional complementarity.
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Katre, Uma V.; Mazumder, Suman; Mohanty, Smita
2013-01-01
Pheromone-binding proteins (PBPs) in lepidopteran moths selectively transport the hydrophobic pheromone molecules across the sensillar lymph to trigger the neuronal response. Moth PBPs are known to bind ligand at physiological pH and release it at acidic pH while undergoing a conformational change. Two molecular switches are considered to play a role in this mechanism: (i) Protonation of His70 and His95 situated at one end of binding pocket, and (ii) Switch of the unstructured C-terminus at the other end of the binding pocket to a helix that enters the pocket. We have reported previously the role of the histidine-driven switch in ligand release for Antheraea polyphemus PBP1 (ApolPBP1). Here we show that the C-terminus plays a role in ligand release and binding mechanism of ApolPBP1. The C-terminus truncated mutants of ApolPBP1 (ApolPBP1ΔP129-V142 and ApolPBP1H70A/H95AΔP129-V142) exist only in the bound conformation at all pH levels, and they fail to undergo pH- or ligand- dependent conformational switch. Although these proteins could bind ligands even at acidic pH unlike the wild-type ApolPBP1, they had ~4 fold reduced affinity towards the ligand at both acidic and physiological pH than that of ApolPBP1wt and ApolPBP1H70A/H95A. Thus, apart from helping in the ligand-release at acidic pH, the C-terminus in ApolPBP1 also plays an important role in ligand binding and/or locking the ligand in the binding pocket. Our results are in stark contrast to those reported for BmorPBP and AtraPBP, where C-terminus truncated proteins had similar or increased pheromone-binding affinity at any pH. PMID:23327454
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Parry, Jesse J.; Chen, Ronald; Andrews, Rebecca; Lears, Kimberly A.
2012-01-01
G protein signaling through human somatostatin receptor subtype 2 (SSTR2) is well known, but the amino acids involved in stimulation of intracellular responses upon ligand binding have not been characterized. We constructed a series of point mutants in SSTR2 at amino acid positions 89, 139, and 140 in attempts to disrupt G protein signaling upon ligand binding. The aspartic acid changes at position 89 to either Ala, Leu, or Arg generated mutant receptors with varying expression profiles and a complete inability to bind somatostatin-14 (SST). Mutations to Asp 139 and Arg 140 also led to varying expression profiles with some mutants maintaining their affinity for SST. Mutation of Arg 140 to Ala resulted in a mutated receptor that had a Bmax and dissociation constant (Kd) similar to wild-type receptor but was still coupled to the G protein as determined in both a cAMP assay and a calcium-release assay. In contrast, mutation of Asp 139 to Asn resulted in a mutated receptor with Bmax and Kd values that were similar to wild type but was uncoupled from G protein-mediated cAMP signaling, but not calcium release. Thus, we identified mutations in SSTR2 that result in either receptor expression levels that are similar to wild type but is completely ablated for ligand binding or a receptor that maintains affinity for SST and is uncoupled from G protein-mediated cAMP signaling. PMID:22495673
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Real-Time Ligand Binding Pocket Database Search Using Local Surface Descriptors
Chikhi, Rayan; Sael, Lee; Kihara, Daisuke
2010-01-01
Due to the increasing number of structures of unknown function accumulated by ongoing structural genomics projects, there is an urgent need for computational methods for characterizing protein tertiary structures. As functions of many of these proteins are not easily predicted by conventional sequence database searches, a legitimate strategy is to utilize structure information in function characterization. Of a particular interest is prediction of ligand binding to a protein, as ligand molecule recognition is a major part of molecular function of proteins. Predicting whether a ligand molecule binds a protein is a complex problem due to the physical nature of protein-ligand interactions and the flexibility of both binding sites and ligand molecules. However, geometric and physicochemical complementarity is observed between the ligand and its binding site in many cases. Therefore, ligand molecules which bind to a local surface site in a protein can be predicted by finding similar local pockets of known binding ligands in the structure database. Here, we present two representations of ligand binding pockets and utilize them for ligand binding prediction by pocket shape comparison. These representations are based on mapping of surface properties of binding pockets, which are compactly described either by the two dimensional pseudo-Zernike moments or the 3D Zernike descriptors. These compact representations allow a fast real-time pocket searching against a database. Thorough benchmark study employing two different datasets show that our representations are competitive with the other existing methods. Limitations and potentials of the shape-based methods as well as possible improvements are discussed. PMID:20455259
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Real-time ligand binding pocket database search using local surface descriptors.
Chikhi, Rayan; Sael, Lee; Kihara, Daisuke
2010-07-01
Because of the increasing number of structures of unknown function accumulated by ongoing structural genomics projects, there is an urgent need for computational methods for characterizing protein tertiary structures. As functions of many of these proteins are not easily predicted by conventional sequence database searches, a legitimate strategy is to utilize structure information in function characterization. Of particular interest is prediction of ligand binding to a protein, as ligand molecule recognition is a major part of molecular function of proteins. Predicting whether a ligand molecule binds a protein is a complex problem due to the physical nature of protein-ligand interactions and the flexibility of both binding sites and ligand molecules. However, geometric and physicochemical complementarity is observed between the ligand and its binding site in many cases. Therefore, ligand molecules which bind to a local surface site in a protein can be predicted by finding similar local pockets of known binding ligands in the structure database. Here, we present two representations of ligand binding pockets and utilize them for ligand binding prediction by pocket shape comparison. These representations are based on mapping of surface properties of binding pockets, which are compactly described either by the two-dimensional pseudo-Zernike moments or the three-dimensional Zernike descriptors. These compact representations allow a fast real-time pocket searching against a database. Thorough benchmark studies employing two different datasets show that our representations are competitive with the other existing methods. Limitations and potentials of the shape-based methods as well as possible improvements are discussed.
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Ligand binding analysis and screening by chemical denaturation shift.
Schön, Arne; Brown, Richard K; Hutchins, Burleigh M; Freire, Ernesto
2013-12-01
The identification of small molecule ligands is an important first step in drug development, especially drugs that target proteins with no intrinsic activity. Toward this goal, it is important to have access to technologies that are able to measure binding affinities for a large number of potential ligands in a fast and accurate way. Because ligand binding stabilizes the protein structure in a manner dependent on concentration and binding affinity, the magnitude of the protein stabilization effect elicited by binding can be used to identify and characterize ligands. For example, the shift in protein denaturation temperature (Tm shift) has become a popular approach to identify potential ligands. However, Tm shifts cannot be readily transformed into binding affinities, and the ligand rank order obtained at denaturation temperatures (≥60°C) does not necessarily coincide with the rank order at physiological temperature. An alternative approach is the use of chemical denaturation, which can be implemented at any temperature. Chemical denaturation shifts allow accurate determination of binding affinities with a surprisingly wide dynamic range (high micromolar to sub nanomolar) and in situations where binding changes the cooperativity of the unfolding transition. In this article, we develop the basic analytical equations and provide several experimental examples. Copyright © 2013 Elsevier Inc. All rights reserved.
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Ligand Binding Analysis and Screening by Chemical Denaturation Shift
Sch n, Arne; Brown, Richard K.; Hutchins, Burleigh M.; Freire, Ernesto
2013-01-01
The identification of small molecule ligands is an important first step in drug development, especially drugs that target proteins with no intrinsic activity. Towards this goal, it is important to have access to technologies that are able to measure binding affinities for a large number of potential ligands in a fast and accurate way. Since ligand binding stabilizes the protein structure in a manner dependent on concentration and binding affinity, the magnitude of the protein stabilization effect elicited by binding can be used to identify and characterize ligands. For example, the shift in protein denaturation temperature (Tm shift) has become a popular approach to identify potential ligands. However, Tm shifts cannot be readily transformed into binding affinities and the ligand rank order obtained at denaturation temperatures (60°C or higher) does not necessarily coincide with the rank order at physiological temperature. An alternative approach is the use of chemical denaturation, which can be implemented at any temperature. Chemical denaturation shifts allow accurate determination of binding affinities with a surprisingly wide dynamic range (high micromolar to sub nanomolar) and in situations in which binding changes the cooperativity of the unfolding transition. In this paper we develop the basic analytical equations and provide several experimental examples. PMID:23994566
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Methyl group reorientation under ligand binding probed by pseudocontact shifts.
Lescanne, Mathilde; Ahuja, Puneet; Blok, Anneloes; Timmer, Monika; Akerud, Tomas; Ubbink, Marcellus
2018-06-02
Liquid-state NMR spectroscopy is a powerful technique to elucidate binding properties of ligands on proteins. Ligands binding in hydrophobic pockets are often in close proximity to methyl groups and binding can lead to subtle displacements of methyl containing side chains to accommodate the ligand. To establish whether pseudocontact shifts can be used to characterize ligand binding and the effects on methyl groups, the N-terminal domain of HSP90 was tagged with caged lanthanoid NMR probe 5 at three positions and titrated with a ligand. Binding was monitored using the resonances of leucine and valine methyl groups. The pseudocontact shifts (PCS) caused by ytterbium result in enhanced dispersion of the methyl spectrum, allowing more resonances to be observed. The effects of tag attachment on the spectrum and ligand binding are small. Significant changes in PCS were observed upon ligand binding, indicating displacements of several methyl groups. By determining the cross-section of PCS iso-surfaces generated by two or three paramagnetic centers, the new position of a methyl group can be estimated, showing displacements in the range of 1-3 Å for methyl groups in the binding site. The information about such subtle but significant changes may be used to improve docking studies and can find application in fragment-based drug discovery.
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Photochemically stable fluorescent heteroditopic ligands for zinc ion.
Zhang, Lu; Zhu, Lei
2008-11-07
Photochemically stable fluorescent heteroditopic ligands (9 and 10) for zinc ion were prepared and studied. Two independent metal coordination-driven photophysical processes, chelation-enhanced fluorescence (CHEF) and internal (or intramolecular) charge transfer (ICT), were designed into our heteroditopic ligand framework. This strategy successfully relates three coordination states of a ligand, non-, mono-, and dicoordinated, to three fluorescence states, fluorescence OFF, ON at one wavelength, and ON at another wavelength. This ligand platform has provided chemical foundation for applications such as the quantification of zinc concentration over broad ranges (Zhang, L.; Clark, R. J.; Zhu, L. Chem.-Eur. J. 2008, 14, 2894-2903) and molecular logic functions (Zhang, L.; Whitfield, W. A.; Zhu, L. Chem. Commun. 2008, 1880-1882). The binding stoichiometries of dipicolylamino and 2,2'-bipyridyl, the two binding sites featured in heteroditopic ligands 7-10, were studied in acetonitrile using both Job's method of continuous variation and isothermal titration calorimetry (ITC). The fluorescence enhancement of 7-10 upon the formation of monozinc complexes (defined as the fluorescence quantum yield ratio of monozinc complex and free ligand) is qualitatively related to the highest occupied molecular orbital (HOMO) energy levels of their fluorophores. This is consistent with our hypothesis on the thermodynamics of the coordination-driven photophysical processes embodied in the designed heteroditopic system, which was supported by cyclic voltammetry studies. In conclusion, compounds 9 and 10 not only possess better photochemical stability but also display a higher degree of fluorescence turn-on upon formation of monozinc complexes than their vinyl counterparts 7 and 8.
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Inhibitory Effects of PPARγ Ligands on TGF-β1–Induced Corneal Myofibroblast Transformation
Jeon, Kye-Im; Kulkarni, Ajit; Woeller, Collynn F.; Phipps, Richard P.; Sime, Patricia J.; Hindman, Holly B.; Huxlin, Krystel R.
2015-01-01
Corneal scarring, whether caused by trauma, laser refractive surgery, or infection, remains a significant problem for humans. Certain ligands for peroxisome proliferator-activated receptor gamma (PPARγ) have shown promise as antiscarring agents in a variety of body tissues. In the cornea, their relative effectiveness and mechanisms of action are still poorly understood. Here, we contrasted the antifibrotic effects of three different PPARγ ligands (15-deoxy-Δ12,14-prostaglandin J2, troglitazone, and rosiglitazone) in cat corneal fibroblasts. Western blot analyses revealed that all three compounds reduced transforming growth factor (TGF)-β1–driven myofibroblast differentiation and up-regulation of α-smooth muscle actin, type I collagen, and fibronectin expression. Because these effects were independent of PPARγ, we ascertained whether they occurred by altering phosphorylation of Smads 2/3, p38 mitogen–activated protein kinase, stress-activated protein kinase, protein kinase B, extracellular signal-regulated kinase, and/or myosin light chain 2. Only p38 mitogen–activated protein kinase phosphorylation was significantly inhibited by all three PPARγ ligands. Finally, we tested the antifibrotic potential of troglitazone in a cat model of photorefractive keratectomy–induced corneal injury. Topical application of troglitazone significantly reduced α-smooth muscle actin expression and haze in the stromal ablation zone. Thus, the PPARγ ligands tested here showed great promise as antifibrotics, both in vitro and in vivo. Our results also provided new evidence for the signaling pathways that may underlie these antifibrotic actions in corneal fibroblasts. PMID:24650561
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Wu, Yaoting; Li, Siming; Gogotsi, Natalie
Two species of monodisperse nanocrystals (NCs) can self-assemble into a variety of complex 2D and 3D periodic structures, or binary NC superlattice (BNSL) films, based on the relative number and size of the NCs. BNSL films offer great promise for both fundamental scientific studies and optoelectronic applications; however, the utility of as-assembled structures has been limited by the insulating ligands that originate from the synthesis of NCs. Here we report the application of an in situ ligand exchange strategy at a liquid–air interface to replace the long synthesis ligands with short ligands while preserving the long-range order of BNSL films.more » This approach is demonstrated for BNSL structures consisting of PbSe NCs of different size combinations and ligands of interest for photovoltaic devices, infrared detectors, and light-emitting diodes. To confirm enhanced coupling introduced by ligand exchange, we show ultrafast (~1 ps) directional carrier transfer across the type-I heterojunction formed by NCs of different sizes within ligand-exchanged BNSL films. In conclusion, this approach shows the potential promise of functional BNSL films, where the local and long-range energy landscape and electronic coupling can be adjusted by tuning NC composition, size, and interparticle spacing.« less
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Testing inhomogeneous solvation theory in structure-based ligand discovery.
Balius, Trent E; Fischer, Marcus; Stein, Reed M; Adler, Thomas B; Nguyen, Crystal N; Cruz, Anthony; Gilson, Michael K; Kurtzman, Tom; Shoichet, Brian K
2017-08-15
Binding-site water is often displaced upon ligand recognition, but is commonly neglected in structure-based ligand discovery. Inhomogeneous solvation theory (IST) has become popular for treating this effect, but it has not been tested in controlled experiments at atomic resolution. To do so, we turned to a grid-based version of this method, GIST, readily implemented in molecular docking. Whereas the term only improves docking modestly in retrospective ligand enrichment, it could be added without disrupting performance. We thus turned to prospective docking of large libraries to investigate GIST's impact on ligand discovery, geometry, and water structure in a model cavity site well-suited to exploring these terms. Although top-ranked docked molecules with and without the GIST term often overlapped, many ligands were meaningfully prioritized or deprioritized; some of these were selected for testing. Experimentally, 13/14 molecules prioritized by GIST did bind, whereas none of the molecules that it deprioritized were observed to bind. Nine crystal complexes were determined. In six, the ligand geometry corresponded to that predicted by GIST, for one of these the pose without the GIST term was wrong, and three crystallographic poses differed from both predictions. Notably, in one structure, an ordered water molecule with a high GIST displacement penalty was observed to stay in place. Inclusion of this water-displacement term can substantially improve the hit rates and ligand geometries from docking screens, although the magnitude of its effects can be small and its impact in drug binding sites merits further controlled studies.
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Shino, Michael Y; Weigt, S Samuel; Li, Ning; Palchevskiy, Vyacheslav; Derhovanessian, Ariss; Saggar, Rajan; Sayah, David M; Gregson, Aric L; Fishbein, Michael C; Ardehali, Abbas; Ross, David J; Lynch, Joseph P; Elashoff, Robert M; Belperio, John A
2013-11-01
After lung transplantation, insults to the allograft generally result in one of four histopathologic patterns of injury: (1) acute rejection, (2) lymphocytic bronchiolitis, (3) organizing pneumonia, and (4) diffuse alveolar damage (DAD). We hypothesized that DAD, the most severe form of acute lung injury, would lead to the highest risk of chronic lung allograft dysfunction (CLAD) and that a type I immune response would mediate this process. Determine whether DAD is associated with CLAD and explore the potential role of CXCR3/ligand biology. Transbronchial biopsies from all lung transplant recipients were reviewed. The association between the four injury patterns and subsequent outcomes were evaluated using proportional hazards models with time-dependent covariates. Bronchoalveolar lavage (BAL) concentrations of the CXCR3 ligands (CXCL9/MIG, CXCL10/IP10, and CXCL11/ITAC) were compared between allograft injury patterns and "healthy" biopsies using linear mixed-effects models. The effect of these chemokine alterations on CLAD risk was assessed using Cox models with serial BAL measurements as time-dependent covariates. There were 1,585 biopsies from 441 recipients with 62 episodes of DAD. An episode of DAD was associated with increased risk of CLAD (hazard ratio, 3.0; 95% confidence interval, 1.9-4.7) and death (hazard ratio, 2.3; 95% confidence interval, 1.7-3.0). There were marked elevations in BAL CXCR3 ligand concentrations during DAD. Furthermore, prolonged elevation of these chemokines in serial BAL fluid measurements predicted the development of CLAD. DAD is associated with marked increases in the risk of CLAD and death after lung transplantation. This association may be mediated in part by an aberrant type I immune response involving CXCR3/ligands.
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Compound activity prediction using models of binding pockets or ligand properties in 3D
Kufareva, Irina; Chen, Yu-Chen; Ilatovskiy, Andrey V.; Abagyan, Ruben
2014-01-01
Transient interactions of endogenous and exogenous small molecules with flexible binding sites in proteins or macromolecular assemblies play a critical role in all biological processes. Current advances in high-resolution protein structure determination, database development, and docking methodology make it possible to design three-dimensional models for prediction of such interactions with increasing accuracy and specificity. Using the data collected in the Pocketome encyclopedia, we here provide an overview of two types of the three-dimensional ligand activity models, pocket-based and ligand property-based, for two important classes of proteins, nuclear and G-protein coupled receptors. For half the targets, the pocket models discriminate actives from property matched decoys with acceptable accuracy (the area under ROC curve, AUC, exceeding 84%) and for about one fifth of the targets with high accuracy (AUC > 95%). The 3D ligand property field models performed better than 95% in half of the cases. The high performance models can already become a basis of activity predictions for new chemicals. Family-wide benchmarking of the models highlights strengths of both approaches and helps identify their inherent bottlenecks and challenges. PMID:23116466
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Xie, Qiuhong; Matsunaga, Shigeru; Shi, Xiaohua; Ogawa, Setsuko; Niimi, Setsuko; Wen, Zhesheng; Tokuyasu, Ken; Machida, Sachiko
2003-11-01
Lectin-like oxidized low-density lipoprotein receptor (LOX-1), a type II membrane protein that can recognize a variety of structurally unrelated macromolecules, plays an important role in host defense and is implicated in atherogenesis. To understand the interaction between human LOX-1 and its ligands, in this study the functional C-type lectin-like domain (CTLD) of LOX-1 was reconstituted at high efficiency from inactive aggregates in Escherichia coli using a refolding technique based on an artificial chaperone. The CD spectra of the purified domain suggested that the domain has alpha-helical structure and the blue shift of Trp residues was observed on refolding of the domain. Like wild-type hLOX-1, the refolded CTLD domain was able to bind modified LDL. Thus, even though CTLD contains six Cys residues that form disulfide bonds, it recovered its specific binding ability on refolding. This suggests that the correct disulfide bonds in CTLD were formed by the artificial chaperone technique. Although the domain lacked N-glycosylation, it showed high affinity for its ligand in surface plasmon resonance experiments. Thus, unglycosylated CTLD is sufficient for binding modified LDL.
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NASA Astrophysics Data System (ADS)
Liu, Guocheng; Chen, Yongqiang; Wang, Xiuli; Chen, Baokuan; Lin, Hongyan
2009-03-01
Three novel Cd(II) coordination polymers, namely, [Cd(Dpq)(1,8-NDC)(H 2O) 2][Cd(Dpq)(1,8-NDC)]·2H 2O ( 1), [Cd(Dpq)(1,4-NDC)(H 2O)] ( 2), and [Cd(Dpq)(2,6-NDC)] ( 3) have been obtained from hydrothermal reactions of cadmium(II) nitrate with the mixed ligands dipyrido [3,2-d:2',3'-f]quinoxaline (Dpq) and three structurally related naphthalene-dicarboxylate ligands [1,8-naphthalene-dicarboxylic acid (1,8-H 2NDC), 1,4-naphthalene-dicarboxylic acid (1,4-H 2NDC), and 2,6-naphthalene-dicarboxylic acid (2,6-H 2NDC)]. Single-crystal X-ray diffraction analysis reveals that the three polymers exhibit novel structures due to different naphthalene-dicarboxylic acid. Compound 1 is a novel cocrystal of left- and right-handed helical chains and binuclear complexes and ultimately packed into a 3D supramolecular structure through hydrogen bonds and π- π stacking interactions. Compound 2 shows a 2D rectangular network (4,4) bridged by 1,4-NDC with two kinds of coordination modes and ultimately packed into a 3D supramolecular structure through inter-layer π- π stacking interactions. Compound 3 is a new 3D coordination polymer with distorted PtS-type network. In addition, the title compounds exhibit blue/green emission in solid state at room temperature.
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Dynamic biochemical tissue analysis detects functional L-selectin ligands on colon cancer tissues
Carlson, Grady E.; Martin, Eric W.; Shirure, Venktesh S.; Malgor, Ramiro; Resto, Vicente A.; Goetz, Douglas J.; Burdick, Monica M.
2017-01-01
A growing body of evidence suggests that L-selectin ligands presented on circulating tumor cells facilitate metastasis by binding L-selectin presented on leukocytes. Commonly used methods for detecting L-selectin ligands on tissues, e.g., immunostaining, are performed under static, no-flow conditions. However, such analysis does not assay for functional L-selectin ligands, specifically those ligands that promote adhesion under shear flow conditions. Recently our lab developed a method, termed dynamic biochemical tissue analysis (DBTA), to detect functional selectin ligands in situ by probing tissues with L-selectin-coated microspheres under hemodynamic flow conditions. In this investigation, DBTA was used to probe human colon tissues for L-selectin ligand activity. The detection of L-selectin ligands using DBTA was highly specific. Furthermore, DBTA reproducibly detected functional L-selectin ligands on diseased, e.g., cancerous or inflamed, tissues but not on noncancerous tissues. In addition, DBTA revealed a heterogeneous distribution of functional L-selectin ligands on colon cancer tissues. Most notably, detection of L-selectin ligands by immunostaining using HECA-452 antibody only partially correlated with functional L-selectin ligands detected by DBTA. In summation, the results of this study demonstrate that DBTA detects functional selectin ligands to provide a unique characterization of pathological tissue. PMID:28282455
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Dynamic biochemical tissue analysis detects functional L-selectin ligands on colon cancer tissues.
Carlson, Grady E; Martin, Eric W; Shirure, Venktesh S; Malgor, Ramiro; Resto, Vicente A; Goetz, Douglas J; Burdick, Monica M
2017-01-01
A growing body of evidence suggests that L-selectin ligands presented on circulating tumor cells facilitate metastasis by binding L-selectin presented on leukocytes. Commonly used methods for detecting L-selectin ligands on tissues, e.g., immunostaining, are performed under static, no-flow conditions. However, such analysis does not assay for functional L-selectin ligands, specifically those ligands that promote adhesion under shear flow conditions. Recently our lab developed a method, termed dynamic biochemical tissue analysis (DBTA), to detect functional selectin ligands in situ by probing tissues with L-selectin-coated microspheres under hemodynamic flow conditions. In this investigation, DBTA was used to probe human colon tissues for L-selectin ligand activity. The detection of L-selectin ligands using DBTA was highly specific. Furthermore, DBTA reproducibly detected functional L-selectin ligands on diseased, e.g., cancerous or inflamed, tissues but not on noncancerous tissues. In addition, DBTA revealed a heterogeneous distribution of functional L-selectin ligands on colon cancer tissues. Most notably, detection of L-selectin ligands by immunostaining using HECA-452 antibody only partially correlated with functional L-selectin ligands detected by DBTA. In summation, the results of this study demonstrate that DBTA detects functional selectin ligands to provide a unique characterization of pathological tissue.
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Tanaka, Atsunari; Shimizu, Toru
2008-12-16
Phosphodiesterase (Ec DOS) from Escherichia coli is a gas-sensor enzyme in which binding of gas molecules, such as O(2), CO, and NO, to the Fe(II)-protoporphyrin IX complex in the sensor domain stimulates phosphodiesterase activity toward cyclic-di-GMP. In this study, we report that external axial ligands, such as cyanide or imidazole, bind to Fe(III)-protoporphyrin IX in the sensor domain and induce a 10- to 11-fold increase (from 8.1 up to 86 min(-1)) in catalysis, which is more substantial than that (6.3 to 7.2-fold) observed for other gas-stimulated Fe(II) heme-bound enzymes. Catalytic activity (50 min(-1)) of the heme-free mutant, H77A, was comparable to that of the ligand-stimulated enzymes. Accordingly, we propose that the heme at the sensor domain inhibits catalysis and that ligand binding to the heme iron complex releases this catalytic suppression. Furthermore, mutations of Met95, Arg97, and Phe113 at the putative heme distal side suppressed the ligand effects on catalysis. The rate constants (19,000 x 10(-5) microM(-1)min(-1)) for cyanide binding to the M95A and M95L mutants of the full-length enzyme were 633-fold higher than that to wild-type Ec DOS (30 x 10(-5) microM(-1)min(-1)). The absorption spectrum of the F113Y mutant suggests that the Tyr O(-) group directly coordinates to the Fe(III) complex and that the cyanide binding rate to the mutant is very slow, compared with those of the wild-type and other mutant proteins. We observed a similar trend in the binding behavior of imidazole to full-length mutant enzymes. Therefore, while Met95 and Phe113 are not direct axial ligands for the Fe(III) complex, catalytic, spectroscopic, and ligand binding evidence suggests that these residues are located in the vicinity of the heme.
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PyPLIF: Python-based Protein-Ligand Interaction Fingerprinting.
Radifar, Muhammad; Yuniarti, Nunung; Istyastono, Enade Perdana
2013-01-01
Structure-based virtual screening (SBVS) methods often rely on docking score. The docking score is an over-simplification of the actual ligand-target binding. Its capability to model and predict the actual binding reality is limited. Recently, interaction fingerprinting (IFP) has come and offered us an alternative way to model reality. IFP provides us an alternate way to examine protein-ligand interactions. The docking score indicates the approximate affinity and IFP shows the interaction specificity. IFP is a method to convert three dimensional (3D) protein-ligand interactions into one dimensional (1D) bitstrings. The bitstrings are subsequently employed to compare the protein-ligand interaction predicted by the docking tool against the reference ligand. These comparisons produce scores that can be used to enhance the quality of SBVS campaigns. However, some IFP tools are either proprietary or using a proprietary library, which limits the access to the tools and the development of customized IFP algorithm. Therefore, we have developed PyPLIF, a Python-based open source tool to analyze IFP. In this article, we describe PyPLIF and its application to enhance the quality of SBVS in order to identify antagonists for estrogen α receptor (ERα). PyPLIF is freely available at http://code.google.com/p/pyplif.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Himanen, J.; Goldgur, Y; Miao, H
2009-01-01
Ephrin (Eph) receptor tyrosine kinases fall into two subclasses (A and B) according to preferences for their ephrin ligands. All published structural studies of Eph receptor/ephrin complexes involve B-class receptors. Here, we present the crystal structures of an A-class complex between EphA2 and ephrin-A1 and of unbound EphA2. Although these structures are similar overall to their B-class counterparts, they reveal important differences that define subclass specificity. The structures suggest that the A-class Eph receptor/ephrin interactions involve smaller rearrangements in the interacting partners, better described by a 'lock-and-key'-type binding mechanism, in contrast to the 'induced fit' mechanism defining the B-class molecules.more » This model is supported by structure-based mutagenesis and by differential requirements for ligand oligomerization by the two subclasses in cell-based Eph receptor activation assays. Finally, the structure of the unligated receptor reveals a homodimer assembly that might represent EphA2-specific homotypic cell adhesion interactions.« less
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Miyake, Ryosuke; Shionoya, Mitsuhiko
2014-06-02
To understand reversible structural switching in crystalline materials, we studied the mechanism of reversible crystal-to-crystal transformation of a tetranuclear Ni(II) macrocycle consisting of artificial β-dipeptides. On the basis of detailed structural analyses and thermodynamic measurements made in a comparison of pseudo-isostructural crystals (NO3 and BF4 salts), we herein discuss how ligand-exchange reactions take place in the crystal due to changes in water content and temperature. Observations of the structural transformation of NO3 salt indicated that a pseudo crystalline phase transformation takes place through concerted ligand-exchange reactions at the four Ni(II) centers of the macrocycle with hydrogen bond switching. A mechanism for this ligand exchange was supported by IR spectroscopy. Thermodynamic measurements suggested that the favorable compensation relationship of the enthalpy changes due to water uptake and structural changes are keys to the reversible structural transformation. On the basis of a comparison with the pseudo-isostructural crystals, it is apparent that the crystal packing structure and the types of counter anions are important factors for facilitating reversible ligand exchange with single crystallinity.
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Mishima, Kazuo; Fujiki, Nobuhiro; Yoshida, Yasushi; Sakurai, Takeshi; Honda, Makoto; Mignot, Emmanuel; Nishino, Seiji
2008-01-01
Study Objective: To determine whether hypocretin receptor gene (hcrtR1 and hcrtR2) expression is affected after long-term hypocretin ligand loss in humans and animal models of narcolepsy. Design: Animal and human study. We measured hcrtR1 and hcrtR2 expression in the frontal cortex and pons using the RT-PCR method in murine models (8-week-old and 27-week-old orexin/ataxin-3 transgenic (TG) hypocretin cell ablated mice and wild-type mice from the same litter, 10 mice for each group), in canine models (8 genetically narcoleptic Dobermans with null mutations in the hcrtR2, 9 control Dobermans, 3 sporadic ligand-deficient narcoleptics, and 4 small breed controls), and in humans (5 narcolepsy-cataplexy patients with hypocretin deficiency (average age 77.0 years) and 5 control subjects (72.6 years). Measurement and Results: 27-week-old (but not 8-week-old) TG mice showed significant decreases in hcrtR1 expression, suggesting the influence of the long-term ligand loss on the receptor expression. Both sporadic narcoleptic dogs and human narcolepsy-cataplexy subjects showed a significant decrease in hcrtR1 expression, while declines in hcrtR2 expression were not significant in these cases. HcrtR2-mutated narcoleptic Dobermans (with normal ligand production) showed no alteration in hcrtR1 expression. Conclusions: Moderate declines in hcrtR expressions, possibly due to long-term postnatal loss of ligand production, were observed in hypocretin-ligand deficient narcoleptic subjects. These declines are not likely to be progressive and complete. The relative preservation of hcrtR2 expression also suggests that hypocretin based therapies are likely to be a viable therapeutic options in human narcolepsy-cataplexy. Citation: Mishima K; Fujiki N; Yoshida Y; Sakurai T; Honda M; Mignot E; Nishino S. Hypocretin receptor expression in canine and murine narcolepsy models and in hypocretin-ligand deficient human narcolepsy. SLEEP 2008;31(8):1119-1126. PMID:18714784
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Searching for new aluminium chelating agents: a family of hydroxypyrone ligands.
Toso, Leonardo; Crisponi, Guido; Nurchi, Valeria M; Crespo-Alonso, Miriam; Lachowicz, Joanna I; Mansoori, Delara; Arca, Massimiliano; Santos, M Amélia; Marques, Sérgio M; Gano, Lurdes; Niclós-Gutíerrez, Juan; González-Pérez, Josefa M; Domínguez-Martín, Alicia; Choquesillo-Lazarte, Duane; Szewczuk, Zbigniew
2014-01-01
Attention is devoted to the role of chelating agents in the treatment of aluminium related diseases. In fact, in spite of the efforts that have drastically reduced the occurrence of aluminium dialysis diseases, they so far constitute a cause of great medical concern. The use of chelating agents for iron and aluminium in different clinical applications has found increasing attention in the last thirty years. With the aim of designing new chelators, we synthesized a series of kojic acid derivatives containing two kojic units joined by different linkers. A huge advantage of these molecules is that they are cheap and easy to produce. Previous works on complex formation equilibria of a first group of these ligands with iron and aluminium highlighted extremely good pMe values and gave evidence of the ability to scavenge iron from inside cells. On these bases a second set of bis-kojic ligands, whose linkers between the kojic chelating moieties are differentiated both in terms of type and size, has been designed, synthesized and characterized. The aluminium(III) complex formation equilibria studied by potentiometry, electrospray ionization mass spectroscopy (ESI-MS), quantum-mechanical calculations and (1)H NMR spectroscopy are here described and discussed, and the structural characterization of one of these new ligands is presented. The in vivo studies show that these new bis-kojic derivatives induce faster clearance from main organs as compared with the monomeric analog. © 2013.
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A web server for analysis, comparison and prediction of protein ligand binding sites.
Singh, Harinder; Srivastava, Hemant Kumar; Raghava, Gajendra P S
2016-03-25
One of the major challenges in the field of system biology is to understand the interaction between a wide range of proteins and ligands. In the past, methods have been developed for predicting binding sites in a protein for a limited number of ligands. In order to address this problem, we developed a web server named 'LPIcom' to facilitate users in understanding protein-ligand interaction. Analysis, comparison and prediction modules are available in the "LPIcom' server to predict protein-ligand interacting residues for 824 ligands. Each ligand must have at least 30 protein binding sites in PDB. Analysis module of the server can identify residues preferred in interaction and binding motif for a given ligand; for example residues glycine, lysine and arginine are preferred in ATP binding sites. Comparison module of the server allows comparing protein-binding sites of multiple ligands to understand the similarity between ligands based on their binding site. This module indicates that ATP, ADP and GTP ligands are in the same cluster and thus their binding sites or interacting residues exhibit a high level of similarity. Propensity-based prediction module has been developed for predicting ligand-interacting residues in a protein for more than 800 ligands. In addition, a number of web-based tools have been integrated to facilitate users in creating web logo and two-sample between ligand interacting and non-interacting residues. In summary, this manuscript presents a web-server for analysis of ligand interacting residue. This server is available for public use from URL http://crdd.osdd.net/raghava/lpicom .
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USDA-ARS?s Scientific Manuscript database
A new facile Ru-catalyzed route to bio-olefins3 from unsaturated fatty acids via readily accessible metal-as-ligand type catalyst precursors, [Ru(CO)2RCO2]n and Ru3(CO)12, will be described. The catalyst apparently functions in a tandem mode by dynamically isomerizing the positions of double bonds i...
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Sigma-2 ligands and PARP inhibitors synergistically trigger cell death in breast cancer cells
DOE Office of Scientific and Technical Information (OSTI.GOV)
McDonald, Elizabeth S.; Mankoff, Julia; Makvandi, Mehran
The sigma-2 receptor is overexpressed in proliferating cells compared to quiescent cells and has been used as a target for imaging solid tumors by positron emission tomography. Recent work has suggested that the sigma-2 receptor may also be an effective therapeutic target for cancer therapy. Poly (ADP-ribose) polymerase (PARP) is a family of enzymes involved in DNA damage response. In this study, we looked for potential synergy of cytotoxicity between PARP inhibitors and sigma-2 receptor ligands in breast cancer cell lines. We showed that the PARP inhibitor, YUN3-6, sensitized mouse breast cancer cell line, EMT6, to sigma-2 receptor ligand (SV119,more » WC-26, and RHM-138) induced cell death determined by cell viability assay and colony forming assay. The PARP inhibitor, olaparib, sensitized tumor cells to a different sigma-2 receptor ligand SW43-induced apoptosis and cell death in human triple negative cell line, MDA-MB-231. Olaparib inhibited PARP activity and cell proliferation, and arrested cells in G2/M phase of the cell cycle in MDA-MB-231 cells. Subsequently cells became sensitized to SW43 induced cell death. In conclusion, the combination of sigma-2 receptor ligands and PARP inhibitors appears to hold promise for synergistically triggering cell death in certain types of breast cancer cells and merits further investigation. - Highlights: • PARPi, YUN3-6 and olaparib, and σ2 ligands, SV119 and SW43, were evaluated. • Mouse and human breast cancer cells, EMT6 and MDA-MB-231 respectively, were used. • YUN3-6 and SV119 synergistically triggered cell death in EMT6 cells. • Olaparib and SW43 additively triggered cell death in MDA-MB-231 cells. • Olaparib arrested cells in G2/M in MDA-MB-231 cells.« less
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High affinity ligands from in vitro selection: Complex targets
Morris, Kevin N.; Jensen, Kirk B.; Julin, Carol M.; Weil, Michael; Gold, Larry
1998-01-01
Human red blood cell membranes were used as a model system to determine if the systematic evolution of ligands by exponential enrichment (SELEX) methodology, an in vitro protocol for isolating high-affinity oligonucleotides that bind specifically to virtually any single protein, could be used with a complex mixture of potential targets. Ligands to multiple targets were generated simultaneously during the selection process, and the binding affinities of these ligands for their targets are comparable to those found in similar experiments against pure targets. A secondary selection scheme, deconvolution-SELEX, facilitates rapid isolation of the ligands to targets of special interest within the mixture. SELEX provides high-affinity compounds for multiple targets in a mixture and might allow a means for dissecting complex biological systems. PMID:9501188
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The coordination chemistry of the neutral tris-2-pyridyl silicon ligand [PhSi(6-Me-2-py)3].
Plajer, Alex J; Colebatch, Annie L; Enders, Markus; García-Romero, Álvaro; Bond, Andrew D; García-Rodríguez, Raúl; Wright, Dominic S
2018-05-22
Difficulties in the preparation of neutral ligands of the type [RSi(2-py)3] (where 2-py is an unfunctionalised 2-pyridyl ring unit) have thwarted efforts to expand the coordination chemistry of ligands of this type. However, simply switching the pyridyl substituents to 6-methyl-pyridyl groups (6-Me-2-py) in the current paper has allowed smooth, high-yielding access to the [PhSi(6-Me-2-py)3] ligand (1), and the first exploration of its coordination chemistry with transition metals. The synthesis, single-crystal X-ray structures and solution dynamics of the new complexes [{PhSi(6-Me-2-py)3}CuCH3CN][PF6], [{PhSi(6-Me-2-py)3}CuCH3CN][CuCl2], [{PhSi(6-Me-2-py)3}FeCl2], [{PhSi(6-Me-2-py)3}Mo(CO)3] and [{PhSi(6-Me-2-py)3}CoCl2] are reported. The paramagnetic Fe2+ and Co2+ complexes show strongly shifted NMR resonances for the coordinated pyridyl units due to large Fermi-contact shifts. However, magnetic anisotropy also leads to considerable pseudo-contact shifts so that both contributions have to be included in the paramagnetic NMR analysis.