Sample records for structure activity relationships

  1. Ecological Structure Activity Relationships

    EPA Science Inventory

    Ecological Structure Activity Relationships, v1.00a, February 2009 ECOSAR (Ecological Structure Activity Relationships) is a personal computer software program that is used to estimate the toxicity of chemicals used in industry and discharged into water. The program predicts...

  2. Structural Antitumoral Activity Relationships of Synthetic Chalcones

    PubMed Central

    Echeverria, Cesar; Santibañez, Juan Francisco; Donoso-Tauda, Oscar; Escobar, Carlos A.; Ramirez-Tagle, Rodrigo

    2009-01-01

    Relationships between the structural characteristic of synthetic chalcones and their antitumoral activity were studied. Treatment of HepG2 cells for 24 h with synthetic 2’-hydroxychalcones resulted in apoptosis induction and dose-dependent inhibition of cell proliferation. The calculated reactivity indexes and the adiabatic electron affinities using the DFT method including solvent effects, suggest a structure-activity relationship between the Chalcones structure and the apoptosis in HepG2 cells. The absence of methoxy substituents in the B ring of synthetic 2’-hydroxychalcones, showed the mayor structure-activity pattern along the series. PMID:19333443

  3. Structure-activity relationships of the nikkomycins.

    PubMed

    Decker, H; Zähner, H; Heitsch, H; König, W A; Fiedler, H P

    1991-08-01

    The structure-activity relationships of different nikkomycins were studied to evaluate the structural requirements for a potent chitin synthase inhibitor. We investigated the transport of the nikkomycins via the peptide transport system of the yeast Yarrowia lipolytica and determined the kinetic parameters for nikkomycin Z uptake [Km = 24 microM, Vmax = 2.2 nmol min-1 (mg dry wt)-1]. We demonstrated that the beta-methyl group of the N-terminal amino acid of dipeptide nikkomycins protects the molecule against peptidase activity in crude cell-extracts of different fungi. Furthermore, the relationship between inhibition constants for chitin synthase, transport of the nikkomycins via the peptide transport system, susceptibility to degradation by cellular proteases and whole-cell activity of the nikkomycins are discussed. PMID:1955867

  4. Structure–Activity Relationships of Classical Cannabinoids

    Microsoft Academic Search

    Raj K. Razdan

    \\u000a In this chapter an overview of the more recent developments in the structure–activity relationships (SARs) of classical cannabinoids\\u000a is discussed, especially the profound pharmacological effects produced by various chemical entities in the side chain at C-3,\\u000a the hydroxyl at C-1, C-11, and hydroxyalkyl chains at C-6. Also cardiovascular studies point to the presence of a novel cannabinoid\\u000a subtype receptor and

  5. Trichothecenes: structure-toxic activity relationships.

    PubMed

    Wu, Qinghua; Dohnal, Vlastimil; Kuca, Kamil; Yuan, Zonghui

    2013-07-01

    Trichothecenes comprise a large family of structurally related toxins mainly produced by fungi belonging to the genus Fusarium. Among trichothecenes, type A and type B are of the most concern due to their broad and highly toxic nature. In order to address structure-activity relationships (SAR) of trichothecenes, relationships between structural features and biological effects of trichothecene mycotoxins in mammalian systems are summarized in this paper. The double bond between C-9-C-10 and the 12,13-epoxide ring are essential structural features for trichothecene toxicity. Removal of these groups results in a complete loss of toxicity. A hydroxyl group at C-3 enhances trichothecene toxicity, while this activity decreases gradually when C-3 is substituted with either hydrogen or an acetoxy group. The presence of a hydroxyl group at C-4 promotes slightly lower toxicity than an acetoxy group at the same position. The toxicity for type B trichothecenes decreases if the substituent at C-4 is changed from acetoxy to hydroxyl or hydrogen at C-4 position. The presence of hydroxyl and hydrogen groups on C-15 decreases the trichothecene toxicity in comparison with an acetoxy group attached to this carbon. Trichothecenes toxicity increases when a macrocyclic ring exists between the C-4 and C-15. At C-8 position, an oxygenated substitution at C-8 is essential for trichothecene toxicity, indicating a decrease in the toxicity if substituent change from isovaleryloxy through hydrogen to the hydroxyl group. The presence of a second epoxy ring at C-7-C-8 reduces the toxicity, whereas epoxidation at C-9-C-10 of some macrocyclic trichothecenes increases the activity. Conjugated trichothecenes could release their toxic precursors after hydrolysis in animals, and present an additional potential risk. The SAR study of trichothecenes should provide some crucial information for a better understanding of trichothecene chemical and biological properties in food contamination. PMID:23869809

  6. THE PRACTICE OF STRUCTURE ACTIVITY RELATIONSHIPS (SAR) IN TOXICOLOGY

    EPA Science Inventory

    Both qualitative and quantitative modeling methods relating chemical structure to biological activity, called structure-activity relationship analyses or SAR, are applied to the prediction and characterization of chemical toxicity. This minireview will discuss some generic issue...

  7. Structure activity relationships of novel antiepileptic drugs.

    PubMed

    Mittapalli, G K; Roberts, E

    2014-01-01

    Despite notable success over years in the discovery and development of new antiepileptic drugs (AEDs), about 30-40% of the patients are resistant to drug treatment. There is a still significant need to develop novel AEDs that demonstrate superior efficacy, broad spectrum of activities and good safety profile. The synaptic vesicle glycoprotein 2A (SV2A), ?-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPA-R) and voltage-gated potassium channels (KCNQ2/Q3) are clinically validated as new molecular targets for epilepsy. The discovery of SV2A as a target for levetiracetam, 2,3-benzodiazepine GYKI 52466 as a non-competitive AMPA-R antagonist and retigabine as a KCNQ2/Q3 channels activator provided a rational basis to develop novel AEDs. The optimization of SV2A binding affinity of levetiracetam led to the discovery of novel high affinity SV2A ligands that displayed superior efficacy and protective index in animal models of epilepsy. The high-throughput screening (HTS) and medicinal chemistry efforts yielded many non-competitive AMPA-R antagonists of which perampanel was recently approved as a first-in-a new class. The efficacy and lack of sub-type selectivity of retigabine prompted many research efforts to discover several potent and selective KCNQ2/Q3 channel activators of distinct chemical scaffolds that are at various stages of clinical development. Despite the known role of galanin and galanin receptor (Gal-R) in epilepsy over a decade, development of potent and brainpenetrant Gal-R agonists is very challenging. The discovery of selective Gal-R2 positive allosteric modulator, CYM 2503, offers a valuable and an alternative approach. The review focuses on the available structure-activity relationships and preclinical efficacy of novel antiepileptic compounds that are distinct from most of the approved AEDs, specifically SV2A ligands, non-competitive AMPA-R antagonists, KCNQ2/Q3 channels activators and Gal-R modulators. PMID:24251563

  8. Unbalance Quantitative Structure Activity Relationship Problem Reduction in Drug Design

    Microsoft Academic Search

    D. Pugazhenthi; S. P. Rajagopalan

    2009-01-01

    Problem statement: Activities of drug molecules can be predicted by Q uantitative Structure Activity Relationship (QSAR) models, which overcome the disadvantage of high cost and long cycle by employing traditional experimental me thods. With the fact that number of drug molecules with positive activity is rather fewer th an that with negatives, it is important to predict molecular activities considering

  9. The structure?activity relationship in herbicidal monosubstituted sulfonylureas

    Microsoft Academic Search

    Zheng-Ming Li; Yi Ma; Luke Guddat; Pei-Quan Cheng; Jian-Guo Wang; Siew S Pang; Yu-Hui Dong; Cheng-Ming Lai; Ling-Xiu Wang; Guo-Feng Jia; Yong-Hong Li; Su-Hua Wang; Jie Liu; Wei-Guang Zhao; Bao-Lei Wang

    2012-01-01

    The herbicide sulfonylurea (SU) belongs to one of the most important class of herbicides worldwide. It is well known for its ecofriendly, extreme low toxicity towards mammals and ultralow dosage application. The original inventor, G Levitt, set out structure-activity relationship (SAR) guidelines for SU structural design to attain superhigh bioactivity. A new approach to SU molecular design has been developed.

  10. Structure-antioxidant activity relationships of flavonoids and phenolic acids.

    PubMed

    Rice-Evans, C A; Miller, N J; Paganga, G

    1996-01-01

    The recent explosion of interest in the bioactivity of the flavonoids of higher plants is due, at least in part, to the potential health benefits of these polyphenolic components of major dietary constituents. This review article discusses the biological properties of the flavonoids and focuses on the relationship between their antioxidant activity, as hydrogen donating free radical scavengers, and their chemical structures. This culminates in a proposed hierarchy of antioxidant activity in the aqueous phase. The cumulative findings concerning structure-antioxidant activity relationships in the lipophilic phase derive from studies on fatty acids, liposomes, and low-density lipoproteins; the factors underlying the influence of the different classes of polyphenols in enhancing their resistance to oxidation are discussed and support the contention that the partition coefficients of the flavonoids as well as their rates of reaction with the relevant radicals define the antioxidant activities in the lipophilic phase. PMID:8743980

  11. Structure-molluscicidal activity relationships of acylphloroglucinols from ferns.

    PubMed

    Socolsky, Cecilia; Borkosky, Susana; Bardón, Alicia

    2011-03-01

    The molluscicidal activity of 12 phloroglucinol derivatives previously isolated from Elaphoglossum piloselloides, E. gayanum, E. yungense, and E. lindbergii, as well as 3 known acylphloroglucinols, now reported from an Argentine collection of Dryopteris wallichiana, was evaluated against the schistosomiasis vector snail Biomphalaria peregrina. Molluscicidal effects were analyzed and compared with those previously observed for 4 acylphloroglucinols from E. piloselloides and their corresponding peracetylated derivatives, in order to draw structure-activity relationships. The most active compounds were the prenylated desaspidins elaphogayanin B and elaphopilosins A and B (LD50 = 1.90, 2.90, and 0.94 ppm, respectively), together with the only evaluated prenylated para-aspidin, elaphopilosin C (LD50 = 2.15 ppm). Quantitative structure-activity relationships (QSAR) were studied by means of a semiempirical method (PM3) for the 24 natural phloroglucinol derivatives included in this paper. The descriptor molecular volume was found to have good correlation with the observed molluscicidal activity (r2 = 0.77). The derived equation can be considered useful to predict the molluscicidal activity of bi and tricyclic acylphloroglucinols. The QSAR analysis showed that there is an optimum volume for high activity, probably related to the size of a receptor's active site. Bigger molecules display lower activity. PMID:21485280

  12. Antioxidant and Prooxidant Behavior of Flavonoids: StructureActivity Relationships

    Microsoft Academic Search

    Guohua Cao; Emin Sofic; Ronald L. Prior

    1997-01-01

    The antioxidant and prooxidant behavior of flavonoids and the related activity-structure relationships were investigated in this study using the oxygen radical absorbance capacity assay. Three different reactive species were used in the assay: 2,2?-azobis(2-amidino-propane) dihydrochloride, a peroxyl radical generator; Cu2+-H2O2, mainly a hydroxyl radical generator; and Cu2+, a transition metal. Flavonoids including flavones, isoflavones, and flavanones acted as antioxidants against

  13. CONSIDERATION OF REACTION INTERMEDIATES IN STRUCTURE-ACTIVITY RELATIONSHIPS: A KEY TO UNDERSTANDING AND PREDICTION

    EPA Science Inventory

    Consideration of Reaction Intermediates in Structure- Activity Relationships: A Key to Understanding and Prediction A structure-activity relationship (SAR) represents an empirical means for generalizing chemical information relative to biological activity, and is frequent...

  14. Piperine and Derivatives: Trends in Structure-Activity Relationships.

    PubMed

    Singh, Inder Pal; Choudhary, Alka

    2015-01-01

    Piperine is the main constituent of pepper, a commonly used kitchen spice and has been reported to possess various pharmacological activities. The structural features, an aromatic ring with a methylenedioxy bridge, a conjugated dienone system and a piperidine ring constituting an amide bond, possessed by the molecule have been considered important for the molecule to exhibit an array of bioactivities. Several modifications of above structural units have affected the biological properties of piperine, either enhancing or in some cases completely abolishing the activity. The present review emphasizes on the synthetic aspects of piperine along with the structure-activity relationships of its derivatives so as to rationalize the discovery of newer piperine based molecules. PMID:25915609

  15. Relationship between antimold activity and molecular structure of cinnamaldehyde analogues.

    PubMed

    Zhang, Yuanyuan; Li, Shujun; Kong, Xianchao

    2013-03-01

    A quantitative structure-activity relationship (QSAR) modeling of the antimold activity of cinnamaldehyde analogues against of Aspergillus niger and Paecilomyces variotii was presented. The molecular descriptors of cinnamaldehyde analogues were calculated by the CODESSA program, and these descriptors were selected by best multi-linear regression method (BMLR). Satisfactory multilinear regression models of Aspergillus niger and Paecilomyces variotii were obtained with R(2)=0.9099 and 0.9444, respectively. The models were also satisfactorily validated using internal validation and leave one out validation. The QSAR models provide the guidance for further synthetic work. PMID:23374870

  16. Structure–Activity Relationship Studies of Pyrrolone Antimalarial Agents

    PubMed Central

    Murugesan, Dinakaran; Kaiser, Marcel; White, Karen L; Norval, Suzanne; Riley, Jennifer; Wyatt, Paul G; Charman, Susan A; Read, Kevin D; Yeates, Clive; Gilbert, Ian H

    2013-01-01

    Previously reported pyrrolones, such as TDR32570, exhibited potential as antimalarial agents; however, while these compounds have potent antimalarial activity, they suffer from poor aqueous solubility and metabolic instability. Here, further structure–activity relationship studies are described that aimed to solve the developability issues associated with this series of compounds. In particular, further modifications to the lead pyrrolone, involving replacement of a phenyl ring with a piperidine and removal of a potentially metabolically labile ester by a scaffold hop, gave rise to derivatives with improved in vitro antimalarial activities against Plasmodium falciparum K1, a chloroquine-and pyrimethamine-resistant parasite strain, with some derivatives exhibiting good selectivity for parasite over mammalian (L6) cells. Three representative compounds were selected for evaluation in a rodent model of malaria infection, and the best compound showed improved ability to decrease parasitaemia and a slight increase in survival. PMID:23918316

  17. Synthesis and structural activity relationship study of antitubercular carboxamides.

    PubMed

    Ugwu, D I; Ezema, B E; Eze, F U; Ugwuja, D I

    2014-01-01

    The unusual structure and chemical composition of the mycobacterial cell wall, the tedious duration of therapy, and resistance developed by the microorganism have made the recurrence of the disease multidrug resistance and extensive or extreme drug resistance. The prevalence of tuberculosis in synergy with HIV/AIDS epidemic augments the risk of developing the disease by 100-fold. The need to synthesize new drugs that will shorten the total duration of effective treatment and/or significantly reduce the dosage taken under DOTS supervision, improve on the treatment of multidrug-resistant tuberculosis which defies the treatment with isoniazid and rifampicin, and provide effective treatment for latent TB infections which is essential for eliminating tuberculosis prompted this review. In this review, we considered the synthesis and structure activity relationship study of carboxamide derivatives with antitubercular potential. PMID:25610646

  18. The structure?activity relationship in herbicidal monosubstituted sulfonylureas

    SciTech Connect

    Li, Zheng-Ming; Ma, Yi; Guddat, Luke; Cheng, Pei-Quan; Wang, Jian-Guo; Pang, Siew S; Dong, Yu-Hui; Lai, Cheng-Ming; Wang, Ling-Xiu; Jia, Guo-Feng; Li, Yong-Hong; Wang, Su-Hua; Liu, Jie; Zhao, Wei-Guang; Wang, Bao-Lei (Nankai); (Queens); (Chinese Aca. Sci.)

    2012-05-24

    The herbicide sulfonylurea (SU) belongs to one of the most important class of herbicides worldwide. It is well known for its ecofriendly, extreme low toxicity towards mammals and ultralow dosage application. The original inventor, G Levitt, set out structure-activity relationship (SAR) guidelines for SU structural design to attain superhigh bioactivity. A new approach to SU molecular design has been developed. After the analysis of scores of SU products by X-ray diffraction methodology and after greenhouse herbicidal screening of 900 novel SU structures synthesized in the authors laboratory, it was found that several SU structures containing a monosubstituted pyrimidine moiety retain excellent herbicidal characteristics, which has led to partial revision of the Levitt guidelines. Among the novel SU molecules, monosulfuron and monosulfuron-ester have been developed into two new herbicides that have been officially approved for field application and applied in millet and wheat fields in China. A systematic structural study of the new substrate-target complex and the relative mode of action in comparison with conventional SU has been carried out. A new mode of action has been postulated.

  19. Quantitative structure activity relationship modelling of peptides and proteins as a tool in food science

    Microsoft Academic Search

    Are Hugo Pripp; Tomas Isaksson; Leszek Stepaniak; Terje Sørhaug; Ylva Ardö

    2005-01-01

    Peptides and proteins contribute to physical properties, biological activities and sensory characteristics of foods. Studies on the isolation and characterisation of peptides and proteins allow compilation of data sets on their structures and properties\\/activities. Quantitative structure activity relationship (QSAR) modelling provides methodology to find mathematical expressions for such relationships which may then be useful for estimating activities of any related

  20. Structure-activity relationships of phomactin derivatives as platelet activating factor antagonists.

    PubMed

    Sugano, M; Sato, A; Saito, K; Takaishi, S; Matsushita, Y; Iijima, Y

    1996-12-20

    Phomactins, natural products isolated from the culture broth of marine fungus Phoma sp., were found to be active as PAF antagonists. This unique carbon skeleton led us to investigate the structure-activity relationship demonstrating that the lipophilicity at C-(7-8), acetoxy, (methoxycarbonyl)oxy, and 3-isoxazolyloxy substitution at C-20, and 2-beta-OH configuration at C-2 are all required for the enhancement of inhibitor activity. PMID:8978857

  1. Structure activity relationships to assess new chemicals under TSCA

    SciTech Connect

    Auletta, A.E. [Environmental Protection Agency, Washington, DC (United States)

    1990-12-31

    Under Section 5 of the Toxic Substances Control Act (TSCA), manufacturers must notify the US Environmental Protection Agency (EPA) 90 days before manufacturing, processing, or importing a new chemical substance. This is referred to as a premanufacture notice (PMN). The PMN must contain certain information including chemical identity, production volume, proposed uses, estimates of exposure and release, and any health or environmental test data that are available to the submitter. Because there is no explicit statutory authority that requires testing of new chemicals prior to their entry into the market, most PMNs are submitted with little or no data. As a result, EPA has developed special techniques for hazard assessment of PMN chemicals. These include (1) evaluation of available data on the chemical itself, (2) evaluation of data on analogues of the PMN, or evaluation of data on metabolites or analogues of metabolites of the PMN, (3) use of quantitative structure activity relationships (QSARs), and (4) knowledge and judgement of scientific assessors in the interpretation and integration of the information developed in the course of the assessment. This approach to evaluating potential hazards of new chemicals is used to identify those that are most in need of addition review of further testing. It should not be viewed as a replacement for testing. 4 tabs.

  2. Nonparametric regression applied to quantitative structure-activity relationships

    PubMed

    Constans; Hirst

    2000-03-01

    Several nonparametric regressors have been applied to modeling quantitative structure-activity relationship (QSAR) data. The simplest regressor, the Nadaraya-Watson, was assessed in a genuine multivariate setting. Other regressors, the local linear and the shifted Nadaraya-Watson, were implemented within additive models--a computationally more expedient approach, better suited for low-density designs. Performances were benchmarked against the nonlinear method of smoothing splines. A linear reference point was provided by multilinear regression (MLR). Variable selection was explored using systematic combinations of different variables and combinations of principal components. For the data set examined, 47 inhibitors of dopamine beta-hydroxylase, the additive nonparametric regressors have greater predictive accuracy (as measured by the mean absolute error of the predictions or the Pearson correlation in cross-validation trails) than MLR. The use of principal components did not improve the performance of the nonparametric regressors over use of the original descriptors, since the original descriptors are not strongly correlated. It remains to be seen if the nonparametric regressors can be successfully coupled with better variable selection and dimensionality reduction in the context of high-dimensional QSARs. PMID:10761152

  3. Structure-antioxidant activity relationships of flavonoids and phenolic acids

    Microsoft Academic Search

    Catherine A. Rice-Evans; Nicholas J. Miller; George Paganga

    1996-01-01

    The recent explosion of interest in the bioactivity of the the flavonoids of higher plants is due, at least in part, to the potential health benefits of these polyphenolic components of major dietary constituents. This review article discusses the biological properties of the flavonoids and focuses on the relationship between their antioxidant activity, as hydrogen donating free radical scavengers, and

  4. Structure-Activity Relationship of Nerve-Highlighting Fluorophores

    PubMed Central

    Gibbs, Summer L.; Xie, Yang; Goodwill, Haley L.; Nasr, Khaled A.; Ashitate, Yoshitomo; Madigan, Victoria J.; Siclovan, Tiberiu M.; Zavodszky, Maria; Tan Hehir, Cristina A.; Frangioni, John V.

    2013-01-01

    Nerve damage is a major morbidity associated with numerous surgical interventions. Yet, nerve visualization continues to challenge even the most experienced surgeons. A nerve-specific fluorescent contrast agent, especially one with near-infrared (NIR) absorption and emission, would be of immediate benefit to patients and surgeons. Currently, there are only three classes of small molecule organic fluorophores that penetrate the blood nerve barrier and bind to nerve tissue when administered systemically. Of these three classes, the distyrylbenzenes (DSBs) are particularly attractive for further study. Although not presently in the NIR range, DSB fluorophores highlight all nerve tissue in mice, rats, and pigs after intravenous administration. The purpose of the current study was to define the pharmacophore responsible for nerve-specific uptake and retention, which would enable future molecules to be optimized for NIR optical properties. Structural analogs of the DSB class of small molecules were synthesized using combinatorial solid phase synthesis and commercially available building blocks, which yielded more than 200 unique DSB fluorophores. The nerve-specific properties of all DSB analogs were quantified using an ex vivo nerve-specific fluorescence assay on pig and human sciatic nerve. Results were used to perform quantitative structure-activity relationship (QSAR) modeling and to define the nerve-specific pharmacophore. All DSB analogs with positive ex vivo fluorescence were tested for in vivo nerve specificity in mice to assess the effect of biodistribution and clearance on nerve fluorescence signal. Two new DSB fluorophores with the highest nerve to muscle ratio were tested in pigs to confirm scalability. PMID:24039960

  5. The relationship between peptide structure and antibacterial activity

    Microsoft Academic Search

    Jon-Paul S Powers; Robert E. W Hancock

    2003-01-01

    Cationic antimicrobial peptides are a class of small, positively charged peptides known for their broad-spectrum antimicrobial activity. These peptides have also been shown to possess anti-viral and anti-cancer activity and, most recently, the ability to modulate the innate immune response. To date, a large number of antimicrobial peptides have been chemically characterized, however, few high-resolution structures are available. Structure–activity studies

  6. Quantitative structure–activity relationships studies for prediction of antimicrobial activity of synthesized disulfonamide derivatives

    Microsoft Academic Search

    Saliha Alyar; Neslihan Özbek; Kübra Kuzuk?ran; Nurcan Karacan

    2011-01-01

    A new series of disulfonamides were synthesized and assayed as antimicrobial agents against Staphylococcus aureus, Bacillus cereus, and Escherichia coli. The quantitative structure–activity relationship analysis (QSAR) was applied to find out the correlation between experimentally\\u000a evaluated antimicrobial activities with various parameters of the compounds using stepwise multiple liner regression method.\\u000a The QSAR analysis revealed that the third-order average connectivity index

  7. Structure-activity relationships in thienodiazepine and benzodiazepine derivatives.

    PubMed

    Chimirri, A; Gitto, R; Grasso, S; Zappalà, M; De Sarro, A; Battista De Sarro, G

    1994-03-01

    The structural and electronic characteristics as well as the anticonvulsant properties and benzodiazepine receptor binding of thieno[3,4-b][1,4]diazepine and 1,5-benzodiazepine derivatives are compared and discussed. The data obtained suggest that the electronic rather than the structural properties appear mainly responsible for the variant degree of anticonvulsant activity exhibited by the tested compounds. PMID:8043171

  8. Cryptocaryol A and B: Total Syntheses, Stereochemical Revision, Structure Elucidation and Structure-Activity Relationship

    PubMed Central

    Wang, Yanping; O’Doherty, George A.

    2013-01-01

    The first total syntheses and structural elucidation of cryptocaryol A and cryptocaryol B were achieved in 23 and 25 linear steps, respectively. The synthesis relied on the use of a key pseudo-Cs symmetric pentaol intermediate, which in a stereo-chemically divergent manner was converted into either enantiomer as well as diastereomers. This synthetic effort enabled the first structure-activity relationships of this class of PDCD4 stabilizing natural products. PMID:23750754

  9. Structure Activity Relationships (SAR) and Pharmacophore Discovery Using Inductive Logic Programming (ILP)

    E-print Network

    Muggleton, Stephen H.

    Structure Activity Relationships (SAR) and Pharmacophore Discovery Using Inductive Logic), a form of machine learning, to derive structure activity relationships (SAR) and to discover pharmacophores is reported. The ILP approach was initially applied to model 1D SARs in terms of the attributes

  10. PREDICTING TOXICOLOGICAL ENDPOINTS OF CHEMICALS USING QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIPS (QSARS)

    EPA Science Inventory

    Quantitative structure-activity relationships (QSARs) are being developed to predict the toxicological endpoints for untested chemicals similar in structure to chemicals that have known experimental toxicological data. Based on a very large number of predetermined descriptors, a...

  11. Precise structure activity relationships in asymmetric catalysis using carbohydrate scaffolds to allow ready fine tuning

    E-print Network

    Davis, Ben G.

    Precise structure activity relationships in asymmetric catalysis using carbohydrate scaffolds construction of 24 stereochemically and functionally diverse carbohydrate ligand structures from a core D construction. Introduction Carbohydrates are powerful sources of chirality for use in syn- thetic asymmetric

  12. Structure-activity relationship of buffalo antibacterial hepcidin analogs.

    PubMed

    Chanu, Khangembam Victoria; Kumar, Ashok; Kumar, Satish

    2011-10-01

    Hepcidin is an anti-microbial peptide expressed predominantly in the liver of many species. Based on the amino acid sequence deduced from buffalo (Bubalus bubalis) hepcidin cDNA (Accession no. EU399814), six peptides Hepc(1-25), Hepc(6-25), Hepc(7-25), Hepc(9-25), Hepc(11-25) and Hepc(15-25) were synthesized using solid-phase fluorenylmethoxycarbonyl (Fmoc) chemistry. CD spectroscopy revealed different spectra of the peptides in different solvents and in all the cases beta-structure was found to be dominant with less alpha-helix as predicted. Quantitation of secondary structure indicated the highest beta-structure for all the six peptides in SDS solution, when used as mimetic for membrane-like environment. The CD spectra of all the peptides taken in water showed that degree of randomness decreased with increase in chain length of the peptide. Out of the six peptides, only Hepc(1-25), Hepc(6-25) and Hepc(7-25) showed antibacterial activity against Staphylococcus aureus (Gram-positive bacteria). The peptides did not show any sensitivity toward E. coli (Gram-negative bacteria). Minimum inhibitory concentration (MIC) showed the lowest value for Hepc(7-25) as an antibacterial agent, followed by Hepc(6-25) and Hepc(1-25). The peptides Hepc(9-25), Hepc(11-25) and Hepc(15-25) with more random structure did not show any antimicrobial activity The study demonstrated that 5 amino acids at N-terminal in buffalo hepcidin can be truncated without loss of antimicrobial activity and further reduction of length of the analog from 20 to 19 amino acids resulted increase in the activity because of increase in beta-structure of the peptide shown by CD spectroscopy. PMID:22165290

  13. Structure-activity relationships of polybiguanides with activity against human immunodeficiency virus type 1.

    PubMed

    Passic, Shendra R; Ferguson, Mary Lee; Catalone, Bradley J; Kish-Catalone, Tina; Kholodovych, Vladyslav; Zhu, Wei; Welsh, William; Rando, Robert; Howett, Mary K; Wigdahl, Brian; Labib, Mohamed; Krebs, Fred C

    2010-12-01

    Previous investigations showing that polydisperse biguanide (PDBG) molecules have activity against human immunodeficiency virus type 1 (HIV-1) also suggested a relationship between PDBG biologic activity and the lengths of hydrocarbon linkers surrounding the positively charged biguanide unit. To better define structure-activity relationships, PDBG molecules with select linker lengths were evaluated for cytotoxicity, anti-HIV-1 activity, and in vivo toxicity. Results of the in vitro experiments demonstrated that increases in linker length (and, therefore, increases in compound lipophilicity) were generally associated with increases in cytotoxicity and antiviral activity against HIV-1. However, a relationship between linker length asymmetry and in vitro therapeutic index (TI) suggested structural specificity in the mechanism of action against HIV-1. Polyethylene hexamethylene biguanide (PEHMB; biguanide units spaced between alternating ethylene and hexamethylene linkers) was found to have the highest in vitro TI (CC??/IC??) among the compounds examined. Recent improvements in PEHMB synthesis and purification have yielded preparations of PEHMB with in vitro TI values of 266 and 7000 against HIV-1 strains BaL and IIIB, respectively. The minimal toxicity of PEHMB relative to polyhexamethylene biguanide (PHMB; biguanide units alternating with hexamethylene linkers) in a murine model of cervicovaginal microbicide toxicity was consistent with considerable differences in cytotoxicity between PEHMB and PHMB observed during in vitro experiments. These structure-activity investigations increase our understanding of PDBG molecules as agents with activity against HIV-1 and provide the foundation for further preclinical studies of PEHMB and other biguanide-based compounds as antiviral and microbicidal agents. PMID:21106331

  14. Structure-activity relationship (SAR) modelling of mosquito larvicides.

    PubMed

    Devillers, J; Doucet-Panaye, A; Doucet, J P

    2015-04-01

    An attempt was made to derive structure-activity models allowing the prediction of the larvicidal activity of structurally diverse chemicals against mosquitoes. A database of 188 chemicals with their activity on Aedes aegypti larvae was constituted from analysis of original publications. The activity values were expressed in log 1/IC50 (concentration required to produce 50% inhibition of larval development, mmol). All the chemicals were encoded by means of CODESSA and autocorrelation descriptors. Partial least squares analysis, classification and regression tree, random forest and boosting regression tree analyses, Kohonen self-organizing maps, linear artificial neural networks, three-layer perceptrons, radial basis function artificial neural networks and support vector machines with linear, polynomial, radial basis function and sigmoid kernels were tested as statistical tools. Because quantitative models did not give good results, a two-class model was designed. The three-layer perceptron significantly outperformed the other statistical approaches regardless of the threshold value used to split the data into active and inactive compounds. The most interesting configuration included eight autocorrelation descriptors as input neurons and four neurons in the hidden layer. This led to more than 96% of good predictions on both the training set and external test set of 88 and 100 chemicals, respectively. From the overall simulation results, new candidate molecules were proposed which will be shortly synthesized and tested. PMID:25864415

  15. Structure-activity relationships for the antifungal activity of selective estrogen receptor antagonists related to tamoxifen.

    PubMed

    Butts, Arielle; Martin, Jennifer A; DiDone, Louis; Bradley, Erin K; Mutz, Mitchell; Krysan, Damian J

    2015-01-01

    Cryptococcosis is one of the most important invasive fungal infections and is a significant contributor to the mortality associated with HIV/AIDS. As part of our program to repurpose molecules related to the selective estrogen receptor modulator (SERM) tamoxifen as anti-cryptococcal agents, we have explored the structure-activity relationships of a set of structurally diverse SERMs and tamoxifen derivatives. Our data provide the first insights into the structural requirements for the antifungal activity of this scaffold. Three key molecular characteristics affecting anti-cryptococcal activity emerged from our studies: 1) the presence of an alkylamino group tethered to one of the aromatic rings of the triphenylethylene core; 2) an appropriately sized aliphatic substituent at the 2 position of the ethylene moiety; and 3) electronegative substituents on the aromatic rings modestly improved activity. Using a cell-based assay of calmodulin antagonism, we found that the anti-cryptococcal activity of the scaffold correlates with calmodulin inhibition. Finally, we developed a homology model of C. neoformans calmodulin and used it to rationalize the structural basis for the activity of these molecules. Taken together, these data and models provide a basis for the further optimization of this promising anti-cryptococcal scaffold. PMID:26016941

  16. Structure-Activity Relationships for the Antifungal Activity of Selective Estrogen Receptor Antagonists Related to Tamoxifen

    PubMed Central

    Butts, Arielle; Martin, Jennifer A.; DiDone, Louis; Bradley, Erin K.; Mutz, Mitchell; Krysan, Damian J.

    2015-01-01

    Cryptococcosis is one of the most important invasive fungal infections and is a significant contributor to the mortality associated with HIV/AIDS. As part of our program to repurpose molecules related to the selective estrogen receptor modulator (SERM) tamoxifen as anti-cryptococcal agents, we have explored the structure-activity relationships of a set of structurally diverse SERMs and tamoxifen derivatives. Our data provide the first insights into the structural requirements for the antifungal activity of this scaffold. Three key molecular characteristics affecting anti-cryptococcal activity emerged from our studies: 1) the presence of an alkylamino group tethered to one of the aromatic rings of the triphenylethylene core; 2) an appropriately sized aliphatic substituent at the 2 position of the ethylene moiety; and 3) electronegative substituents on the aromatic rings modestly improved activity. Using a cell-based assay of calmodulin antagonism, we found that the anti-cryptococcal activity of the scaffold correlates with calmodulin inhibition. Finally, we developed a homology model of C. neoformans calmodulin and used it to rationalize the structural basis for the activity of these molecules. Taken together, these data and models provide a basis for the further optimization of this promising anti-cryptococcal scaffold. PMID:26016941

  17. Structure activity relationship (SAR) study of benzimidazole scaffold for different biological activities: A mini-review.

    PubMed

    Yadav, Geeta; Ganguly, Swastika

    2015-06-01

    Benzimidazoles are the fused heterocyclic ring systems which form an integral part of vitamin B12 and have been luring many researchers all over the world to assess their potential therapeutic significance. They are known for their crucial role in numerous diseases via various mechanisms. Substitution of benzimidazole nucleus is a crucial step in the drug discovery process. Therefore, it is necessary to gather the latest information along with the earlier information to understand the present status of benzimidazole nucleus in drug discovery. In the present review, benzimidazole derivatives with different pharmacological activities are described on the basis of SAR study using structural substitution pattern around the benzimidazole nucleus and aims to review the reported work related to the chemistry and pharmacological activities of benzimidazole derivatives during recent years. The present manuscript to the best of our knowledge is the first compilation on synthesis and medicinal aspects including structure-activity relationships of benzimidazole reported to date. PMID:25479684

  18. Structure-activity relationship of celecoxib and rofecoxib for the membrane permeabilizing activity.

    PubMed

    Yamakawa, Naoki; Suzuki, Koichiro; Yamashita, Yasunobu; Katsu, Takashi; Hanaya, Kengo; Shoji, Mitsuru; Sugai, Takeshi; Mizushima, Tohru

    2014-04-15

    Non-steroidal anti-inflammatory drugs (NSAIDs) achieve their anti-inflammatory effect by inhibiting cyclooxygenase activity. We previously suggested that in addition to cyclooxygenase-inhibition at the gastric mucosa, NSAID-induced gastric mucosal cell death is required for the formation of NSAID-induced gastric lesions in vivo. We showed that celecoxib exhibited the most potent membrane permeabilizing activity among the NSAIDs tested. In contrast, we have found that the NSAID rofecoxib has very weak membrane permeabilizing activity. To understand the membrane permeabilizing activity of coxibs in terms of their structure-activity relationship, we separated the structures of celecoxib and rofecoxib into three parts, synthesized hybrid compounds by substitution of each of the parts, and examined the membrane permeabilizing activities of these hybrids. The results suggest that the sulfonamidophenyl subgroup of celecoxib or the methanesulfonylphenyl subgroup of rofecoxib is important for their potent or weak membrane permeabilizing activity, respectively. These findings provide important information for design and synthesis of new coxibs with lower membrane permeabilizing activity. PMID:24650702

  19. SIMPLIFYING COMPLEX QSAR'S (QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIPS) IN TOXICITY STUDIES WITH MULTIVARIATE STATISTICS

    EPA Science Inventory

    During the past several decades many quantitative structure-activity relationships (QSAR's) have been derived from relatively small data sets of chemicals in a homologous series and selected empirical observations. An alternative approach is to analyze large data sets consisting ...

  20. MOLECULAR INTERACTION POTENTIALS FOR THE DEVELOPMENT OF STRUCTURE-ACTIVITY RELATIONSHIPS

    EPA Science Inventory

    Abstract One reasonable approach to the analysis of the relationships between molecular structure and toxic activity is through the investigation of the forces and intermolecular interactions responsible for chemical toxicity. The interaction between the xenobiotic and the bio...

  1. Quantitative Structure--Activity Relationship Modeling of Rat Acute Toxicity by Oral Exposure

    EPA Science Inventory

    Background: Few Quantitative Structure-Activity Relationship (QSAR) studies have successfully modeled large, diverse rodent toxicity endpoints. Objective: In this study, a combinatorial QSAR approach has been employed for the creation of robust and predictive models of acute toxi...

  2. Structure-activity relationships of the hypertrehalosemic hormone from the cockroach Blaberus discoidalis Serville 

    E-print Network

    Ford, Mary Stahlschmidt

    1988-01-01

    STRUCTURE-ACTIVITY RELATIONSHIPS OF THE HYPERTREHALOSEMIC HORMONE FROM THE COCKROACH Q~~~ ~DQQ~~I SERVILLE A Thesis by MARY STAHLSCHMIDT FORD Submitted to the Graduate College of Texas A&M University in partial fulfillment of the requirements... for the degree of MASTER OF SCIENCE May 1988 Major Subject: Veterinary Microbiology STRUCTURE-ACTIVITY RELATIONSHIP'S OF THE HYPERTREHALOSEMIC HORMONE FROM THE COCKROACH BLAB ERUS DIS COIDALIS SERVILLE A Thesis by MARY STAHLSCHMIDT FORD Approved...

  3. Developmental toxicity and structure-activity relationships of ochratoxin A and related compounds in Hydra attenuata 

    E-print Network

    Taylor, Monica Ann

    1988-01-01

    DEVELOPMENTAL TOXICITY AND STRUCTURE-ACTIVITY RELATIONSHIPS OF OCHRATOXIN A AND RELATED COMPOUNDS IN HYDRA ATTENUATA A Thesis by MONICA ANN TAYLOR Submitted to the Office of Graduate Studies of Texas ARM University in Partial fulfillment... of the requirements for the degree of MASTER OF SCIENCE December 1988 Major Subject: Food Science and Technology DEVELOPMENTAL TOXICITY AND STRUCTURE-ACTIVITY RELATIONSHIPS OF OCHRATOXIN A AND RELATED COMPOUNDS IN ~HY R ATTENUATA A Thesis by MONICA ANN TAYLOR...

  4. Advance in dietary polyphenols as ?-glucosidases inhibitors: a review on structure-activity relationship aspect

    Microsoft Academic Search

    Jianbo Xiao; Guoyin Kai; Koichiro Yamamoto; Xiaoqing Chen

    2012-01-01

    The dietary polyphenols as ?-glucosidases inhibitors have attracted great interest among researchers. The aim of this review is to give an overview of the research reports on the structure-activity relationship of dietary polyphenols inhibiting ?-glucosidases. The molecular structures influence the inhibition are the following: 1) The hydroxylation and galloylation of flavonoids including catechins improve the inhibitory activity. 2) The glycosylation

  5. Structure–radical scavenging activity relationships of phenolic compounds from traditional Chinese medicinal plants

    Microsoft Academic Search

    Yi-Zhong Cai; Mei Sun; Jie Xing; Qiong Luo; Harold Corke

    2006-01-01

    Traditional Chinese medicinal plants associated with anticancer contain a wide variety of natural phenolic compounds with various structural features and possessing widely differing antioxidant activity. The structure–radical scavenging activity relationships of a large number of representative phenolic compounds (e.g., flavanols, flavonols, chalcones, flavones, flavanones, isoflavones, tannins, stilbenes, curcuminoids, phenolic acids, coumarins, lignans, and quinones) identified in the traditional Chinese medicinal

  6. Isothiocyanate synthetic analogs: biological activities, structure-activity relationships and synthetic strategies.

    PubMed

    Milelli, Andrea; Fimognari, Carmela; Ticchi, Nicole; Neviani, Paolo; Minarini, Anna; Tumiatti, Vincenzo

    2014-01-01

    Sulforaphane is a natural product that is constantly under biological investigation for its unique biological properties. This naturally occurring isothiocyanate (ITC) and its analogs are the main components of cruciferous vegetables, such as cauliflower, watercress, broccoli, cabbage, Brussels sprouts, widely used as chemopreventive agents. Due to their interesting biological profiles, natural ITCs have been exploited as starting point to develop new synthetic analogs. The present mini-review briefly highlights the most important biological actions of selected new synthetic ITCs focusing on their structure-activity relationships and related synthetic strategies. PMID:25373847

  7. Structure-activity relationships of 44 halogenated compounds for iodotyrosine deiodinase-inhibitory activity.

    PubMed

    Shimizu, Ryo; Yamaguchi, Masafumi; Uramaru, Naoto; Kuroki, Hiroaki; Ohta, Shigeru; Kitamura, Shigeyuki; Sugihara, Kazumi

    2013-12-01

    The aim of this study was to investigate the possible influence of halogenated compounds on thyroid hormone metabolism via inhibition of iodotyrosine deiodinase (IYD) activity. The structure-activity relationships of 44 halogenated compounds for IYD-inhibitory activity were examined in vitro using microsomes of HEK-293 T cells expressing recombinant human IYD. The compounds examined were 17 polychlorinated biphenyls (PCBs), 15 polybrominated diphenyl ethers (PBDEs), two agrichemicals, five antiparasitics, two pharmaceuticals and three food colorants. Among them, 25 halogenated phenolic compounds inhibited IYD activity at the concentration of 1×10(-4)M or 6×10(-4)M. Rose bengal was the most potent inhibitor, followed by erythrosine B, phloxine B, benzbromarone, 4'-hydroxy-2,2',4-tribromodiphenyl ether, 4-hydroxy-2,3',3,4'-tetrabromodiphenyl ether, 4-hydroxy-2',3,4',5,6'-pentachlorobiphenyl, 4'-hydroxy-2,2',4,5'-tetrabromodiphenyl ether, triclosan, and 4-hydroxy-2,2',3,4',5-pentabromodiphenyl ether. However, among PCBs and PBDEs without a hydroxyl group, including their methoxylated metabolites, none inhibited IYD activity. These results suggest that halogenated compounds may disturb thyroid hormone homeostasis via inhibition of IYD, and that the structural requirements for IYD-inhibitory activity include halogen atom and hydroxyl group substitution on a phenyl ring. PMID:24012475

  8. Probing structure-antifouling activity relationships of polyacrylamides and polyacrylates.

    PubMed

    Zhao, Chao; Zhao, Jun; Li, Xiaosi; Wu, Jiang; Chen, Shenfu; Chen, Qiang; Wang, Qiuming; Gong, Xiong; Li, Lingyan; Zheng, Jie

    2013-07-01

    We have synthesized two different polyacrylamide polymers with amide groups (polySBAA and polyHEAA) and two corresponding polyacrylate polymers without amide groups (polySBMA and polyHEA), with particular attention to the evaluation of the effect of amide group on the hydration and antifouling ability of these systems using both computational and experimental approaches. The influence of polymer architectures of brushes, hydrogels, and nanogels, prepared by different polymerization methods, on antifouling performance is also studied. SPR and ELISA data reveal that all polymers exhibit excellent antifouling ability to repel proteins from undiluted human blood serum/plasma, and such antifouling ability can be further enhanced by presenting amide groups in polySBAA and polyHEAA as compared to polySBMA and polyHEA. The antifouling performance is positively correlated with the hydration properties. Simulations confirm that four polymers indeed have different hydration characteristics, while all presenting a strong hydration overall. Integration of amide group with pendant hydroxyl or sulfobetaine group in polymer backbones is found to increase their surface hydration of polymer chains and thus to improve their antifouling ability. Importantly, we present a proof-of-concept experiment to synthesize polySBAA nanogels, which show a switchable property between antifouling and pH-responsive functions driven by acid-base conditions, while still maintaining high stability in undiluted fetal bovine serum and minimal toxicity to cultured cells. This work provides important structural insights into how very subtle structural changes in polymers can yield great improvement in biological activity, specifically the inclusion of amide group in polymer backbone/sidechain enables to obtain antifouling materials with better performance for biomedical applications. PMID:23562049

  9. Extracellular melanogenesis inhibitory activity and the structure-activity relationships of ugonins from Helminthostachys zeylanica roots.

    PubMed

    Yamauchi, Kosei; Mitsunaga, Tohru; Itakura, Yuki; Batubara, Irmanida

    2015-07-01

    Ugonin J, K, and L, which are luteolin derivatives, were isolated from Helminthostachys zeylanica roots by a series of chromatographic separations of a 50% ethanol/water extract. They were identified using nuclear magnetic resonance (NMR), ultraviolet (UV) spectra, and ultra-performance liquid chromatography coupled to time-of-flight mass spectrometry (UPLC-TOF-MS). In this study, the intra and extracellular melanogenic activity of the ugonins were determined using B16 melanoma cells. The results showed that ugonin J at 12.5, 25, and 50?M reduced extracellular melanin contents to 75, 16, and 14%, respectively, compared to the control. This indicates that ugonin J showed a stronger activity than arbutin, used as the positive control. Moreover, ugonin K showed a more potent inhibition with 19, 8, and 9% extracellular melanin reduction at the same concentrations, than that shown by ugonin J. In contrast, ugonin L did not inhibit intra- or extracellular melanogenic activity. Furthermore, in order to investigate the structure-activity relationships of the ugonins, the intra- and extracellular melanogenic activity of luteolin, methylluteolin, quercetin, eriodictyol, apigenin, and chrysin were determined. Consequently, it was suggested that the catechol and flavone skeleton of ugonin K is essential for the extracellular melanogenic inhibitory activity, and the low polarity substituent groups on the A ring of ugonin K may increase the activity. PMID:25979512

  10. Development of Computational Tools for Use in Quantitative Structure-Activity and Structure-Property Relationships

    NASA Astrophysics Data System (ADS)

    Dixon, Steven L.

    Computational tools are developed to relate theoretical aspects of molecular structure to experimental chemical behavior. The assumption that a causal relationship exists between molecular structure and chemical behavior is the fundamental premise that underlies the fields of quantitative structure-activity relationships (QSAR) and quantitative structure-property relationships (QSPR). Generation of a QSAR or QSPR involves the characterization of chemical structure in terms of numerical indices, and the development of mathematical models that correlate these indices with biological activities or physicochemical properties. Tools are developed in this thesis for use at three important stages of this process. A fast quantum mechanical molecular modeling technique based on a modified extended Huckel approach is developed for placing molecules in realistic energy-minimized conformations. The extended Huckel neglect-of-differential-overlap (EHNDO) method utilizes a one-electron approximation, semiempirical parameterization, and an efficient BFGS geometry optimization. The calculated molecular geometries from EHNDO are as accurate as those produced by the two-electron AM1 method, and the EHNDO geometry optimization is approximately three times faster. A new empirical method for calculating atomic charges is developed to characterize electronic structure. These charges are used in combination with the concepts of induction and resonance to arrive at an empirical model for pK _ a estimation in organic acids and bases. The PKACHG method generates partial atomic charges that yield accurate predictions of electric dipole moment, and the pK_ a model is accurate over wide ranges of acidity and basicity. Finally, nonlinear mathematical modeling techniques are investigated as a means of generating QSARs and QSPRs that contain stronger connections between calculated structure and experimental chemical behavior. A computational neural network program, QNET, is developed and outfitted with an efficient BFGS optimization for network training. A quadratic fitting routine, QUADFIT, is proposed as a fast alternative to neural networks. Both QNET and QUADFIT utilize external cross-validation during model development to prevent experimental data from being overfit. In a QSAR study of amine toxicity, QNET significantly outperforms conventional linear regression, and both QNET and QUADFIT yield post-model predictions that are considerably more accurate than those of linear regression.

  11. Quantitative structure-activity relationship of antifungal activity of rosin derivatives.

    PubMed

    Wang, Hui; Nguyen, Thi Thanh Hien; Li, Shujun; Liang, Tao; Zhang, Yuanyuan; Li, Jian

    2015-01-15

    To develop new rosin-based wood preservatives with good antifungal activity, 24 rosin derivatives were synthesized, bioassay tested with Trametes versicolor and Gloeophyllum trabeum, and subjected to analysis of their quantitative structure-activity relationships (QSAR). A QSAR analysis using Ampac 9.2.1 and Codessa 2.7.16 software built two QSAR models of antifungal ratio for T. versicolor and G. trabeum with values of R(2)=0.9740 and 0.9692, respectively. Based on the models, tri-N-(3-hydroabietoxy-2-hydroxy) propyl-triethyl ammonium chloride was designed and the bioassay test result proved its better inhibitory effect against the two selected fungi as expected. PMID:25466709

  12. ESTIMATION OF ELECTRON AFFINITY BASED ON STRUCTURE ACTIVITY RELATIONSHIPS

    EPA Science Inventory

    Electron affinity for a wide range of organic molecules was calculated from molecular structure using the chemical reactivity models developed in SPARC. hese models are based on fundamental chemical structure theory applied to the prediction of chemical reactivities for organic m...

  13. A descriptor of amino acids: SVRG and its application to peptide quantitative structure–activity relationship

    Microsoft Academic Search

    J. Tong; T. Che; Y. Li; P. Wang; X. Xu; Y. Chen

    2011-01-01

    In this work, a descriptor, SVRG (principal component scores vector of radial distribution function descriptors and geometrical descriptors), was derived from principal component analysis (PCA) of a matrix of two structural variables of coded amino acids, including radial distribution function index (RDF) and geometrical index. SVRG scales were then applied in three panels of peptide quantitative structure–activity relationships (QSARs) which

  14. STRUCTURE-ACTIVITY RELATIONSHIPS FOR SCREENING ORGANIC CHEMICALS FOR POTENTIAL ECOTOXICITY EFFECTS

    EPA Science Inventory

    The paper presents structure-activity relationships (QSAR) for estimating the bioconcentration factor and acute toxicity of some classes of industrial chemicals using only the n-octanol/water partition coefficient (Log P) which is derived from chemical structure. The bioconcentra...

  15. Structural Relationships between Social Activities and Longitudinal Trajectories of Depression among Older Adults

    ERIC Educational Resources Information Center

    Hong, Song-Iee; Hasche, Leslie; Bowland, Sharon

    2009-01-01

    Purpose: This study examines the structural relationships between social activities and trajectories of late-life depression. Design and Methods: Latent class analysis was used with a nationally representative sample of older adults (N = 5,294) from the Longitudinal Study on Aging II to classify patterns of social activities. A latent growth curve…

  16. Structure-Activity Relationship of Benzophenanthridine Alkaloids from Zanthoxylum rhoifolium Having Antimicrobial Activity

    PubMed Central

    Tavares, Luciana de C.; Zanon, Graciane; Weber, Andréia D.; Neto, Alexandre T.; Mostardeiro, Clarice P.; Da Cruz, Ivana B. M.; Oliveira, Raul M.; Ilha, Vinicius; Dalcol, Ionara I.; Morel, Ademir F.

    2014-01-01

    Zanthoxylum rhoifolium (Rutaceae) is a plant alkaloid that grows in South America and has been used in Brazilian traditional medicine for the treatment of different health problems. The present study was designed to evaluate the antimicrobial activity of the steam bark crude methanol extract, fractions, and pure alkaloids of Z. rhoifolium. Its stem bark extracts exhibited a broad spectrum of antimicrobial activity, ranging from 12.5 to 100 µg/mL using bioautography method, and from 125 to 500 µg/mL in the microdilution bioassay. From the dichloromethane basic fraction, three furoquinoline alkaloids (1–3), and nine benzophenanthridine alkaloids (4–12) were isolated and the antimicrobial activity of the benzophenanthridine alkaloids is discussed in terms of structure-activity relationships. The alkaloid with the widest spectrum of activity was chelerythrine (10), followed by avicine (12) and dihydrochelerythrine (4). The minimal inhibitory concentrations of chelerythrine, of 1.50 µg/mL for all bacteria tested, and between 3.12 and 6.25 µg/mL for the yeast tested, show this compound to be a more powerful antimicrobial agent when compared with the other active alkaloids isolated from Z. rhoifolium. To verify the potential importance of the methylenedioxy group (ring A) of these alkaloids, chelerythrine was selected to represent the remainder of the benzophenanthridine alkaloids isolated in this work and was subjected to a demethylation reaction giving derivative 14. Compared to chelerythrine, the derivative (14) was less active against the tested bacteria and fungi. Kinetic measurements of the bacteriolytic activities of chelerythrine against the bacteria Bacillus subtilis (Gram-positive) and Escherichia coli (Gram-negative) were determined by optical density based on real time assay, suggesting that its mechanism of action is not bacteriolytic. The present study did not detect hemolytic effects of chelerythrine on erythrocytes and found a protective effect considering the decrease in TBARS and AOPP (advanced oxidized protein products) levels when compared to the control group. PMID:24824737

  17. Structure-activity relationship of benzophenanthridine alkaloids from Zanthoxylum rhoifolium having antimicrobial activity.

    PubMed

    Tavares, Luciana de C; Zanon, Graciane; Weber, Andréia D; Neto, Alexandre T; Mostardeiro, Clarice P; Da Cruz, Ivana B M; Oliveira, Raul M; Ilha, Vinicius; Dalcol, Ionara I; Morel, Ademir F

    2014-01-01

    Zanthoxylum rhoifolium (Rutaceae) is a plant alkaloid that grows in South America and has been used in Brazilian traditional medicine for the treatment of different health problems. The present study was designed to evaluate the antimicrobial activity of the steam bark crude methanol extract, fractions, and pure alkaloids of Z. rhoifolium. Its stem bark extracts exhibited a broad spectrum of antimicrobial activity, ranging from 12.5 to 100 µg/mL using bioautography method, and from 125 to 500 µg/mL in the microdilution bioassay. From the dichloromethane basic fraction, three furoquinoline alkaloids (1-3), and nine benzophenanthridine alkaloids (4-12) were isolated and the antimicrobial activity of the benzophenanthridine alkaloids is discussed in terms of structure-activity relationships. The alkaloid with the widest spectrum of activity was chelerythrine (10), followed by avicine (12) and dihydrochelerythrine (4). The minimal inhibitory concentrations of chelerythrine, of 1.50 µg/mL for all bacteria tested, and between 3.12 and 6.25 µg/mL for the yeast tested, show this compound to be a more powerful antimicrobial agent when compared with the other active alkaloids isolated from Z. rhoifolium. To verify the potential importance of the methylenedioxy group (ring A) of these alkaloids, chelerythrine was selected to represent the remainder of the benzophenanthridine alkaloids isolated in this work and was subjected to a demethylation reaction giving derivative 14. Compared to chelerythrine, the derivative (14) was less active against the tested bacteria and fungi. Kinetic measurements of the bacteriolytic activities of chelerythrine against the bacteria Bacillus subtilis (Gram-positive) and Escherichia coli (Gram-negative) were determined by optical density based on real time assay, suggesting that its mechanism of action is not bacteriolytic. The present study did not detect hemolytic effects of chelerythrine on erythrocytes and found a protective effect considering the decrease in TBARS and AOPP (advanced oxidized protein products) levels when compared to the control group. PMID:24824737

  18. Structure–activity relationship studies on quorum sensing ComX ROE2 pheromone

    Microsoft Academic Search

    Masahiro Okada; Hisao Yamaguchi; Isao Sato; Soo Jeong Cho; David Dubnau; Youji Sakagami

    2007-01-01

    The ComX pheromone is a posttranslationally modified oligopeptide that stimulates natural genetic competence in Bacillus subtilis. Various ComXRO-E-2 analogs were synthesized and their biological activities were studied to investigate structure–activity relationships. These results showed that the minimal active unit was the tripeptide, [3–5]ComXRO-E-2, and all residues except the modified tryptophan residue were replaceable by alanine without total loss of activity.

  19. Flavonoid antioxidants: chemistry, metabolism and structure-activity relationships

    Microsoft Academic Search

    Kelly E Heim; Anthony R Tagliaferro; Dennis J Bobilya

    2002-01-01

    Flavonoids are a class of secondary plant phenolics with significant antioxidant and chelating properties. In the human diet, they are most concentrated in fruits, vegetables, wines, teas and cocoa. Their cardioprotective effects stem from the ability to inhibit lipid peroxidation, chelate redox-active metals, and attenuate other processes involving reactive oxygen species. Flavonoids occur in foods primarily as glycosides and polymers

  20. Structure–activity relationships for ?-calcitonin gene-related peptide

    PubMed Central

    Watkins, Harriet A; Rathbone, Dan L; Barwell, James; Hay, Debbie L; Poyner, David R

    2013-01-01

    Calcitonin gene-related peptide (CGRP) is a member of the calcitonin (CT) family of peptides. It is a widely distributed neuropeptide implicated in conditions such as neurogenic inflammation. With other members of the CT family, it shares an N-terminal disulphide-bonded ring which is essential for biological activity, an area of potential ?-helix, and a C-terminal amide. CGRP binds to the calcitonin receptor-like receptor (CLR) in complex with receptor activity-modifying protein 1 (RAMP1), a member of the family B (or secretin-like) GPCRs. It can also activate other CLR or calcitonin-receptor/RAMP complexes. This 37 amino acid peptide comprises the N-terminal ring that is required for receptor activation (residues 1–7); an ?-helix (residues 8–18), a region incorporating a ?-bend (residues 19–26) and the C-terminal portion (residues 27–37), that is characterized by bends between residues 28–30 and 33–34. A few residues have been identified that seem to make major contributions to receptor binding and activation, with a larger number contributing either to minor interactions (which collectively may be significant), or to maintaining the conformation of the bound peptide. It is not clear if CGRP follows the pattern of other family B GPCRs in binding largely as an ?-helix. LINKED ARTICLES This article is part of a themed section on Neuropeptides. To view the other articles in this section visit http://dx.doi.org/10.1111/bph.2013.170.issue-7 PMID:23186257

  1. Structure-activity relationship of immunostimulatory effects of phthalates

    PubMed Central

    Larsen, Søren T; Nielsen, Gunnar D

    2008-01-01

    Background Some chemicals, including some phthalate plasticizers, have been shown to have an adjuvant effect in mice. However, an adjuvant effect, defined as an inherent ability to stimulate the humoral immune response, was only observed after exposure to a limited number of the phthalates. An adjuvant effect may be due to the structure or physicochemical characteristics of the molecule. The scope of this study was to investigate which molecular characteristics that determine the observed adjuvant effect of the most widely used phthalate plasticizer, the di-(2-ethylhexyl) phthalate (DEHP), which is documented as having a strong adjuvant effect. To do so, a series of nine lipophilic compounds with structural and physicochemical relations to DEHP were investigated. Results Adjuvant effect of phthalates and related compounds were restricted to the IgG1 antibody formation. No effect was seen on IgE. It appears that lipophilicity plays a crucial role, but lipophilicity does not per se cause an adjuvant effect. In addition to lipophilicity, a phthalate must also possess specific stereochemical characteristics in order for it to have adjuvant effect. Conclusion The adjuvant effect of phthalates are highly influenced by both stereochemical and physico-chemical properties. This knowledge may be used in the rational development of plasticizers without adjuvant effect as well as in the design of new immunological adjuvants. PMID:18976460

  2. Derivatives of Ergot-alkaloids: Molecular structure, physical properties, and structure-activity relationships

    NASA Astrophysics Data System (ADS)

    Ivanova, Bojidarka B.; Spiteller, Michael

    2012-09-01

    A comprehensive screening of fifteen functionalized Ergot-alkaloids, containing bulk aliphatic cyclic substituents at D-ring of the ergoline molecular skeleton was performed, studying their structure-active relationships and model interactions with ?2A-adreno-, serotonin (5HT2A) and dopamine D3 (D3A) receptors. The accounted high affinity to the receptors binding loops and unusual bonding situations, joined with the molecular flexibility of the substituents and the presence of proton accepting/donating functional groups in the studied alkaloids, may contribute to further understanding the mechanisms of biological activity in vivo and in predicting their therapeutic potential in central nervous system (CNS), including those related the Schizophrenia. Since the presented correlation between the molecular structure and properties, was based on the comprehensively theoretical computational and experimental physical study on the successfully isolated derivatives, through using routine synthetic pathways in a relatively high yields, marked these derivatives as 'treasure' for further experimental and theoretical studied in areas such as: (a) pharmacological and clinical testing; (b) molecular-drugs design of novel psychoactive substances; (c) development of the analytical protocols for determination of Ergot-alkaloids through a functionalization of the ergoline-skeleton, and more.

  3. Strong nonadditivity as a key structure-activity relationship feature: distinguishing structural changes from assay artifacts.

    PubMed

    Kramer, Christian; Fuchs, Julian E; Liedl, Klaus R

    2015-03-23

    Nonadditivity in protein-ligand affinity data represents highly instructive structure-activity relationship (SAR) features that indicate structural changes and have the potential to guide rational drug design. At the same time, nonadditivity is a challenge for both basic SAR analysis as well as many ligand-based data analysis techniques such as Free-Wilson Analysis and Matched Molecular Pair analysis, since linear substituent contribution models inherently assume additivity and thus do not work in such cases. While structural causes for nonadditivity have been analyzed anecdotally, no systematic approaches to interpret and use nonadditivity prospectively have been developed yet. In this contribution, we lay the statistical framework for systematic analysis of nonadditivity in a SAR series. First, we develop a general metric to quantify nonadditivity. Then, we demonstrate the non-negligible impact of experimental uncertainty that creates apparent nonadditivity, and we introduce techniques to handle experimental uncertainty. Finally, we analyze public SAR data sets for strong nonadditivity and use recourse to the original publications and available X-ray structures to find structural explanations for the nonadditivity observed. We find that all cases of strong nonadditivity (??pKi and ??pIC50 > 2.0 log units) with sufficient structural information to generate reasonable hypothesis involve changes in binding mode. With the appropriate statistical basis, nonadditivity analysis offers a variety of new attempts for various areas in computer-aided drug design, including the validation of scoring functions and free energy perturbation approaches, binding pocket classification, and novel features in SAR analysis tools. PMID:25760829

  4. [Rough sets theory in structure-activity relationship analysis of quaternary pyridinium compounds].

    PubMed

    Krysi?ski, J

    1991-12-01

    Relationship between chemical structure and antimicrobial activity of 53 quaternary pyridinium compounds is analysed using the theory of rough sets. The compounds are described by 8 attributes concerning structure and are divided into 5 classes of activity. The description builds up an information system. Using the rough sets approach a smallest set of attributes significant for a high quality of classification has been found. A decision algorithm has been derived from the information system showing important relations between structure and activity. It may be helpful in supporting decisions concerning synthesis of new antimicrobial compounds. PMID:1818327

  5. Structure-activity relationships (SAR) and structure-kinetic relationships (SKR) of bicyclic heteroaromatic acetic acids as potent CRTh2 antagonists II: lead optimization.

    PubMed

    Alonso, Juan Antonio; Andrés, Miriam; Bravo, Mónica; Calbet, Marta; Eastwood, Paul R; Eichhorn, Peter; Esteve, Cristina; Ferrer, Manel; Gómez, Elena; González, Jacob; Mir, Marta; Moreno, Imma; Petit, Silvia; Roberts, Richard S; Sevilla, Sara; Vidal, Bernat; Vidal, Laura; Vilaseca, Pere; Zanuy, Miriam

    2014-11-01

    Extensive structure-activity relationship (SAR) and structure-kinetic relationship (SKR) studies in the bicyclic heteroaromatic series of CRTh2 antagonists led to the identification of several molecules that possessed both excellent binding and cellular potencies along with long receptor residence times. A small substituent in the bicyclic core provided an order of magnitude jump in dissociation half-lives. Selected optimized compounds demonstrated suitable pharmacokinetic profiles. PMID:25437505

  6. Synthesis and Structure activity relationships of EGCG Analogues, A Recently Identified Hsp90 Inhibitor

    PubMed Central

    Khandelwal, Anuj; Hall, Jessica

    2014-01-01

    Epigallocatechin-3-gallate (EGCG), the principal polyphenol isolated from green tea, was recently shown to inhibit Hsp90, however structure-activity relationships for this natural product have not yet been produced. Herein, we report the synthesis and biological evaluation of EGCG analogues to establish structure-activity relationships between EGCG and Hsp90. All four rings as well as the linker connecting the C- and the D-rings were systematically investigated, which led to the discovery of compounds that inhibit Hs90 and display improvement in efficacy over EGCG. Anti-proliferative activity of all the analogues was determined against MCF-7 and SKBr3 cell lines and Hsp90 inhibitory activity of four most potent analogues was further evaluated by western blot analyses and degradation of Hsp90-dependent client proteins. Prenyl substituted aryl ester of 3,5-dihydroxychroman-3-ol ring system was identified as novel scaffold that exhibit Hsp90 inhibitory activity. PMID:23834230

  7. Structure-Activity Relationship Study of Novel Peptoids That Mimic the Structure of Antimicrobial Peptides.

    PubMed

    Mojsoska, Biljana; Zuckermann, Ronald N; Jenssen, Håvard

    2015-07-01

    The constant emergence of new bacterial strains that resist the effectiveness of marketed antimicrobials has led to an urgent demand for and intensive research on new classes of compounds to combat bacterial infections. Antimicrobial peptoids comprise one group of potential candidates for antimicrobial drug development. The present study highlights a library of 22 cationic amphipathic peptoids designed to target bacteria. All the peptoids share an overall net charge of +4 and are 8 to 9 residues long; however, the hydrophobicity and charge distribution along the abiotic backbone varied, thus allowing an examination of the structure-activity relationship within the library. In addition, the toxicity profiles of all peptoids were assessed in human red blood cells (hRBCs) and HeLa cells, revealing the low toxicity exerted by the majority of the peptoids. The structural optimization also identified two peptoid candidates, 3 and 4, with high selectivity ratios of 4 to 32 and 8 to 64, respectively, and a concentration-dependent bactericidal mode of action against Gram-negative Escherichia coli. PMID:25941221

  8. Representation of molecular structure using quantum topology with inductive logic programming in structure-activity relationships.

    PubMed

    Buttingsrud, Bård; Ryeng, Einar; King, Ross D; Alsberg, Bjørn K

    2006-06-01

    The requirement of aligning each individual molecule in a data set severely limits the type of molecules which can be analysed with traditional structure activity relationship (SAR) methods. A method which solves this problem by using relations between objects is inductive logic programming (ILP). Another advantage of this methodology is its ability to include background knowledge as 1st-order logic. However, previous molecular ILP representations have not been effective in describing the electronic structure of molecules. We present a more unified and comprehensive representation based on Richard Bader's quantum topological atoms in molecules (AIM) theory where critical points in the electron density are connected through a network. AIM theory provides a wealth of chemical information about individual atoms and their bond connections enabling a more flexible and chemically relevant representation. To obtain even more relevant rules with higher coverage, we apply manual postprocessing and interpretation of ILP rules. We have tested the usefulness of the new representation in SAR modelling on classifying compounds of low/high mutagenicity and on a set of factor Xa inhibitors of high and low affinity. PMID:17054018

  9. Structure-Activity Relationship for Thiohydantoin Androgen Receptor Antagonists for Castration-Resistant Prostate Cancer (CRPC)

    PubMed Central

    Jung, Michael E.; Ouk, Samedy; Yoo, Dongwon; Sawyers, Charles L.; Chen, Charlie; Tran, Chris; Wongvipat, John

    2011-01-01

    A structure-activity relationship study was carried out on a series of thiohydantoins and their analogues 14 which led to the discovery of 92 (MDV3100) as the clinical candidate for the treatment of hormone refractory prostate cancer. PMID:20218717

  10. Partial Least Squares Modeling and Genetic Algorithm Optimization in Quantitative StructureActivity Relationships

    Microsoft Academic Search

    K. Hasegawa; K. Funatsu

    2000-01-01

    Quantitative structure-activity relationship (QSAR) studies based on chemometric techniques are reviewed. Partial least squares (PLS) is introduced as a novel robust method to replace classical methods such as multiple linear regression (MLR). Advantages of PLS compared to MLR are illustrated with typical applications. Genetic algorithm (GA) is a novel optimization technique which can be used as a search engine in

  11. STRUCTURE-ACTIVITY RELATIONSHIPS AND ESTIMATION TECHNIQUES FOR BIODEGRADATION OF XENOBIOTICS

    EPA Science Inventory

    The Current status of structure-activity relationships for the biodegradation of xenobiotics is reviewed. esults are presented of a pilot study on biodegradation Constants obtained from Computer databases. ew analyses for a relatively large number of anilines and phenols are pres...

  12. Total Synthesis and Structure-Activity Relationship of Glycoglycerolipids from Marine Organisms

    PubMed Central

    Zhang, Jun; Li, Chunxia; Yu, Guangli; Guan, Huashi

    2014-01-01

    Glycoglycerolipids occur widely in natural products, especially in the marine species. Glycoglycerolipids have been shown to possess a variety of bioactivities. This paper will review the different methodologies and strategies for the synthesis of biological glycoglycerolipids and their analogs for bioactivity assay. In addition, the bioactivities and structure-activity relationship of the glycoglycerolipids are also briefly outlined. PMID:24945415

  13. A Robust StructureActivity Relationship (SAR) Model for Esters that Cause Skin Irritation in Humans

    Microsoft Academic Search

    Jeffrey S. Smith; Orest T. Macina; Nancy B. Sussman; Michael I. Luster; Meryl H. Karol

    2000-01-01

    A structure-activity relationship (SAR) model has been devel- oped to discriminate skin irritant from nonirritant esters. The model is based on the physicochemical properties of 42 esters that were tested in humans for skin irritation. Nineteen physicochem- ical parameters that represent transport, electronic, and steric properties were calculated for each chemical. Best subsets regres- sion analysis indicated candidate models for

  14. ESR study on the structure–antioxidant activity relationship of tea catechins and their epimers

    Microsoft Academic Search

    Qiong Guo; Baolu Zhao; Shengrong Shen; Jingwu Hou; Jungai Hu; Wenjuan Xin

    1999-01-01

    The purpose of this study is to examine the relationship between the free radical scavenging activities and the chemical structures of tea catechins ((?)-epigallocatechin gallate (EGCG), (?)-epigallocatechin (EGC) and (?)-epicatechin (EC)) and their corresponding epimers ((?)-gallocatechin gallate (GCG), (?)-gallocatechin (GC) and (+)-catechin ((+)-C)). With electron spin resonance (ESR) we investigated their scavenging effects on superoxide anions (O?·2) generated in the

  15. Synthetic ceramide analogues as skin permeation enhancers: structure–Activity relationships

    Microsoft Academic Search

    Kate?ina Vávrová; Alexandr Hrabálek; Pavel Doležal; Lucie Šámalová; Karel Palát; Jarmila Zbytovská; Tomáš Holas; Jana Klimentová

    2003-01-01

    The study presents new information about the structure–activity relationships of the skin permeation enhancers. A series of ceramide analogues including eight different polar head groups and six different chain lengths was synthesised. The compounds were evaluated as permeation enhancers in vitro using porcine skin. The physico-chemical parameters of the tested compounds obtained by computer modelling were used to evaluate, by

  16. Relationship between the antifreeze activities and the chemical structures of polyols

    NASA Astrophysics Data System (ADS)

    Baruch, Eti; Belostotskii, Anatoly M.; Mastai, Yitzhak

    2008-02-01

    In this paper, we study the antifreeze activities of aqueous solutions of carbohydrates by Scanning Calorimetry (DSC) technique. The observed antifreeze activity of carbohydrates is correlated to the chemical structures of the carbohydrates. Based on the DSC results, we develop a simple molecular model aimed at explaining the antifreeze activity of carbohydrates. Our molecular model demonstrates that carbohydrates with unique chemical structures that possessing a certain spatial O-O distance of 4.2-4.5 Å between the hydroxyl groups are essential for antifreeze activity. Additionally the structure-antifreeze activity relationship of the carbohydrates may be easily explained within the limits of the concept of their complementarity to the surface of the hexagonal ice. Overall our results provide new physical insights on the role of the complementary pattern of carbohydrates to ice surfaces and their antifreeze activity.

  17. Quantitative structure-activity relationships of antimicrobial fatty acids and derivatives against Staphylococcus aureus.

    PubMed

    Zhang, Hui; Zhang, Lu; Peng, Li-juan; Dong, Xiao-wu; Wu, Di; Wu, Vivian Chi-Hua; Feng, Feng-Qin

    2012-02-01

    Fatty acids and derivatives (FADs) are resources for natural antimicrobials. In order to screen for additional potent antimicrobial agents, the antimicrobial activities of FADs against Staphylococcus aureus were examined using a microplate assay. Monoglycerides of fatty acids were the most potent class of fatty acids, among which monotridecanoin possessed the most potent antimicrobial activity. The conventional quantitative structure-activity relationship (QSAR) and comparative molecular field analysis (CoMFA) were performed to establish two statistically reliable models (conventional QSAR: R(2)=0.942, Q(2)(LOO)=0.910; CoMFA: R(2)=0.979, Q(2)=0.588, respectively). Improved forecasting can be achieved by the combination of these two models that provide a good insight into the structure-activity relationships of the FADs and that may be useful to design new FADs as antimicrobial agents. PMID:22302421

  18. Structure-activity relationships (SAR) and structure-kinetic relationships (SKR) of pyrrolopiperidinone acetic acids as CRTh2 antagonists.

    PubMed

    Andrés, Miriam; Buil, Maria Antonia; Calbet, Marta; Casado, Oscar; Castro, Jordi; Eastwood, Paul R; Eichhorn, Peter; Ferrer, Manel; Forns, Pilar; Moreno, Imma; Petit, Silvia; Roberts, Richard S

    2014-11-01

    Pyrrolopiperidinone acetic acids (PPAs) were identified as highly potent CRTh2 receptor antagonists. In addition, many of these compounds displayed slow-dissociation kinetics from the receptor. Structure-kinetic relationship (SKR) studies allowed optimisation of the kinetics to give potent analogues with long receptor residence half-lives of up to 23 h. Low permeability was a general feature of this series, however oral bioavailability could be achieved through the use of ester prodrugs. PMID:25437503

  19. Structure–Activity Relationship of Halophenols as a New Class of Protein Tyrosine Kinase Inhibitors

    PubMed Central

    Feng, Xiu E.; Zhao, Wan Yi; Ban, Shu Rong; Zhao, Cheng Xiao; Li, Qing Shan; Lin, Wen Han

    2011-01-01

    A series of new benzophenone and diphenylmethane halophenol derivatives were prepared. Their structures were established based on 1H NMR, 13C NMR and HRMS data. All prepared compounds were screened for their in vitro protein tyrosine kinase (PTK) inhibitory activities. The effects of modification of the linker, functional groups and substituted positions at the phenyl ring on PTK inhibitory activity were investigated. Twelve halophenols showed significant PTK inhibitory activity. Among them, compounds 6c, 6d, 7d, 9d, 10d, 11d and 13d exhibited stronger activities than that of genistein, the positive reference compound. The results gave a relatively full and definite description of the structure–activity relationship and provided a foundation for further design and structure optimization of the halophenols. PMID:22016647

  20. Progress in Studies on Rutaecarpine. II.-Synthesis and Structure-Biological Activity Relationships.

    PubMed

    Son, Jong-Keun; Chang, Hyeun Wook; Jahng, Yurngdong

    2015-01-01

    Rutaecarpine is a pentacyclic indolopyridoquinazolinone alkaloid found in Evodia rutaecarpa and other related herbs. It has a variety of intriguing biological properties, which continue to attract the academic and industrial interest. Studies on rutaecarpine have included isolation from new natural sources, development of new synthetic methods for its total synthesis, the discovery of new biological activities, metabolism, toxicology, and establishment of analytical methods for determining rutaecarpine content. The present review focuses on the synthesis, biological activities, and structure-activity relationships of rutaecarpine derivatives, with respect to their antiplatelet, vasodilatory, cytotoxic, and anticholinesterase activities. PMID:26111170

  1. Synthesis and biological activities of Schiff bases of gabapentin with different aldehydes and ketones: a structure–activity relationship study

    Microsoft Academic Search

    Lingappa Mallesha; Kikkeri N. Mohana; Bantal Veeresh

    A series of novel gabapentin derivatives 6a–k and 7a–f were synthesized, and their biological activities were determined. The chemical structures were confirmed by elemental analyses,\\u000a UV–visible, FT-IR, and 1H NMR spectral studies. The structure–activity relationships (SAR) for anticonvulsant and antioxidant activities were discussed.\\u000a Compounds 7a–f were evaluated for their possible anticonvulsant activity by Maximal Electroshock Seizure (MES) test, and their

  2. Structure-activity relationship of bile alcohols as human farnesoid X receptor agonist.

    PubMed

    Iguchi, Yusuke; Kihira, Kenji; Nishimaki-Mogami, Tomoko; Une, Mizuho

    2010-01-01

    FXR (farnesoid X receptor) is a bile acid-activated nuclear receptor that regulates not only the biosynthesis and enterohepatic circulation of bile acids, but also triglyceride, cholesterol and glucose metabolism. FXR-mediated signaling pathways have become promising novel drug targets for the treatment of common metabolic and hepatic diseases. With the aim of uncovering novel modulators of FXR and further elucidating the molecular basis of FXR activation, we investigated the structure-activity relationships of a variety of naturally occurring sterols structurally related to bile acids in terms of their FXR agonist activity. Here, we report that the ability of bile alcohols to activate FXR varied with the position and number of hydroxyl groups existing in the steroid side chain of bile alcohols. In addition, we showed that the shortening of the steroid side chain of bile acids as well as bile alcohols resulted in a decline of the ability of these agents to activate FXR. Thus, we provide new insights into the structure-activity relationships of bile acids and bile alcohols as FXR agonists. PMID:19913569

  3. Nuclear receptor engineering based on novel structure activity relationships revealed by farnesyl pyrophosphate

    PubMed Central

    Goyanka, Ritu; Das, Sharmistha; Samuels, Herbert H.; Cardozo, Timothy

    2010-01-01

    Nuclear receptors (NRs) comprise the second largest protein family targeted by currently available drugs, acting via specific ligand interactions within the ligand binding domain (LBD). Recently, farnesyl pyrophosphate (FPP) was shown to be a unique promiscuous NR ligand, activating a subset of NR family members and inhibiting wound healing in skin. The current study aimed at visualizing the unique basis of FPP interaction with multiple receptors in order to identify general structure–activity relationships that operate across the NR family. Docking of FPP to the 3D structures of the LBDs of a diverse set of NRs consistently revealed an electrostatic FPP pyrophosphate contact with an NR arginine conserved in the NR family, a hydrophobic farnesyl contact with NR helix-12 and a ligand binding pocket volume between 300 and 430 Å3 as the minimal requirements for FPP activation of any NR. Lack of any of these structural features appears to render a given NR resistant to FPP activation. We used these structure–activity relationships to rationally design and successfully engineer several mutant human estrogen receptors that retain responsiveness to estradiol but no longer respond to FPP. PMID:20817759

  4. Cannabimimetic Indoles, Pyrroles, and Indenes: Structure–Activity Relationships and Receptor Interactions

    Microsoft Academic Search

    John W. Huffman

    \\u000a A number of years ago it was found that 1-aminoalkyl-3-aroylindoles have affinity for the canabinoid receptor that is expressed\\u000a in the central nervous system (CB1 receptor). More than 100 of these aminoalkylindoles were prepared and structure–activity\\u000a relationships (SARs) were developed for these compounds. Subsequently it was found that the aminoalkyl substituent could be\\u000a replaced by a straight chain alkyl group

  5. Multivariate quantitative structure-activity relationships for the aquatic toxicity of technical nonionic surfactants

    Microsoft Academic Search

    Lise-Lott Uppgård; Åsa Lindgren; Michael Sjöström; Svante Wold

    2000-01-01

    The aquatic toxicity of 36 technical nonionic surfactants (ethoxylated fatty alcohols) was examined toward two freshwater\\u000a animal species, the fairy shrimp Thamnocephalus playtyurus and the rotifer Brachionus calyciflorus. Responses of the two species to the surfactants were generally similar. A multivariate-quantitative structure-activity relationship\\u000a (M-QSAR) model was developed from the data. The M-QSAR model consisted of a partial least squares model

  6. Quantitative structure—Activity relationships for skin irritation and corrosivity of neutral and electrophilic organic chemicals

    Microsoft Academic Search

    M. D. Barratt

    1996-01-01

    Quantitative structure-activity relationships (QSARs) have been derived by relating skin irritation and corrosivity data of neutral and electrophilic organic chemicals to their log(octanol\\/water partition coefficient) (logP), molecular volume, dipole moment and 1\\/molecular weight. Datasets were analysed using stepwise regression, discriminant and principal components analysis. Discriminant analysis between irritant and non-irritant neutral and electrophilic organic chemicals using the above parameters, which

  7. [Advances in the structure-activity relationship study of natural flavonoids and its derivatives].

    PubMed

    Zhong, Jian-Qing; Li, Bo; Jia, Qi; Li, Yi-Ming; Zhu, Wei-Liang; Chen, Kai-Xian

    2011-06-01

    Flavonoids are a large class of compounds widely distributed in nature. Many pharmacological activities of flavonoids have been reported such as anti-cancer, antioxidant, anti-inflammatory, hepatoprotective, antithrombotic, vasodilator, antiviral, antibacterial, antiallergic, and so on. In recent years, domestic and foreign research groups choose natural flavonoids and optimize their chemical structures in order to develop a number of new derivatives with stronger pharmacological activities. As part of the mechanisms are not clear, we need to strengthen in-depth research in the SAR (structure-activity relationship) study for targeted and efficient structure optimization. This paper systematically summarize current researches in the SAR studies of flavonoids and their derivatives, which can serve as a reference for synthesizing new flavonoid derivatives. PMID:21882520

  8. Exploring the structure-activity relationships of ABCC2 modulators using a screening approach.

    PubMed

    Wissel, Gloria; Kudryavtsev, Pavel; Ghemtio, Leo; Tammela, Päivi; Wipf, Peter; Yliperttula, Marjo; Finel, Moshe; Urtti, Arto; Kidron, Heidi; Xhaard, Henri

    2015-07-01

    ABCC2 is a transporter with key influence on liver and kidney pharmacokinetics. In order to explore the structure-activity relationships of compounds that modulate ABCC2, and by doing so gain insights into drug-drug interactions, we screened a library of 432 compounds for modulators of radiolabeled ?-estradiol 17-(?-d-glucuronide) (EG) and fluorescent 5(6)-carboxy-2',7'-dichlorofluorescein transport (CDCF) in membrane vesicles. Following the primary screen at 80?M, dose-response curves were used to investigate in detail 86 compounds, identifying 16 low ?M inhibitors and providing data about the structure-activity relationships in four series containing 19, 24, 10, and eight analogues. Measurements with the CDCF probe were consistently more robust than for the EG probe. Only one compound was clearly probe-selective with a 50-fold difference in the IC50s obtained by the two assays. We built 24 classification models using the SVM and fused-XY Kohonen methods, revealing molecular descriptors related to number of rings, solubility and lipophilicity as important to distinguish inhibitors from inactive compounds. This study is to the best of our knowledge the first to provide details about structure-activity relationships in ABCC2 modulation. PMID:25935289

  9. Structure-Activity Relationship for Fe(III)-Salen-Like Complexes as Potent Anticancer Agents

    PubMed Central

    Ghanbari, Zahra; Housaindokht, Mohammad R.; Izadyar, Mohammad; Bozorgmehr, Mohammad R.; Eshtiagh-Hosseini, Hossein; Bahrami, Ahmad R.; Matin, Maryam M.; Khoshkholgh, Maliheh Javan

    2014-01-01

    Quantitative structure activity relationship (QSAR) for the anticancer activity of Fe(III)-salen and salen-like complexes was studied. The methods of density function theory (B3LYP/LANL2DZ) were used to optimize the structures. A pool of descriptors was calculated: 1497 theoretical descriptors and quantum-chemical parameters, shielding NMR, and electronic descriptors. The study of structure and activity relationship was performed with multiple linear regression (MLR) and artificial neural network (ANN). In nonlinear method, the adaptive neuro-fuzzy inference system (ANFIS) was applied in order to choose the most effective descriptors. The ANN-ANFIS model with high statistical significance (R2train = 0.99, RMSE = 0.138, and Q2LOO = 0.82) has better capability to predict the anticancer activity of the new compounds series of this family. Based on this study, anticancer activity of this compound is mainly dependent on the geometrical parameters, position, and the nature of the substituent of salen ligand. PMID:24955417

  10. Structure-activity relationship study of trifluoromethylketones: inhibitors of insect juvenile hormone esterase.

    PubMed

    Doucet, J P; Doucet-Panaye, A; Devillers, J

    2013-01-01

    The juvenile hormone esterase (JHE) regulates juvenile hormone titre in insect hemolymph during its larval development. It has been suggested that JHE could be targeted for use in insect control. This enzyme can also be considered as involved in the phenomenon of endocrine disruption by xenobiotics in beneficial insects. Consequently, there is a need to know the characteristics of the molecules able to act on the JHE. Trifluoromethylketones (TFKs) are the most potent JHE inhibitors found to date and different quantitative structure-activity relationships (QSARs) have been derived for this group of chemicals. In this context, a set of 181 TFKs (118 active and 63 inactive compounds), tested on Trichoplusia ni for their JHE inhibition activity and described by physico-chemical descriptors, was split into different training and test sets to derive structure-activity relationship (SAR) models from support vector classification (SVC). A SVC model including 88 descriptors and derived from a Gaussian kernel was selected for its predictive performances. Another model computed only with 13 descriptors was also selected due to its mechanistic interpretability. This study clearly illustrates the difficulty in capturing the essential structural characteristics of the TFKs explaining their JHE inhibitory activity. PMID:23721304

  11. Structure-activity relationship for Fe(III)-salen-like complexes as potent anticancer agents.

    PubMed

    Ghanbari, Zahra; Housaindokht, Mohammad R; Izadyar, Mohammad; Bozorgmehr, Mohammad R; Eshtiagh-Hosseini, Hossein; Bahrami, Ahmad R; Matin, Maryam M; Khoshkholgh, Maliheh Javan

    2014-01-01

    Quantitative structure activity relationship (QSAR) for the anticancer activity of Fe(III)-salen and salen-like complexes was studied. The methods of density function theory (B3LYP/LANL2DZ) were used to optimize the structures. A pool of descriptors was calculated: 1497 theoretical descriptors and quantum-chemical parameters, shielding NMR, and electronic descriptors. The study of structure and activity relationship was performed with multiple linear regression (MLR) and artificial neural network (ANN). In nonlinear method, the adaptive neuro-fuzzy inference system (ANFIS) was applied in order to choose the most effective descriptors. The ANN-ANFIS model with high statistical significance (R (2) train = 0.99, RMSE = 0.138, and Q (2) LOO = 0.82) has better capability to predict the anticancer activity of the new compounds series of this family. Based on this study, anticancer activity of this compound is mainly dependent on the geometrical parameters, position, and the nature of the substituent of salen ligand. PMID:24955417

  12. Identification and structure-activity relationship study of carvacrol derivatives as Mycobacterium tuberculosis chorismate mutase inhibitors.

    PubMed

    Alokam, Reshma; Jeankumar, Variam Ullas; Sridevi, Jonnalagadda Padma; Matikonda, Siddharth Sai; Peddi, Santosh; Alvala, Mallika; Yogeeswari, Perumal; Sriram, Dharmarajan

    2014-08-01

    In the present study, we identified carvacrol, a major phenolic component of oregano oil as a novel small molecule inhibitor of Mycobacterium tuberculosis (MTB) chorismate mutase (CM) enzyme with IC50 of 1.06 ± 0.4 µM. Virtual screening of the BITS-Pilani in-house database using the crystal structure of the MTB CM bound transition state intermediate (PDB: 2FP2) as framework identified carvacrol as a potential lead. Further various carvacrol derivatives were evaluated in vitro for their ability to inhibit MTB CM enzyme, whole cell MTB and cytotoxicity as steps toward the derivation of structure-activity relationships (SAR) and lead optimization. PMID:24090423

  13. Immunomodulatory effects of methoxylated flavonoids from two Chromolaena species: structure-activity relationships.

    PubMed

    Taleb-Contini, S H; Kanashiro, A; Kabeya, L M; Polizello, A C M; Lucisano-Valim, Y M; Oliveira, D C R

    2006-07-01

    Excessive generation of reactive oxygen species (ROS) by polymorphonuclear leukocytes (PMNL) is involved in the pathology of many inflammatory diseases. Compounds isolated from natural sources with antioxidant activity can be helpful to inhibit and/or modulate the oxidative damage associated with PMNL-derived ROS. The present study investigated the relationship between the chemical structure of five methoxylated flavonoids, isolated from Chromolaena hirsuta and Chromolaena squalida, and their inhibitory activity on ROS generation by opsonized zymosan-stimulated PMNL. The antioxidant efficacy of the studied flavonoids, assessed by luminol-dependent chemiluminescence, was dependent on the position and number of methoxy and hydroxy groups. PMID:16619335

  14. Structure–Activity Relationship Studies of the Tricyclic Indoline Resistance-Modifying Agent

    PubMed Central

    2015-01-01

    Previously we discovered a tricyclic indoline, N-[2-(6-bromo-4-methylidene-2,3,4,4a,9,9a-hexahydro-1H-carbazol-4a-yl)ethyl]-4-chlorobenzene-1-sulfonamide (1, Of1), from bioinspired synthesis of a highly diverse polycyclic indoline alkaloid library, that selectively resensitizes methicillin-resistant Staphylococcus aureus strains to ?-lactam antibiotics. Herein, we report a thorough structure–activity relationship investigation of 1, which identified regions of 1 that tolerate modifications without compromising activity and afforded the discovery of a more potent analogue with reduced mammalian toxicity. PMID:24694192

  15. Use of selected toxicology information resources in assessing relationships between chemical structure and biological activity.

    PubMed Central

    Wassom, J S

    1985-01-01

    This paper addresses the subject of the use of selected toxicology information resources in assessing relationships between chemical structure and specific biological end points. To assist the researcher in how to access the primary literature of genetic toxicology, teratogenesis, and carcinogenesis, three specific specialized information centers are discussed--Environmental Mutagen Information Center, Environmental Teratology Information Center, and Environmental Carcinogenesis Information Center. Also included are descriptions of information resources that contain evaluated (peer-reviewed) biological research results. The U.S. Environmental Protection Agency Genetic Toxicology Program, the International Agency for Research on Cancer Monographs, and the Toxicology Data Bank are the best sources currently available to obtain peer-reviewed results for compounds tested for genotoxicity, carcinogenicity, and other toxicological end points. The value of published information lies in its use. It has become evident that most information cannot be accepted at face value for interpretation and analysis when subjected to stringent quality evaluation criteria. This deficit can be corrected by rigid editorship and the cognizance of authors. Increased interest in alternative methods to in vivo animal testing will be exemplified by use of short-term bioassays and in structure-activity relationship studies. With respect to this latter area, it must be remembered that mechanically (computer generated) derived data cannot substitute, at least at this stage, for data obtained from actual animal testing. The future of structure-activity relationship studies will rest only in their use as a predictive tool. PMID:4065070

  16. Structure-activity relationships of lanostane-type triterpenoids from Ganoderma lingzhi as ?-glucosidase inhibitors.

    PubMed

    Fatmawati, Sri; Kondo, Ryuichiro; Shimizu, Kuniyoshi

    2013-11-01

    A series of lanostane-type triterpenoids, identified as ganoderma alcohols and ganoderma acids, were isolated from the fruiting body of Ganoderma lingzhi. Some of these compounds were confirmed as active inhibitors of the in vitro human recombinant aldose reductase. This paper aims to explain the structural requirement for ?-glucosidase inhibition. Our structure-activity studies of ganoderma alcohols showed that the OH substituent at C-3 and the double-bond moiety at C-24 and C-25 are necessary to increase ?-glucosidase inhibitory activity. The structure-activity relationships of ganoderma acids revealed that the OH substituent at C-11 is an important feature and that the carboxylic group in the side chain is essential for the recognition of ?-glucosidase inhibitory activity. Moreover, the double-bond moiety at C-20 and C-22 in the side chain and the OH substituent at C-3 of ganoderma acids improve ?-glucosidase inhibitory activity. These results provide an approach with which to consider the structural requirements of lanostane-type triterpenoids from G. lingzhi. An understanding of these requirements is considered necessary in order to improve a new type of ?-glucosidase inhibitor. PMID:24070782

  17. Thyroid hormone structure-activity relationships: molecular structure of 3,5,3'-triiodothyropropionic acid.

    PubMed

    Cody, V

    1988-01-01

    The crystal and molecular structures of 3,5,3'-triiodothyropropionic acid (T3P), determined as an N-diethanolamine salt, were carried out and the results are compared with those of other thyroid hormone structures. These data show that T3P has an unusual conformation with the diphenyl ether bridge outside the range normally observed for other thyroactive acid structures and has the largest deviations from the ideal skewed conformation predicted for 3,5-diiodothyroactive compounds. These conformational properties are not observed in the structures of thyroformic or acetic acid analogues. Biochemical data indicate that thyropropionic acid analogue activity differs from that other acid analogues which could imply that their metabolism and activity can be controlled differently from that of other hormone metabolites. PMID:3168955

  18. Peptidic HIV integrase inhibitors derived from HIV gene products: structure-activity relationship studies

    PubMed Central

    Suzuki, Shintaro; Maddali, Kasthuraiah; Hashimoto, Chie; Urano, Emiko; Ohashi, Nami; Tanaka, Tomohiro; Ozaki, Taro; Arai, Hiroshi; Tsutsumi, Hiroshi; Narumi, Tetsuo; Nomura, Wataru; Yamamoto, Naoki; Pommier, Yves; Komano, Jun A.

    2010-01-01

    Structure-activity relationship studies were conducted on HIV integrase (IN) inhibitory peptides which were found by the screening of an overlapping peptide library derived from HIV-1 gene products. Since these peptides located in the second helix of Vpr are considered to have an alpha-helical conformation, Glu-Lys pairs were introduced into the i and i+4 positions to increase the helicity of the lead compound possessing an octa-arginyl group. Ala-scan was also performed on the lead compound for the identification of the amino acid residues responsible for the inhibitory activity. The results indicated the importance of an alpha-helical structure for the expression of inhibitory activity, and presented a binding model of integrase and the lead compound. PMID:20708407

  19. Investigation on the substitution effects of the flavonoids as potent anticancer agents: a structure–activity relationships study

    Microsoft Academic Search

    Xiao-Bing Wang; Wei Liu; Lei Yang; Qing-Long Guo; Ling-Yi Kong

    Three series of flavonoid analogues substituted with different aminomethyl substitutions at C-6, C-7, and C-8 were designed\\u000a and synthesized for the structure–activity relationship studies as potent anticancer agents. The prepared analogues were evaluated\\u000a for their in vitro inhibitory activity against the growth of the hepatic cancer cell lines HepG2 and SMMC-7721. Structure–activity\\u000a relationships indicated that not only the compounds with

  20. Structure-Activity Relationship of Fenamates as Slo2.1 Channel Activators

    PubMed Central

    Garg, Priyanka

    2012-01-01

    Niflumic acid, 2-{[3-(trifluoromethyl)phenyl]amino}pyridine-3-carboxylic acid (NFA), a nonsteroidal anti-inflammatory drug that blocks cyclooxygenase (COX), was shown previously to activate [Na+]i-regulated Slo2.1 channels. In this study, we report that other fenamates, including flufenamic acid, mefenamic acid, tolfenamic acid, meclofenamic acid, and a phenyl acetic acid derivative, diclofenac, also are low-potency (EC50 = 80 ?M to 2.1 mM), partial agonists of human Slo2.1 channels heterologously expressed in Xenopus oocytes. Substituent analysis determined that N-phenylanthranilic acid was the minimal pharmacophore for fenamate activation of Slo2.1 channels. The effects of fenamates were biphasic, with an initial rapid activation phase followed by a slow phase of current inhibition. Ibuprofen, a structurally dissimilar COX inhibitor, did not activate Slo2.1. Preincubation of oocytes with ibuprofen did not significantly alter the effects of NFA, suggesting that neither channel activation nor inhibition is associated with COX activity. A point mutation (A278R) in the pore-lining S6 segment of Slo2.1 increased the sensitivity to activation and reduced the inhibition induced by NFA. Together, our results suggest that fenamates bind to two sites on Slo2.1 channels: an extracellular accessible site to activate and a cytoplasmic accessible site in the pore to inhibit currents. PMID:22851714

  1. Synthesis and Structure Activity Relationship of 3-Hydroxypyridin-2-thione Based Histone Deacetylase Inhibitors

    PubMed Central

    Sodji, Quaovi H.; Patil, Vishal; Kornacki, James R.; Mrksich, Milan; Oyelere, Adegboyega K.

    2014-01-01

    We have previously identified 3-hydroxypyridin-2-thione (3HPT) as a novel zinc binding group for histone deacetylase (HDAC) inhibition. Early structure activity relationship (SAR) studies led to various small molecules possessing selective inhibitory activity against HDAC6 or HDAC8 but are devoid of HDAC1 inhibition. To further delineate the depth of the SAR of 3HPT-derived HDAC inhibitors (HDACi), we have extended the SAR studies to include the linker region and the surface recognition group to optimize the HDAC inhibition. The current efforts resulted in the identification of two lead compounds 10d and 14e with potent HDAC6 and HDAC8 activities, but that are inactive against HDAC1. These new HDACi possess anti-cancer activities against various cancer cell lines including Jurkat J-?1 against which SAHA and the previously disclosed 3HPT-derived HDACi were inactive. PMID:24304348

  2. Prediction of compounds in different local structure-activity relationship environments using emerging chemical patterns.

    PubMed

    Namasivayam, Vigneshwaran; Gupta-Ostermann, Disha; Balfer, Jenny; Heikamp, Kathrin; Bajorath, Jürgen

    2014-05-27

    Active compounds can participate in different local structure-activity relationship (SAR) environments and introduce different degrees of local SAR discontinuity, depending on their structural and potency relationships in data sets. Such SAR features have thus far mostly been analyzed using descriptive approaches, in particular, on the basis of activity landscape modeling. However, compounds in different local SAR environments have not yet been predicted. Herein, we adapt the emerging chemical patterns (ECP) method, a machine learning approach for compound classification, to systematically predict compounds with different local SAR characteristics. ECP analysis is shown to accurately assign many compounds to different local SAR environments across a variety of activity classes covering the entire range of observed local SARs. Control calculations using random forests and multiclass support vector machines were carried out and a variety of statistical performance measures were applied. In all instances, ECP calculations yielded comparable or better performance than controls. The approach presented herein can be applied to predict compounds that complement local SARs or prioritize compounds with different SAR characteristics. PMID:24803014

  3. Inhibition of LOX by flavonoids: a structure-activity relationship study.

    PubMed

    Ribeiro, Daniela; Freitas, Marisa; Tomé, Sara M; Silva, Artur M S; Porto, Graça; Cabrita, Eurico J; Marques, M Manuel B; Fernandes, Eduarda

    2014-01-24

    The lipoxygenase (LOX) products have been identified as mediators of a series of inflammatory diseases, namely rheumatoid arthritis, inflammatory bowel disease, psoriasis, allergic rhinitis, atherosclerosis and certain types of cancer. Hence, LOX inhibitors are of interest for the modulation of these phenomena and resolution of the inflammatory processes. During LOX activity, peroxyl radical complexes are part of the reaction and may function as sources of free radicals. Thus antioxidants, such as flavonoids, capable of inhibiting lipid peroxidation and scavenging free radicals, may act as LOX inhibitors. The aim of this work was to assess the structure-activity relationship among a series of flavonoids concerning 5-LOX inhibition, through a systematic study of the inhibition of the formation of LTB4 in human neutrophils. The type of inhibition of the flavonoids was further studied using soybean LOX, type I, and Saturation Transfer Difference (1)H NMR (STD-(1)H NMR) was used to characterize the binding epitopes of the compounds to LOX-1. The obtained results reinforce flavonoids as effective inhibitors of LTB4 production in human neutrophils. It was also possible to establish a structure/activity relationship for the inhibitory activity and the type of inhibition. PMID:24368208

  4. StructureActivity Relationships for Inhibition of Cysteine Protease Activity and Development of Plasmodium falciparum by Peptidyl Vinyl Sulfones

    Microsoft Academic Search

    Bhaskar R. Shenai; Belinda J. Lee; Alejandro Alvarez-Hernandez; Pek Y. Chong; Cory D. Emal; R. Jeffrey Neitz; William R. Roush; Philip J. Rosenthal

    2003-01-01

    The Plasmodium falciparum cysteine proteases falcipain-2 and falcipain-3 appear to be required for hemo- globin hydrolysis by intraerythrocytic malaria parasites. Previous studies showed that peptidyl vinyl sulfone inhibitors of falcipain-2 blocked the development of P. falciparum in culture and exerted antimalarial effects in vivo. We now report the structure-activity relationships for inhibition of falcipain-2, falcipain-3, and parasite development by 39

  5. Structure-Antifungal Activity Relationships of Polyene Antibiotics of the Amphotericin B Group

    PubMed Central

    Tevyashova, Anna N.; Olsufyeva, Evgenia N.; Solovieva, Svetlana E.; Printsevskaya, Svetlana S.; Reznikova, Marina I.; Trenin, Aleksei S.; Galatenko, Olga A.; Treshalin, Ivan D.; Pereverzeva, Eleonora R.; Mirchink, Elena P.; Isakova, Elena B.; Zotchev, Sergey B.

    2013-01-01

    A comprehensive comparative analysis of the structure-antifungal activity relationships for the series of biosynthetically engineered nystatin analogues and their novel semisynthetic derivatives, as well as amphotericin B (AMB) and its semisynthetic derivatives, was performed. The data obtained revealed the significant influence of the structure of the C-7 to C-10 polyol region on the antifungal activity of these polyene antibiotics. Comparison of positions of hydroxyl groups in the antibiotics and in vitro antifungal activity data showed that the most active are the compounds in which hydroxyl groups are in positions C-8 and C-9 or positions C-7 and C-10. Antibiotics with OH groups at both C-7 and C-9 had the lowest activity. The replacement of the C-16 carboxyl with methyl group did not significantly affect the in vitro antifungal activity of antibiotics without modifications at the amino group of mycosamine. In contrast, the activity of the N-modified derivatives was modulated both by the presence of CH3 or COOH group in the position C-16 and by the structure of the modifying substituent. The most active compounds were tested in vivo to determine the maximum tolerated doses and antifungal activity on the model of candidosis sepsis in leukopenic mice (cyclophosphamide-induced). Study of our library of semisynthetic polyene antibiotics led to the discovery of compounds, namely, N-(l-lysyl)-BSG005 (compound 3n) and, especially, l-glutamate of 2-(N,N-dimethylamino)ethyl amide of S44HP (compound 2j), with high antifungal activity that were comparable in in vitro and in vivo tests to AMB and that have better toxicological properties. PMID:23716057

  6. Structure-Activity Relationship Studies of 3-epi-Deoxynegamycin Derivatives as Potent Readthrough Drug Candidates.

    PubMed

    Hamada, Keisuke; Taguchi, Akihiro; Kotake, Masaya; Aita, Suguru; Murakami, Saori; Takayama, Kentaro; Yakushiji, Fumika; Hayashi, Yoshio

    2015-06-11

    (+)-Negamycin (1), a natural dipeptidic antibiotic bearing a hydrazide structure, exhibits a readthrough activity toward the nonsense mutation of the dystrophin gene and restores dystrophin expression in muscles of Duchenne muscular dystrophy model mdx mice. Herein to develop more potent readthrough compounds, we performed a structure-activity relationship (SAR) study of 3-epi-deoxynegamycin (2), which is also another natural readthrough compound with little antimicrobial activity, focusing on the main carbon chain length. We found that one carbon atom shorter derivative 9b shows a higher readthrough activity than 1 and 2. Further derivatization at the carboxylic acid part of 9b demonstrates that its meta-chlorobenzyl ester derivative 17e, which has a higher ClogP value, exhibits a more potent readthrough activity than 9b. Interestingly, in the cell-free protein expression system, the readthrough activity of 17e drastically decreases compared to that in the cell-based assay. These results suggest that benzyl ester-type derivatives enhance the hydrophobicity and function as prodrugs to produce active compound 9b in living cell systems. PMID:26101575

  7. In vivo structure-activity relationship studies support allosteric targeting of a dual specificity phosphatase.

    PubMed

    Korotchenko, Vasiliy N; Saydmohammed, Manush; Vollmer, Laura L; Bakan, Ahmet; Sheetz, Kyle; Debiec, Karl T; Greene, Kristina A; Agliori, Christine S; Bahar, Ivet; Day, Billy W; Vogt, Andreas; Tsang, Michael

    2014-07-01

    Dual specificity phosphatase 6 (DUSP6) functions as a feedback attenuator of fibroblast growth factor signaling during development. In vitro high throughput chemical screening attempts to discover DUSP6 inhibitors have yielded limited success. However, in vivo whole-organism screens of zebrafish identified compound 1 (BCI) as an allosteric inhibitor of DUSP6. Here we designed and synthesized a panel of analogues to define the structure-activity relationship (SAR) of DUSP6 inhibition. In vivo high-content analysis in transgenic zebrafish, coupled with cell-based chemical complementation assays, identified structural features of the pharmacophore of 1 that were essential for biological activity. In vitro assays of DUSP hyperactivation corroborated the results from in vivo and cellular SAR. The results reinforce the notion that DUSPs are druggable through allosteric mechanisms and illustrate the utility of zebrafish as a model organism for in vivo SAR analyses. PMID:24909879

  8. Phomentrioloxin, a fungal phytotoxin with potential herbicidal activity, and its derivatives: a structure-activity relationship study.

    PubMed

    Cimmino, Alessio; Andolfi, Anna; Zonno, Maria Chiara; Boari, Angela; Troise, Ciro; Motta, Andrea; Vurro, Maurizio; Ash, Gavin; Evidente, Antonio

    2013-10-01

    Phomentrioloxin is a phytotoxic geranylcyclohexenetriol produced in liquid culture by Phomopsis sp. (teleomorph: Diaporthe gulyae), a potential mycoherbicide proposed for the control of the annual weed Carthamus lanatus. In this study, seven derivatives obtained by chemical modifications of the toxin were assayed for phytotoxic, antimicrobial, and zootoxic activities, and the structure-activity relationships were examined. Each compound was tested on nonhost weedy and agrarian plants, fungi, Gram+ and Gram- bacteria, and on brine shrimp larvae. The results provide insights into an investigation of the structural requirements for activity. The hydroxy groups at C-2 and C-4 appeared to be important features for the phytotoxicity, as well as an unchanged cyclohexentriol ring. A role seemed also to be played by the unsaturations of the geranyl side chain. These findings could be useful for understanding the mechanisms of action of new natural products, for identifying the active sites, and possibly in devising new herbicides of natural origin. PMID:24083323

  9. FISH ACUTE TOXICITY SYNDROMES: APPLICATION TO THE DEVELOPMENT OF MECHANISM-SPECIFIC QSARS (QUANTITATIVE STRUCTURE ACTIVITY RELATIONSHIPS)

    EPA Science Inventory

    Predictive models based on quantitative structure activity relationships (QSARs), are used as rapid screening tools to identify potentially hazardous chemicals. Several QSARs are now available that predict the acute toxicity of narcotic-industrial chemicals. Predictions for compo...

  10. Cytochrome P450 Family 1 Inhibitors and Structure-Activity Relationships

    PubMed Central

    Liu, Jiawang; Sridhar, Jayalakshmi; Foroozesh, Maryam

    2014-01-01

    With the widespread use of O-alkoxyresorufin dealkylation assays since the 1990’s, thousands of inhibitors of cytochrome P450 family 1 enzymes (P450s 1A1, 1A2, and 1B1) have been identified and studied. Generally, planar polycyclic molecules such as polycyclic aromatic hydrocarbons, stilbenoids, and flavonoids are considered to potentially be effective inhibitors of these enzymes. However, the details of structure-activity relationships and selectivity of these inhibitors are still ambiguous. In this review, we thoroughly discuss the selectivity of many representative P450 family 1 inhibitors reported in the past 20 years through a meta-analysis. PMID:24287985

  11. Structure-activity relationship of synthetic pheromone components in sex communication of click beetles (Coleoptera, Elateridae).

    PubMed

    Siirde, K; Lääts, K; Erm, A; Kogerman, A; Kudryavtsev, I; Ismailov, V; Pristavko, V

    1993-08-01

    It has been shown earlier that various geranyl and (E,E)-farnesyl esters are major components of natural sex pheromones of click beetles,Agriotes. In addition, some isomeric terpene esters have an inhibiting or synergistic influence upon the sex communication of some species ofAgriotes. In this paper the influence of synthetic terpene esters in pheromone compositions on the sex communication of differentAgriotes species occurring in different climatic zones has been studied. The relationship between the biological activity of sex attractants and their chemical structure has been established. PMID:24249227

  12. Synthesis and structure-activity relationships of novel benzoxaboroles as a new class of antimalarial agents.

    PubMed

    Zhang, Yong-Kang; Plattner, Jacob J; Freund, Yvonne R; Easom, Eric E; Zhou, Yasheen; Gut, Jiri; Rosenthal, Philip J; Waterson, David; Gamo, Francisco-Javier; Angulo-Barturen, Inigo; Ge, Min; Li, Zhiya; Li, Lingchao; Jian, Yong; Cui, Han; Wang, Hailong; Yang, Jian

    2011-01-15

    A series of boron-containing benzoxaborole compounds was designed and synthesized for a structure-activity relationship investigation surrounding 7-(HOOCCH(2)CH(2))-1,3-dihydro-1-hydroxy-2,1-benzoxaborole (1) with the goal of discovering a new antimalarial treatment. Compound 1 demonstrates the best potency (IC(50)=26nM) against Plasmodium falciparum and has good drug-like properties, with low molecular weight (206.00), low ClogP (0.86) and high water solubility (750?g/mL at pH 7). PMID:21195617

  13. Synthesis and structure-activity relationships studies of brartemicin analogs as anti-invasive agents.

    PubMed

    Jiang, Yong-Li; Miyanaga, Satoshi; Han, Xiu-Zhen; Tang, Long-Qiang; Igarashi, Yasuhiro; Saiki, Ikuo; Liu, Zhao-Peng

    2013-09-01

    Brartemicin is a trehalose-based inhibitor of tumor cell invasion produced by the actinomycete of the genus Nonomuraea. In order to find more potent anti-invasive agents and study the structure-activity relationships, a series of 19 brartemicin analogs were prepared via two synthetic routes from ?,?-D-trehalose and evaluated for their anti-invasive activities. Compound 4f, 6,6'-bis(2,3-dimethoxybenzoyl)-?,?-D-trehalose, was more potent than the natural brartemicin. It inhibited the invasion of murine colon 26-L5, colon carcinoma SW620, melanoma B16-BL6 and breast MDA-MB-231 cells with IC50 values of 0.15, 2.35, 4.12 and 2.61 ?M, respectively. Analog 4p, 6,6'-bis(3,4-dimethoxycinnamoyl)-?,?-D-trehalose, was as potent as brartemicin against invasion of murine colon 26-L5 carcinoma cells in vitro. The structure-activity relationships of these novel trehalose-based compounds were summarized. PMID:23652604

  14. Structure-activity relationship study of bone morphogenetic protein (BMP) signaling inhibitors

    PubMed Central

    Cuny, Gregory D.; Yu, Paul B.; Laha, Joydev K.; Xing, Xuechao; Liu, Ji-Feng; Lai, Carol S.; Deng, Donna Y.; Sachidanandan, Chetana; Bloch, Kenneth D.; Peterson, Randall T.

    2008-01-01

    A structure-activity relationship study of dorsomorphin, a previously identified inhibitor of SMAD 1/5/8 phosphorylation by bone morphogenetic protein (BMP) type 1 receptors ALK2, 3, and 6, revealed that increased inhibitory activity could be accomplished by replacing the pendent 4-pyridine ring with 4-quinoline. The activity contributions of various nitrogen atoms in the core pyrazolo[1,5-a]pyrimidine ring were also examined by preparing and evaluating pyrrolo[1,2-a]pyrimidine and pyrazolo[1,5-a]pyridine derivatives. In addition, increased mouse liver microsome stability was achieved by replacing the ether substituent on the pendent phenyl ring with piperazine. Finally, an optimized compound 13 (LDN-193189 or DM-3189) demonstrated moderate pharmacokinetic characteristics (e.g. plasma t1/2 = 1.6 h) following intraperitoneal administration in mice. These studies provide useful molecular probes for examining the in vivo pharmacology of BMP signaling inhibition. PMID:18621530

  15. Discovery of thiochroman and chroman derivatives as pure antiestrogens and their structure-activity relationship.

    PubMed

    Kanbe, Yoshitake; Kim, Myung-Hwa; Nishimoto, Masahiro; Ohtake, Yoshihito; Kato, Nobuaki; Tsunenari, Toshiaki; Taniguchi, Kenji; Ohizumi, Iwao; Kaiho, Shin-ichi; Morikawa, Kazumi; Jo, Jae-Chon; Lim, Hyun-Suk; Kim, Hak-Yeop

    2006-07-15

    In order to develop pure antiestrogens, a series of 7-hydroxy-3-(4-hydroxyphenyl)-3-methylchroman and 7-hydroxy-3-(4-hydroxyphenyl)-3-methylthiochroman derivatives with sulfoxide containing side chains at the 4-position were designed, synthesized, and evaluated. Among them, compounds 14b and 24b functioned as pure antiestrogens with the ability to downregulate ER, and their in vitro and in vivo antiestrogen activities were similar to those of ICI182,780. In addition, the structure-activity relationship indicated that the (3RS,4RS)-configuration between the 3- and 4-position, the methyl group at the 3-position, the 9-methylene chain between the scaffold and the sulfoxide moiety, and the terminal perfluoroalkyl moiety play an important role in increasing estrogen receptor binding and oral antiestrogen activities. PMID:16580210

  16. Antitumor activity of norditerpenoid dilactones in Podocarpus plants: structure-activity relationship on in vitro cytotoxicity against Yoshida sarcoma.

    PubMed

    Hayashi, Y; Matsumoto, T; Tashiro, T

    1979-06-01

    The in vitro cytotoxicity of norditerpenoid dilactones isolated from Podocarpus plants was determined against cultured Yoshida sarcoma cells. The dilactones involved 15 natural lactones as well as their derivatives, which include appropriate modifications necessary to the estimation of the structure-activity relationship. The unsaturated system on the B/C ring portion, the dienolide or the epoxyenolide moiety, is essential for the activity, but the gamma-lactone group on the A/B ring portion is not. Other oxygenated substituents on the skeletal carbons, such as hydroxyl, acyloxyl, or epoxide group, also show some significant effect. PMID:572795

  17. Fundamental Structure-Activity Relationships of Titanium Dioxide-Based Photocatalysts

    NASA Astrophysics Data System (ADS)

    Roberts, Charles A.

    Heterogeneous photocatalysis has been identified as a means of using renewable solar energy to produce the sustainable, non-carbon fuel H 2 and a variety of useful chemical intermediates. Currently, however, heterogeneous photocatalytic reactions are too inefficient to be industrially relevant and a deeper understanding of the effect of fundamental photocatalytic material properties on photoactivity is needed to further enhance the yields of desired products. In the general field of heterogeneous catalysis, structure-activity relationships aid in the rational design of improved catalysts and this ideology was applied to photocatalytic reactions over TiO2 based photocatalysts and model supported TiO2/SiO2 catalysts in this study. The model supported TiO2/SiO2 catalysts contain well-defined TiOx nanodomain structures that vary in domain size and electronic structure and greatly facilitate the determination of structure-photoactivity relationships. These catalysts were used in reactor studies during photocatalytic water splitting and cyclohexane photo-oxidation, and were monitored for production of H2 and cyclohexanone, respectively. It was found that for both reactions the trend in photoactivity for the TiOx nanodomains proceeded as: pure TiO2 (anatase) (24 nm) > TiO2 (anatase) nanoparticles (4--11 nm) > polymeric surface TiO5 (˜1 nm) > surface isolated TiO4 (˜0.4 nm). Photoluminescence (PL) spectroscopy was employed to yield insight into how exciton generation and recombination are related to TiOx domain size and, thus, to the photoactivity of the examined reactions. Transient PL decay studies determined that the larger bulk structure found in TiO 2 (anatase) nanoparticles (NPs) acts as a reservoir for excitons exhibiting slow recombination kinetics, which have an increased opportunity to participate in photochemistry at the surface active sites. The reactions were also studied using in situ attenuated total reflectance (ATR) Fourier transform infrared spectroscopy (FTIR) to observe the formation of adsorbed intermediates and products. For cyclohexane photo-oxidation, cyclohexanone intermediates and products were identified and the high photoactivity of the unsupported TiO2 (anatase) NPs was attributed to improved product desorption characteristics. The identification of intermediates during water splitting is made difficult by the extremely high absorption of infrared wavelengths by H2O. ATR-FTIR and Raman spectroscopy measurements were performed during photocatalytic splitting of water in an attempt to confirm the surface reaction intermediates currently identified in the literature and evidence for both superoxide (O2-) and peroxide (O2 2-) adsorbed species were found by ATR-FTIR, but no surface Ti-OOH was detected by Raman. Finally, alternate Ti-containing structures, titanate and TiO2 (anatase) nanotubes, were characterized with Raman spectroscopy and screened for their photocatalytic activity. Depending on the photo-reaction (4-chlorophenol decomposition or water splitting), thermal treatment to form the anatase phase in the nanotubular structure is a benefit to photoactivity due to the increased crystallinity. For water splitting, however, the structure-activity relationship found for supported TiO 2/SiO2 holds, and the presence of a larger bulk structure yields the best H2 production photoactivity. The structure-photoactivity relationship in this dissertation exists for two different photo-reactions and is expected to be a beneficial aid to future studies on the rational design of new and novel photocatalysts.

  18. Quantitative structure activity relationship (QSAR) of competitive N-methyl-D-aspartate (NMDA) antagonists

    NASA Astrophysics Data System (ADS)

    Korkut, Anil; Varnali, Tereza

    Glutamic acid is an excitatory amino acid neurotransmitter in the mammalian central nervous system and the NMDA molecule binds to NMDA-type glutamic acid receptors as a glutamic acid analogue, in vitro. The NMDA-type glutamic acid receptors are known for their function in many neural processes, such as neural plasticity, learning and memory. In addition, excessive NMDA receptor activity has been shown to be related to neurodegenerative diseases like epilepsy so the design of new NMDA antagonists has extra importance as potent drugs for various neural diseases. Potential antagonist molecules are usually synthesized and their activity is measured by experimental techniques. Here, computational chemistry methods are applied to develop a model, which allows one to predict the activity of potent competitive NMDA antagonists. First, various molecular parameters are calculated for a series of competitive NMDA antagonists with known activity values and those parameters are used to make a regression analysis which provides a model that relates the computationally calculated parameters to experimentally determined activity values. By the quantitative structure activity relationship (QSAR) model developed here, it is possible to predict the activity of a potent drug before its synthesis since only theoretically determined molecular parameters are used for the prediction.

  19. Structure-activity relationships and molecular modeling of sphingosine kinase inhibitors.

    PubMed

    Baek, Dong Jae; MacRitchie, Neil; Anthony, Nahoum G; Mackay, Simon P; Pyne, Susan; Pyne, Nigel J; Bittman, Robert

    2013-11-27

    The design, synthesis, and evaluation of the potency of new isoform-selective inhibitors of sphingosine kinases 1 and 2 (SK1 and SK2), the enzyme that catalyzes the phosphorylation of d-erythro-sphingosine to produce the key signaling lipid, sphingosine 1-phosphate, are described. Recently, we reported that 1-(4-octylphenethyl)piperidin-4-ol (RB-005) is a selective inhibitor of SK1. Here we report the synthesis of 43 new analogues of RB-005, in which the lipophilic tail, polar headgroup, and linker region were modified to extend the structure-activity relationship profile for this lead compound, which we explain using modeling studies with the recently published crystal structure of SK1. We provide a basis for the key residues targeted by our profiled series and provide further evidence for the ability to discriminate between the two isoforms using pharmacological intervention. PMID:24164513

  20. Structure–Activity Relationships and Molecular Modeling of Sphingosine Kinase Inhibitors

    PubMed Central

    2013-01-01

    The design, synthesis, and evaluation of the potency of new isoform-selective inhibitors of sphingosine kinases 1 and 2 (SK1 and SK2), the enzyme that catalyzes the phosphorylation of d-erythro-sphingosine to produce the key signaling lipid, sphingosine 1-phosphate, are described. Recently, we reported that 1-(4-octylphenethyl)piperidin-4-ol (RB-005) is a selective inhibitor of SK1. Here we report the synthesis of 43 new analogues of RB-005, in which the lipophilic tail, polar headgroup, and linker region were modified to extend the structure–activity relationship profile for this lead compound, which we explain using modeling studies with the recently published crystal structure of SK1. We provide a basis for the key residues targeted by our profiled series and provide further evidence for the ability to discriminate between the two isoforms using pharmacological intervention. PMID:24164513

  1. Electrochemical behavior of indolone-N-oxides: relationship to structure and antiplasmodial activity.

    PubMed

    Reybier, Karine; Nguyen, Thi Hoang Yen; Ibrahim, Hany; Perio, Pierre; Montrose, Armelle; Fabre, Paul-Louis; Nepveu, Françoise

    2012-12-01

    Indolone-N-oxides exert high parasiticidal activity at the nanomolar level in vitro against Plasmodium falciparum, the parasite responsible for malaria. The bioreductive character of these molecules was investigated using cyclic voltammetry and EPR spectroelectrochemistry to examine the relationship between electrochemical behavior and antimalarial activity and to understand their mechanisms of action. For all the compounds (37 compounds) studied, the voltammograms recorded in acetonitrile showed a well-defined and reversible redox couple followed by a second complicated electron transfer. The first reduction (-0.88Vrelationship between electrochemical behavior and indolone-N-oxide structure can be established for compounds with R(1)=-OCH(3), R(2)=H, and electron-withdrawing substituents on the phenyl group at R(3). The results help in the design of new molecules with more potent in vivo antimalarial activity. PMID:22771836

  2. Quantitative structure-activity relationships of imidazolium oximes as nerve agent antidotes

    SciTech Connect

    Musallam, H.A.; Foye, W.O.; Hansch, C.; Harris, R.N.; Engle, R.R.

    1993-05-13

    Organophosphorus-containing pesticides and chemical warfare agents are potent inhibitors of synaptic acetylcholinesterase, a key regulator of cholinergic neurotransmission. These nerve agents have for many years constituted a serious threat to military personnel. These threats stimulated considerable efforts to develop effective medical countermeasures. Several potential drugs have been found recently which are capable of protecting animals from lethal levels of nerve agents. A recent U. S. Army Medical Research and Development Command drug development project synthesized a large number of imidazolium oximes. These compounds were found to possess strong antidotal activity against one of the most lethal nerve agents, soman. The Army's approach, like most conventional drug discovery approaches, depended primarily on the trial and error method. This research was carried out to determine if these potential nerve agent antidotes could have been discovered through the use of Quantitative Structure Activity-Relationships (QSAR) technique.

  3. Threshold-based structure-activity relationships of pyrazines with bell-pepper flavor.

    PubMed

    Buchbauer, G; Klein, C T; Wailzer, B; Wolschann, P

    2000-09-01

    Quantitative structure activity relationships (QSAR) and comparative molecular field analysis (CoMFA) are applied in order to explain the aroma of 46 bell-pepper aroma compounds. Biological activities log(1/c) values are used, where c stands for the detection threshold value of the aroma compound in water. Results of conventional QSAR and CoMFA are both satisfactory in statistical significance and predictive ability. We construct a qualitative model using the graphic features of CoMFA together with the results of "classical" QSAR analysis, which is performed by multiple linear regression. Finally, the human olfactory detection threshold values of excluded pyrazines are successfully predicted. This makes CoMFA and QSAR two important tools for designing new aroma compounds and in elucidating the mechanism of odor-receptor interaction. PMID:10995349

  4. The Effect of Nano Confinement on the C-H Activation and its Corresponding Structure-Activity Relationship

    NASA Astrophysics Data System (ADS)

    Shao, Jing; Yuan, Linghua; Hu, Xingbang; Wu, Youting; Zhang, Zhibing

    2014-11-01

    The C-H activation of methane, ethane, and t-butane on inner and outer surfaces of nitrogen-doped carbon nanotube (NCNTs) are investigated using density functional theory. It includes NCNTs with different diameters, different N and O concentrations, and different types (armchair and zigzag). A universal structure-reactivity relationship is proposed to characterize the C-H activation occurring both on the inner and outer surfaces of the nano channel. The C-O bond distance, spin density and charge carried by active oxygen are found to be highly related to the C-H activation barriers. Based on these theoretical results, some useful strategies are suggested to guide the rational design of more effective catalysts by nano channel confinement.

  5. The effect of nano confinement on the C-h activation and its corresponding structure-activity relationship.

    PubMed

    Shao, Jing; Yuan, Linghua; Hu, Xingbang; Wu, Youting; Zhang, Zhibing

    2014-01-01

    The C-H activation of methane, ethane, and t-butane on inner and outer surfaces of nitrogen-doped carbon nanotube (NCNTs) are investigated using density functional theory. It includes NCNTs with different diameters, different N and O concentrations, and different types (armchair and zigzag). A universal structure-reactivity relationship is proposed to characterize the C-H activation occurring both on the inner and outer surfaces of the nano channel. The C-O bond distance, spin density and charge carried by active oxygen are found to be highly related to the C-H activation barriers. Based on these theoretical results, some useful strategies are suggested to guide the rational design of more effective catalysts by nano channel confinement. PMID:25428459

  6. Phosphodiesterase type IV inhibition. Structure-activity relationships of 1,3-disubstituted pyrrolidines.

    PubMed

    Feldman, P L; Brackeen, M F; Cowan, D J; Marron, B E; Schoenen, F J; Stafford, J A; Suh, E M; Domanico, P L; Rose, D; Leesnitzer, M A

    1995-04-28

    The synthesis of 1,3-disubstituted pyrrolidines 2 and their activities as type IV phosphodiesterase (PDE) inhibitors are described. Various groups were appended to the nitrogen of the pyrrolidine nucleus to enable structure-activity relationships to be assessed. Groups which render the pyrrolidine nitrogen of 2 nonbasic yielded potent PDE-IV inhibitors. Analogs of amides, carbamates, and ureas of 2 were synthesized to determine the effects that substitution on these functional groups had on PDE-IV inhibitor potency. The structural requirements for PDE-IV inhibitor potency differed among the three classes. A representative amide, carbamate, and urea (2c,d,h) were shown to be > 50-fold selective for inhibiting PDE-IV versus representative PDEs from families I-III and V. Furthermore, these same three inhibitors demonstrated potent functional activity (IC50 < 1 microM) by inhibiting tumor necrosis factor-alpha (TNF-alpha) release from lipopolysaccharide (LPS)-activated purified human peripheral blood monocytes and mouse peritoneal macrophages. These compounds were also tested orally in LPS-injected mice and demonstrated dose-dependent inhibition of serum TNF-alpha levels. PMID:7739009

  7. Investigations on Inhibitors of Hedgehog Signal Pathway: A Quantitative Structure-Activity Relationship Study

    PubMed Central

    Zhu, Ruixin; Liu, Qi; Tang, Jian; Li, Huiliang; Cao, Zhiwei

    2011-01-01

    The hedgehog signal pathway is an essential agent in developmental patterning, wherein the local concentration of the Hedgehog morphogens directs cellular differentiation and expansion. Furthermore, the Hedgehog pathway has been implicated in tumor/stromal interaction and cancer stem cell. Nowadays searching novel inhibitors for Hedgehog Signal Pathway is drawing much more attention by biological, chemical and pharmological scientists. In our study, a solid computational model is proposed which incorporates various statistical analysis methods to perform a Quantitative Structure-Activity Relationship (QSAR) study on the inhibitors of Hedgehog signaling. The whole QSAR data contain 93 cyclopamine derivatives as well as their activities against four different cell lines (NCI-H446, BxPC-3, SW1990 and NCI-H157). Our extensive testing indicated that the binary classification model is a better choice for building the QSAR model of inhibitors of Hedgehog signaling compared with other statistical methods and the corresponding in silico analysis provides three possible ways to improve the activity of inhibitors by demethylation, methylation and hydroxylation at specific positions of the compound scaffold respectively. From these, demethylation is the best choice for inhibitor structure modifications. Our investigation also revealed that NCI-H466 served as the best cell line for testing the activities of inhibitors of Hedgehog signal pathway among others. PMID:21686166

  8. Structure-Activity Relationships of Neplanocin A Analogues as S-Adenosylhomocysteine Hydrolase Inhibitors and Their Antiviral and Antitumor Activities.

    PubMed

    Chandra, Girish; Moon, Yang Won; Lee, Yoonji; Jang, Ji Yong; Song, Jayoung; Nayak, Akshata; Oh, Kawon; Mulamoottil, Varughese A; Sahu, Pramod K; Kim, Gyudong; Chang, Tong-Shin; Noh, Minsoo; Lee, Sang Kook; Choi, Sun; Jeong, Lak Shin

    2015-06-25

    On the basis of the potent inhibitory activity of neplanocin A (1) against S-adenosylhomocysteine (AdoHcy) hydrolase, we analyzed the comprehensive structure-activity relationships by modifying the adenine and carbasugar moiety of 1 to find the pharmacophore in the active site of the enzyme. The introduction of 7-deazaadenine instead of adenine eliminated the inhibitory activity against the AdoHcy hydrolase, while 3-deazaadenine maintained the inhibitory activity of the enzyme, indicating that N-7 is essential for its role as a hydrogen bonding acceptor. The substitution of hydrogen at the 6'-position with fluorine increased the inhibitory activity of the enzyme. The one-carbon homologation at the 5'-position generally decreased the inhibitory activity of the enzyme, indicating that steric repulsion exists. A molecular docking study also supported these experimental data. In this study, 6'-fluoroneplanocin A (2) was the most potent inhibitor of AdoHcy hydrolase (IC50 = 0.24 ?M). It showed a potent anti-VSV activity (EC50 = 0.43 ?M) and potent anticancer activity in all the human tumor cell lines tested. PMID:26010585

  9. Structure-composition-activity relationships in transition-metal oxide and oxyhydroxide oxygen-evolution electrocatalysts

    NASA Astrophysics Data System (ADS)

    Trotochaud, Lena

    Solar water-splitting is a potentially transformative renewable energy technology. Slow kinetics of the oxygen evolution reaction (OER) limit the efficiency of solar-watersplitting devices, thus constituting a hurdle to widespread implementation of this technology. Catalysts must be stable under highly oxidizing conditions in aqueous electrolyte and minimally absorb light. A grand goal of OER catalysis research is the design of new materials with higher efficiencies enabled by comprehensive understanding of the fundamental chemistry behind catalyst activity. However, little progress has been made towards this goal to date. This dissertation details work addressing major challenges in the field of OER catalysis. Chapter I introduces the current state-of-the-art and challenges in the field. Chapter II highlights work using ultra-thin films as a platform for fundamental study and comparison of catalyst activity. Key results of this work are (1) the identification of a Ni0.9Fe0.1OOH catalyst displaying the highest OER activity in base to date and (2) that in base, many transition-metal oxides transform to layered oxyhydroxide materials which are the active catalysts. The latter result is critical in the context of understanding structure-activity relationships in OER catalysts. Chapter III explores the optical properties of these catalysts, using in situ spectroelectrochemistry to quantify their optical absorption. A new figure-of-merit for catalyst performance is developed which considers both optical and kinetic losses due to the catalyst and describes how these factors together affect the efficiency of composite semiconductor/catalyst photoanodes. In Chapter IV, the fundamental structure-composition-activity relationships in Ni1--xFexOOH catalysts are systematically investigated. This work shows that nearly all previous studies of Ni-based catalysts were likely affected by the presence of Fe impurities, a realization which holds significant weight for future study of Ni-based catalyst materials. Chapter V discusses the synthesis of tin-titanium oxide nanoparticles with tunable lattice constants. These materials could be used to make high-surface-area supports for thin layers of OER catalysts, which is important for maximizing catalyst surface area, minimizing the use of precious-metal catalysts, and optimizing 3D structure for enhanced mass/bubble transport. Finally, Chapter VI summarizes this work and outlines directions for future research.

  10. In vitro anti-cancer activity and structure–activity relationships of natural products isolated from fruits of Panax ginseng

    Microsoft Academic Search

    Wei Wang; Yuqing Zhao; Elizabeth R. Rayburn; Donald L. Hill; Hui Wang; Ruiwen Zhang

    2007-01-01

    Purpose  \\u000a Panax ginseng and its extracts have long been used for medical purposes; there is increasing interest in developing ginseng products as\\u000a cancer preventive or therapeutic agents. The present study was designed to determine biological structure–activity relationships\\u000a (SAR) for saponins present in Panax ginseng fruits.\\u000a \\u000a \\u000a \\u000a Methods  Eleven saponins were extracted from P. ginseng fruits and purified by use of D101 resin

  11. Targeted Mutations of Bacillus anthracis Dihydrofolate Reductase Condense Complex Structure-Activity Relationships

    SciTech Connect

    J Beierlein; N Karri; A Anderson

    2011-12-31

    Several antifolates, including trimethoprim (TMP) and a series of propargyl-linked analogues, bind dihydrofolate reductase from Bacillus anthracis (BaDHFR) with lower affinity than is typical in other bacterial species. To guide lead optimization for BaDHFR, we explored a new approach to determine structure-activity relationships whereby the enzyme is altered and the analogues remain constant, essentially reversing the standard experimental design. Active site mutants of the enzyme, Ba(F96I)DHFR and Ba(Y102F)DHFR, were created and evaluated with enzyme inhibition assays and crystal structures. The affinities of the antifolates increase up to 60-fold with the Y102F mutant, suggesting that interactions with Tyr 102 are critical for affinity. Crystal structures of the enzymes bound to TMP and propargyl-linked inhibitors reveal the basis of TMP resistance and illuminate the influence of Tyr 102 on the lipophilic linker between the pyrimidine and aryl rings. Two new inhibitors test and validate these conclusions and show the value of the technique for providing new directions during lead optimization.

  12. Structure-activity relationships for chloro- and nitrophenol toxicity in the pollen tube growth test

    SciTech Connect

    Schueuermann, G. [UFZ Centre for Environmental Research, Leipzig (Germany). Dept. of Chemical Ecotoxicology; Somashekar, R.K. [Bangalore Univ. (India). Dept. of Botany; Kristen, U. [Univ. Hamburg (Germany). Inst. fuer Allgemeine Botanik

    1996-10-01

    Acute toxicity of 10 chlorophenols and 10 nitrophenols with identical substitution patterns is analyzed with the pollen tube growth (PTG) test. Concentration values of 50% growth inhibition (IC50) between 0.1 and 300 mg/L indicate that the absolute sensitivity of this alternative biotest is comparable to conventional aquatic test systems. Analysis of quantitative structure-activity relationships using lipophilicity (log K{sub ow}), acidity (pK{sub a}), and quantum chemical parameters to model intrinsic acidity, solvation interactions, and nucleophilicity reveals substantial differences between the intraseries trends of log IC50. With chlorophenols, a narcotic-type relationship is derived, which, however, shows marked differences in slope and intercept when compared to reference regression equations for polar narcosis. Regression analysis of nitrophenol toxicity suggests interpretation in terms of two modes of action: oxidative uncoupling activity is associated with a pK{sub a} window from 3.8 to 8.5, and more acidic congeners with diortho-substitution show a transition from uncoupling to a narcotic mode of action with decreasing pK{sub a} and log K{sub ow}. Model calculations for phenol nucleophilicity suggest that differences in the phenol readiness for glucuronic acid conjugation as a major phase-II detoxication pathway have no direct influence on acute PTG toxicity of the compounds.

  13. Development and Validation of Quantitative Structure-Activity Relationship Models for Compounds Acting on Serotoninergic Receptors

    PubMed Central

    ?ydek, Gra?yna; Brzezi?ska, El?bieta

    2012-01-01

    A quantitative structure-activity relationship (QSAR) study has been made on 20 compounds with serotonin (5-HT) receptor affinity. Thin-layer chromatographic (TLC) data and physicochemical parameters were applied in this study. RP2 TLC 60F254 plates (silanized) impregnated with solutions of propionic acid, ethylbenzene, 4-ethylphenol, and propionamide (used as analogues of the key receptor amino acids) and their mixtures (denoted as S1–S7 biochromatographic models) were used in two developing phases as a model of drug-5-HT receptor interaction. The semiempirical method AM1 (HyperChem v. 7.0 program) and ACD/Labs v. 8.0 program were employed to calculate a set of physicochemical parameters for the investigated compounds. Correlation and multiple linear regression analysis were used to search for the best QSAR equations. The correlations obtained for the compounds studied represent their interactions with the proposed biochromatographic models. The good multivariate relationships (R2 = 0.78–0.84) obtained by means of regression analysis can be used for predicting the quantitative effect of biological activity of different compounds with 5-HT receptor affinity. “Leave-one-out” (LOO) and “leave-N-out” (LNO) cross-validation methods were used to judge the predictive power of final regression equations. PMID:22619602

  14. Cytotoxic constituents from Brazilian red propolis and their structure-activity relationship.

    PubMed

    Li, Feng; Awale, Suresh; Tezuka, Yasuhiro; Kadota, Shigetoshi

    2008-05-15

    Several classes of flavonoids [flavanoids (1-10), flavonol (11), isoflavones (12-18), isoflavanones (19-22), isoflavans (23-26), chalcones (27-30), auronol (31), pterocarpans (32-37), 2-arylbenzofuran (38), and neoflavonoid (39)] and lignans (40-42) isolated from the MeOH extract of Brazilian red propolis were investigated for their cytotoxic activity against a panel of six different cancer cell lines including murine colon 26-L5 carcinoma, murine B16-BL6 melanoma, murine Lewis lung carcinoma, human lung A549 adenocarcinoma, human cervix HeLa adenocarcinoma, and human HT-1080 fibrosarcoma cell lines. Based on the observed results, structure-activity relationships were discussed. Among the tested compounds, 7-hydroxy-6-methoxyflavanone (3) exhibited the most potent activity against B16-BL6 (IC(50), 6.66microM), LLC (IC(50), 9.29microM), A549 (IC(50), 8.63microM), and HT-1080 (IC(50), 7.94microM) cancer cell lines, and mucronulatol (26) against LLC (IC(50), 8.38microM) and A549 (IC(50), 9.9microM) cancer cell lines. These activity data were comparable to those of the clinically used anticancer drugs, 5-fluorouracil and doxorubicin, against the tested cell lines, suggesting that 3 and 26 are the good candidates for future anticancer drug development. PMID:18440233

  15. Disubstituted amino-, nitroso-, and nitrofluorenes: a physicochemical basis for structure-activity relationships in Salmonella typhimurium

    SciTech Connect

    Vance, W.A.; Wang, Y.Y.; Okamoto, H.S.

    1987-01-01

    Twenty-nine derivatives of fluorene were tested for mutagenic potency in four strains of Salmonella typhimurium with and/or without S9 microsomal activation. The effects of a second functional group on the mutagenic activity of an amino-nitroso-, and nitrofluorene were correlated with its physical and chemical properties. When the functional group is conjugated by resonance, both inductive and resonance effects are determinants of mutagenic potency. Electron-withdrawing groups such as the halogens (F, Cl, Br, and I), nitro, nitroso, and cyano at C-7 increased the mutagenic potency of 2-nitrofluorene. Acetylation of a hydroxy or an amino group at C-7 increased the mutagenic potency of 2-nitrofluorene. The physical properties of a second functional group are expected to exert their effect(s) at three points in the metabolic activation of 2,7-disubstituted fluorene derivatives: 1) initial reduction of the nitro group (redox effect), 2) stabilization of the hydroxylamine (inductive effect), and 3) stabilization/destabilization of the nitrenium ion (resonance and inductive effects). The relationships between the physical properties of a second functional group and their effects on biological activities of nitro- and aminofluorenes in the Ames Salmonella assay may be of predictive value in a first approximation of both the mutagenic and carcinogenic potency of chemicals with comparable structures such as fluoranthene and biphenyl.

  16. Immunostimulation by Synthetic Lipopeptide-Based Vaccine Candidates: Structure-Activity Relationships

    PubMed Central

    Zaman, Mehfuz; Toth, Istvan

    2013-01-01

    Peptide-based vaccines offer several advantages over conventional whole organism or protein approaches by offering improved purity and specificity in inducing immune response. However, peptides alone are generally non-immunogenic. Concerns remain about the toxicity of adjuvants which are critical for immunogenicity of synthetic peptides. The use of lipopeptides in peptide vaccines is currently under intensive investigation because potent immune responses can be generated without the use of adjuvant (thus are self-adjuvanting). Several lipopeptides derived from microbial origin, and their synthetic versions or simpler fatty acid moieties impart this self-adjuvanting activity by signaling via Toll-like receptor 2 (TLR2). Engagement of this innate immune receptor on antigen-presenting cell leads to the initiation and development of potent immune responses. Therefore optimization of lipopeptides to enhance TLR2-mediated activation is a promising strategy for vaccine development. Considerable structure-activity relationships that determine TLR2 binding and consequent stimulation of innate immune responses have been investigated for a range of lipopeptides. In this mini review we address the development of lipopeptide vaccines, mechanism of TLR2 recognition, and immune activation. An overview is provided of the best studied lipopeptide vaccine systems. PMID:24130558

  17. The structure-activity relationship of urea derivatives as anti-tuberculosis agents.

    PubMed

    Brown, Joshua R; North, Elton J; Hurdle, Julian G; Morisseau, Christophe; Scarborough, Jerrod S; Sun, Dianqing; Korduláková, Jana; Scherman, Michael S; Jones, Victoria; Grzegorzewicz, Anna; Crew, Rebecca M; Jackson, Mary; McNeil, Michael R; Lee, Richard E

    2011-09-15

    The treatment of tuberculosis is becoming more difficult due to the ever increasing prevalence of drug resistance. Thus, it is imperative that novel anti-tuberculosis agents, with unique mechanisms of action, be discovered and developed. The direct anti-tubercular testing of a small compound library led to discovery of adamantyl urea hit compound 1. In this study, the hit was followed up through the synthesis of an optimization library. This library was generated by systematically replacing each section of the molecule with a similar moiety until a clear structure-activity relationship was obtained with respect to anti-tubercular activity. The best compounds in this series contained a 1-adamantyl-3-phenyl urea core and had potent activity against Mycobacterium tuberculosis plus an acceptable therapeutic index. It was noted that the compounds identified and the pharmacophore developed is consistent with inhibitors of epoxide hydrolase family of enzymes. Consequently, the compounds were tested for inhibition of representative epoxide hydrolases: M. tuberculosis EphB and EphE; and human soluble epoxide hydrolase. Many of the optimized inhibitors showed both potent EphB and EphE inhibition suggesting the antitubercular activity is through inhibition of multiple epoxide hydrolase enzymes. The inhibitors also showed potent inhibition of humans soluble epoxide hydrolase, but limited cytotoxicity suggesting that future studies must be towards increasing the selectivity of epoxide hydrolase inhibition towards the M. tuberculosis enzymes. PMID:21840723

  18. Structure-activity relationships for antibacterial to antifungal conversion of kanamycin to amphiphilic analogues.

    PubMed

    Fosso, Marina; AlFindee, Madher N; Zhang, Qian; Nziko, Vincent de Paul Nzuwah; Kawasaki, Yukie; Shrestha, Sanjib K; Bearss, Jeremiah; Gregory, Rylee; Takemoto, Jon Y; Chang, Cheng-Wei Tom

    2015-05-01

    Novel fungicides are urgently needed. It was recently reported that the attachment of an octyl group at the O-4? position of kanamycin B converts this antibacterial aminoglycoside into a novel antifungal agent. To elucidate the structure-activity relationship (SAR) for this phenomenon, a lead compound FG03 with a hydroxyl group replacing the 3?-NH2 group of kanamycin B was synthesized. FG03's antifungal activity and synthetic scheme inspired the synthesis of a library of kanamycin B analogues alkylated at various hydroxyl groups. SAR studies of the library revealed that for antifungal activity the O-4? position is the optimal site for attaching a linear alkyl chain and that the 3?-NH2 and 6?-OH groups of the kanamycin B parent molecule are not essential for antifungal activity. The discovery of lead compound, FG03, is an example of reviving clinically obsolete drugs like kanamycin by simple chemical modification and an alternative strategy for discovering novel antimicrobials. PMID:25826012

  19. Structure-activity relationship of a u-type antimicrobial microemulsion system.

    PubMed

    Zhang, Hui; Taxipalati, Maierhaba; Yu, Liyi; Que, Fei; Feng, Fengqin

    2013-01-01

    The structure-activity relationship of a U-type antimicrobial microemulsion system containing glycerol monolaurate and ethanol at a 1?1 mass ratio as oil phase and Tween 20 as surfactant were investigated along a water dilution line at a ratio of 80?20 mass% surfactant/oil phase, based on a pseudo-ternary phase diagram. The differential scanning calorimetry results showed that in the region of up to 33% water, all water molecules are confined to the hydrophilic core of the reverse micelles, leading to the formation of w/o microemulsion. As the water content increases, the water gains mobility, and transforms into bicontinuous in the region of 33-39% water, and finally the microemulsion become o/w in the region of above 39% water. The microstructure characterization was confirmed by the dynamic light scattering measurements and freeze-fracture transmission electron microscope observation. The antimicrobial activity assay using kinetics of killing analysis demonstrated that the microemulsions in w/o regions exhibited relatively high antimicrobial activity against Escherichia coli and Staphylococcus aureus due to the antimicrobial oil phase as the continuous phase, while the antimicrobial activity started to decrease when the microemulsions entered the bicontinuous region, and decreased rapidly as the water content increased in the o/w region, as a result of the dilution of antimicrobial oil droplets in the aqueous continuous phase. PMID:24204605

  20. Structure-Activity Relationship of a U-Type Antimicrobial Microemulsion System

    PubMed Central

    Zhang, Hui; Taxipalati, Maierhaba; Yu, Liyi; Que, Fei; Feng, Fengqin

    2013-01-01

    The structure-activity relationship of a U-type antimicrobial microemulsion system containing glycerol monolaurate and ethanol at a 1?1 mass ratio as oil phase and Tween 20 as surfactant were investigated along a water dilution line at a ratio of 80?20 mass% surfactant/oil phase, based on a pseudo-ternary phase diagram. The differential scanning calorimetry results showed that in the region of up to 33% water, all water molecules are confined to the hydrophilic core of the reverse micelles, leading to the formation of w/o microemulsion. As the water content increases, the water gains mobility, and transforms into bicontinuous in the region of 33–39% water, and finally the microemulsion become o/w in the region of above 39% water. The microstructure characterization was confirmed by the dynamic light scattering measurements and freeze-fracture transmission electron microscope observation. The antimicrobial activity assay using kinetics of killing analysis demonstrated that the microemulsions in w/o regions exhibited relatively high antimicrobial activity against Escherichia coli and Staphylococcus aureus due to the antimicrobial oil phase as the continuous phase, while the antimicrobial activity started to decrease when the microemulsions entered the bicontinuous region, and decreased rapidly as the water content increased in the o/w region, as a result of the dilution of antimicrobial oil droplets in the aqueous continuous phase. PMID:24204605

  1. The Structure Activity Relationship of Urea Derivatives as Anti-Tuberculosis Agents

    PubMed Central

    Brown, Joshua R.; North, Elton J.; Hurdle, Julian G.; Morisseau, Christophe; Scarborough, Jerrod S.; Sun, Dianqing; Korduláková, Jana; Scherman, Michael S.; Jones, Victoria; Grzegorzewicz, Anna; Crew, Rebecca M.; Jackson, Mary; McNeil, Michael R.; Lee, Richard E.

    2011-01-01

    The treatment of tuberculosis is becoming more difficult due to the ever increasing prevalence of drug resistance. Thus, it is imperative that novel anti-tuberculosis agents, with unique mechanisms of action, be discovered and developed. The direct anti-tubercular testing of a small compound library led to discovery of adamantyl urea hit compound 1. In this study, the hit was followed up through the synthesis of an optimization library. This library was generated by systematically replacing each section of the molecule with a similar moiety until a clear structure activity relationship was obtained with respect to anti-tubercular activity. The best compounds in this series contained a 1-adamantyl-3-phenyl urea core and had potent activity against Mycobacterium tuberculosis plus an acceptable therapeutic index. It was noted that the compounds identified and the pharmacophore developed is consistent with inhibitors of epoxide hydrolase family of enzymes. Consequently, the compounds were tested for inhibition of representative epoxide hydrolases: M. tuberculosis EphB and EphE; and human soluble epoxide hydrolase. Many of the optimized inhibitors showed both potent EphB and EphE inhibition suggesting the antitubercular activity is through inhibition of multiple epoxide hydrolyase enzymes. The inhibitors also showed potent inhibition of humans soluble expoxide hydrolyase, but limited cytotoxicity suggesting that future studies must be towards increasing the selectivity of epoxide hydrolyase inhibition towards the M. tuberculosis enzymes. PMID:21840723

  2. Improved Quantitative Structure-Activity Relationship Models to Predict Antioxidant Activity of Flavonoids in Chemical, Enzymatic, and Cellular Systems

    PubMed Central

    Khlebnikov, Andrei I.; Schepetkin, Igor A.; Domina, Nina G.; Kirpotina, Liliya N.; Quinn, Mark T.

    2007-01-01

    Quantitative structure-activity relationship (QSAR) models are useful in understanding how chemical structure relates to the biological activity of natural and synthetic chemicals and for design of newer and better therapeutics. In the present study, 46 flavonoids and related polyphenols were evaluated for direct/indirect antioxidant activity in three different assay systems of increasing complexity (chemical, enzymatic, and intact phagocytes). Based on these data, two different QSAR models were developed using i) physicochemical and structural (PC&S) descriptors to generate multiparameter partial least squares (PLS) regression equations derived from optimized molecular structures of the tested compounds and ii) a partial 3D comparison of the 46 compounds with local fingerprints obtained from fragments of the molecules by the frontal polygon (FP) method. We obtained much higher QSAR correlation coefficients (r) for flavonoid end-point antioxidant activity in all 3 assay systems using the FP method (0.966, 0.948, and 0.965 for datasets in evaluated in the biochemical, enzymatic, and whole cells assay systems, respectively). Furthermore, high leave-one-out cross-validation coefficients (q2) of 0.907, 0.821, and 0.897 for these datasets, respectively, indicated enhanced predictive ability and robustness of the model. Using the FP method, structural fragments (submolecules) responsible for the end-point antioxidant activity in the three assay systems were also identified. To our knowledge, this is the first QSAR model derived for description of flavonoid direct/indirect antioxidant effects in a cellular system, and this model could form the basis for further drug development of flavonoid-like antioxidant compounds with therapeutic potential. PMID:17166721

  3. Predicting toxicity of benzene derivatives by molecular hologram derived quantitative structure-activity relationships (QSARS).

    PubMed

    Cui, S; Wang, X; Liu, S; Wang, L

    2003-06-01

    Holographic quantitative structure-activity relationship (HQSAR) is an emerging QSAR technique with the combined application of molecular hologram, which encodes the frequency of occurrence of various molecular fragment types, and the subsequent partial least squares (PLS) regression analysis. Based on molecular hologram, alignment-free QSAR models could be rapidly and easily developed with highly statistical significance and predictive ability. In this paper, the toxicity data for a series of 83 benzene derivatives to the autotrophic Chlorella vulgaris (IGC50, negative logarithmic form of 6-h 50% population growth inhibition concentration in mmol/l) were subjected to HQSAR analysis and this resulted in a model with a high predictive ability. The robustness and predictive ability of the model were validated by "leave-one-out" (LOO) cross-validation procedure and an external testing set. The influence of fragment distinction parameters and fragment size on the quality of the HQSAR model have been also discussed. PMID:12854655

  4. Structure-Activity Relationship of Semicarbazone EGA Furnishes Photoaffinity Inhibitors of Anthrax Toxin Cellular Entry.

    PubMed

    Jung, Michael E; Chamberlain, Brian T; Ho, Chi-Lee C; Gillespie, Eugene J; Bradley, Kenneth A

    2014-04-10

    EGA, 1, prevents the entry of multiple viruses and bacterial toxins into mammalian cells by inhibiting vesicular trafficking. The cellular target of 1 is unknown, and a structure-activity relationship study was conducted in order to develop a strategy for target identification. A compound with midnanomolar potency was identified (2), and three photoaffinity labels were synthesized (3-5). For this series, the expected photochemistry of the phenyl azide moiety is a more important factor than the IC50 of the photoprobe in obtaining a successful photolabeling event. While 3 was the most effective reversible inhibitor of the series, it provided no protection to cells against anthrax lethal toxin (LT) following UV irradiation. Conversely, 5, which possessed weak bioactivity in the standard assay, conferred robust irreversible protection vs LT to cells upon UV photolysis. PMID:24900841

  5. Structure–Activity Relationship of Semicarbazone EGA Furnishes Photoaffinity Inhibitors of Anthrax Toxin Cellular Entry

    PubMed Central

    2014-01-01

    EGA, 1, prevents the entry of multiple viruses and bacterial toxins into mammalian cells by inhibiting vesicular trafficking. The cellular target of 1 is unknown, and a structure–activity relationship study was conducted in order to develop a strategy for target identification. A compound with midnanomolar potency was identified (2), and three photoaffinity labels were synthesized (3–5). For this series, the expected photochemistry of the phenyl azide moiety is a more important factor than the IC50 of the photoprobe in obtaining a successful photolabeling event. While 3 was the most effective reversible inhibitor of the series, it provided no protection to cells against anthrax lethal toxin (LT) following UV irradiation. Conversely, 5, which possessed weak bioactivity in the standard assay, conferred robust irreversible protection vs LT to cells upon UV photolysis. PMID:24900841

  6. Quantitative Structure-Activity Relationship Studies of 4-Imidazolyl- 1,4-dihydropyridines as Calcium Channel Blockers

    PubMed Central

    Hadizadeh, Farzin; Vahdani, Saadat; Jafarpour, Mehrnaz

    2013-01-01

    Objective(s): The structure- activity relationship of a series of 36 molecules, showing L-type calcium channel blocking was studied using a QSAR (quantitative structure–activity relationship) method. Materials and Methods: Structures were optimized by the semi-empirical AM1 quantum-chemical method which was also used to find structure-calcium channel blocking activity trends. Several types of descriptors, including electrotopological, structural and thermodynamics were used to derive a quantitative relationship between L-type calcium channel blocking activity and structural properties. The developed QSAR model contributed to a mechanistic understanding of the investigated biological effects. Results: Multiple linear regressions (MLR) was employed to model the relationships between molecular descriptors and biological activities of molecules using stepwise method and genetic algorithm as variable selection tools. The accuracy of the proposed MLR model was illustrated using cross-validation, and Y-randomisation -as the evaluation techniques. Conclusion: The predictive ability of the model was found to be satisfactory and could be used for designing a similar group of 1,4- dihydropyridines , based on a pyridine structure core which can block calcium channels. PMID:24106595

  7. Insight into the antimicrobial activities of coprisin isolated from the dung beetle, Copris tripartitus, revealed by structure-activity relationships.

    PubMed

    Lee, Eunjung; Kim, Jin-Kyoung; Shin, Soyoung; Jeong, Ki-Woong; Shin, Areum; Lee, Juneyoung; Lee, Dong Gun; Hwang, Jae-Sam; Kim, Yangmee

    2013-02-01

    The novel 43-residue, insect defensin-like peptide coprisin, isolated from the dung beetle, Copris tripartitus, is a potent antibiotic with bacterial cell selectivity, exhibiting antimicrobial activities against Gram-positive and Gram-negative bacteria without exerting hemolytic activity against human erythrocytes. Tests against Staphylococcus aureus using fluorescent dye leakage and depolarization measurements showed that coprisin targets the bacterial cell membrane. To understand structure-activity relationships, we determined the three-dimensional structure of coprisin in aqueous solution by nuclear magnetic resonance spectroscopy, which showed that coprisin has an amphipathic ?-helical structure from Ala(19) to Arg(28), and ?-sheets from Gly(31) to Gln(35) and Val(38) to Arg(42). Coprisin has electropositive regions formed by Arg(28), Lys(29), Lys(30), and Arg(42) and ITC results proved that coprisin and LPS have electrostatically driven interactions. Using measurements of nitric oxide release and inflammatory cytokine production, we provide the first verification of the anti-inflammatory activity and associated mechanism of an insect defensin, demonstrating that the anti-inflammatory actions of the defensin-like peptide, coprisin, are initiated by suppressing the binding of LPS to toll-like receptor 4, and subsequently inhibiting the phosphorylation of p38 mitogen-activated protein kinase and nuclear translocation of NF-kB. In conclusion, we have demonstrated that an amphipathic helix and an electropositive surface in coprisin may play important roles in its effective interaction with bacterial cell membranes and, ultimately, in its high antibacterial activity and potent anti-inflammatory activity. In addition to elucidating the antimicrobial action of coprisin, this work may provide insight into the mechanism of action of insect defense systems. PMID:23137439

  8. Development of an information-intensive structure–activity relationship model and its application to human respiratory chemical sensitizers

    Microsoft Academic Search

    A. R. Cunningham; S. L. Cunningham; D. M. Consoer; S. T. Moss; M. H. Karol

    2005-01-01

    Structure–activity relationship (SAR) models are recognized as powerful tools to predict the toxicologic potential of new or untested chemicals and also provide insight into possible mechanisms of toxicity. Models have been based on physicochemical attributes and structural features of chemicals. We describe herein the development of a new SAR modeling algorithm called cat-SAR that is capable of analyzing and predicting

  9. Structure–activity relationship study of acridine analogs as haspin and DYRK2 kinase inhibitors

    PubMed Central

    Cuny, Gregory D.; Robin, Maxime; Ulyanova, Natalia P.; Patnaik, Debasis; Pique, Valerie; Casano, Gilles; Liu, Ji-Feng; Lin, Xiangjie; Xian, Jun; Glicksman, Marcie A.; Stein, Ross L.; Higgins, Jonathan M. G.

    2011-01-01

    Haspin is a serine/threonine kinase required for completion of normal mitosis that is highly expressed during cell proliferation, including in a number of neoplasms. Consequently, it has emerged as a potential therapeutic target in oncology. A high throughput screen of approximately 140,000 compounds identified an acridine analog as a potent haspin kinase inhibitor. Profiling against a panel of 270 kinases revealed that the compound also exhibited potent inhibitory activity for DYRK2, another serine/threonine kinase. An optimization study of the acridine series revealed that the structure–activity relationship (SAR) of the acridine series for haspin and DYRK2 inhibition had many similarities. However, several structural differences were noted that allowed generation of a potent haspin kinase inhibitor (33, IC50 <60 nM) with 180-fold selectivity over DYRK2. In addition, a moderately potent DYRK2 inhibitor (41, IC50 <400 nM) with a 5.4-fold selectivity over haspin was also identified. PMID:20836251

  10. Structure-activity relationship study of acridine analogs as haspin and DYRK2 kinase inhibitors

    PubMed Central

    Cuny, Gregory D.; Robin, Maxime; Ulyanova, Natalia P.; Patnaik, Debasis; Pique, Valerie; Casano, Gilles; Liu, Ji-Feng; Lin, Xiangjie; Xian, Jun; Glicksman, Marcie A.; Stein, Ross L.; Higgins, Jonathan M.G.

    2010-01-01

    Haspin is a serine/threonine kinase required for completion of normal mitosis that is highly expressed during cell proliferation, including in a number of neoplasms. Consequently, it has emerged as a potential therapeutic target in oncology. A high throughput screen of approximately 140,000 compounds identified an acridine analog as a potent haspin kinase inhibitor. Profiling against a panel of 270 kinases revealed that the compound also exhibited potent inhibitory activity for DYRK2, another serine/threonine kinase. An optimization study of the acridine series revealed that the structure-activity relationship (SAR) of the acridine series for haspin and DYRK2 inhibition had many similarities. However, several structural differences were noted that allowed generation of a potent haspin kinase inhibitor (33, IC50 < 60 nM) with 180-fold selectivity over DYRK2. In addition, a moderately potent DYRK2 inhibitor (41, IC50 < 400 nM) with a 5.4-fold selectivity over haspin was also identified. PMID:20529681

  11. Quantitative structure-activity relationships and the prediction of MHC supermotifs.

    PubMed

    Doytchinova, Irini A; Guan, Pingping; Flower, Darren R

    2004-12-01

    The underlying assumption in quantitative structure-activity relationship (QSAR) methodology is that related chemical structures exhibit related biological activities. We review here two QSAR methods in terms of their applicability for human MHC supermotif definition. Supermotifs are motifs that characterise binding to more than one allele. Supermotif definition is the initial in silico step of epitope-based vaccine design. The first QSAR method we review here--the additive method--is based on the assumption that the binding affinity of a peptide depends on contributions from both amino acids and the interactions between them. The second method is a 3D-QSAR method: comparative molecular similarity indices analysis (CoMSIA). Both methods were applied to 771 peptides binding to 9 HLA alleles. Five of the alleles (A*0201, A*0202, A*0203, A*0206 and A*6802) belong to the HLA-A2 superfamily and the other four (A*0301, A*1101, A*3101 and A*6801) to the HLA-A3 superfamily. For each superfamily, supermotifs defined by the two QSAR methods agree closely and are supported by many experimental data. PMID:15542370

  12. Structure-activity relationships of quinolone agents against mycobacteria: effect of structural modifications at the 8 position.

    PubMed Central

    Renau, T E; Gage, J W; Dever, J A; Roland, G E; Joannides, E T; Shapiro, M A; Sanchez, J P; Gracheck, S J; Domagala, J M; Jacobs, M R; Reynolds, R C

    1996-01-01

    A series of quinolones with substitutions at the 8 position has been prepared as part of a study to examine the relationship between structural modifications at this position and activity against mycobacteria. The compounds were prepared by procedures described in the literature and were evaluated for their activities against Mycobacterium fortuitum and Mycobacterium smegmatis. The activities of the compounds against these two organisms were used as a measure of Mycobacterium tuberculosis activity. The results demonstrate that the contribution of the 8 position to antimycobacterial activity was dependent on the substituent at N-1 and was in the order (i) COMe approximately CBr > CCI > CH approximately CF approximately COEt > N > CCF3 when N-1 was cyclopropyl; (ii) N approximately CH > CF > COMe when N-1 was 2,4-difluorophenyl; (iii) N > or = CH when N-1 was tert-butyl; and (iv) N > CH when N-1 was ethyl. In general, derivatives with piperazine substitutions at C-7 were slightly less active against mycobacteria than the analogs with pyrrolidine substitutions, regardless of the pattern of substitution at the 8 position. Several of the best compounds were evaluated for their potential side effects as well as their activities against Mycobacterium aurum, Mycobacterium avium-M. intracellulare, and M. tuberculosis. These agents exhibited biological profiles similar to or better than those of the positive controls ciprofloxacin and sparfloxacin. PMID:8891145

  13. 6-Nitrobenzimidazole derivatives: potential phosphodiesterase inhibitors: synthesis and structure-activity relationship.

    PubMed

    Khan, K M; Shah, Zarbad; Ahmad, V U; Ambreen, N; Khan, M; Taha, M; Rahim, F; Noreen, S; Perveen, S; Choudhary, M I; Voelter, W

    2012-02-15

    6-Nitrobenzimidazole derivatives (1-30) synthesized and their phosphodiesterase inhibitory activities determined. Out of thirty tested compounds, ten showed a varying degrees of phosphodiesterase inhibition with IC(50) values between 1.5±0.043 and 294.0±16.7 ?M. Compounds 30 (IC(50)=1.5±0.043 ?M), 1 (IC(50)=2.4±0.049 ?M), 11 (IC(50)=5.7±0.113 ?M), 13 (IC(50)=6.4±0.148 ?M), 14 (IC(50)=10.5±0.51 ?M), 9 (IC(50)=11.49±0.08 ?M), 3 (IC(50)=63.1±1.48 ?M), 10 (IC(50)=120.0±4.47 ?M), and 6 (IC(50)=153.2±5.6 ?M) showed excellent phosphodiesterase inhibitory activity, much superior to the standard EDTA (IC(50)=274±0.007 ?M), and thus are potential molecules for the development of a new class of phosphodiesterase inhibitors. A structure-activity relationship is evaluated. All compounds are characterized by spectroscopic parameters. PMID:22264761

  14. Structure-activity relationship of hybrids of Cinchona alkaloids and bile acids with in vitro antiplasmodial and antitrypanosomal activities.

    PubMed

    Leverrier, Aurélie; Bero, Joanne; Cabrera, Julián; Frédérich, Michel; Quetin-Leclercq, Joëlle; Palermo, Jorge A

    2015-07-15

    In this work, a series of hybrid compounds were tested as antiparasitic substances. These hybrids were prepared from bile acids and a series of antiparasitic Cinchona alkaloids by the formation of a covalent C-C bond via a decarboxylative Barton-Zard reaction between the two entities. The bile acids showed only weak antiparasitic properties, but all the hybrids exhibited high in vitro activities (IC50: 0.48-5.39 ?M) against Trypanosoma brucei. These hybrids were more active than their respective parent alkaloids (up to a 135 fold increase in activity), and displayed good selectivity indices. Aditionally, all these compounds inhibited the in vitro growth of a chloroquine-sensitive strain of Plasmodium falciparum (3D7: IC50: 36.1 nM to 8.72 ?M), and the most active hybrids had IC50s comparable to that of artemisinin (IC50: 36 nM). Some structure-activity relationships among the group of 48 hybrids are discussed. The increase in antiparasitic activity may be explained by an improvement in bioavailability, since the more lipophilic derivatives showed the lowest IC50s. PMID:26063305

  15. Structure–Activity Relationship Study of the Cleistriosides and Cleistetrosides for Antibacterial/Anticancer Activity

    PubMed Central

    2012-01-01

    Two known cleistriosides and six known cleistetrosides were synthesized and evaluated for anticancer and antibacterial activities. This study, for the first time, reports anticancer activity and comprehensively the antibacterial activity for these oligosaccharide natural products. In addition, two new unnatural cleistetroside analogues were synthesized and tested. Biological activities for the 10 oligosaccharides against B. subtilis were found to range between 4 and >64 ?M and for NCI-H460 human lung cancer epithelial cells between 7.5 and 90.9 ?M. Similar activities were found for seven of the oligosaccharides against the NCI panel of 60 cell lines. The degree of acylation and location of the specific acetate groups had significant effects on the anticancer and antibacterial activity of both the cleistriosides and the cleistetrosides. PMID:23543830

  16. Iridium Oxide Coatings with Templated Porosity as Highly Active Oxygen Evolution Catalysts: Structure-Activity Relationships.

    PubMed

    Bernicke, Michael; Ortel, Erik; Reier, Tobias; Bergmann, Arno; Ferreira de Araujo, Jorge; Strasser, Peter; Kraehnert, Ralph

    2015-06-01

    Iridium oxide is the catalytic material with the highest stability in the oxygen evolution reaction (OER) performed under acidic conditions. However, its high cost and limited availability demand that IrO2 is utilized as efficiently as possible. We report the synthesis and OER performance of highly active mesoporous IrO2 catalysts with optimized surface area, intrinsic activity, and pore accessibility. Catalytic layers with controlled pore size were obtained by soft-templating with micelles formed from amphiphilic block copolymers poly(ethylene oxide)-b-poly(butadiene)-b-poly(ethylene oxide). A systematic study on the influence of the calcination temperature and film thickness on the morphology, phase composition, accessible surface area, and OER activity reveals that the catalytic performance is controlled by at least two independent factors, that is, accessible surface area and intrinsic activity per accessible site. Catalysts with lower crystallinity show higher intrinsic activity. The catalyst surface area increases linearly with film thickness. As a result of the templated mesopores, the pore surface remains fully active and accessible even for thick IrO2 films. Even the most active multilayer catalyst does not show signs of transport limitations at current densities as high as 75?mA?cm(-2) . PMID:25958795

  17. Resorcylic Acid Lactones with Cytotoxic and NF-?B Inhibitory Activities and Their Structure-activity Relationships

    PubMed Central

    Ayers, Sloan; Graf, Tyler N.; Adcock, Audrey F.; Kroll, David J.; Matthew, Susan; Carcache de Blanco, Esperanza J.; Shen, Qi; Swanson, Steven M.; Wani, Mansukh C.; Pearce, Cedric J.; Oberlies, Nicholas H.

    2011-01-01

    As part of our ongoing investigation of filamentous fungi for anticancer leads, an active fungal extract was identified from the Mycosynthetix library (MSX 63935; related to Phoma sp.). The initial extract exhibited cytotoxic activity against the H460 (human non-small cell lung carcinoma) and SF268 (human astrocytoma) cell lines and was selected for further study. Bioactivity-directed fractionation yielded resorcylic acid lactones (RALs) 1 (a new natural product) and 3 (a new compound) and the known RALs zeaenol (2), 5E-7-oxozeaenol (4), 5Z-7-oxozeaenol (5) and LL-Z1640-1 (6). Reduction of 5E-7-oxozeaenol (4) with sodium borohydride produced 3, which allowed assignment of the absolute configuration of 3. Other known resorcylic acid lactones (7–12) were purchased and assayed in parallel for cytotoxicity with isolated 1–6 to investigate structure-activity relationships in the series. Moreover, the isolated compounds (1–6) were examined for activity in a suite of biological assays, including antibacterial, mitochondria transmembrane potential, and NF-?B. In the latter assay, compounds 1 and 5 displayed sub-micromolar activities that were on par with the positive control, and as such, these compounds may serve as a lead scaffold for future medicinal chemistry studies. PMID:21513293

  18. Effects of resveratrol and its derivatives on lipopolysaccharide-induced microglial activation and their structure-activity relationships.

    PubMed

    Meng, Xue-Lian; Yang, Jing-Yu; Chen, Guo-Liang; Wang, Li-Hui; Zhang, Li-Jia; Wang, Shu; Li, Jie; Wu, Chun-Fu

    2008-07-10

    The inhibitory effects of 21 resveratrol derivatives on lipopolysaccharide (LPS)-induced nitric oxide (NO) production in microglia and their structure-activity relationships were studied. It was found, for the first time, that certain resveratrol derivatives that have 3,5-dimethoxyl groups in the A-ring, such as (E)-4-(3,5-dimethoxystyryl)phenol (pterostilbene, compound 2), or have substituted the B-ring of resveratrol with quinolyl, such as (E)-5-[2-(quinolin-4-yl)vinyl]benzene-1,3-diol (compound 18) and (E)-4-(3,5-dimethoxystyryl)quinoline (compound 19), strongly inhibited NO production. Compounds 2, 18, and 19 reduced LPS-induced protein and mRNA expression of inducible NO synthase (iNOS), but did not display direct NO-scavenging activity up to 30 microM in sodium nitroprusside (SNP) solution. Moreover, compounds 2, 18, and 19 could also significantly inhibit the production of TNF-alpha by LPS-activated microglia. Further studies revealed that compounds 2, 18, and 19 inhibited LPS-induced NO and TNF-alpha production in microglia by blocking IkappaBalpha phosphorylation and degradation. The potent inhibitory effects of compounds 2, 18, and 19 on microglial activation suggest their potential for treatment of neurodegenerative diseases accompanied by microglial activation. PMID:18513711

  19. Structure-Activity Relationships, Pharmacokinetics, and in Vivo Activity of CYP11B2 and CYP11B1 Inhibitors.

    PubMed

    Papillon, Julien P N; Adams, Christopher M; Hu, Qi-Ying; Lou, Changgang; Singh, Alok K; Zhang, Chun; Carvalho, Jose; Rajan, Srinivan; Amaral, Adam; Beil, Michael E; Fu, Fumin; Gangl, Eric; Hu, Chii-Whei; Jeng, Arco Y; LaSala, Daniel; Liang, Guiqing; Logman, Michael; Maniara, Wieslawa M; Rigel, Dean F; Smith, Sherri A; Ksander, Gary M

    2015-06-11

    CYP11B2, the aldosterone synthase, and CYP11B1, the cortisol synthase, are two highly homologous enzymes implicated in a range of cardiovascular and metabolic diseases. We have previously reported the discovery of LCI699, a dual CYP11B2 and CYP11B1 inhibitor that has provided clinical validation for the lowering of plasma aldosterone as a viable approach to modulate blood pressure in humans, as well normalization of urinary cortisol in Cushing's disease patients. We now report novel series of aldosterone synthase inhibitors with single-digit nanomolar cellular potency and excellent physicochemical properties. Structure-activity relationships and optimization of their oral bioavailability are presented. An illustration of the impact of the age of preclinical models on pharmacokinetic properties is also highlighted. Similar biochemical potency was generally observed against CYP11B2 and CYP11B1, although emerging structure-selectivity relationships were noted leading to more CYP11B1-selective analogs. PMID:25953419

  20. Blood-brain barrier permeability mechanisms in view of quantitative structure-activity relationships (QSAR).

    PubMed

    Bujak, Renata; Struck-Lewicka, Wiktoria; Kaliszan, Micha?; Kaliszan, Roman; Markuszewski, Micha? J

    2015-04-10

    The goal of the present paper was to develop a quantitative structure-activity relationship (QSAR) method using a simple statistical approach, such as multiple linear regression (MLR) for predicting the blood-brain barrier (BBB) permeability of chemical compounds. The "best" MLR models, comprised logP and either molecular mass (M) or isolated atomic energy (E(isol)), tested on a structurally diverse set of 66 compounds, is characterized the by correlation coefficients (R) around 0.8. The obtained models were validated using leave-one-out (LOO) cross-validation technique and the correlation coefficient of leave-one-out- R(LOO)(2) (Q(2)) was at least 0.6. Analysis of a case from legal medicine demonstrated informative value of our QSAR model. To best authors' knowledge the present study is a first application of the developed QSAR models of BBB permeability to case from the legal medicine. Our data indicate that molecular energy-related descriptors, in combination with the well-known descriptors of lipophilicity may have a supportive value in predicting blood-brain distribution, which is of utmost importance in drug development and toxicological studies. PMID:25703237

  1. Quantitative structure-activity relationships of nitroaromatics toxicity to the algae (Scenedesmus obliguus).

    PubMed

    Yan, Xiu-Fen; Xiao, He-Ming; Gong, Xue-Dong; Ju, Xue-Hai

    2005-04-01

    The DFT-B3LYP method, with the basis set 6-311G( * *), was employed to calculate the molecular geometries and electronic structures of 25 nitroaromatics. The acute toxicity (-lgEC(50)) of these compounds to the algae (Scenedesmus obliguus) along with hydrophobicity described by logK(OW), and two quantum chemical parameters-energy of the lowest unoccupied molecular orbital, E(LUMO), and the charge of the nitro group, [ForQ(NO2), were used to establish the quantitative structure-activity relationships (QSARs). For 18 mononitro derivatives, the hydrophobicity parameter logK(OW) could interpret the toxic mechanism successfully. Dinitro aromatic compounds were susceptible to be reduced to aniline for their electrophilic nature. Their toxicity was controlled mainly by electronic factors instead of hydrophobicity. The electronic parameters, E(LUMO) and Q(NO2), were used to yield the following model: -lg EC(50) = 3.746 - 25.053 E(LUMO) + 6.481 Q(NO2) (n=22, R=0.926, SE=0.206, F=56.854, P<0.001). The predicted toxic values using the above equation are in good agreement with the experimental values. PMID:15788169

  2. Structure-activity relationships of phenylpropanoids as antifeedants for the pine weevil Hylobius abietis.

    PubMed

    Bohman, B; Nordlander, G; Nordenhem, H; Sunnerheim, K; Borg-Karlson, A-K; Unelius, C R

    2008-03-01

    Ethyl cinnamate has been isolated from the bark of Pinus contorta in the search for antifeedants for the pine weevil, Hylobius abietis. Based on this lead compound, a number of structurally related compounds were synthesized and tested. The usability of the Topliss scheme, a flow diagram previously used in numerous structure-activity relationship (SAR) studies, was evaluated in an attempt to find the most potent antifeedants. The scheme was initially followed stepwise; subsequently, all compounds found in the scheme were compared. In total, 51 phenylpropanoids were tested and analyzed for SARs by using arguments from the field of medicinal chemistry (rational drug design). Individual Hansch parameters based on hydrophobicity, steric, and electronic properties were examined. The effects of position and numbers of substituents on the aromatic ring, the effects of conjugation in the molecules, and the effects of the properties of the parent alcohol part of the esters were also evaluated. It proved difficult to find strong SARs derived from single physicochemical descriptors, but our study led to numerous new, potent, phenylpropanoid antifeedants for the pine weevil. Among the most potent were methyl 3-phenylpropanoates monosubstituted with chloro, fluoro, or methyl groups and the 3,4-dichlorinated methyl 3-phenylpropanoate. PMID:18311506

  3. Quantitative structure-activity relationships for the toxicity of chlorophenols to mammalian submitochondrial particles.

    PubMed

    Argese, E; Bettiol, C; Giurin, G; Miana, P

    1999-04-01

    The toxicity of a series of chlorophenols, determined by a short-term in vitro assay utilizing mammalian submitochondrial particles, was related to the physicochemical and structural properties of these compounds. Quantitative Structure-Activity Relationships were defined by correlating EC50 values with six molecular descriptors, chosen to represent lipophilic, electronic and steric effects: the n-octanol/water partition coefficient (log Kow), the constant of Hammett (sigma sigma), the acid dissociation constant (pKa), the first order valence molecular connectivity index (1 chi v), the perimeter of the efficacious section (sigma D) and the melting point (m.p.). The results of regression analysis showed that log Kow is the most successful descriptor, indicating that the ability of chlorophenols to partition into the lipid bilayer of the mitochondrial membrane has an important role in determining their toxic effects. These results are consistent with a molecular mechanism of uncoupling action based on the chemiosmotic theory and on the protonophoric properties of chlorophenols. The quality of the QSAR models confirms the suitability of the SMP assay as a short-term prediction tool for aquatic toxicity of environmental pollutants acting on respiratory functions. PMID:10101866

  4. Some methods of obtaining quantitative structure-activity relationships for quantities of environmental interest

    SciTech Connect

    Charton, M.

    1985-09-01

    Methods are described for obtaining quantitative structure-activity relationships (QSAR) for the estimation of quantities of environmental interest. Toxicities of alkylamines and of alkyl alkanoates are well correlated by the alkyl bioactivity branching equation (ABB). Narcotic activities of 1,1-disubstituted ethylenes are correlated by the intermolecular forces bioactivity (IMF) equation. When the data set has a limited number of substituents in equivalent positions the group number (GN) equation, derivable from the IMF equation, can be used for correlation. It has been successfully applied to aqueous solubilities, 1-octanol-water partition coefficients, and bioaccumulation factors and ecological magnifications for organochlorine compounds. A combination of the omega method for combining data sets for different organisms with the GN equation has been used to correlate toxicities of organochlorine insecticides in two species of fish. Toxicities of carbamates have been correlated by a combination of the zeta method and the IMFB equation. The ABB and the GN equations are particularly useful in that they generally do not require parameter tables, and that the parameters they use are error-free. The methods presented here, as shown by the examples given, should make it possible to establish a collection of QSAR for toxicities, bioaccumulation factors, aqueous solubilities, partition coefficients, and other properties of sets of compounds of environmental interest. 29 references.

  5. Structure-activity relationship in PAF-acether. 3. Hydrophobic contribution to agonistic activity.

    PubMed

    Godfroid, J J; Broquet, C; Jouquey, S; Lebbar, M; Heymans, F; Redeuilh, C; Steiner, E; Michel, E; Coeffier, E; Fichelle, J

    1987-05-01

    The synthesis of some selected PAF-acether homologues with an alkoxy-chain length from C1 to C20 in position 1 is described. All agonist activities are closely correlated among themselves and with the calculated fatty-chain hydrophobicity. After a discussion on recent published results and comparison with our data, we conclude that the ether oxide function is absolutely essential at the glycerol 1-position for potent agonist activity and that potency correlates well with hydrophobicity parameters. We indicate the importance of steric and configurational constraints. PMID:3572968

  6. [Application of the rough sets theory to the analysis of structure-activity relationships of pyridinium antifungal compounds].

    PubMed

    Krysi?ski, J

    1994-04-01

    Relationships between chemical structure and antifungal activity of 72 quaternary pyridinium chlorides were analysed using the method of rough sets. In the information system the compounds are described by eight condition attributes and divided into three classes of activity. Using the rough sets approach a smallest set of four condition attributes significant for a high quality of classification and accuracy of classes has been found. The resulting decision algorithm describes relations between structure and antifungal activity in terms of significant condition attributes. It may be helpful in predicting structures of new antifungal compounds to be synthesized. PMID:8204024

  7. [Rough sets theory in the analysis of structure-activity relationships of quaternary quinolinium- and isoquinolinium compounds].

    PubMed

    Krysinski, J

    1991-11-01

    Relationship between chemical structure and antimicrobial activity of 72 quaternary quinolinium and isoquinolinium compounds is analyzed using the theory of rough sets. The compounds are described by 11 attributes concerning structure and are divided into 3 classes of activity. The description builds up on information system. Using the rough sets approach a smallest set of attributes significant for a high quality of classification has been found. A decision algorithm has been driven from the information system showing up important relations between structure and activity. This may be helpful in supporting decisions concerning synthesis of new antimicrobial compounds. PMID:1804057

  8. Structure–Activity Relationships for Antioxidant Activities of a Series of Flavonoids in a Liposomal System

    Microsoft Academic Search

    Arti Arora; Muraleedharan G. Nair; Gale M. Strasburg

    1998-01-01

    Structurally diverse plant phenolics were examined for their abilities to inhibit lipid peroxidation induced either by Fe(II) and Fe(III) metal ions or by azo-derived peroxyl radicals in a liposomal membrane system. The antioxidant abilities of flavonoids were compared with those of coumarin and tert-butylhydroquinone (TBHQ). The antioxidant efficacies of these compounds were evaluated on the basis of their abilities to

  9. Analysis of the Internal Representations Developed by Neural Networks for Structures Applied to Quantitative Structure-Activity Relationship Studies of Benzodiazepines

    E-print Network

    Sperduti, Alessandro

    Analysis of the Internal Representations Developed by Neural Networks for Structures Applied by principal component analysis. This analysis shows that the networks are able to discover relevant structural to Quantitative Structure-Activity Relationship Studies of Benzodiazepines A. Micheli, A. Sperduti,*, and A

  10. Moving around the molecule: Relationship between chemical structure and in vivo activity of synthetic cannabinoids

    PubMed Central

    Wiley, Jenny L.; Marusich, Julie A.; Huffman, John W.

    2013-01-01

    Originally synthesized for research purposes, indole- and pyrrole-derived synthetic cannabinoids are the most common psychoactive compounds contained in abused products marketed as “spice” or “herbal incense.” While CB1 and CB2 receptor affinities are available for most of these research chemicals, in vivo pharmacological data are sparse. In mice, cannabinoids produce a characteristic profile of dose-dependent effects: antinociception, hypothermia, catalepsy and suppression of locomotion. In combination with receptor binding data, this tetrad battery has been useful in evaluation of the relationship between the structural features of synthetic cannabinoids and their in vivo cannabimimetic activity. Here, published tetrad studies are reviewed and additional in vivo data on synthetic cannabinoids are presented. Overall, the best predictor of likely cannabimimetic effects in the tetrad tests was good CB1 receptor affinity. Further, retention of good CB1 affinity and in vivo activity was observed across a wide array of structural manipulations of substituents of the prototypic aminoalkylindole molecule WIN55,212-2, including substitution of an alkyl for the morpholino group, replacement of an indole core with a pyrrole or phenylpyrrole, substitution of a phenylacetyl or tetramethylcyclopropyl group for JWH-018’s naphthoyl, and halogenation of the naphthoyl group. This flexibility of cannabinoid ligand-receptor interactions has been a particular challenge for forensic scientists who have struggled to identify and regulate each new compound as it has appeared on the drug market. One of the most pressing future research needs is determination of the extent to which the pharmacology of these synthetic cannabinoids may differ from those of classical cannabinoids. PMID:24071522

  11. Structure-Activity Relationships of Constrained Phenylethylamine Ligands for the Serotonin 5-HT2 Receptors

    PubMed Central

    Isberg, Vignir; Paine, James; Leth-Petersen, Sebastian; Kristensen, Jesper L.; Gloriam, David E.

    2013-01-01

    Serotonergic ligands have proven effective drugs in the treatment of migraine, pain, obesity, and a wide range of psychiatric and neurological disorders. There is a clinical need for more highly 5-HT2 receptor subtype-selective ligands and the most attention has been given to the phenethylamine class. Conformationally constrained phenethylamine analogs have demonstrated that for optimal activity the free lone pair electrons of the 2-oxygen must be oriented syn and the 5-oxygen lone pairs anti relative to the ethylamine moiety. Also the ethyl linker has been constrained providing information about the bioactive conformation of the amine functionality. However, combined 1,2-constriction by cyclization has only been tested with one compound. Here, we present three new 1,2-cyclized phenylethylamines, 9–11, and describe their synthetic routes. Ligand docking in the 5-HT2B crystal structure showed that the 1,2-heterocyclized compounds can be accommodated in the binding site. Conformational analysis showed that 11 can only bind in a higher-energy conformation, which would explain its absent or low affinity. The amine and 2-oxygen interactions with D3.32 and S3.36, respectively, can form but shift the placement of the core scaffold. The constraints in 9–11 resulted in docking poses with the 4-bromine in closer vicinity to 5.46, which is polar only in the human 5-HT2A subtype, for which 9–11 have the lowest affinity. The new ligands, conformational analysis and docking expand the structure-activity relationships of constrained phenethylamines and contributes towards the development of 5-HT2 receptor subtype-selective ligands. PMID:24244317

  12. Structure-Activity Relationship (SAR) of Withanolides to Inhibit Hsp90 for Its Activity in Pancreatic Cancer Cells

    PubMed Central

    Gu, Mancang; Yu, Yanke; Gunaherath, G. M. Kamal B; Leslie Gunatilaka, A. A.; Li, Dapeng; Sun, Duxin

    2013-01-01

    Withaferin A (WA), a naturally occurring steroidal lactone, directly binds to Hsp90 and leads to the degradation of Hsp90 client protein. The purpose of this study is to investigate the structure activity relationship (SAR) of withanolides for their inhibition of Hsp90 and anti-proliferative activities in pancreatic cancer cells. In pancreatic cancer Panc-1 cells, withaferin A (WA) and its four analogues withanolide E (WE), 4-hydroxywithanolide E (HWE), 3-aziridinylwithaferin A (AzWA) inhibited cell proliferation with IC50 ranged from 1.0 to 2.8 ?M. WA, WE, HWE, and AzWA also induced caspase-3 activity by 21-, 6-, 11- and 15-fold, respectively, in Panc-1 cells, while withaperuvin (WP) did not show any activity. Our data showed that WA, WE, HWE, and AzWA, but not WP, all directly bound to Hsp90 and induced Hsp90 aggregation, hence inhibited Hsp90 chaperone activity to induce degradation of Hsp90 client proteins Akt and Cdk4 through proteasome-dependent pathway in pancreatic cancer cells. However, only WA, HWE and AzWA disrupted Hsp90-Cdc37 complexes but not WE and WP. SAR study suggested that the C-5(6)-epoxy functional group contributes considerably for withanolide to bind to Hsp90, inhibit Hsp90 chaperone activity, and result in Hsp90 client protein depletion. Meanwhile, the hydroxyl group at C-4 of ring A may enhance withanolide to inhibit Hsp90 activity and disrupt Hsp90-Cdc37 interaction. These SAR data provide possible mechanisms of anti-proliferative action of withanolides. PMID:23887853

  13. Structure-activity relationship of the tocopherol-regeneration reaction by catechins.

    PubMed

    Mukai, Kazuo; Mitani, Shuji; Ohara, Keishi; Nagaoka, Shin-Ichi

    2005-05-01

    The reaction rates (k(r)) of 5,7-diisopropyl-tocopheroxyl radical (Toc) with catechins (epicatechin (EC), epicatechin gallate (ECG), epigallocatechin (EGC), epigallocatechin gallate (EGCG)) and related compounds (methyl gallate (MG), 4-methylcatechol (MC), and 5-methoxyresorcinol (MR)) have been measured by stopped-flow spectrophotometer. The k(r) values increased in the order of MR < < MG < EC < MC approximately ECG < EGC < EGCG in ethanol and 2-propanol/H(2)O (5/1, v/v) solutions, indicating that the reactivity of the OH groups in catechins increased in the order of resorcinol A-ring < < gallate G-ring < catechol B-ring < pyrogallol B-ring. The catechins which have lower oxidation potentials show higher reactivities. The rate constants for catechins in micellar solution showed notable pH dependence with one or two peaks around pH 9-11, because of the dissociation of various phenolic hydroxyl protons in catechins. The structure-activity relationship in the free-radical-scavenging reaction by catechins has been clarified by the detailed analyses of the pH dependence of k(r) values. The reaction rates increased remarkably with increasing the anionic character of catechins, that is, the electron-donating capacity of catechins. The mono anion form at catechol B-and resorcinol A-rings and dianion form at pyrogallol B-and gallate G-rings show the highest activity for free-radical-scavenging. It was found that catechins (EC, ECG, EGC, and EGCG) have activity similar to or higher than that of vitamin C in vitamin E regeneration at pH 7-12 in micellar solution. PMID:15808422

  14. Chlorine Contribution to Quantitative Structure and Activity Relationship Models of Disinfection By-Products' Quantum Chemical Descriptors and Toxicities

    Microsoft Academic Search

    Fang Wang

    2009-01-01

    Quantitative Structure-Activity Relationship (QSAR) has been applied extensively in predicting toxicity of Disinfection By-Products (DBPs) in drinking water. Among many toxicological properties, acute and chronic toxicities of DBPs have been widely used in health risk assessment of DBPs. These toxicities are correlated with molecular properties, which are usually correlated with molecular descriptors. The primary goals of this thesis are: 1)

  15. Chlorine contribution to quantitative structure and activity relationship models of disinfection by-products' quantum chemical descriptors and toxicities

    Microsoft Academic Search

    Fang Wang

    2010-01-01

    Quantitative Structure-Activity Relationship (QSAR) has been applied extensively in predicting toxicity of Disinfection By-Products (DBPs) in drinking water. Among many toxicological properties, acute and chronic toxicities of DBPs have been widely used in health risk assessment of DBPs. These toxicities are correlated with molecular properties, which are usually correlated with molecular descriptors. The primary goals of this thesis are: (1)

  16. Quantitative structure–activity relationship analysis of acute toxicity of diverse chemicals to Daphnia magna with whole molecule descriptors

    Microsoft Academic Search

    M. Moosus; U. Maran

    2011-01-01

    Quantitative structure–activity relationship analysis and estimation of toxicological effects at lower-mid trophic levels provide first aid means to understand the toxicity of chemicals. Daphnia magna serves as a good starting point for such toxicity studies and is also recognized for regulatory use in estimating the risk of chemicals. The ECOTOX database was queried and analysed for available data and a

  17. The relationship between the structure of plastoquinone derivatives and their biological activity in Photosystem II of spinach chloroplasts

    Microsoft Academic Search

    Ben-Li Liu; Arnold J. Hoff; Lian-Quan Gu; Liang-Bi Li; Pei-Zhen Zhou

    1991-01-01

    The relationship between the structure of reconstituted plastoquinone derivatives and their ability to recover the Hill reaction was investigated by extraction and reconstitution of lyophilized chloroplasts from spinach, followed by monitoring DCIP photoreduction at 600 nm. The results show that: It is not essential that the plastoquinone side chain be an isoprenoid or a phytol; the activity increases with increasing

  18. IN VIVO AND IN VITRO STRUCTURE-DOSIMETRY-ACTIVITY RELATIONSHIPS OF SUBSTITUTED PHENOLS IN DEVELOPMENTAL TOXICITY ASSAYS

    EPA Science Inventory

    Structure-dosimetry-activity relationships (SDARs) of a series of substituted phenols were evaluated following exposure of gestation day 11 rats in vivo and in comparable stage embryos in vitro. n the in vivo study, 27 congeners were assayed and log p (a term used synonymously wi...

  19. Quantitative structure-activity relationship of organophosphate compounds based on molecular interaction fields descriptors.

    PubMed

    Zhao, Jinsong; Yu, Shuxia

    2013-03-01

    By using multi-block partial least-squares (MBPLS) method, quantitative structure-activity relationship (QSAR) between 35 organophosphate compounds (OP) and their 24h acute toxicities towards the housefly (Musca nebulo L.) was built on the molecular interaction fields (MIF) descriptors, which were obtained with O, N and DRY as probes, and then normalised with block unscaled weights (BUW) technique. The best QSAR model had 8 principal components, with the coefficient of determination R(2)=0.995 and that of leave-one-out cross-validation Q(2)=0.865, and the corresponding standard deviation of error 0.076 and 0.361, respectively. Block importance in the prediction (BIP) for O, N and DRY probe were 1.030, 0.962 and 1.007, respectively. Contour map of variable coefficients showed that hydrogen bonding between the O atom in PO and the NH groups in acetylcholinesterase (AChE) played an important role in the interaction between OP and AChE. Meanwhile, the hydrophobicity of OP also had significant contribution. QSAR based on the MIF descriptors could be a potential means to interpret the mechanisms of ligand-receptor interaction when the receptor was well known. PMID:23348103

  20. Development of quantitative structure-activity relationships and its application in rational drug design.

    PubMed

    Yang, Guang-Fu; Huang, Xiaoqin

    2006-01-01

    Over forty years have elapsed since Hansch and Fujita published their pioneering work of quantitative structure-activity relationships (QSAR). Following the introduction of Comparative Molecular Field Analysis (CoMFA) by Cramer in 1998, other three-dimensional QSAR methods have been developed. Currently, combination of classical QSAR and other computational techniques at three-dimensional level is of greatest interest and generally used in the process of modern drug discovery and design. During the last several decades, a number of different mythologies incorporating a range of molecular descriptors and different statistical regression ways have been proposed and successfully applied in developing of new drugs, thus QSAR method has been proven to be indispensable in not only the reliable prediction of specific properties of new compounds, but also the help to elucidate the possible molecular mechanism of the receptor-ligand interactions. Here, we review the recent developments in QSAR and their applications in rational drug design, focusing on the reasonable selection of novel molecular descriptors and the construction of predictive QSAR models by the help of advanced computational techniques. PMID:17168765

  1. Deep neural nets as a method for quantitative structure-activity relationships.

    PubMed

    Ma, Junshui; Sheridan, Robert P; Liaw, Andy; Dahl, George E; Svetnik, Vladimir

    2015-02-23

    Neural networks were widely used for quantitative structure-activity relationships (QSAR) in the 1990s. Because of various practical issues (e.g., slow on large problems, difficult to train, prone to overfitting, etc.), they were superseded by more robust methods like support vector machine (SVM) and random forest (RF), which arose in the early 2000s. The last 10 years has witnessed a revival of neural networks in the machine learning community thanks to new methods for preventing overfitting, more efficient training algorithms, and advancements in computer hardware. In particular, deep neural nets (DNNs), i.e. neural nets with more than one hidden layer, have found great successes in many applications, such as computer vision and natural language processing. Here we show that DNNs can routinely make better prospective predictions than RF on a set of large diverse QSAR data sets that are taken from Merck's drug discovery effort. The number of adjustable parameters needed for DNNs is fairly large, but our results show that it is not necessary to optimize them for individual data sets, and a single set of recommended parameters can achieve better performance than RF for most of the data sets we studied. The usefulness of the parameters is demonstrated on additional data sets not used in the calibration. Although training DNNs is still computationally intensive, using graphical processing units (GPUs) can make this issue manageable. PMID:25635324

  2. Quantitative structure-activity relationships for weak acid respiratory uncouplers to Vibrio fisheri

    SciTech Connect

    Schultz, T.W. [Univ. of Tennessee, Knoxville, TN (United States). Coll. of Veterinary Medicine; Cronin, M.T.D. [Liverpool John Moores Univ. (United Kingdom). School of Pharmacy and Chemistry

    1997-02-01

    Acute toxicity values of 16 organic compounds thought to elicit their response via the weak acid respiratory uncoupling mechanism of toxic action were secured from the literature. Regression analysis of toxicities revealed that a measured 5-min V. fisheri potency value can be used as a surrogate for the 30-min value. Regression analysis of toxicity versus hydrophobicity, measured as the 1-octanol/water partition coefficient (log K{sub ow}), was used to formulate a quantitative structure-activity relationship (QSAR). The equation log pT{sub 30}{sup {minus}1} = 0.489(log K{sub ow}) + 0.126 was found to be a highly predictive model. This V. fisheri QSAR is statistically similar to QSARs generated from weak acid uncoupler potency data for Pimephales promelas survivability and Tetrahymena pyriformis population growth impairment. This work, therefore, suggests that the weak acid respiratory uncoupling mechanism of toxic action is present in V. fisheri, and as such is not restricted to mitochondria-containing organisms.

  3. Selective depletion of mutant p53 by cancer chemopreventive isothiocyanates and its structure-activity relationships

    PubMed Central

    Wang, Xiantao; Di Pasqua, Anthony J.; Govind, Sudha; McCracken, Erin; Hong, Charles; Mi, Lixin; Mao, Yuehua; Wu, Jessie Yu-Chieh; Tomita, York; Woodrick, Jordan C.; Fine, Robert L.; Chung, Fung-Lung

    2011-01-01

    Isothiocyanates (ITCs) derived from cruciferous vegetables induce apoptosis in cancer cells. We demonstrate that certain naturally-occurring ITCs selectively deplete mutant p53, but not the wild type, and do so via a transcription-independent mechanism. Direct p53 binding followed by conformational changes appears to be a mechanism by which mutant p53 is depleted. Structure-activity relationship studies (SARs) using naturally-occurring and synthetic ITCs show that depletion is influenced by the ITC side chain moiety. Furthermore, we show that cells with p53 mutations are more sensitive to cytotoxicity induced by phenethyl isothiocyanate (PEITC) than those with the wild type. 2,2-diphenylethyl ITC, a synthetic ITC and one of the most potent depletors of mutant p53 studied, induces apoptosis to the greatest extent in mutant p53 breast cancer cells. Collectively, this study shows that mutant p53 depletion may be an important novel target for cancer chemoprevention and therapy by natural and synthetic ITCs. PMID:21241062

  4. Structure-activity relationships of triterpenoid derivatives extracted from Gymnema inodorum leaves on glucose absorption.

    PubMed

    Shimizu, K; Ozeki, M; Iino, A; Nakajyo, S; Urakawa, N; Atsuchi, M

    2001-06-01

    The leaves of Gymnema inodorum (GI) have been known to be effective for some diseases including diabetes mellitus, rheumatic arthritis and gout. The crude saponin mixtures extracted from GI leaves inhibited glucose absorption in the isolated intestinal tract and suppressed the increased blood glucose in rats. In this study, we examined the relationship between chemical structure and pharmacological activity of the four components from GI leave extracts (GiA-1, GiA-2, GiA-5 and GiA-7). These components were the derivatives of (3beta,4alpha,16beta)-16,23,28-trihydroxyolean-12-en-3-yl-beta-D-glucopyranosiduroic acid. GiA-2, GiA-5 and GiA-7 that have suppressive effects on the high K+-induced contraction, an increase in deltaPD and the increased blood glucose level in the glucose tolerance test have -H at the 21st position and -CH2OH at 4beta of aglycon. On the other hand, GiA-1 that does not have any effects on the three parameters mentioned above has -H at the 21st position and -CH3 at 4beta of aglycon. In conclusion, it is suggested that the inhibitory effect of triterpenoids in Gymnema leaves on glucose absorption from the intestinal tract relies on -CH2OH at 4beta. PMID:11459125

  5. CORAL: quantitative structure-activity relationship models for estimating toxicity of organic compounds in rats.

    PubMed

    Toropova, A P; Toropov, A A; Benfenati, E; Gini, G; Leszczynska, D; Leszczynski, J

    2011-09-01

    For six random splits, one-variable models of rat toxicity (minus decimal logarithm of the 50% lethal dose [pLD50], oral exposure) have been calculated with CORAL software (http://www.insilico.eu/coral/). The total number of considered compounds is 689. New additional global attributes of the simplified molecular input line entry system (SMILES) have been examined for improvement of the optimal SMILES-based descriptors. These global SMILES attributes are representing the presence of some chemical elements and different kinds of chemical bonds (double, triple, and stereochemical). The "classic" scheme of building up quantitative structure-property/activity relationships and the balance of correlations (BC) with the ideal slopes were compared. For all six random splits, best prediction takes place if the aforementioned BC along with the global SMILES attributes are included in the modeling process. The average statistical characteristics for the external test set are the following: n = 119 ± 6.4, R(2) = 0.7371 ± 0.013, and root mean square error = 0.360 ± 0.037. PMID:21656789

  6. Discovery and Structure Activity Relationship of Small Molecule Inhibitors of Toxic ?-Amyloid-42 Fibril Formation*

    PubMed Central

    Kroth, Heiko; Ansaloni, Annalisa; Varisco, Yvan; Jan, Asad; Sreenivasachary, Nampally; Rezaei-Ghaleh, Nasrollah; Giriens, Valérie; Lohmann, Sophie; López-Deber, María Pilar; Adolfsson, Oskar; Pihlgren, Maria; Paganetti, Paolo; Froestl, Wolfgang; Nagel-Steger, Luitgard; Willbold, Dieter; Schrader, Thomas; Zweckstetter, Markus; Pfeifer, Andrea; Lashuel, Hilal A.; Muhs, Andreas

    2012-01-01

    Increasing evidence implicates A? peptides self-assembly and fibril formation as crucial events in the pathogenesis of Alzheimer disease. Thus, inhibiting A? aggregation, among others, has emerged as a potential therapeutic intervention for this disorder. Herein, we employed 3-aminopyrazole as a key fragment in our design of non-dye compounds capable of interacting with A?42 via a donor-acceptor-donor hydrogen bond pattern complementary to that of the ?-sheet conformation of A?42. The initial design of the compounds was based on connecting two 3-aminopyrazole moieties via a linker to identify suitable scaffold molecules. Additional aryl substitutions on the two 3-aminopyrazole moieties were also explored to enhance ?-? stacking/hydrophobic interactions with amino acids of A?42. The efficacy of these compounds on inhibiting A? fibril formation and toxicity in vitro was assessed using a combination of biophysical techniques and viability assays. Using structure activity relationship data from the in vitro assays, we identified compounds capable of preventing pathological self-assembly of A?42 leading to decreased cell toxicity. PMID:22891248

  7. Cytotoxic Activity and Three-Dimensional Quantitative Structure Activity Relationship of 2-Aryl-1,8-naphthyridin-4-ones

    PubMed Central

    Kim, Yong Jin; Kim, Eun Ae; Chung, Mi Lyang

    2009-01-01

    A series of substituted 2-arylnaphthyridin-4-one analogues, which were previously synthesized in our laboratory, were evaluated for their in vitro cytotoxic activity against human lung cancer A549 and human renal cancer Caki-2 cells using MTT assay. Some compounds (11, 12, and 13) showed stronger cytotoxicity than colchicine against both tumor cell lines, and compound 13 exhibited the most potent activity with IC50 values of 2.3 and 13.4 µM, respectively. Three-dimensional quantitative structure activity relationship (3D-QSAR) studies of comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were performed. Predictive 3D-QSAR models were obtained with q2 values of 0.869 and 0.872 and r2ncv values of 0.983 and 0.993 for CoMFA and CoMSIA, respectively. These results demonstrate that CoMFA and CoMSIA models could be reliably used in the design of novel cytotoxic agents. PMID:20054500

  8. Synthesis, Biological Evaluation and Structure-Activity Relationships of Dithiolethiones as Inducers of Cytoprotective Phase 2 Enzymes

    PubMed Central

    Munday, Rex; Zhang, Yuesheng; Paonessa, Joseph D.; Munday, Christine M.; Wilkins, Alistair L.; Babu, Jacob

    2010-01-01

    Dithiolethiones are a family of promising cancer chemopreventive agents, and induction of Phase 2 enzymes is key to their chemopreventive activities. Two dithiolethiones have been evaluated in humans for cancer prevention. While some chemopreventive activities were detected in several human studies, potential side effects are a concern. Herein, we report structure-activity relationships of 25 dithiolethiones. Several compounds show exceedingly potent and bladder specific activity in Phase 2 enzyme induction. Structural features responsible for such activity, as well as those inhibiting the activity, are discussed. Moreover, the compounds activate and depend on Nrf2 for their inductive activities. Nrf2 is a major transcriptional stimulator of cytoprotective genes and is critical for cancer prevention. Thus, several new dithiolethiones that are highly promising for bladder cancer prevention have been identified. Because the compounds act specifically in the bladder, the likelihood of potential systemic toxicity may be low. PMID:20481594

  9. Multivariate Analysis of Conserved SequenceStructure Relationships in Kinesins: Coupling of the Active Site

    E-print Network

    Cross, Robert

    Multivariate Analysis of Conserved Sequence­Structure Relationships in Kinesins: Coupling-domain motion lies near a conserved glycine at position 292. Statistical coupling analysis revealed a network coupling analysis; RMSF, root mean square fluctuation; PDB, protein data bank. E-mail address

  10. Quantitative Structure Activity Relationship for Inhibition of Human Organic Cation/Carnitine Transporter (OCTN2)

    PubMed Central

    Diao, Lei; Ekins, Sean; Polli, James E.

    2010-01-01

    Organic cation/carnitine transporter (OCTN2; SLC22A5) is an important transporter for L-carnitine homeostasis, but can be inhibited by drugs, which may cause L-carnitine deficiency and possibly other OCTN2-mediated drug-drug interactions. One objective was to develop a quantitative structure–activity relationship (QSAR) of OCTN2 inhibitors, in order to predict and identify other potential OCTN2 inhibitors and infer potential clinical interactions. A second objective was to assess two high renal clearance drugs that interact with OCTN2 in vitro (cetirizine and cephaloridine) for possible OCTN2-mediated drug-drug interactions. Using previously generated in vitro data of 22 drugs, a 3D quantitative pharmacophore model and a Bayesian machine learning model were developed. The four pharmacophore features include two hydrophobic groups, one hydrogen-bond acceptor, and one positive ionizable center. The Bayesian machine learning model was developed using simple interpretable descriptors and function class fingerprints of maximum diameter 6 (FCFP_6). An external test set of 27 molecules, including 15 newly identified OCTN2 inhibitors, and a literature test set of 22 molecules were used to validate both models. The computational models afforded good capability to identify structurally diverse OCTN2 inhibitors, providing a valuable tool to predict new inhibitors efficiently. Inhibition results confirmed our previously observed association between rhabdomyolysis and Cmax/Ki ratio. The two high renal clearance drugs cetirizine and cephaloridine were found not to be OCTN2 substrates and their diminished elimination by other drugs is concluded not to be mediated by OCTN2. PMID:20831193

  11. [Perspective of predictive toxicity assessment of in vivo repeated dose toxicity using structural activity relationship].

    PubMed

    Ono, Atsushi

    2010-01-01

    Tens of thousands of existing chemicals have been widely used for manufacture, agriculture, household and other purposes in worldwide. Only approximately 10% of chemicals have been assessed for human health hazard. The health hazard assessment of residual large number of chemicals for which little or no information of their toxicity is available is urgently needed for public health. However, the conduct of traditional toxicity tests which involves using animals for all of these chemicals would be economically impractical and ethically unacceptable. (Quantitative) Structure-Activity Relationships [(Q)SARs] are expected as method to have the potential to estimate hazards of chemicals from their structure, while reducing time, cost and animal testing currently needed. Therefore, our studies have been focused on evaluation of available (Q)SAR systems for estimating in vivo repeated toxicity on the liver. The results from our preliminary analysis showed the distribution for LogP of the chemicals which have potential to induce liver toxicity was bell-shape and indicating the possibility to estimate liver toxicity of chemicals from their physicochemical property. We have developed (Q)SAR models to in vivo liver toxicity using three commercially available systems (DEREK, ADMEWorks and MultiCASE) as well as combinatorial use of publically available chemoinformatic tools (CDK, MOSS and WEKA). Distinct data-sets of the 28-day repeated dose toxicity test of new and existing chemicals evaluated in Japan were used for model development and performance test. The results that concordances of commercial systems and public tools were almost same which below 70% may suggest currently attainable knowledge of in silico estimation of complex biological process, though it possible to obtain complementary and enhanced performance by combining predictions from different programs. In future, the combinatorial application of in silico and in vitro tests might provide more accurate information which support regulatory decisions. At the same time, an appropriate strategy to use (Q)SAR for of the efficiency and accuracy in chemical management is necessary. PMID:21381395

  12. Does electron-correlation has any role in the quantitative structure-activity relationships?

    PubMed

    Vikas; Reenu; Chayawan

    2013-05-01

    For developing quantitative structure-activity relationships (QSARs), quantum-mechanical molecular descriptors based on the state-of-the-art quantum-mechanical methods such as Hartree-Fock (HF) method and density-functional theory (DFT), are now routinely employed. The validity of these quantum-mechanical methods, however, rests on the accurate estimation of electron-correlation energy. This work analyses the role of electron-correlation, using correlation energy as a molecular descriptor, in the QSARs. In particular, QSAR models, for the mutagenic activity of a set of nitrated polycyclic aromatic hydrocarbons (nitro-PAHs), are examined for the role of electron-correlation through state-of-the-art external validation parameters such as concordance correlation coefficient and recently proposed predictive squared correlation coefficients, namely, QF1(2), QF2(2), and QF3(2) etc. The electron-correlation contribution to the highest occupied and lowest unoccupied molecular orbital (HOMO/LUMO) energies is also analyzed. QSAR models based on the semi-empirical quantum-mechanical methods like PM6 and RM1 are also compared. It is found that the models, developed using electron-correlation contribution of the quantum-mechanical descriptors, are not only robust but also relatively more predictive than those developed with the HF and DFT descriptors. The latter are found to be even less reliable than PM6 and RM1 descriptors based models, which show comparable robustness and predictivity with those developed using electron correlation based descriptors. The external predictivity of model based on semi-empirical descriptors can be improved if electron-correlation contribution of the quantum-mechanical descriptors is explicitly included in the model. This work reports the first-ever use of electron-correlation energy and its contribution to the HOMO/LUMO energies as molecular descriptors. PMID:23501159

  13. Broad spectrum antibacterial and antifungal polymeric paint materials: synthesis, structure-activity relationship, and membrane-active mode of action.

    PubMed

    Hoque, Jiaul; Akkapeddi, Padma; Yadav, Vikas; Manjunath, Goutham B; Uppu, Divakara S S M; Konai, Mohini M; Yarlagadda, Venkateswarlu; Sanyal, Kaustuv; Haldar, Jayanta

    2015-01-28

    Microbial attachment and subsequent colonization onto surfaces lead to the spread of deadly community-acquired and hospital-acquired (nosocomial) infections. Noncovalent immobilization of water insoluble and organo-soluble cationic polymers onto a surface is a facile approach to prevent microbial contamination. In the present study, we described the synthesis of water insoluble and organo-soluble polymeric materials and demonstrated their structure-activity relationship against various human pathogenic bacteria including drug-resistant strains such as methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococci (VRE), and beta lactam-resistant Klebsiella pneumoniae as well as pathogenic fungi such as Candida spp. and Cryptococcus spp. The polymer coated surfaces completely inactivated both bacteria and fungi upon contact (5 log reduction with respect to control). Linear polymers were more active and found to have a higher killing rate than the branched polymers. The polymer coated surfaces also exhibited significant activity in various complex mammalian fluids such as serum, plasma, and blood and showed negligible hemolysis at an amount much higher than minimum inhibitory amounts (MIAs). These polymers were found to have excellent compatibility with other medically relevant polymers (polylactic acid, PLA) and commercial paint. The cationic hydrophobic polymer coatings disrupted the lipid membrane of both bacteria and fungi and thus showed a membrane-active mode of action. Further, bacteria did not develop resistance against these membrane-active polymers in sharp contrast to conventional antibiotics and lipopeptides, thus the polymers hold great promise to be used as coating materials for developing permanent antimicrobial paint. PMID:25541751

  14. A novel quantitative structure–activity relationship model for prediction of biomagnification factor of some organochlorine pollutants

    Microsoft Academic Search

    Mohammad Hossein Fatemi; Elham Baher

    2009-01-01

    The biomagnification factor (BMF) is an important property for toxicology and environmental chemistry. In this work, quantitative\\u000a structure–activity relationship (QSAR) models were used for the prediction of BMF for a data set including 30 polychlorinated\\u000a biphenyls and 12 organochlorine pollutants. This set was divided into training and prediction sets. The result of diversity\\u000a test reveals that the structure of the

  15. Mechanism-Based Quantitative Structure–Activity Relationships on Toxicity of Selected Herbicides to Chlorella vulgaris and Raphidocelis subcapitata

    Microsoft Academic Search

    Guanghui Ding; Xue Li; Fan Zhang; Jingwen Chen; Liping Huang; Xianliang Qiao

    2009-01-01

    Four quantitative structure-activity relationships were developed for toxicity of selected photosynthesis (PHS) inhibitors\\u000a and acetolactate synthase (ALS) inhibitors to Chlorella Vulgaris and Raphidocelis subcapitata using a mechanism-based approach. These models have good fitness and predictive ability. The potential of electron transfer,\\u000a intermolecular interactions with weak electron-transfer, and intermolecular dispersive interactions between PHS inhibitors\\u000a and the active site of action are

  16. Identification and structure–activity relationships of ortho-biphenyl carboxamides as potent Smoothened antagonists inhibiting the Hedgehog signaling pathway

    Microsoft Academic Search

    Stefan Peukert; Rishi K. Jain; Adrian Geisser; Yingchuan Sun; Rui Zhang; Aaron Bourret; Adam Carlson; Jennifer DaSilva; Arun Ramamurthy; Joseph F. Kelleher

    2009-01-01

    Ortho-biphenyl carboxamides, originally prepared as inhibitors of microsomal triglyceride transfer protein (MTP) have been identified as novel inhibitors of the Hedgehog signaling pathway. Structure–activity relationship studies for this class of compounds reduced MTP inhibitory activity and led to low nanomolar Hedgehog inhibitors. Binding assays revealed that the compounds act as antagonists of Smoothened and show cross-reactivity for both the human

  17. Quantitative structure–activity relationship study of nonpeptide antagonists of CXCR2 using stepwise multiple linear regression analysis

    Microsoft Academic Search

    Jahan B. Ghasemi; Parvin Zohrabi; Habibollah Khajehsharifi

    2010-01-01

    \\u000a Abstract  The chemokine receptor CXCR2 plays an important role in recruiting granulocytes to sites of inflammation and has been proposed\\u000a as an important therapeutic target. A linear quantitative structure–activity relationship model is presented for modeling\\u000a and predicting biological activities of CXCR2 antagonists. The model was produced by using the multiple linear regression\\u000a technique on a database that consists of 55 nonpeptide

  18. Ginsenosides as Anticancer Agents: In vitro and in vivo Activities, Structure–Activity Relationships, and Molecular Mechanisms of Action

    PubMed Central

    Nag, Subhasree Ashok; Qin, Jiang-Jiang; Wang, Wei; Wang, Ming-Hai; Wang, Hui; Zhang, Ruiwen

    2012-01-01

    Conventional chemotherapeutic agents are often toxic not only to tumor cells but also to normal cells, limiting their therapeutic use in the clinic. Novel natural product anticancer compounds present an attractive alternative to synthetic compounds, based on their favorable safety and efficacy profiles. Several pre-clinical and clinical studies have demonstrated the anticancer potential of Panax ginseng, a widely used traditional Chinese medicine. The anti-tumor efficacy of ginseng is attributed mainly to the presence of saponins, known as ginsenosides. In this review, we focus on how ginsenosides exert their anticancer effects by modulation of diverse signaling pathways, including regulation of cell proliferation mediators (CDKs and cyclins), growth factors (c-myc, EGFR, and vascular endothelial growth factor), tumor suppressors (p53 and p21), oncogenes (MDM2), cell death mediators (Bcl-2, Bcl-xL, XIAP, caspases, and death receptors), inflammatory response molecules (NF-?B and COX-2), and protein kinases (JNK, Akt, and AMP-activated protein kinase). We also discuss the structure–activity relationship of various ginsenosides and their potentials in the treatment of various human cancers. In summary, recent advances in the discovery and evaluation of ginsenosides as cancer therapeutic agents support further pre-clinical and clinical development of these agents for the treatment of primary and metastatic tumors. PMID:22403544

  19. Synthesis and quantitative structure-activity relationships study for phenylpropenamide derivatives as inhibitors of hepatitis B virus replication.

    PubMed

    Yang, Jing; Ma, Min; Wang, Xue-Ding; Jiang, Xing-Jun; Zhang, Yuan-Yuan; Yang, Wei-Qing; Li, Zi-Cheng; Wang, Xi-Hong; Yang, Bin; Ma, Meng-Lin

    2015-06-24

    A series of new phenylpropenamide derivatives containing different substituents was synthesized, characterized and evaluated for their anti-hepatitis B virus (HBV) activities. The quantitative structure-activity relationships (QSAR) of phenylpropenamide compound have been studied. The 2D-QSAR models, based on DFT and multiple linear regression analysis methods, revealed that higher values of total energy (TE) and lower entropy (S(?)) enhanced the anti-HBV activities of the phenylpropenamide molecules. Predictive 3D-QSAR models were established using SYBYL multifit molecular alignment rule. The optimum models were all statistically significant with cross-validated and conventional coefficients, indicating that they were reliable enough for activity prediction. PMID:26057705

  20. Structure-Activity Relationship Study of the Plant-Derived Decapeptide OSIP108 Inhibiting Candida albicans Biofilm Formation

    PubMed Central

    Delattin, Nicolas; De Brucker, Katrijn; Craik, David J.; Cheneval, Olivier; De Coninck, Barbara; Thevissen, Karin

    2014-01-01

    We performed a structure-activity relationship study of the antibiofilm plant-derived decapeptide OSIP108. Introduction of positively charged amino acids R, H, and K resulted in an up-to-5-fold-increased antibiofilm activity against Candida albicans compared to native OSIP108, whereas replacement of R9 resulted in complete abolishment of its antibiofilm activity. By combining the most promising amino acid substitutions, we found that the double-substituted OSIP108 analogue Q6R/G7K had an 8-fold-increased antibiofilm activity. PMID:24913176

  1. Quantitative structure activities relationships of some 2-mercaptoimidazoles as CCR2 inhibitors using genetic algorithm-artificial neural networks

    PubMed Central

    Saghaie, L; Shahlaei, M; Fassihi, A

    2013-01-01

    Quantitative relationships between structures of twenty six of 2-mercaptoimidazoles as C-C chemokine receptor type 2 (CCR2) inhibitors were assessed. Modeling of the biological activities of compounds of interest as a function of molecular structures was established by means of genetic algorithm multivariate linear regression (GA-MLR) and genetic algorithm (GA-ANN). The results showed that, the pIC50 values calculated by GA-ANN are in good agreement with the experimental data, and the performance of the artificial neural networks regression model is superior to the multivariate linear regression-based (MLR) model. With respect to the obtained results, it can be deduced that there is a non-linear relationship between the pIC50 s and the calculated structural descriptors of the 2-mercaptoimidazoles. The obtained models were able to describe about 78% and 93% of the variance in the experimental activity of molecules in training set, respectively. The study provided a novel and effective approach for predicting biological activities of 2-mercaptoimidazole derivatives as CCR2 inhibitors and disclosed that combined genetic algorithm and GA-ANN can be used as a powerful chemometric tools for quantitative structure activity relationship (QSAR) studies. PMID:24019819

  2. Quantitative structure activity relationship and risk analysis of some pesticides in the goat milk

    PubMed Central

    2013-01-01

    The detection and quantification of different pesticides in the goat milk samples collected from different localities of Faisalabad, Pakistan was performed by HPLC using solid phase microextraction. The analysis showed that about 50% milk samples were contaminated with pesticides. The mean±SEM levels (ppm) of cyhalothrin, endosulfan, chlorpyrifos and cypermethrin were 0.34±0.007, 0.063±0.002, 0.034±0.002 and 0.092±0.002, respectively; whereas, methyl parathion was not detected in any of the analyzed samples. Quantitative structure activity relationship (QSAR) models were suggested to predict the residues of unknown pesticides in the goat milk using their known physicochemical characteristics including molecular weight (MW), melting point (MP), and log octanol to water partition coefficient (Ko/w) in relation to the characteristics such as pH, % fat, specific gravity and refractive index of goat milk. The analysis revealed good correlation coefficient (R2 = 0.985) for goat QSAR model. The coefficients for Ko/w and refractive index for the studied pesticides were higher in goat milk. This suggests that these are better determinants for pesticide residue prediction in the milk of these animals. Based upon the determined pesticide residues and their provisional tolerable daily intakes, risk analysis was also conducted which showed that daily intake levels of pesticide residues including cyhalothrin, chlorpyrifos and cypermethrin in present study are 2.68, 5.19 and 2.71 times higher, respectively in the goat milk. This intake of pesticide contaminated milk might pose health hazards to humans in this locality. PMID:23369514

  3. Synthesis, antioxidant activity and structure-activity relationships for a new series of 2-(N-acylaminoethyl)indoles with melatonin-like cytoprotective activity.

    PubMed

    Spadoni, Gilberto; Diamantini, Giuseppe; Bedini, Annalida; Tarzia, Giorgio; Vacondio, Federica; Silva, Claudia; Rivara, Mirko; Mor, Marco; Plazzi, Pier Vincenzo; Zusso, Morena; Franceschini, Davide; Giusti, Pietro

    2006-04-01

    5-Methoxy-2-(N-acetylaminoethyl)indole (5d), a melatonin analogue derived from the transposition of the acetylaminoethyl side chain from C3 to C2 of the indole nucleus, had been previously characterized as a low affinity antagonist at MT1 and MT2 membrane receptors; this molecule is endowed with good in vitro antioxidant and cytoprotective potency in rat cerebellar cell cultures, comparable to or better than those of melatonin. In order to further investigate the role of structure-antioxidant activity relationships in cytoprotection, the structure of 5d was systematically modulated to design a new series of compounds. The 5-methoxy group was replaced by substituents with different electronic and lipophilic properties and it was moved to a different position on the indole ring. Other modifications of the lead structure involved the methylation of the indole nitrogen or its replacement by a sulfur atom. The side chain was also modified either increasing its lipophilicity or introducing an ionisable acid group. The antioxidant activity of this set of compounds was evaluated by the ABTS and conjugated dienes (CD) assays, while their cytoprotection was evaluated against kainate-induced cytotoxicity in cultured cerebellar neurons. In both antioxidant assays, the shift of the 5-methoxy group to the 4-position of the indole nucleus led to the most active radical scavenger (9), more potent than the parent compound and melatonin in the antioxidant tests, but much less effective as a cytoprotectant. Sharp structure-activity relationships were registered for cytoprotection, where the maintenance of the 5-alkoxy-2-(N-acylaminoethyl)indole scaffold appeared as the key feature to confer both antioxidant and cytoprotective activity to the structure. Some derivatives of the set, however, together with the most potent 5d, maintained a significant antioxidant and cytoprotective effect and could be employed as tools for in vivo pharmacological investigations on neuroprotective efficacy of melatonin-related indoles. PMID:16499563

  4. Coumarins isolated from Angelica gigas inhibit acetylcholinesterase: structure-activity relationships.

    PubMed

    Kang, S Y; Lee, K Y; Sung, S H; Park, M J; Kim, Y C

    2001-05-01

    Acetylcholinesterase (AChE) inhibitory activity-guided fractionation of Angelica gigas led to isolation and identification of a new coumarin, peucedanone (12), and isolation of 11 known coumarins. Among them, decursinol (1) represented the highest inhibitory activity toward AChE in vitro. The correlation of the inhibitory activities of the coumarins toward AChE with their chemical structures was studied. PMID:11374978

  5. Structure-activity relationship for the binding of nucleoside ligands to adenosine kinase from Toxoplasma gondii.

    PubMed

    Iltzsch, M H; Uber, S S; Tankersley, K O; el Kouni, M H

    1995-05-17

    One hundred and twenty-eight purine nucleoside analogs were evaluated as ligands of Toxoplasma gondii adenosine kinase (EC 2.7.1.20) by examining their ability to inhibit this enzyme in vitro. Inhibition was quantified by determining apparent Ki (appKi) values for those compounds that inhibited this enzyme by greater than 10% at a concentration of 1 mM. Two compounds, N6-(p-methoxybenzoyl)adenosine and 7-iodo-7-deazaadenosine (iodotubercidin), were found to bind to the enzyme (appKi = 3.9 and 1.6 microM, respectively) better than adenosine. On the basis of these data, a structure-activity relationship for the binding of ligands to T. gondii adenosine kinase was formulated using adenosine as a reference compound. It was concluded that the following structural features of purine nucleoside analogs are required or strongly preferred for binding: (1) "pyridine-type" endocyclic nitrogens at the 1- and 3-positions; (2) an exocyclic hydrogen at the 2-position; (3) 6-position exocyclic substituents in the lactim tautomeric form; (4) a "pyridine-type" endocyclic nitrogen at the 7-position or hydrophobic exocyclic substituents attached to an endocyclic carbon at the 7-position; (5) an endocyclic methine or "pyridine-type" nitrogen at the 8-position; (6) an endocyclic nitrogen at the 9-position; (7) a pentose or "pentose-like" (e.g. hydroxylated cyclopentene) moiety attached to the 9-position nitrogen; (8) hydroxyl groups at the 2'- and 3'-positions in a ribose configuration; (9) a hydroxymethyl or methyl (i.e. 5'-deoxy) group at the 5'-position; (10) a beta-D-nucleoside configuration; and (11) an anti conformation around the N-glycosidic bond. In addition, there appears to be a "pocket" in the catalytic site of T. gondii adenosine kinase, adjacent to the 6-position of adenosine, that can accommodate large (preferably unsaturated or aromatic) substituents (e.g. phenyl). These findings provide the basis for the rational design of additional ligands of T. gondii adenosine kinase. PMID:7763293

  6. Structure-activity relationships (SAR) and structure-kinetic relationships (SKR) of bicyclic heteroaromatic acetic acids as potent CRTh2 antagonists I.

    PubMed

    Alonso, Juan Antonio; Andrés, Miriam; Bravo, Mónica; Buil, Maria Antonia; Calbet, Marta; Castro, Jordi; Eastwood, Paul R; Eichhorn, Peter; Esteve, Cristina; Gómez, Elena; González, Jacob; Mir, Marta; Petit, Silvia; Roberts, Richard S; Vidal, Bernat; Vidal, Laura; Vilaseca, Pere; Zanuy, Miriam

    2014-11-01

    A knowledge-based design strategy led to the discovery of several new series of potent and orally bioavailable CRTh2 antagonists where a bicyclic heteroaromatic ring serves as the central core. Structure-kinetic relationships (SKR) opened up the possibility of long receptor residence times. PMID:25437504

  7. Oximes: Inhibitors of Human Recombinant Acetylcholinesterase. A Structure-Activity Relationship (SAR) Study

    PubMed Central

    Sepsova, Vendula; Karasova, Jana Zdarova; Korabecny, Jan; Dolezal, Rafael; Zemek, Filip; Bennion, Brian J.; Kuca, Kamil

    2013-01-01

    Acetylcholinesterase (AChE) reactivators were developed for the treatment of organophosphate intoxication. Standard care involves the use of anticonvulsants (e.g., diazepam), parasympatolytics (e.g., atropine) and oximes that restore AChE activity. However, oximes also bind to the active site of AChE, simultaneously acting as reversible inhibitors. The goal of the present study is to determine how oxime structure influences the inhibition of human recombinant AChE (hrAChE). Therefore, 24 structurally different oximes were tested and the results compared to the previous eel AChE (EeAChE) experiments. Structural factors that were tested included the number of pyridinium rings, the length and structural features of the linker, and the number and position of the oxime group on the pyridinium ring. PMID:23959117

  8. A Binding Site Model and Structure-Activity Relationships for the Rat A3 Adenosine Receptor

    PubMed Central

    VAN GALEN, PHILIP J. M.; VAN BERGEN, ANDREW H.; GALLO-RODRIGUEZ, CAROLA; MELMAN, NELI; OLAH, MARK E.; IJZERMAN, AD P.; STILES, GARY L.; JACOBSON, KENNETH A.

    2012-01-01

    SUMMARY A novel adenosine receptor, the A3 receptor, has recently been cloned. We have systematically investigated the hitherto largely unexplored structure-activity relationships (SARs) for binding at A3 receptors, using 125I-N6-2-(4-aminophenyl)ethyladenosine as a radioligand and membranes from Chinese hamster ovary cells stably transfected with the rat A3-cDNA. As is the case for A1 and A2a, receptors, substitutions at the N6 and 5? positions of adenosine, the prototypic agonist ligand, may yield fairly potent compounds. However, the highest affinity and A3 selectivity is found for N6,5?-disubstituted compounds, in contrast to A1 and A2a receptors. Thus, N6-benzyladenosine-5?-N-ethylcarboxamide is highly potent (Ki, 6.8 nM) and moderately selective (13- and 14-fold versus A1 and A2a). The N6 region of the A3 receptor also appears to tolerate hydrophilic substitutions, in sharp contrast to the other subtypes. Potencies of N6,5?-disubstituted compounds in inhibition of adenylate cyclase via A3 receptors parallel their high affinity in the binding assay. None of the typical xanthine or nonxanthine (A1/A2) antagonists tested show any appreciable affinity for rat A3 receptors. 1,3-Dialkylxanthines did not antagonize the A3 agonist-induced inhibition of adenylate cyclase. A His residue in helix 6 that is absent in A3 receptors but present in A1/A2 receptors may be causal in this respect. In a molecular model for the rat A3 receptor, this mutation, together with an increased bulkiness of residues surrounding the ligand, make antagonist binding unfavorable when compared with a previously developed A1 receptor model. Second, this A3 receptor model predicted similarities with A1 and A2 receptors in the binding requirements for the ribose moiety and that xanthine-7-ribosides would bind to rat A3 receptors. This hypothesis was supported experimentally by the moderate affinity (Ki 6 ?M) of 7-riboside of 1,3-dibutylxanthine, which appears to be a partial agonist at rat A3 receptors. The model presented here, which is consistent with the detailed SAR found in this study, may serve to suggest future chemical modification, site-directed mutagenesis, and SAR studies to further define essential characteristics of the ligand-receptor interaction and to develop even more potent and selective A3 receptor ligands. PMID:8022403

  9. Structure-activity relationships of the prototypical TRPM8 agonist icilin.

    PubMed

    De Petrocellis, Luciano; Ortar, Giorgio; Schiano Moriello, Aniello; Serum, Eric M; Rusterholz, David B

    2015-06-01

    A series of structural analogues of the TRPM8 agonist icilin was prepared. The compounds were examined for their ability to exert agonist or antagonist effects in HEK-293 cells expressing the TRPM8 receptor. Most structural modifications of the icilin structure largely met with diminished TRPM8 agonist activity. Cinnamamide 'open-chain' analogs of icilin, however, demonstrated significant antagonistic actions at the TRPM8 receptor. Optimal potency (IC50=73nM) was observed in the 3-iodo derivative 18l. PMID:25935641

  10. Bronchodilation and structure-activity relationship studies on new 6-substituted benzimidazo[1,2-c]quinazolines.

    PubMed

    Bahekar, R H; Rao, A R

    2000-08-01

    Two series of 6-substituted benzimidazo[1,2-c]quinazolines (Ia-p and IIa-l) have been synthesized and characterized. The compounds were evaluated for their bronchodilator activity, in vitro and in vivo. All the test compounds exhibited good activity both in vivo and in vitro methods. The structure-activity relationships based on the results obtained for these series have also been studied. In the 6-alkyl substituted compounds II, a longer alkyl chain and a 4-substitution by an electron-withdrawing group in compounds I, showed more activity. The presence of halogens altered the biological activity in both series. Among the compounds tested, 10-iodo-6-(n-propyl)-benzimidazol[1,2-c]quinazoline (II) was found to be the most potent (% protection = 75%; relative activity = 1.1). PMID:10994154

  11. Quantitative structure activity relationships of some pyridine derivatives as corrosion inhibitors of steel in acidic medium.

    PubMed

    El Ashry, El Sayed H; El Nemr, Ahmed; Ragab, Safaa

    2012-03-01

    Quantum chemical calculations using the density functional theory (B3LYP/6-31G DFT) and semi-empirical AM1 methods were performed on ten pyridine derivatives used as corrosion inhibitors for mild steel in acidic medium to determine the relationship between molecular structure and their inhibition efficiencies. Quantum chemical parameters such as total negative charge (TNC) on the molecule, energy of highest occupied molecular orbital (E (HOMO)), energy of lowest unoccupied molecular orbital (E (LUMO)) and dipole moment (?) as well as linear solvation energy terms, molecular volume (Vi) and dipolar-polarization (?) were correlated to corrosion inhibition efficiency of ten pyridine derivatives. A possible correlation between corrosion inhibition efficiencies and structural properties was searched to reduce the number of compounds to be selected for testing from a library of compounds. It was found that theoretical data support the experimental results. The results were used to predict the corrosion inhibition of 24 related pyridine derivatives. PMID:21695505

  12. Structure–activity relationships of compounds targeting mycobacterium tuberculosis 1-deoxy- d-xylulose 5-phosphate synthase

    Microsoft Academic Search

    Jialin Mao; Hyungjin Eoh; Rong He; Yuehong Wang; Baojie Wan; Scott G. Franzblau; Dean C. Crick; Alan P. Kozikowski

    2008-01-01

    We report on a target-based approach to identify possible Mycobacteriumtuberculosis DXS inhibitors from the structure of a known transketolase inhibitor. A small focused library of analogs was assembled in order to begin elucidating some meaningful structure–activity relationships of 3-(4-chloro-phenyl)-5-benzyl-4H-pyrazolo[1,5-a]pyrimidin-7-one. Ultimately we found that 2-methyl-3- (4-fluorophenyl)-5-(4-methoxy-phenyl)-4H-pyrazolo[1,5-a]pyrimidin-7-one, although still weak, was able to inhibit M. tuberculosis DXS with an IC50 of 10.6?M.

  13. Structure-activity relationship study of phenylpyrazole derivatives as a novel class of anti-HIV agents.

    PubMed

    Mizuhara, Tsukasa; Kato, Takayuki; Hirai, Atsushi; Kurihara, Hideki; Shimada, Yasuhiro; Taniguchi, Masahiko; Maeta, Hideki; Togami, Hiroaki; Shimura, Kazuya; Matsuoka, Masao; Okazaki, Shiho; Takeuchi, Tomoki; Ohno, Hiroaki; Oishi, Shinya; Fujii, Nobutaka

    2013-08-15

    The structure-activity relationship of phenylpyrazole derivative 1 was investigated for the development of novel anti-HIV agents. Initial efforts revealed that the diazenyl group can be replaced by an aminomethylene group. In addition, we synthesized various derivatives by the reductive amination of benzaldehydes with 5-aminopyrazoles and carried out parallel structural optimization on the benzyl group and the pyrazole ring. This optimization led to a six-fold more potent derivative 32j than the lead compound 1, and this derivative has a 3',4'-dichloro-(1,1'-biphenyl)-3-yl group. PMID:23845222

  14. Synthesis and structure–activity relationships of indole and benzimidazole piperazines as histamine H 4 receptor antagonists

    Microsoft Academic Search

    Nalan Terzioglu; Richard M. van Rijn; Remko A. Bakker; Iwan J. P. De Esch; Rob Leurs

    2004-01-01

    We describe the structure–activity relationships for a series of ligands structurally related to the recently identified (5-chloro-1H-indol-2-yl)-(4-methyl-piperazin-1-yl)-methanone (1) as histamine H4 receptor (H4R) antagonists. Furthermore, we identified related benzimidazoles as novel lead compounds for the H4R. The ligands have been evaluated by radioligand displacement studies and functional assays for their interaction with both the human histamine H3 and H4 receptors

  15. Design, synthesis, and structure-activity relationships of novel 6,7-disubstituted-4-phenoxyquinoline derivatives as potential antitumor agents.

    PubMed

    Tang, Qidong; Zhao, Yanfang; Du, Xinming; Chong, Lian'e; Gong, Ping; Guo, Chun

    2013-11-01

    Two series of quinoline derivatives bearing the pyridine/pyrimidine scaffold were synthesized, and evaluated for their c-Met kinase inhibitory activity and antiproliferative activity against 5 cancer cell lines (HT-29, H460, MKN-45, A549, and U87MG) were evaluated in vitro. Most compounds showed moderate to excellent potency, and compared to foretinib, the most promising analog 18b (c-Met half-maximal inhibitory concentration [IC??] = 1.39 nM) showed a 7.3-fold increase in activity against HT-29 cell line in vitro. Structure-activity relationship studies indicated that regulation of the electron density on the pyridine/pyrimidine ring to a proper degree was a key factor in improving the antitumor activity. PMID:24012712

  16. Structure activity relationship of plumbagin in BRCA1 related cancer cells.

    PubMed

    K A, Thasni; T, Ratheeshkumar; G, Rojini; K C, Sivakumar; Nair, Rakesh Sathish; G, Srinivas; Banerji, Asoke; Somasundaram, Veena; Srinivas, Priya

    2013-05-01

    It has been shown earlier that plumbagin, a naturally occurring naphthaquinone has specific anticancer activity in BRCA1 blocked ovarian cancer cells. Plumbagin can induce estrogen dependent cell signaling and apoptosis in BRCA1 blocked ovarian cancer cells. Being a reactive oxygen species (ROS) generator and apoptosis inducing agent, plumbagin has immense potential as a promising anticancer agent. In this study we analyzed whether there would be increased anticancer activity if the positions of the functional groups on plumbagin were altered and further to analyze the detailed molecular mechanism of action of the lead molecule. Methods like MTT assay, apoptosis analysis by flow cytometry, assessment of mitochondrial membrane potential-??m , suppression subtractive hybridization, microarray, molecular docking and estrogen receptor-DNA binding activity by electrophoresis mobility shift assay (EMSA) were adopted for assessing the anticancer activity. Consequently we found that, plumbagin was the most potent anticancer agent when compared to structurally related compounds. The anti-cancer activities were in the order plumbagin > 1,4-naphthaquinone > juglone > lawsone > menadione. Molecular docking studies showed that plumbagin could be well docked in the receptor ligand complex of TRAIL-DR5 complexes to activate the extrinsic pathway of apoptosis. Since the antiproliferative activity of plumbagin could be reduced by inhibiting ER?, we speculated that plumbagin interferes with the binding of ER? to ERE and we confirmed this by EMSA. This study clearly indicates that plumbagin can induce multiple pathways of apoptosis and cell cycle arrest in BRCA1 blocked cells compared to unblocked cells. PMID:22290577

  17. Quantitative structure-activity relationship (QSAR) studies for predicting activation of the ryanodine receptor type 1 channel complex (RyR1) by polychlorinated biphenyl (PCB) congeners

    Microsoft Academic Search

    Sierra Rayne; Kaya Forest

    2010-01-01

    A quantitative structure-activity relationship (QSAR) was developed to predict the congener specific ryanodine receptor type RyR1 activity of all 209 polychlorinated biphenyl (PCB) congeners. A three-variable QSAR equation was obtained via stepwise forward linear regression on an unsupervised forward selection reduced data set from an initial database. Application of the QSAR towards predicting EC2x values for all 209 PCB congeners

  18. Rapid preparation of rare ginsenosides by acid transformation and their structure-activity relationships against cancer cells

    PubMed Central

    Quan, Kai; Liu, Qun; Wan, Jin-Yi; Zhao, Yi-Jing; Guo, Ru-Zhou; Alolga, Raphael N.; Li, Ping; Qi, Lian-Wen

    2015-01-01

    The anticancer activities of ginsenosides are widely reported. The structure-activity relationship of ginsenosides against cancer is not well elucidated because of the unavailability of these compounds. In this work, we developed a transformation method to rapidly produce rare dehydroxylated ginsenosides by acid treatment. The optimized temperature, time course, and concentration of formic acid were 120°C, 4?h and 0.01%, respectively. From 100?mg of Rh1, 8.3?mg of Rk3 and 18.7?mg of Rh4 can be produced by acid transformation. Similarly, from 100?mg of Rg3, 7.4?mg of Rk1 and 15.1?mg of Rg5 can be produced. From 100?mg of Rh2, 8.3?mg of Rk2 and 12.7?mg of Rh3 can be generated. Next, the structure-activity relationships of 23 ginsenosides were investigated by comparing their cytotoxic effects on six human cancer cells, including HCT-116, HepG2, MCF-7, Hela, PANC-1, and A549. The results showed that: (1) the cytotoxic effect of ginsenosides is inversely related to the sugar numbers; (2) sugar linkages rank as C-3 > C-6 > C-20; (3) the protopanaxadiol-type has higher activities; (4) having the double bond at the terminal C20-21 exhibits stronger activity than that at C20-22; and (5) 20(S)-ginsenosides show stronger effects than their 20(R)-stereoisomers. PMID:25716943

  19. Rapid preparation of rare ginsenosides by acid transformation and their structure-activity relationships against cancer cells.

    PubMed

    Quan, Kai; Liu, Qun; Wan, Jin-Yi; Zhao, Yi-Jing; Guo, Ru-Zhou; Alolga, Raphael N; Li, Ping; Qi, Lian-Wen

    2015-01-01

    The anticancer activities of ginsenosides are widely reported. The structure-activity relationship of ginsenosides against cancer is not well elucidated because of the unavailability of these compounds. In this work, we developed a transformation method to rapidly produce rare dehydroxylated ginsenosides by acid treatment. The optimized temperature, time course, and concentration of formic acid were 120°C, 4 h and 0.01%, respectively. From 100 mg of Rh1, 8.3 mg of Rk3 and 18.7 mg of Rh4 can be produced by acid transformation. Similarly, from 100 mg of Rg3, 7.4 mg of Rk1 and 15.1 mg of Rg5 can be produced. From 100 mg of Rh2, 8.3 mg of Rk2 and 12.7 mg of Rh3 can be generated. Next, the structure-activity relationships of 23 ginsenosides were investigated by comparing their cytotoxic effects on six human cancer cells, including HCT-116, HepG2, MCF-7, Hela, PANC-1, and A549. The results showed that: (1) the cytotoxic effect of ginsenosides is inversely related to the sugar numbers; (2) sugar linkages rank as C-3 > C-6 > C-20; (3) the protopanaxadiol-type has higher activities; (4) having the double bond at the terminal C20-21 exhibits stronger activity than that at C20-22; and (5) 20(S)-ginsenosides show stronger effects than their 20(R)-stereoisomers. PMID:25716943

  20. Non-linear quantitative structure-activity relationship for adenine derivatives as competitive inhibitors of adenosine deaminase

    SciTech Connect

    Sadat Hayatshahi, Sayyed Hamed [Department of Biophysics, Faculty of Science, Tarbiat Modares University, P.O. Box: 14115/175, Tehran (Iran, Islamic Republic of) ; Abdolmaleki, Parviz [Department of Biophysics, Faculty of Science, Tarbiat Modares University, P.O. Box: 14115/175, Tehran (Iran, Islamic Republic of) ]. E-mail: parviz@modares.ac.ir; Safarian, Shahrokh [Department of Biology, Faculty of Science, Tehran University, P.O. Box: 13155-6455, Tehran (Iran, Islamic Republic of) ; Khajeh, Khosro [Department of Biochemistry, Faculty of Science, Tarbiat Modares University, P.O. Box: 14115/175, Tehran (Iran, Islamic Republic of)

    2005-12-16

    Logistic regression and artificial neural networks have been developed as two non-linear models to establish quantitative structure-activity relationships between structural descriptors and biochemical activity of adenosine based competitive inhibitors, toward adenosine deaminase. The training set included 24 compounds with known k {sub i} values. The models were trained to solve two-class problems. Unlike the previous work in which multiple linear regression was used, the highest of positive charge on the molecules was recognized to be in close relation with their inhibition activity, while the electric charge on atom N1 of adenosine was found to be a poor descriptor. Consequently, the previously developed equation was improved and the newly formed one could predict the class of 91.66% of compounds correctly. Also optimized 2-3-1 and 3-4-1 neural networks could increase this rate to 95.83%.

  1. Synthesis and structure–activity relationships of serotonin derivatives effect on ?-glucosidase inhibition

    Microsoft Academic Search

    Toshiyuki Takahashi; Mitsuo Miyazawa

    The ?-glucosidase inhibitory activities of serotonin derivatives were evaluated. Two serotonin derivatives, N-p-coumaroyl serotonin (2) and N-caffeoyl serotonin (4) exhibited most potent inhibition on ?-glucosidase, whereas, cinnamic acid derivatives were less efficient. Furthermore,\\u000a we analyzed their structural importance for ?-glucosidase inhibition. The linkage of cinnamic acid moiety and serotonin moiety\\u000a and the olefin in cinnamic acid moiety of serotonin derivatives

  2. Structure-activity relationship study of E6 as a novel necroptosis inducer.

    PubMed

    Mou, Jianfeng; Park, Ann; Cai, Yu; Yuan, Junying; Yuan, Chengye

    2015-08-01

    Necroptosis inducers represent a promising potential treatment for drug-resistant cancer. We herein describe the structure modification of E6, which was identified recently as a potent and selective necroptosis inducer. The studies described herein demonstrate for the first time that functionalized biphenyl derivatives possess necroptosis inducer activity. Furthermore, these studies have led to the identification of two promising compounds (5h and 5j) that can be used for further optimization studies as well as mechanism of action investigations. PMID:26048796

  3. Hydroxylated Polychlorinated Biphenyls (PCBs) as Estrogens and Antiestrogens: Structure–Activity Relationships

    Microsoft Academic Search

    K. Connor; K. Ramamoorthy; M. Moore; M. Mustain; I. Chen; S. Safe; T. Zacharewski; B. Gillesby; A. Joyeux; P. Balaguer

    1997-01-01

    The effects of structure on the estrogenicity and antiestrogenicity of hydroxylated polychlorinated biphenyls were investigated using the following estrogen-sensitive assays: competitive binding to the rat and mouse cytosolic estrogen receptor (ER); immature rat and mouse uterine wet weight, peroxidase and progesterone receptor (PR) levels; induction of luciferase activity in HeLa cells stably transfected with a Gal4:human ER chimera and a

  4. Structure-activity relationships of larvicidal monoterpenes and derivatives against Aedes aegypti Linn.

    PubMed

    Santos, Sandra R L; Melo, Manuela A; Cardoso, Andrea Valença; Santos, Roseli L C; de Sousa, Damião P; Cavalcanti, Sócrates C H

    2011-06-01

    In the search for larvicidal compounds against Aedes aegypti L. (Diptera: Culicidae), a collection of monoterpenes were selected and evaluated. R- and S-limonene exhibited the highest larvicidal potency (LC(50)=27 and 30 ppm, respectively), followed by ?-terpinene (LC(50)=56 ppm) and RS-carvone (LC(50)=118 ppm). Structural characteristics which may contribute to the understanding of the larvicidal activity of monoterpenes were empirically identified. The presence of heteroatoms in the basic hydrocarbon structure decreases larvicidal potency. Conjugated and exo double bonds appear to increase larvicidal potency. Replacement of double bonds by more reactive epoxides decreases the larvicidal potency. The presence of hydroxyls in the cyclic structure resulted in decreased potency, probably due to increased polarity indicanting that lipophilicity seems to play an important role in increasing the larvicidal potency in this set of compounds. PMID:21376365

  5. Biofunctional constituent isolated from Citrullus colocynthis fruits and structure-activity relationships of its analogues show acaricidal and insecticidal efficacy.

    PubMed

    Jeon, Ju-Hyun; Lee, Hoi-Seon

    2014-08-27

    The acaricidal and insecticidal potential of the active constituent isolated from Citrullus colocynthis fruits and its structurally related analogues was evaluated by performing leaf disk, contact toxicity, and fumigant toxicity bioassays against Tetranychus urticae, Sitophilus oryzae, and Sitophilus zeamais adults. The active constituent of C. colocynthis fruits was isolated by chromatographic techniques and was identified as 4-methylquinoline on the basis of spectroscopic analyses. To investigate the structure-activity relationships, 4-methylquinoline and its structural analogues were tested against mites and two insect pests. On the basis of the LC50 values, 7,8-benzoquinoline was the most effective against T. urticae. Quinoline, 8-hydroxyquinoline, 2-methylquinoline, 4-methylquinoline, 6-methylquinoline, 8-methylquinoline, and 7,8-benzoquinoline showed high insecticidal activities against S. oryzae and S. zeamais regardless of the application method. These results indicate that introduction of a functional group into the quinoline skeleton and changing the position of the group have an important influence on the acaricidal and insecticidal activities. Furthermore, 4-methylquinoline isolated from C. colocynthis fruits, along with its structural analogues, could be effective natural pesticides for managing spider mites and stored grain weevils. PMID:25110971

  6. Cucurbitane glycosides derived from mogroside IIE: structure-taste relationships, antioxidant activity, and acute toxicity.

    PubMed

    Wang, Lei; Yang, Ziming; Lu, Fenglai; Liu, Jinglei; Song, Yunfei; Li, Dianpeng

    2014-01-01

    Mogroside IIE is a bitter triterpenoid saponin which is the main component of unripe Luo Han Guo fruit and a precursor of the commercially available sweetener mogroside V. In this study, we developed an enzymatic glycosyl transfer method, by which bitter mogroside IIE could be converted into a sweet triterpenoid saponin mixture. The reactant concentration, temperature, pH and buffer system were studied. New saponins with the ?-glucose group were isolated from the resulting mixtures, and the structures of three components of the extract were determined. The structure-taste relationships of these derivatives were also studied together with those of the natural mogrosides. The number and stereoconfiguration of glucose groups present in the mogroside molecules were found to be the main factor to determine the sweet or bitter taste of a compound. The antioxidant and food safety properties were initially evaluated by their radical scavenging ability and via 7 day mice survival tests, respectively. The results showed that the sweet triterpenoid saponin mixture has the same favorable physiological and safety characteristics as the natural mogrosides. PMID:25140446

  7. Pharmacophore modeling and 3D quantitative structure-activity relationship analysis of febrifugine analogues as potent antimalarial agent.

    PubMed

    Sen, Debanjan; Chatterjee, Tapan Kumar

    2013-01-01

    Febrifugine and its derivatives are effective against Plasmodium falciparum. Using PHASE algorithm, a five-point pharmacophore model with two hydrogen bond acceptor (A), one positively ionizable (P) and two aromatic rings (R), was developed to derive a predictive ligand-based statistically significant 3D-quantitative structure-activity relationship (QSAR) model (r(2) = 0.972, SD = 0.3, F = 173.4, Q(2) = 0.712, RMSE = 0.3, Person-R = 0.94, and r(2) pred = 0.8) to explicate the structural attributes crucial for antimalarial activity. The developed pharmacophore model and 3D QSAR model can be a substantial tool for virtual screening and related antimalarial drug discovery research. PMID:23662282

  8. Pharmacophore modeling and 3D quantitative structure-activity relationship analysis of febrifugine analogues as potent antimalarial agent

    PubMed Central

    Sen, Debanjan; Chatterjee, Tapan Kumar

    2013-01-01

    Febrifugine and its derivatives are effective against Plasmodium falciparum. Using PHASE algorithm, a five-point pharmacophore model with two hydrogen bond acceptor (A), one positively ionizable (P) and two aromatic rings (R), was developed to derive a predictive ligand-based statistically significant 3D-quantitative structure-activity relationship (QSAR) model (r2 = 0.972, SD = 0.3, F = 173.4, Q2 = 0.712, RMSE = 0.3, Person-R = 0.94, and r2pred = 0.8) to explicate the structural attributes crucial for antimalarial activity. The developed pharmacophore model and 3D QSAR model can be a substantial tool for virtual screening and related antimalarial drug discovery research. PMID:23662282

  9. Anti-listerial activity and structure-activity relationships of the six major tyrocidines, cyclic decapeptides from Bacillus aneurinolyticus.

    PubMed

    Spathelf, Barbara M; Rautenbach, Marina

    2009-08-01

    Six major tyrocidines, purified from the antibiotic tyrothricin complex produced by Bacillus aneurinolyticus, showed significant lytic and growth inhibitory activity towards the gram+ bacteria, Micrococcus luteus and Listeria monocytogenes, but not against the gram- bacterium, Escherichia coli. The isolated natural tyrocidines were in particular more active against the leucocin A (antimicrobial peptide) resistant strain, L. monocytogenes B73-MR1, than the sensitive L. monocytogenes B73 strain. Remarkably similar structure-activity trends toward the three gram+ bacteria were found between growth inhibition and different physicochemical parameters (solution amphipathicity, theoretical lipophilicity, side-chain surface area and mass-over-charge ratio). PMID:19586775

  10. Inhibitors of HCV NS5B polymerase: Synthesis and structure–activity relationships of N-alkyl-4-hydroxyquinolon-3-yl-benzothiadiazine sulfamides

    Microsoft Academic Search

    A. Chris Krueger; Darold L. Madigan; Wen W. Jiang; Warren M. Kati; Dachun Liu; Yaya Liu; Clarence J. Maring; Sherie Masse; Keith F. McDaniel; Tim Middleton; Hongmei Mo; Akhteruzzaman Molla; Debra Montgomery; John K. Pratt; Todd W. Rockway; Rong Zhang; Dale J. Kempf

    Substituted N-alkyl-4-hydroxyquinolon-3-yl-benzothiadiazine sulfamides were investigated as inhibitors of genotype 1 HCV polymerase. Structure–activity relationship patterns for this class of compounds are discussed.

  11. Inhibitors of HCV NS5B polymerase: Synthesis and structure–activity relationships of N-alkyl-4-hydroxyquinolon-3-yl-benzothiadiazine sulfamides

    Microsoft Academic Search

    A. Chris Krueger; Darold L. Madigan; Wen W. Jiang; Warren M. Kati; Dachun Liu; Yaya Liu; Clarence J. Maring; Sherie Masse; Keith F. McDaniel; Tim Middleton; Hongmei Mo; Akhteruzzaman Molla; Debra Montgomery; John K. Pratt; Todd W. Rockway; Rong Zhang; Dale J. Kempf

    2006-01-01

    Substituted N-alkyl-4-hydroxyquinolon-3-yl-benzothiadiazine sulfamides were investigated as inhibitors of genotype 1 HCV polymerase. Structure–activity relationship patterns for this class of compounds are discussed.

  12. Synthesis, Structure?Activity Relationship, and Pharmacological Profile of Analogs of The ASIC-3 Inhibitor A-317567

    PubMed Central

    2009-01-01

    The synthesis, structure?activity relationship (SAR), and pharmacological evaluation of analogs of the acid-sensing ion channel (ASIC) inhibitor A-317567 are reported. It was found that the compound with an acetylenic linkage was the most potent ASIC-3 channel blocker. This compound reversed mechanical hypersensitivity in the rat iodoacetate model of osteoarthritis pain, although sedation was noted. Sedation was also observed in ASIC-3 knockout mice, questioning whether sedation and antinociception are mediated via a non-ASIC-3 specific mechanism. PMID:22778804

  13. Effects of taurine analogues on chloride channel conductance of rat skeletal muscle fibers: a structure-activity relationship investigation

    Microsoft Academic Search

    S. Pierno; D. Tricarico; A. Luca; F. Campagna; A. Carotti; G. Casini; D. Conte Camerino

    1994-01-01

    In rat skeletal muscle, taurine was proposed to interact with a low affinity binding site on sarcolemmal phospholipids near chloride channel, increasing chloride conductance (GCI). In an attempt to evaluate the structure-activity relationship between taurine and its binding site, a series of N-azacycloalkenyl analogues of taurine (A: N-(1'aza-cyclopenten-2'yl)-2-aminoethane sulfonic acid; B: N-(1'-aza-cyclopenten-2'-yl)-2-aminoethane sulfonic acid; C: N-(1'aza-cyclopenten-2'-yl)-3-amino-propane sulfonic acid; D: N-(1'aza-cyclopenten-2'-yl)-3-aminopropane

  14. Pyridine derivatives: structure-activity relationships causing parkinsonism-like symptoms.

    PubMed

    Bachurin, S O; Tkachenko, S E; Lermontova, N N

    1991-01-01

    In recent years, sufficient evidence has surfaced to implicate low-molecular-weight organic compounds in certain known neurological disorders. At this time, 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) is considered the compound capable of inducing conditions most similar to idiopathic parkinsonism in clinical, biochemical, and histopathological characteristics. Substances containing MPTP-like fragments are used as herbicides, drugs and intermediates in the synthesis of many heterocyclic compounds. The mechanistic study of toxic MPTP action has enabled development of criteria for appraising potential parkinsonogenic properties of similar chemical structures. Key features of MPTP action include the following: 1. Ability to pass through the blood-brain barrier (BBB). 2. Enzymatic biotransformation to the neuroactive form (pyridine metabolites). 3. Transfer to neurons via a neuromediator reuptake system. 4. Action on intracellular targets. This review discusses data concerning the effects of metabolite structure on the major steps in the neurotropic action mechanism of MPTP-like compounds. Special attention is focused on the key steps defining the selectivity of MPTP's neuronal action, i.e., the activation step caused by monoamine oxidase (MAO) and interaction with the dopamine (DA) reuptake system. Most structural MPTP analogs (including certain pesticide preparations) used in our experiments and described in the literature exhibit no degenerative MPTP-like properties. This is probably related to the fact that each consecutive stage in the MPTP neurotoxicity mechanism makes rather stringent demands on metabolite structure. The number of structures which concurrently meet the requirements of all the processes is finite. This, however, does not invalidate the hypotheses concerning the ecotoxic nature of idiopathic parkinsonism. Possible ecotoxins may have only a partial, presymptomatic effect which, however, promotes age-related neurodegenerative processes and accelerates development of parkinsonism. This concept necessitates designing special tests of the possible neurotoxic properties of compounds found in the environment which may be functional MPTP analogs. PMID:1771272

  15. Cellular Localization of Dieldrin and Structure–Activity Relationship of Dieldrin Analogues in Dopaminergic Cells

    PubMed Central

    Allen, Erin M. G.; Florang, Virginia R.; Davenport, Laurie L.; Jinsmaa, Yunden; Doorn, Jonathan A.

    2015-01-01

    The incidence of Parkinson’s disease (PD) correlates with environmental exposure to pesticides, such as the organochlorine insecticide, dieldrin. Previous studies found an increased concentration of the pesticide in the striatal region of the brains of PD patients and also that dieldrin adversely affects cellular processes associated with PD. These processes include mitochondrial function and reactive oxygen species production. However, the mechanism and specific cellular targets responsible for dieldrin-mediated cellular dysfunction and the structural components of dieldrin contributing to its toxicity (toxicophore) have not been fully defined. In order to identify the toxicophore of dieldrin, a structure–activity approach was used, with the toxicity profiles of numerous analogues of dieldrin (including aldrin, endrin, and cis-aldrin diol) assessed in PC6-3 cells. The MTT and lactate dehydrogenase (LDH) assays were used to monitor cell viability and membrane permeability after treatment with each compound. Cellular assays monitoring ROS production and extracellular dopamine metabolite levels were also used. Structure and stereochemistry for dieldrin were found to be very important for toxicity and other end points measured. Small changes in structure for dieldrin (e.g., comparison to the stereoisomer endrin) yielded significant differences in toxicity. Interestingly, the cis-diol metabolite of dieldrin was found to be significantly more toxic than the parent compound. Disruption of dopamine catabolism yielded elevated levels of the neurotoxin, 3,4-dihydroxyphenylacetaldehyde, for many organochlorines. Comparisons of the toxicity profiles for each dieldrin analogue indicated a structure-specific effect important for elucidating the mechanisms of dieldrin neurotoxicity. PMID:23763672

  16. Hepatoprotection of sesquiterpenoids: a quantitative structure-activity relationship (QSAR) approach.

    PubMed

    Vinholes, Juliana; Rudnitskaya, Alisa; Gonçalves, Pedro; Martel, Fátima; Coimbra, Manuel A; Rocha, Sílvia M

    2014-03-01

    The relative hepatoprotection effect of fifteen sesquiterpenoids, commonly found in plants and plant-derived foods and beverages was assessed. Endogenous lipid peroxidation (assay A) and induced lipid peroxidation (assay B) were evaluated in liver homogenates from Wistar rats by the thiobarbituric acid reactive species test. Sesquiterpenoids with different chemical structures were tested: trans,trans-farnesol, cis-nerolidol, (-)-?-bisabolol, trans-?-farnesene, germacrene D, ?-humulene, ?-caryophyllene, isocaryophyllene, (+)-valencene, guaiazulene, (-)-?-cedrene, (+)-aromadendrene, (-)-?-neoclovene, (-)-?-copaene, and (+)-cyclosativene. Ascorbic acid was used as a positive antioxidant control. With the exception of ?-humulene, all the sesquiterpenoids under study (1mM) were effective in reducing the malonaldehyde levels in both endogenous and induced lipid peroxidation up to 35% and 70%, respectively. The 3D-QSAR models developed, relating the hepatoprotection activity with molecular properties, showed good fit (Radj(2) 0.819 and 0.972 for the assays A and B, respectively) with good prediction power (Q(2)>0.950 and SDEP<2%, for both models A and B). A network of effects associated with structural and chemical features of sesquiterpenoids such as shape, branching, symmetry, and presence of electronegative fragments, can modulate the hepatoprotective activity observed for these compounds. PMID:24176316

  17. Synthesis and structure-activity relationship of N-(cinnamyl) chitosan analogs as antimicrobial agents.

    PubMed

    Badawy, Mohamed E I; Rabea, Entsar I

    2013-06-01

    The current study focuses on the preparation of new N-(cinnamyl) chitosan derivatives as antimicrobial agents against nine types of crop-threatening pathogens. Chitosan was reacted with a set of aromatic cinnamaldehyde analogs by reductive amination involving formation of the corresponding imines, followed by reduction with sodium borohydride to produce N-(cinnamyl) chitosan derivatives. The structural characterization was confirmed by (1)H and (13)C NMR spectroscopy and the degrees of substitution ranged from 0.08 to 0.28. The antibacterial activity was evaluated in vitro by minimum inhibitory concentration (MIC) against Agrobacterium tumefaciens and Erwinia carotovora. A higher inhibition activity was obtained by N-(?-methylcinnamyl) chitosan with MIC 1275 and 1025 mg/L against A. tumefaciens and E. carotovora, respectively followed by N-(o-methoxycinnamyl) chitosan (MIC=1925 and 1550 mg/L, respectively). The antifungal assessment was evaluated in vitro by mycelial radial growth technique against Alternaria alternata, Botrytis cinerea, Botryodiplodia theobromae, Fusarium oxysporum, Fusarium solani, Pythium debaryanum and Phytophthora infestans. N-(o-methoxycinnamyl) chitosan showed the highest antifungal activity among the tested compounds against the airborne fungi A. alternata, B. cinerea, Bd. theobromae and Ph. infestans with EC?? of 672, 796, 980 and 636 mg/L, respectively. However, N-(p-N-dimethylaminocinnamyl) chitosan was the most active against the soil born fungi F. oxysporum, F. solani and P. debaryanum (EC50=411, 566 and 404 mg/L, respectively). On the other hand, the chitosan derivatives caused significant reduction in spore germination of A. alternata, B. cinerea, F. oxysporum and F. solani compared to chitosan and the reduction in spore germination was higher than that of the mycelia inhibition. The synthesis and characterization of new chitosan derivatives are ongoing in our laboratory aiming to obtain derivatives with higher antimicrobial activities and used as safe alternatives to harmful microbicides. PMID:23511055

  18. Structure-activity relationships of siRNA carriers based on sequence-defined oligo (ethane amino) amides.

    PubMed

    Fröhlich, Thomas; Edinger, Daniel; Kläger, Raphaela; Troiber, Christina; Salcher, Edith; Badgujar, Naresh; Martin, Irene; Schaffert, David; Cengizeroglu, Arzu; Hadwiger, Philipp; Vornlocher, Hans-Peter; Wagner, Ernst

    2012-06-28

    Sequence defined oligo (ethane amino) amides produced by solid-phase supported synthesis using different building blocks and molecular shapes were tested for structure-activity relationships in siRNA delivery. Efficient reporter gene knockdown was obtained in a variety of cell lines using either branched three-armed structures, or lipid-modified structures with i-shape, T-shape, U-shape configuration. For the majority of structures (apart from U-shapes), the presence of 2 or 3 cysteines was strictly required for polyplex stabilization and silencing activity. Although all four building blocks contain the ethylenediamine proton sponge motif, only oligomers assembled with the tetraethylenepentamine based amino acids (Stp, Gtp, Ptp) but not with the triethylenetetramine based amino acid (Gtt) were able to mediate efficient gene silencing. For the lipopolymeric structures, out of the tested saturated (from C4 to C18) and unsaturated (C18) fatty acid moieties, two proximate oleic acids or linolic acids provided the oligomers with the best gene silencing activity and also pH specific lytic activity at pH 5.5, presumably facilitating endosomal escape of the polyplexes. Evaluation of oligomer chain length revealed a minimal number of at least two oligo (ethane amino) building blocks per oligomer arm as necessary for the vast majority of structures, but only marginal changes were found with higher numbers (structures with up to 60 ethane amino nitrogens were evaluated). Two promising carriers (T-shape 49, i-shape 229) were also evaluated for EG5 siRNA delivery. This resulted in tumor cell cycle arrest, and appearance of mitotic monoastral spindles both in vitro and in vivo upon systemic delivery. Repeated intratumoral treatment with EG5 siRNA polyplexes significantly reduced Neuro2A-eGFPLuc tumor growth in a siRNA-specific manner. PMID:22465674

  19. Structure-activity relationship of imidazothiadiazole analogs for the binding to the ecdysone receptor of insect cells.

    PubMed

    Yokoi, Taiyo; Minami, Saki; Nakagawa, Yoshiaki; Miyagawa, Hisashi

    2015-05-01

    Diacylhydrazines are the first non-steroidal ecdysone agonists, and five compounds are used as insecticides in agriculture. After the discovery of diacylhydrazine-type compounds, numerous non-steroidal structures were reported as ecdysone agonists. Among various ecdysone agonists, imidazothiadiazoles are reported to be very potent in vitro; however, the experimental detail for the structure identification and bioassays are not stated in the paper (Holmwood and Schindler, Bioorg. Med. Chem. 17, 4064-4070, 2009). In our present study, we synthesized 18 imidazothiadiazole-type compounds and confirmed the chemical structures by spectrometric analyses. The binding activity of the synthesized compounds to the ecdysone receptor was evaluated in terms of the concentration required for 50% inhibition of [(3)H]ponasterone A incorporation [IC50 (M)] into lepidopteran (Sf-9), coleopteran (BCRL-Lepd-SL1), and dipteran (NIAS-AeAl2) cells. 6-(2-Chlorophenyl)-2-(trifluoromethyl)imidazo[2,1-b] [1,3,4]-thiadiazol-5-yl)acrylamide analogs with CONHR (secondary amide) were very potent against Sf-9 cells, but further alkylation (tertiary amide: CONR2) decreased the activity dramatically. Additionally, a primary amide analog (CONH2) was inactive. The activity also decreased 150-fold by the saturation of olefin region of the acrylamide moiety. In addition, various substituents were introduced at the 2-position of the imidazothiadiazole ring to disclose the physicochemical properties of the substituents which are important for receptor binding. The activity increased by 7500-fold with the introduction of the CF2CF2CF3 group compared to the unsubstituted compound against Sf-9 cells. Quantitative structure-activity relationship analysis for these substituents indicated that hydrophobic and electron-withdrawing groups were favorable for binding. Some of the compounds with strong receptor binding activity showed good larvicidal activity against Spodoptera litura. In contrast, the binding affinity of imidazothiadiazole analogs was low or not observed against dipteran and coleopteran cells. PMID:25987219

  20. Structure-immunomodulating activity relationships of a pectic arabinogalactan from Vernonia kotschyana Sch. Bip. ex Walp.

    PubMed

    Nergard, Cecilie Sogn; Kiyohara, Hiroaki; Reynolds, James C; Thomas-Oates, Jane E; Matsumoto, Tsukasa; Yamada, Haruki; Michaelsen, Terje E; Diallo, Drissa; Paulsen, Berit Smestad

    2005-08-15

    Structure and immunological characteristics of the pectic arabinogalactan Vk2a (previously reported as Vk100A2a) from the roots of Vernonia kotschyana Sch. Bip. ex Walp. were investigated after enzymatic digestion of the galacturonan moiety and the side chains of the rhamnogalacturonan structure of Vk2a. endo-alpha-D-(1-->4)-Polygalacturonase digestion released the high molecular weight 'hairy region' (Vk2a-HR) and oligogalacturonides. Vk2a-HR consisted of GalA (4-linked) and Rha (2- or 2,4-linked) in a 1:1 ratio, with 60% of Rha branched at C-4. The Rha located in the rhamnogalacturonan core was branched randomly by Gal units. Vk2a-HR was rich in neutral sugars such as Araf 5- (12.2%) and 3,5-substituted (12.8%) and terminally- (14.1%) linked and Gal 4- (13.0%), 3- (0.9%), 6- (2.2%) and 3,6- (1.1%) substituted. Arabinans with chain lengths up to 11 units were identified. Araf residues were attached to C-3 of alpha-L-(1-->5)-Araf chains and to C-4 of Gal residues. Single Gal units and chains of beta-D-(1-->6)-linked galacto di- to penta-saccharides were attached to a beta-D-(1-->3)-galactan core. All the enzyme resistant fractions expressed potent complement fixation and induction of B-cell mitogenic activity, and the present study indicates that there may be several and possibly structurally different active sites involved in the bioactivity of Vk2a. The bioactive sites may be located both in the more peripheral parts of the molecule but also in the inner core of the 'hairy region' or in larger enzyme-resistant chains. PMID:15979597

  1. Minimal-length short hairpin RNAs: The relationship of structure and RNAi activity

    PubMed Central

    Ge, Qing; Ilves, Heini; Dallas, Anne; Kumar, Pavan; Shorenstein, Joshua; Kazakov, Sergei A.; Johnston, Brian H.

    2010-01-01

    Small hairpin RNAs (shRNAs) are widely used in RNAi studies and typically consist of a stem of 19–29 base pairs (bp), a loop of at least 4 nucleotides (nt), and a dinucleotide overhang at the 3? end. Compared with shRNAs with 21–29 bp stems, we have found that shRNAs with 19-bp or shorter stems (sshRNAs) possess some unique structure–activity features that depend on whether the antisense strand is positioned 5? or 3? to the loop (L- or R-type sshRNAs, respectively). L sshRNAs can have IC50s in the very low picomolar range, and sshRNAs with nominal loop sizes of 1 or 4 nt were at least as active as those with longer loops. L sshRNAs remained highly potent even when the 3? end of the antisense strand was directly linked with the 5? end of the sense strand. In this case, the sense strand can be shorter than the antisense strand, and the loop can be formed entirely by the 3? end of the antisense strand. Monomer sshRNAs are not processed by recombinant Dicers in vitro. Although they can form dimers that are sometimes Dicer substrates, their RNAi activity is not dependent on the formation of such structures. Our findings have implications for the mechanism of action of sshRNAs, and the ability to design highly potent shRNAs with minimal length is encouraging for the prospects of the therapeutic use of direct-delivered shRNAs. PMID:19952116

  2. Structural investigations of T854A mutation in EGFR and identification of novel inhibitors using structure activity relationships

    PubMed Central

    2015-01-01

    Background The epidermal growth factor receptor (EGFR) is a member of the ErbB family that is involved in a number of processes responsible for cancer development and progression such as angiogenesis, apoptosis, cell proliferation and metastatic spread. Malfunction in activation of protein tyrosine kinases has been shown to result in uncontrolled cell growth. The EGFR TK domain has been identified as suitable target in cancer therapy and tyrosine kinase inhibitors such as erlotinib have been used for treatment of cancer. Mutations in the region of the EGFR gene encoding the tyrosine kinase (TK) domain causes altered responses to EGFR TK inhibitors (TKI). In this paper we perform molecular dynamics simulations and PCA analysis on wild-type and mutant (T854A) structures to gain insight into the structural changes observed in the target protein upon mutation. We also report two novel inhibitors identified by combined approach of QSAR model development. Results The wild-type and mutant structure was observed to be stable for 26 ns and 24 ns respectively. In PCA analysis, the mutant structure proved to be more flexible than wild-type. We developed a 3D-QSAR model using 38 thiazolyl-pyrazoline compounds which was later used for prediction of inhibitory activity of natural compounds of ZINC library. The 3D-QSAR model was proved to be robust by the statistical parameters such as r2 (0.9751), q2(0.9491) and pred_r2(0.9525). Conclusion Analysis of molecular dynamics simulations results indicate stability loss and increased flexibility in the mutant structure. This flexibility results in structural changes which render the mutant protein drug resistant against erlotinib. We report two novel compounds having high predicted inhibitory activity to EGFR TK domain with both wild-type and mutant structure. PMID:26041145

  3. Virulence Factor-activity Relationships: Workshop Summary

    EPA Science Inventory

    The concept or notion of virulence factor?activity relationships (VFAR) is an approach for identifying an analogous process to the use of qualitative structure?activity relationships (QSAR) for identifying new microbial contaminants. In QSAR, it is hypothesized that, for new chem...

  4. Antipodal crambescin A2 homologues from the marine sponge Pseudaxinella reticulata. Antifungal structure-activity relationships.

    PubMed

    Jamison, Matthew T; Molinski, Tadeusz F

    2015-03-27

    Investigation of antifungal natural products from the marine sponge Pseudaxinella reticulata from the Bahamas led to the discovery of new crambescin homologues (1, 2) and enantiomers (3, 4) of known natural products. The cyclic-guanidine structures were solved through analysis of 2D NMR, MS-MS, and CD data. The absolute configurations of 1-4 were established as 13R-opposite of known homologues reported from Crambe crambe obtained from the Mediterranean Sea-by comparison of their CD spectra with predicted Cotton effects obtained from DFT calculations. Antifungal activities of 1-4 against the pathogenic strains Candida albicans and Cryptococcus sp. were observed to correlate potency (MIC50 and MIC90) with the length of the alkyl side chain. PMID:25738226

  5. Side effects of anabolic androgenic steroids: pathological findings and structure-activity relationships.

    PubMed

    Büttner, Andreas; Thieme, Detlef

    2010-01-01

    Side effects of anabolic steroids with relevance in forensic medicine are mainly due to life-threatening health risks with potential fatal outcome and cases of uncertain limitations of criminal liability after steroid administration. Both problems are typically associated with long-term abuse and excessive overdose of anabolic steroids. Side effects may be due to direct genomic or nongenomic activities (myotrophic, hepatotoxic), can result from down-regulation of endogenous biosynthesis (antiandrogenic) or be indirect consequence of steroid biotransformation (estrogenic).Logically, there are no systematic clinical studies available and the number of causally determined fatalities is fairly limited. The following compilation reviews typical abundant observations in cases where nonnatural deaths (mostly liver failure and sudden cardiac death) were concurrent with steroid abuse. Moreover, frequent associations between structural characteristics and typical side effects are summarized. PMID:20020376

  6. Acaricidal constituents isolated from Sinapis alba L. seeds and structure-activity relationships.

    PubMed

    Lim, Jeong-Hyeon; Kim, Hyung-Wook; Jeon, Ju-Hyun; Lee, Hoi-Seon

    2008-11-12

    Allyl isothiocyanate (AITC) and phenethyl isothiocyanate (PEITC) were isolated from Sinapis alba L. seeds and their effects against Dermatophagoides farinae and D. pteronyssinus were evaluated using the impregnated fabric disk method. The LD 50 values of their compounds and derivatives were then compared with those of a commercial acaricide, benzyl benzoate. On the basis of the LD 50 values against D. farinae, PEITC (0.21 microg/cm(2)) was the most toxic, followed by benzyl isothiocyanate (0.55 microg/cm(2)), phenyl isothiocyanate (1.09 microg/cm(2)), butyl isothiocyanate (1.24 microg/cm(2)), and AITC (1.36 microg/cm(2)); acetyl isothiocyanate (195.01 microg/cm(2)) was the least toxic. In addition, the acaricidal effects of AITC and PEITC against D. farinae were 7.4- and 47.8-fold greater than those of benzyl benzoate, respectively. Against D. pteronyssinus, PEITC was the most toxic (0.19 microg/cm(2)), followed by benzyl isothiocyanate (0.77 microg/cm(2)), phenyl isothiocyanate (1.37 microg/cm(2)), butyl isothiocyanate (1.50 microg/cm(2)), and AITC (2.88 microg/cm(2)); acetyl isothiocyanate (168.82 microg/cm(2)) was the least toxic. AITC and PEITC were 3.3- and 50.4-fold more active than benzyl benzoate against D. pteronyssinus, respectively. Taken together, these findings indicate that AITC, PEITC, and partial derivatives may be useful as preventive agents against dust mites. In addition, these results indicate that structure-activity is related to the aromatic structure, the number of carbon atoms, and the compounds hydrophobicity. PMID:18844359

  7. Toward establishing structure-activity relationships for oxygenated coumarins as differentiation inducers of promonocytic leukemic cells.

    PubMed

    Riveiro, María E; Maes, Dominick; Vázquez, Ramiro; Vermeulen, Monica; Mangelinckx, Sven; Jacobs, Jan; Debenedetti, Silvia; Shayo, Carina; De Kimpe, Norbert; Davio, Carlos

    2009-09-15

    The presumption that some coumarins might be lead compounds in the search for new differentiation agents against leukemia is based on the fact that natural coumarins, 5-(3-methyl-2-butenyloxy)-6,7-methylenedioxycoumarin (C-2) and 5-methoxy-6,7-methylenedioxycoumarin (C-1) inhibit proliferation and induce differentiation in U-937 cells [Riveiro, M. E.; Shayo, C.; Monczor, F.; Fernandez, N.; Baldi, A.; De Kimpe, N.; Rossi, J.; Debenedetti, S.; Davio, C. Cancer Lett.2004, 210, 179-188]. These promising findings prompted us to investigate the anti-leukemia activity of a broader range of related polyoxygenated coumarins. Twenty related natural or synthetically prepared coumarins, including a range of 5-substituted ayapin derivatives which have become easy accessible via newly developed synthesis methods, were evaluated, where treatments with 5-(2,3-dihydroxy-3-methylbutoxy)-6,7-methylenedioxycoumarin (D-3) and 5-(2-hydroxy-3-methoxy-3-methylbutoxy)-6,7-methylenedioxycoumarin (D-2) were able to inhibit the cell growth and induce the differentiation of U-937 cells after 48 h treatment. These results provide insight into the correlation between some structural properties of polyoxygenated coumarins and their in vitro leukemic differentiation activity. PMID:19716307

  8. Uniform 2 nm gold nanoparticles supported on iron oxides as active catalysts for CO oxidation reaction: structure-activity relationship

    NASA Astrophysics Data System (ADS)

    Guo, Yu; Gu, Dong; Jin, Zhao; Du, Pei-Pei; Si, Rui; Tao, Jing; Xu, Wen-Qian; Huang, Yu-Ying; Senanayake, Sanjaya; Song, Qi-Sheng; Jia, Chun-Jiang; Schüth, Ferdi

    2015-03-01

    Uniform Au nanoparticles (~2 nm) with narrow size-distribution (standard deviation: 0.5-0.6 nm) supported on both hydroxylated (Fe_OH) and dehydrated iron oxide (Fe_O) have been prepared by either deposition-precipitation (DP) or colloidal-deposition (CD) methods. Different structural and textural characterizations were applied to the dried, calcined and used gold-iron oxide samples. Transmission electron microscopy (TEM) and high-resolution TEM (HRTEM) showed high homogeneity in the supported Au nanoparticles. The ex situ and in situ X-ray absorption fine structure (XAFS) characterization monitored the electronic and short-range local structure of active gold species. The synchrotron-based in situ X-ray diffraction (XRD), together with the corresponding temperature-programmed reduction by hydrogen (H2-TPR), indicated a structural evolution of the iron-oxide supports, correlating to their reducibility. An inverse order of catalytic activity between DP (Au/Fe_OH < Au/Fe_O) and CD (Au/Fe_OH > Au/Fe_O) was observed. Effective gold-support interaction results in a high activity for gold nanoparticles, locally generated by the sintering of dispersed Au atoms on the oxide support in the DP synthesis, while a hydroxylated surface favors the reactivity of externally introduced Au nanoparticles on Fe_OH support for the CD approach. This work reveals why differences in the synthetic protocol translate to differences in the catalytic performance of Au/FeOx catalysts with very similar structural characteristics in CO oxidation.

  9. Analysis of structure-activity relationships in renin substrate analogue inhibitory peptides.

    PubMed

    Hui, K Y; Carlson, W D; Bernatowicz, M S; Haber, E

    1987-08-01

    On the basis of the minimal octapeptide sequence of the renin substrate, a series of peptides was synthesized containing (3S,4S)-4-amino-3-hydroxy-6-methylheptanoic acid (statine) or (3S,4S)-4-amino-3-hydroxy-5-phenylpentanoic acid (AHPPA) at the P1P1' position. Some of these peptides also contained Nin-formyltryptophan at the P5, P3, or P3' position. Renin-inhibitory potency varied over a wide range (from inactive to IC50 = 3 nM). Potency was reduced by at least 10-fold when the peptide was shortened by two residues at either the amino or carboxy terminus. The AHPPA-containing inhibitors were several-fold less potent than the statine-containing inhibitors. Analysis of models for the three-dimensional structure of inhibitors at the active site of human renin suggests that the diminished potency of the AHPPA peptides in comparison with the statine-containing peptides was caused by a shift in the peptide backbone due to a steric conflict between the phenyl ring of the AHPPA residue and the S1 subsite. The importance of the side chain and the 3(S)-hydroxyl group of the statine residue was demonstrated by substituting 5-aminovaleric acid for a dipeptide unit at the P1P1' position, which resulted in a peptide devoid of renin-inhibitory activity. Substitutions of other basic amino acids for histidine at the P2 position caused a great loss in potency, possibly due to disruption of a hydrogen bond as suggested by molecular modeling. Studies on the plasma renins of four nonhuman species suggest that the isoleucine-histidine segment at the P2'P3' position is important to defining the human specificity of the substrate. This work suggests a number of properties important to the design of potent renin inhibitors, and demonstrates the usefulness of three-dimensional models in the interpretation of structure-activity data. PMID:3302256

  10. Inhibitory effect of tanshinones on rat CYP3A2 and CYP2C11 activity and its structure-activity relationship.

    PubMed

    Wang, Xin; Yeung, John H K

    2011-06-01

    This study investigated the effect of tanshinones on rat liver microsomal CYP3A2 and 2C11 activity and explored the structure-activity relationship of tanshinones with CYP3A activity. Cryptotanshinone, tanshinone I and tanshinone IIA were competitive CYP3A2 inhibitors (K(i) = 199-243 ?M) and CYP2C11 inhibitors (K(i) = 91-118 ?M). Dihydrotanshinone was not only a noncompetitive inhibitor of CYP3A2 (K(i) = 110 ?M), but also a competitive CYP2C11 inhibitor (K(i) = 55 ?M). The structural difference between dihydrotanshinone and tanshinone I at C-15 position of furan ring resulted in the different modes of inhibition on CYP3A activity. PMID:21262326

  11. Cytotoxic and antioxidant effects of methoxylated stilbene analogues on HepG2 hepatoma and Chang liver cells: Implications for structure activity relationship.

    PubMed

    Hasiah, A H; Ghazali, A R; Weber, J F F; Velu, S; Thomas, N F; Inayat Hussain, S H

    2011-02-01

    Stilbenes possess a variety of biological activities including chemopreventive activity. This study was conducted to evaluate the structural activity relationships of six methoxylated stilbene analogues with respect to their cytotoxic effects and antioxidant activities on HepG2 hepatoma and Chang liver cells. The cytotoxic and total antioxidant activities of six stilbene analogues were determined by MTT and Ferric Reducing Antioxidant Power (FRAP) assays, respectively. We found that the cis-methoxylated stilbene: (Z)-3,4,4'-trimethoxystilbene was the most potent and selective antiproliferative agent (IC?? 89 µM) in HepG2 cells. For the total antioxidant activity, compounds possessing hydroxyl groups at the 4' position namely (E)-3-methoxy-4'-hydroxystilbene, (E)-3,5-dimethoxy-4'-hydroxystilbene (pterostilbene), (E)-4-methoxy-4'-hydroxystilbene showed the highest antioxidant activity. Structure activity relationship studies of these compounds demonstrated that the cytotoxic effect and antioxidant activities of the tested compounds in this study were structurally dependent. PMID:20385705

  12. Mammalian olfactory receptors: molecular mechanisms of odorant detection, 3D-modeling, and structure-activity relationships.

    PubMed

    Persuy, Marie-Annick; Sanz, Guenhaël; Tromelin, Anne; Thomas-Danguin, Thierry; Gibrat, Jean-François; Pajot-Augy, Edith

    2015-01-01

    This chapter describes the main characteristics of olfactory receptor (OR) genes of vertebrates, including generation of this large multigenic family and pseudogenization. OR genes are compared in relation to evolution and among species. OR gene structure and selection of a given gene for expression in an olfactory sensory neuron (OSN) are tackled. The specificities of OR proteins, their expression, and their function are presented. The expression of OR proteins in locations other than the nasal cavity is regulated by different mechanisms, and ORs display various additional functions. A conventional olfactory signal transduction cascade is observed in OSNs, but individual ORs can also mediate different signaling pathways, through the involvement of other molecular partners and depending on the odorant ligand encountered. ORs are engaged in constitutive dimers. Ligand binding induces conformational changes in the ORs that regulate their level of activity depending on odorant dose. When present, odorant binding proteins induce an allosteric modulation of OR activity. Since no 3D structure of an OR has been yet resolved, modeling has to be performed using the closest G-protein-coupled receptor 3D structures available, to facilitate virtual ligand screening using the models. The study of odorant binding modes and affinities may infer best-bet OR ligands, to be subsequently checked experimentally. The relationship between spatial and steric features of odorants and their activity in terms of perceived odor quality are also fields of research that development of computing tools may enhance. PMID:25623335

  13. Thermodynamics of engineered gold binding peptides: establishing the structure-activity relationships.

    PubMed

    Seker, Urartu Ozgur Safak; Wilson, Brandon; Kulp, John L; Evans, John S; Tamerler, Candan; Sarikaya, Mehmet

    2014-07-14

    Adsorption behavior of a gold binding peptide was experimentally studied to achieve kinetics and thermodynamics parameters toward understanding of the binding of an engineered peptide onto a solid metal surface. The gold-binding peptide, GBP1, was originally selected using a cell surface display library and contains 14 amino acid residues. In this work, single- and three-repeats of GBP1 were used to assess the effects of two parameters: molecular architecture versus secondary structure on adsorption on to gold substrate. The adsorption measurements were carried out using surface plasmon resonance (SPR) spectroscopy at temperatures ranging from 10 to 55 °C. At all temperatures, two different regimes of peptide adsorption were observed, which, based on the model, correspond to two sets of thermodynamics values. The values of enthalpy, ?H(ads), and entropy, ?S(ads), in these two regimes were determined using the van't Hoff approach and Gibbs-Helmholtz relationship. In general, the values of enthalpy for both peptides are negative indicating GBP1 binding to gold is an exothermic phenomenon and that the binding of three repeat gold binding peptide (3l-GBP1) is almost 5 times tighter than that for the single repeat (l-GBP1). More intriguing result is that the entropy of adsorption for the 3l-GBP1 is negative (-43.4 ± 8.5 cal/(mol K)), while that for the l-GBP1 is positive (10.90 ± 1.3 cal/(mol K)). Among a number of factors that synergistically contribute to the decrease of entropy, long-range ordered self-assembly of the 3l-GBP1 on gold surface is the most effective, probably through both peptide-solid and peptide-peptide intermolecular interactions. Additional adsorption experiments were conducted in the presence of 2,2,2-trifluoroethanol (TFE) to determine how the conformational structures of the biomolecules responded to the environmental perturbation. We found that the peptides differ in their conformational responses to the change in solution conditions; while l-GBP does not fold in the presence of TFE, 3l-GBP1 adopted two types of secondary structure (?-strand, ?-helix) and that peptide's binding to the solid is enhanced by the presence of low percentages of TFE solvent. Not only do these kinetics and thermodynamics results provide adsorption behavior and binding of genetically engineered peptides for inorganics (GEPI), but they could also provide considerable insights into fundamental understanding peptide molecular recognition and their selective specificity for the solids. Moreover, comprehensive work described herein suggests that multiple repeat forms of the solid binding peptides possess a conformational component that can be exploited to further tailor affinity and binding of a given sequence to a solid material followed by ordered assembly as a convenient tool in future practical applications. PMID:24892212

  14. Synthesis and Structure-Activity Relationship Study of 1-Phenyl-1-(quinazolin-4-yl)ethanols as Anticancer Agents.

    PubMed

    Kuroiwa, Kenta; Ishii, Hirosuke; Matsuno, Kenji; Asai, Akira; Suzuki, Yumiko

    2015-03-12

    A quinazoline derivative PVHD121 (1a) was shown to have strong antiproliferative activity against various tumor-derived cell lines, including A549 (lung), NCI-H460 (lung), HCT116 (colon), MCF7 (breast), PC3 (prostate), and HeLa (cervical) cells with IC50 values from 0.1 to 0.3 ?M. A structure-activity relationship (SAR) study at the 2- and 4-position of the quinazoline core lead to the discovery of more potent anticancer agents (14, 16, 17, 19, 24, and 31). The results of an in vitro tubulin polymerization assay and fluorescent-based colchicine site competition assay with purified tubulin indicated that 1a inhibits tubulin polymerization by binding to the colchicine site. PMID:25815147

  15. 1,5-Benzodiazepine derivatives as potential antimicrobial agents: design, synthesis, biological evaluation, and structure-activity relationships.

    PubMed

    Wang, Lan-Zhi; Li, Xiao-Qing; An, Ying-Shuang

    2015-05-01

    36 Novel 1,5-benzodiazepine derivatives were rationally designed and synthesized according to the principle of superposition of bioactive substructures by the combination of 1,5-benzodiazepines, thiophene or thiazole and ester group. The structures of the target compounds have been characterized by IR, (1)H NMR, (13)C NMR, MS and elemental analysis. The structure of was further determined using X-ray single crystal diffraction. All synthesized 1,5-benzodiazepine derivatives were evaluated for their in vitro antimicrobial activity against C. neoformans, C. neoformans clinical isolates, C. albicans, E. coli and S. aureus. The bioactive assay results revealed that most of the 1,5-benzodiazepine derivatives exhibited considerable potency against all of the tested strains. In particular, compounds and (MIC: 2-6 ?g mL(-1), MFC: 10-14 ?g mL(-1)) exhibited excellent antifungal activity and were found to be 32-64 and 9-12.8 times more potent than the reference drugs against C. neoformans, respectively. Moreover, compound (MIC: 40 ?g mL(-1)) displayed equipotent antibacterial activity against E. coli and S. aureus compared to the reference drugs. The most potent of the synthesized compounds and were further studied by evaluating their cytotoxicities, and the results showed that they had relatively low level cytotoxicity for BV2 cell. A preliminary study of the structure-activity relationship revealed that substituents in the phenyl ring and the thiophene ring had a great effect on the antimicrobial activity of these compounds. In addition, the thiazole ring at C2 may be a pharmacophore of these compounds and COOC2H5 group at C3 is the best substituent for the maintenance of antimicrobial activities at low concentrations (1.5625 ?g per disc). PMID:25875695

  16. Insights into the structure-activity relationships of chiral 1,2-diaminophenylalkane platinum(II) anticancer derivatives.

    PubMed

    Berger, Gilles; Fusaro, Luca; Luhmer, Michel; Czapla-Masztafiak, Joanna; Lipiec, Ewelina; Szlachetko, Jakub; Kayser, Yves; Fernandes, Daniel L A; Sá, Jacinto; Dufrasne, François; Bombard, Sophie

    2015-07-01

    The structure-activity relationships of chiral 1,2-diaminophenylalkane platinum(II) anticancer derivatives are studied, including interactions with telomeric- and genomic-like DNA sequences, the pKa of their diaqua species, structural properties obtained from DFT calculations and resonant X-ray emission spectroscopy. The binding modes of the compounds to telomeric sequences were elucidated, showing no major differences with conventional cis-platinum(II) complexes like cisplatin, supporting that the cis-square planar geometry governs the binding of small Pt(II) complexes to G4 structures. Double-stranded DNA platination kinetics and acid-base constants of the diaqua species of the compounds were measured and compared, highlighting a strong steric dependence of the DNA-binding kinetics, but independent to stereoisomerism. Structural features of the compounds are discussed on the basis of dispersion-corrected DFT, showing that the most active series presents conformers for which the platinum atom is well devoid of steric hindrance. If reactivity indices derived from conceptual DFT do not show evidences for different reactivity between the compounds, RXES experiments provide new insight into the availability of platinum orbitals for binding to nucleophiles. PMID:25982100

  17. Synthesis and structure-activity relationships of novel cationic lipids with anti-inflammatory and antimicrobial activities.

    PubMed

    Myint, Melissa; Bucki, Robert; Janmey, Paul A; Diamond, Scott L

    2015-07-15

    Certain membrane-active cationic steroids are known to also possess both anti-inflammatory and antimicrobial properties. This combined functionality is particularly relevant for potential therapies of infections associated with elevated tissue damage, for example, cystic fibrosis airway disease, a condition characterized by chronic bacterial infections and ongoing inflammation. In this study, six novel cationic glucocorticoids were synthesized using beclomethasone, budesonide, and flumethasone. Products were either monosubstituted or disubstituted, containing one or two steroidal groups, respectively. In vitro evaluation of biological activities demonstrated dual anti-inflammatory and antimicrobial properties with limited cytotoxicity for all synthesized compounds. Budesonide-derived compounds showed the highest degree of both glucocorticoid and antimicrobial properties within their respective mono- and disubstituted categories. Structure-activity analyses revealed that activity was generally related to the potency of the parent glucocorticoid. Taken together, these data indicate that these types of dual acting cationic lipids can be synthesized with the appropriate starting steroid to tailor activities as desired. PMID:26004577

  18. Amide-Modified Prenylcysteine based Icmt Inhibitors: Structure Activity Relationships, Kinetic Analysis and Cellular Characterization

    PubMed Central

    Majmudar, Jaimeen D.; Hodges-Loaiza, Heather B.; Hahne, Kalub; Donelson, James L.; Song, Jiao; Shrestha, Liza; Harrison, Marietta L.; Hrycyna, Christine A.; Gibbs, Richard A.

    2012-01-01

    Human protein isoprenylcysteine carboxyl methyltransferase (hIcmt) is the enzyme responsible for the ?-carboxyl methylation of the C-termimal isoprenylated cysteine of CaaX proteins, including Ras proteins. This specific posttranslational methylation event has been shown to be important for cellular transformation by oncogenic Ras isoforms. This finding led to interest in hIcmt inhibitors as potential anti-cancer agents. Previous analog studies based on N-acetyl-S-farnesylcysteine identified two prenylcysteine-based low micromolar inhibitors (1a and 1b) of hIcmt, each bearing a phenoxyphenyl amide modification. In this study, a focused library of analogs of 1a and 1b was synthesized and screened versus hIcmt, delineating structural features important for inhibition. Kinetic characterization of the most potent analogs 1a and 1b established that both inhibitors exhibited mixed-mode inhibition and that the competitive component predominated. Using the Cheng – Prusoff method, the Ki values were determined from the IC50 values. Analog 1a has a KIC of 1.4 ± 0.2 ?M and a KIU of 4.8 ± 0.5 ?M while 1b has a KIC of 0.5 ± 0.07 ?M and a KIU of 1.9 ± 0.2 ?M. Cellular evaluation of 1b revealed that it alters the subcellular localization of GFP-KRas, and also inhibits both Ras activation and Erk phosphorylation in Jurkat cells. PMID:22142613

  19. Structure-activity relationships of the thujaplicins for inhibition of human tyrosinase.

    PubMed

    Yoshimori, Atsushi; Oyama, Takahiro; Takahashi, Satoshi; Abe, Hideaki; Kamiya, Takanori; Abe, Takehiko; Tanuma, Sei-ichi

    2014-11-01

    Tyrosinase inhibitors have become increasingly critical agents in cosmetic, agricultural, and medicinal products. Although a large number of tyrosinase inhibitors have been reported, almost all the inhibitors were unfortunately evaluated by using commercial available mushroom tyrosinase. Here, we examined the inhibitory effects of three isomers of thujaplicin (?, ?, and ?) on human tyrosinase and analyzed their binding modes using homology model and docking studies. As the results, ?-thujaplicin was found to strongly inhibit human tyrosinase with the IC50 of 1.15 ?M, extremely superior to a well-known tyrosinase inhibitor kojic acid (IC50 = 571.17 ?M). MM-GB/SA binding free energy decomposition analyses suggested that the potent inhibitory activity of ?-thujaplicin may be due to the interactions with His367, Ile368, and Val377 (hot spot amino acid residues) in human tyrosinase. Furthermore, the binding mode of ?-thujaplicin indicated that Val377 and Ser380 may cause van der Waals clashes with the isopropyl group of ?-thujaplicin. These results provide a novel structural insight into the hot spot of human tyrosinase for the specific binding of ?-thujaplicin and a way to optimize not only thujaplicins but also other lead compounds as specific inhibitors for human tyrosinase in a rational manner. PMID:25288494

  20. Designing Anti-Influenza Aptamers: Novel Quantitative Structure Activity Relationship Approach Gives Insights into Aptamer – Virus Interaction

    PubMed Central

    Musafia, Boaz; Oren-Banaroya, Rony; Noiman, Silvia

    2014-01-01

    This study describes the development of aptamers as a therapy against influenza virus infection. Aptamers are oligonucleotides (like ssDNA or RNA) that are capable of binding to a variety of molecular targets with high affinity and specificity. We have studied the ssDNA aptamer BV02, which was designed to inhibit influenza infection by targeting the hemagglutinin viral protein, a protein that facilitates the first stage of the virus’ infection. While testing other aptamers and during lead optimization, we realized that the dominant characteristics that determine the aptamer’s binding to the influenza virus may not necessarily be sequence-specific, as with other known aptamers, but rather depend on general 2D structural motifs. We adopted QSAR (quantitative structure activity relationship) tool and developed computational algorithm that correlate six calculated structural and physicochemical properties to the aptamers’ binding affinity to the virus. The QSAR study provided us with a predictive tool of the binding potential of an aptamer to the influenza virus. The correlation between the calculated and actual binding was R2?=?0.702 for the training set, and R2?=?0.66 for the independent test set. Moreover, in the test set the model’s sensitivity was 89%, and the specificity was 87%, in selecting aptamers with enhanced viral binding. The most important properties that positively correlated with the aptamer’s binding were the aptamer length, 2D-loops and repeating sequences of C nucleotides. Based on the structure-activity study, we have managed to produce aptamers having viral affinity that was more than 20 times higher than that of the original BV02 aptamer. Further testing of influenza infection in cell culture and animal models yielded aptamers with 10 to 15 times greater anti-viral activity than the BV02 aptamer. Our insights concerning the mechanism of action and the structural and physicochemical properties that govern the interaction with the influenza virus are discussed. PMID:24846127

  1. Synthesis and structure–activity relationships of quaternary ammonium cephalosporins with 3-pyrazolylpyridinium derivatives

    Microsoft Academic Search

    Kwan Young Chang; Sung Hoon Kim; Ghilsoo Nam; Jae Hong Seo; Joong Hyup Kim; Deok-Chan Ha

    2000-01-01

    Cephalosporins with 3-pyazolylpyridinium at C-3 position, which is supposed to exhibit synergic activity of ceftazidime and cefoselis, were synthesized and their antibacterial activity against Gram-positive and Gram-negative was inspected.

  2. Structure?Activity Relationships of Antimicrobial Gallic Acid Derivatives from Pomegranate and Acacia Fruit Extracts against Potato Bacterial Wilt Pathogen.

    PubMed

    Farag, Mohamed A; Al-Mahdy, Dalia A; Salah El Dine, Riham; Fahmy, Sherifa; Yassin, Aymen; Porzel, Andrea; Brandt, Wolfgang

    2015-06-01

    Bacterial wilts of potato, tomato, pepper, and or eggplant caused by Ralstonia solanacearum are among the most serious plant diseases worldwide. In this study, the issue of developing bactericidal agents from natural sources against R. solanacearum derived from plant extracts was addressed. Extracts prepared from 25 plant species with antiseptic relevance in Egyptian folk medicine were screened for their antimicrobial properties against the potato pathogen R. solancearum by using the disc-zone inhibition assay and microtitre plate dilution method. Plants exhibiting notable antimicrobial activities against the tested pathogen include extracts from Acacia arabica and Punica granatum. Bioactivity-guided fractionation of A. arabica and P. granatum resulted in the isolation of bioactive compounds 3,5-dihydroxy-4-methoxybenzoic acid and gallic acid, in addition to epicatechin. All isolates displayed significant antimicrobial activities against R. solanacearum (MIC values 0.5-9?mg/ml), with 3,5-dihydroxy-4-methoxybenzoic acid being the most effective one with a MIC value of 0.47?mg/ml. We further performed a structure-activity relationship (SAR) study for the inhibition of R. solanacearum growth by ten natural, structurally related benzoic acids. PMID:26080741

  3. Structure–Activity Relationships among Antifungal Nylon-3 Polymers: Identification of Materials Active against Drug-Resistant Strains of Candida albicans

    PubMed Central

    2015-01-01

    Fungal infections are a major challenge to human health that is heightened by pathogen resistance to current therapeutic agents. Previously, we were inspired by host-defense peptides to develop nylon-3 polymers (poly-?-peptides) that are toxic toward the fungal pathogen Candida albicans but exert little effect on mammalian cells. Based on subsequent analysis of structure–activity relationships among antifungal nylon-3 polymers, we have now identified readily prepared cationic homopolymers active against strains of C. albicans that are resistant to the antifungal drugs fluconazole and amphotericin B. These nylon-3 polymers are nonhemolytic. In addition, we have identified cationic–hydrophobic copolymers that are highly active against a second fungal pathogen, Cryptococcus neoformans, and moderately active against a third pathogen, Aspergillus fumigatus. PMID:24606327

  4. Structure activity relationship of phenolic diterpenes from Salvia officinalis as activators of the nuclear factor E2-related factor 2 pathway.

    PubMed

    Fischedick, Justin T; Standiford, Miranda; Johnson, Delinda A; Johnson, Jeffrey A

    2013-05-01

    Nuclear factor E2-related factor 2 (Nrf2) is a transcription factor known to activate cytoprotective genes which may be useful in the treatment of neurodegenerative disease. In order to better understand the structure activity relationship of phenolic diterpenes from Salvia officinalis L., we isolated carnosic acid, carnosol, epirosmanol, rosmanol, 12-methoxy-carnosic acid, sageone, and carnosaldehyde using polyamide column, centrifugal partition chromatography, and semi-preparative high performance liquid chromatography. Isolated compounds were screened in vitro for their ability to active the Nrf2 and general cellular toxicity using mouse primary cortical cultures. All compounds except 12-methoxy-carnosic acid were able to activate the antioxidant response element. Furthermore both carnosol and carnoasldehyde were able to induce Nrf2-dependent gene expression as well as protect mouse primary cortical neuronal cultures from H(2)O(2) induced cell death. PMID:23507152

  5. Synthesis, Antifungal Activity and Structure-Activity Relationships of Novel 3-(Difluoromethyl)-1-methyl-1H-pyrazole-4-carboxylic Acid Amides.

    PubMed

    Du, Shijie; Tian, Zaimin; Yang, Dongyan; Li, Xiuyun; Li, Hong; Jia, Changqing; Che, Chuanliang; Wang, Mian; Qin, Zhaohai

    2015-01-01

    A series of novel 3-(difluoromethyl)-1-methyl-1H-pyrazole-4-carboxylic acid amides were synthesized and their activities were tested against seven phytopathogenic fungi by an in vitro mycelia growth inhibition assay. Most of them displayed moderate to excellent activities. Among them N-(2-(5-bromo-1H-indazol-1-yl)phenyl)-3-(difluoro-methyl)-1-methyl-1H-pyrazole-4-carboxamide (9m) exhibited higher antifungal activity against the seven phytopathogenic fungi than boscalid. Topomer CoMFA was employed to develop a three-dimensional quantitative structure-activity relationship model for the compounds. In molecular docking, the carbonyl oxygen atom of 9m could form hydrogen bonds towards the hydroxyl of TYR58 and TRP173 on SDH. PMID:26007171

  6. Structure activity relationship of phenolic diterpenes from Salvia officinalis as activators of the nuclear factor E2-related factor 2 pathway

    PubMed Central

    Fischedick, Justin T; Standiford, Miranda; Johnson, Delinda A.; Johnson, Jeffrey A.

    2013-01-01

    Nuclear factor E2-related factor 2 (Nrf2) is a transcription factor known to activate cytoprotective genes which may be useful in the treatment of neurodegenerative disease. In order to better understand the structure activity relationship of phenolic diterpenes from Salvia officinalis L., we isolated carnosic acid, carnosol, epirosmanol, rosmanol, 12-methoxy-carnosic acid, sageone, and carnosaldehyde using polyamide column, centrifugal partition chromatography, and semi-preparative high performance liquid chromatography. Isolated compounds were screened in-vitro for their ability to active the Nrf2 and general cellular toxicity using mouse primary cortical cultures. All compounds except 12-methoxy-carnosic acid were able to activate the antioxidant response element. Furthermore both carnosol and carnoasldehyde were able to induce Nrf2-dependent gene expression as well as protect mouse primary cortical neuronal cultures from H2O2 induced cell death. PMID:23507152

  7. Dietary flavonoids modulate CYP2C to improve drug oral bioavailability and their qualitative/quantitative structure-activity relationship.

    PubMed

    Wang, Hong-Jaan; Pao, Li-Heng; Hsiong, Cheng-Huei; Shih, Tung-Yuan; Lee, Meei-Shyuan; Hu, Oliver Yoa-Pu

    2014-03-01

    This study aims to improve the drug oral bioavailability by co-administration with flavonoid inhibitors of the CYP2C isozyme and to establish qualitative and quantitative (QSAR) structure-activity relationships (SAR) between flavonoids and CYP2C. A total of 40 naturally occurring flavonoids were screened in vitro for CYP2C inhibition. Enzyme activity was determined by measuring conversion of tolbutamide to 4-hydroxytolbutamide by rat liver microsomes. The percent inhibition and IC50 of each flavonoid were calculated and used to develop SAR and QSAR. The most effective flavonoid was orally co-administered in vivo with a cholesterol-reducing drug, fluvastatin, which is normally metabolized by CYP2C. The most potent CYP2C inhibitor identified in vitro was tamarixetin (IC50 = 1.4 ?M). This flavonoid enhanced the oral bioavailability of fluvastatin in vivo, producing a >2-fold increase in the area under the concentration-time curve and in the peak plasma concentration. SAR analysis indicated that the presence of a 2,3-double bond in the C ring, hydroxylation at positions 5, 6, and 7, and glycosylation had important effects on flavonoid-CYP2C interactions. These findings should prove useful for predicting the inhibition of CYP2C activity by other untested flavonoid-like compounds. In the present study, tamarixetin significantly inhibited CYP2C activity in vitro and in vivo. Thus, the use of tamarixetin could improve the therapeutic efficacy of drugs with low bioavailability. PMID:24431079

  8. Design, synthesis and structure-activity relationships of novel 4-phenoxyquinoline derivatives containing pyridazinone moiety as potential antitumor agents.

    PubMed

    Zhou, Shunguang; Liao, Huimin; He, Chao; Dou, Yanan; Jiang, Mingyan; Ren, Lixiang; Zhao, Yanfang; Gong, Ping

    2014-08-18

    A series of novel 4-phenoxyquinoline derivatives containing pyridazinone moiety were synthesized and evaluated for their in vitro cytotoxic activity against five cancer cell lines (HT-29, H460, A549, MKN-45, and U87MG). Most of the compounds exhibited moderate-to-significant cytotoxicity and high selectivity against one or more cell lines. Compounds 15a, 20a, 15b, 15c, 20d, and 16e were further examined for their inhibitory activity against c-Met kinase. The most promising compound 15a (c-Met half-maximal inhibitory concentration [IC50] = 2.15 nM) showed remarkable cytotoxicity against HT-29, H460, and A549 cell lines with IC50 values of 0.10 ?M, 0.13 ?M, and 0.05 ?M, respectively, and thus it was 1.5- to 2.3-fold more potent than foretinib. Their preliminary structure-activity relationships (SARs) studies indicate that electron-withdrawing groups on the terminal phenyl rings are beneficial for improving the antitumor activity. PMID:24996144

  9. Discovery of Tricyclic Clerodane Diterpenes as Sarco/Endoplasmic Reticulum Ca(2+)-ATPase Inhibitors and Structure-Activity Relationships.

    PubMed

    De Ford, Christian; Calderón, Carlos; Sehgal, Pankaj; Fedosova, Natalya U; Murillo, Renato; Olesen, Claus; Nissen, Poul; Møller, Jesper V; Merfort, Irmgard

    2015-06-26

    Tricyclic clerodane diterpenes (TCDs) are natural compounds that often show potent cytotoxicity for cancer cells, but their mode of action remains elusive. A computationally based similarity search (CDRUG), combined with principal component analysis (ChemGPS-NP) and docking calculations (GOLD 5.2), suggested TCDs to be inhibitors of the sarco/endoplasmic reticulum Ca(2+)-ATPase (SERCA) pump, which is also the target of the sesquiterpene lactone thapsigargin. Biochemical studies were performed with 11 TCDs on purified rabbit skeletal muscle sarcoplasmic reticulum membranes, which are highly enriched with the SERCA1a isoform. Casearborin D (2) exhibited the highest affinity, with a KD value of 2 ?M and giving rise to complete inhibition of SERCA1a activity. Structure-activity relationships revealed that functionalization of two acyl side chains (R1 and R4) and the hydrophobicity imparted by the aliphatic chain at C-9, as well as a C-3,C-4 double bond, play crucial roles for inhibitory activity. Docking studies also suggested that hydrophobic interactions in the binding site, especially with Phe256 and Phe834, may be important for a strong inhibitory activity of the TCDs. In conclusion, a novel class of SERCA inhibitory compounds is presented. PMID:25993619

  10. Structure-activity relationships and optimization of 3,5-dichloropyridine derivatives as novel P2X(7) receptor antagonists.

    PubMed

    Lee, Won-Gil; Lee, So-Deok; Cho, Joong-Heui; Jung, Younghwan; Kim, Jeong-hyun; Hien, Tran T; Kang, Keon-Wook; Ko, Hyojin; Kim, Yong-Chul

    2012-04-26

    Screening of a library of chemical compounds showed that the dichloropyridine-based analogue 9 was a novel P2X(7) receptor antagonist. To optimize its activity, we assessed the structure-activity relationships (SAR) of 9, focusing on the hydrazide linker, the dichloropyridine skeleton, and the hydrophobic acyl (R(2)) group. We found that the hydrazide linker and the 3,5-disubstituted chlorides in the pyridine skeleton were critical for P2X(7) antagonistic activity and that the presence of hydrophobic polycycloalkyl groups at the R(2) position optimized antagonistic activity. In the EtBr uptake assay in hP2X(7)-expressing HEK293 cells, the optimized antagonists, 51 and 52, had IC(50) values of 4.9 and 13 nM, respectively. The antagonistic effects of 51 and 52 were paralleled by their ability to inhibit the release of the pro-inflammatory cytokine, IL-1?, by LPS/IFN-?/BzATP stimulation of THP-1 cells (IC(50) = 1.3 and 9.2 nM, respectively). In addition, 52 strongly inhibited iNOS/COX-2 expression and NO production in THP-1 cells, further indicating that this compound blocks inflammatory signaling and suggesting that the dichloropyridine analogues may be useful in developing P2X(7) receptor targeted anti-inflammatory agents. PMID:22400713

  11. Structure-activity relationship of quinazolinedione inhibitors of calcium-independent phosphodiesterase.

    PubMed

    Lowe, J A; Archer, R L; Chapin, D S; Chen, J B; Helweg, D; Johnson, J L; Koe, B K; Lebel, L A; Moore, P F; Nielsen, J A

    1991-02-01

    A series of quinazolinediones and azaquinazolinediones is described which possess potent inhibitory activity toward the calcium-independent phosphodiesterase enzyme (CaIPDE). In vivo testing showed that this in vitro activity translates to animal models predictive of chronic diseases such as depression and inflammation. These results support the hypothesis that inhibition of CaIPDE may lead to useful activity in such chronic diseases. PMID:1995886

  12. Structure activity relationship study of burkholdine analogues toward simple antifungal agents.

    PubMed

    Konno, Hiroyuki; Abumi, Kanako; Sasaki, Yasuhiro; Yano, Shigekazu; Nosaka, Kazuto

    2015-08-15

    Cyclic and linear lipopeptides, burkholdine analogues, were synthesized by conventional Fmoc-SPPS and cyclisation with DIPC/HOBt in the solution phase. Synthesized peptides were evaluated for antifungal activities with MIC values against Saccharomyces cerevisiae and Aspergillus oryzae. As a result, the stereochemistry of the amino acid residues and sequences of burkholdine analogues exerted a significant influence on antifungal activities. In addition, we found a linear burkholdine analogue with moderate antifungal activities. PMID:26077490

  13. Synthesis and structure-activity relationship (SAR) of novel perfluoroalkyl-containing quaternary ammonium salts

    Microsoft Academic Search

    Jian-Ying Sun; Jing Li; Xiao-Long Qiu; Feng-Ling Qing

    2005-01-01

    A new series of perfluoroalkyl-containing quaternary ammonium compounds were prepared and examined for their antibacterial activities. The perfluoroalkyl-containing quaternary ammonium salts mainly exhibited excellent antibacterial activity for the Gram-positive strain such as Staphylococcus aureus, the MIC (minimal inhibitory concentration) values was between 2.5 and 10?g\\/mL and the MBC (minimal bactericidal concentration) values were 20?g\\/mL. They all showed weak activity against

  14. Synthesis and structure-activity relationship studies of furan-ring fused chalcones as antiproliferative agents.

    PubMed

    Saito, Yusuke; Kishimoto, Maho; Yoshizawa, Yuko; Kawaii, Satoru

    2015-02-01

    As part of our continuing investigation of flavonoid derivatives as potential anticancer substances, the synthesis of 25 cinnamoyl derivatives of benzofuran as furan-fused chalcones was carried-out and these compounds were further evaluated for their antiproliferative activity towards HL60 promyelocytic leukemia cells. In comparison with 2',4'-dihydroxychalcone, attachment of a furan moiety on the A-ring enhanced activity by more than twofold. Benzofurans may be useful in the design of biologically active flavonoids. PMID:25667461

  15. Insights into Structure-Activity Relationships in the C-Terminal Region of Divercin V41, a Class IIa Bacteriocin with High-Level Antilisterial Activity?

    PubMed Central

    Rihakova, Jitka; Petit, Vanessa W.; Demnerova, Katerina; Prévost, Hervé; Rebuffat, Sylvie; Drider, Djamel

    2009-01-01

    Divercin V41 (DvnV41) is a class IIa bacteriocin with potent antilisterial activity isolated from Carnobacterium divergens V41. Previously, we expressed from a synthetic gene, in Escherichia coli Origami, a recombinant DvnV41 designated DvnRV41, which possesses four additional amino acids (AMDP) in the N-terminal region that result from enzymatic cleavage and retains the initial DvnV41 activity. To unravel the relationship between the structure of DvnRV41 and its particularly elevated activity, we produced by site-directed mutagenesis eight variants in which a single amino acid replacement was specifically introduced into the sequence. The point mutations were designed to change either conserved residues in class IIa bacteriocins or residues specific to DvnV41 located mainly in the C-terminal region. The fusion proteins were purified from the cytosoluble fractions by immobilized affinity chromatography. DvnRV41 and its variants were released from the fusion proteins by enzymatic cleavage, using enterokinase. The purity of DvnRV41 and of the variants was checked by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, high-performance liquid chromatography, and mass spectrometry. The antibacterial activity of DvnRV41 and its variants was assessed using different indicator strains, including Listeria monocytogenes EGDe and Enterococcus faecalis JH2-2. The activity of all of the variants appeared to be less than the activity of DvnRV41. The decrease in activity did not appear to be related to a global conformational change, as determined by circular dichroism. Overall, the variants of DvnRV41 produced in the present study provide interesting insights into structure-activity relationships of class IIa bacteriocins. PMID:19181835

  16. Holographic quantitative structure-activity relationship for prediction acute toxicity of benzene derivatives to the guppy (Poecilia reticulata).

    PubMed

    Huang, Hong; Wang, Xiao-dong; Dai, Xuan-li; Yu, Ya-juan; Wang, Lian-sheng

    2004-01-01

    Holographic quantitative structure-activity relationship (HQSAR) is an emerging QSAR technique with the combined application of molecular hologram, which encoded the frequency of occurrence of various molecular fragment types, and the subsequent partial least squares (PLS) regression analysis. In this paper, the acute toxicity data to the guppy (Poecilia reticulata) for a series of 56 substituted benzenes, phenols, aromatic amines and nitro-aromatics were subjected and this resulted in a model with a high predictive ability. The influence of fragment size and fragment distinction parameters on the quality of HQSAR model was investigated. The robustness and predictive ability of the model were also validated by leave-one-out (LOO) cross-validation procedure and external testing data set. PMID:15272716

  17. The application of structure-activity relationships (SARs) in the aquatic toxicity evaluation of discrete organic chemicals.

    PubMed

    Clements, R G; Nabholz, J V; Zeeman, M G; Auer, C M

    1995-01-01

    The Office of Pollution Prevention and Toxics (OPPT), United States Environmental Protection Agency (USEPA) routinely uses structure-activity relationships (SAR) for the aquatic hazard assessment of new chemicals submitted under Section 5 of the Toxic Substances Control Act (TSCA). With 15 years of experience and the general acceptance of toxicity predictions based on SARs, OPPT has expanded the use and application of the methodology to include existing chemicals used in printing, dry cleaning, and paint stripping. SAR analysis has also been used in the hazard evaluation of the U.S. and EU/OECD high production volume (HPV) chemicals. This paper describes the assumptions, limitations, and methodology for the use of SARs to evaluate large sets of discrete organic chemicals. PMID:8564855

  18. Towards a systematic analysis of human short-chain dehydrogenases/reductases (SDR): Ligand identification and structure-activity relationships.

    PubMed

    Bhatia, Chitra; Oerum, Stephanie; Bray, James; Kavanagh, Kathryn L; Shafqat, Naeem; Yue, Wyatt; Oppermann, Udo

    2015-06-01

    Short-chain dehydrogenases/reductases (SDRs) constitute a large, functionally diverse branch of enzymes within the class of NAD(P)(H) dependent oxidoreductases. In humans, over 80 genes have been identified with distinct metabolic roles in carbohydrate, amino acid, lipid, retinoid and steroid hormone metabolism, frequently associated with inherited genetic defects. Besides metabolic functions, a subset of atypical SDR proteins appears to play critical roles in adapting to redox status or RNA processing, and thereby controlling metabolic pathways. Here we present an update on the human SDR superfamily and a ligand identification strategy using differential scanning fluorimetry (DSF) with a focused library of oxidoreductase and metabolic ligands to identify substrate classes and inhibitor chemotypes. This method is applicable to investigate structure-activity relationships of oxidoreductases and ultimately to better understand their physiological roles. PMID:25526675

  19. Structure-Activity Relationship Studies on the Mosquito Toxicity and Biting Deterrency of Callicarpenal Derivatives

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Callicarpenal (13,14,15,16-tetranor-3-cleroden-12-al) has previously demonstrated significant mosquito bite-deterring activity against Aedes aegypti and Anopheles stephensi in addition to repellent activity against host-seeking nymphs of the blacklegged tick, Ixodes scapularis. In the present study...

  20. Synthesis and insight into the structure-activity relationships of chalcones as antimalarial agents.

    PubMed

    Tadigoppula, Narender; Korthikunta, Venkateswarlu; Gupta, Shweta; Kancharla, Papireddy; Khaliq, Tanvir; Soni, Awakash; Srivastava, Rajeev Kumar; Srivastava, Kumkum; Puri, Sunil Kumar; Raju, Kanumuri Siva Rama; Wahajuddin; Sijwali, Puran Singh; Kumar, Vikash; Mohammad, Imran Siddiqi

    2013-01-10

    Licochalcone A (I), isolated from the roots of Chinese licorice, is the most promising antimalarial compound reported so far. In continuation of our drug discovery program, we isolated two similar chalcones, medicagenin (II) and munchiwarin (III), from Crotalaria medicagenia , which exhibited antimalarial activity against Plasmodium falciparum . A library of 88 chalcones were synthesized and evaluated for their in vitro antimalarial activity. Among these, 67, 68, 74, 77, and 78 exhibited good in vitro antimalarial activity against P. falciparum strains 3D7 and K1 with low cytotoxicity. These chalcones also showed reduction in parasitemia and increased survival time of Swiss mice infected with Plasmodium yoelii (strain N-67). Pharmacokinetic studies indicated that low oral bioavailability due to poor ADME properties. Molecular docking studies revealed the binding orientation of these inhibitors in active sites of falcipain-2 (FP-2) enzyme. Compounds 67, 68, and 78 showed modest inhibitory activity against the major hemoglobin degrading cysteine protease FP-2. PMID:23270565

  1. Three-dimensional quantitative structure-activity relationship study on antioxidant capacity of curcumin analogues

    NASA Astrophysics Data System (ADS)

    Chen, Bohong; Zhu, Zhibo; Chen, Min; Dong, Wenqi; Li, Zhen

    2014-03-01

    A comparative molecular similarity indices analysis (CoMSIA) was performed on a set of 27 curcumin-like diarylpentanoid analogues with the radical scavenging activities. A significant cross-validated correlation coefficient Q2 (0.784), SEP (0.042) for CoMSIA were obtained, indicating the statistical significance of the correlation. Further we adopt a rational approach toward the selection of substituents at various positions in our scaffold,and finally find the favored and disfavoured regions for the enhanced antioxidative activity. The results have been used as a guide to design compounds that, potentially, have better activity against oxidative damage.

  2. Structure-activity relationships of substituted 1H-indole-2-carboxamides as CB1 receptor allosteric modulators.

    PubMed

    Nguyen, Thuy; German, Nadezhda; Decker, Ann M; Li, Jun-Xu; Wiley, Jenny L; Thomas, Brian F; Kenakin, Terry P; Zhang, Yanan

    2015-05-01

    A series of substituted 1H-indole-2-carboxamides structurally related to compounds Org27569 (1), Org29647 (2) and Org27759 (3) were synthesized and evaluated for CB1 allosteric modulating activity in calcium mobilization assays. Structure-activity relationship studies showed that the modulation potency of this series at the CB1 receptor was enhanced by the presence of a diethylamino group at the 4-position of the phenyl ring, a chloro or fluoro group at the C5 position and short alkyl groups at the C3 position on the indole ring. The most potent compound (45) had an IC?? value of 79 nM which is ?2.5 and 10 fold more potent than the parent compounds 3 and 1, respectively. These compounds appeared to be negative allosteric modulators at the CB1 receptor and dose-dependently reduced the Emax of agonist CP55,940. These analogs may provide the basis for further optimization and use of CB1 allosteric modulators. PMID:25797163

  3. Structure–Activity Relationships of Acetolactate Synthase Inhibition among New Benzenesulfonylureas in Rice ( Oryza sativa) and Barnyardgrass ( Echinochloa crus-galli var. oryzicola)

    Microsoft Academic Search

    I. T. Hwang; Y. K. Ko; T. J. Kim; D. W. Kim; K. Y. Cho

    2000-01-01

    Structure–activity relationships of 15 new benzenesulfonylurea derivatives were investigated using acetolactate synthase (ALS) assays in vitro and in vivo in rice (Oryza sativa) and barnyardgrass (Echinochloa crus-galli var. oryzicola). In vitro ALS activities of both rice and barnyardgrass were significantly inhibited by the compounds with smaller numbers of carbon atoms and ?-fluorine substituents in the R radical of the new

  4. Structure-based approach to pharmacophore identification, in silico screening, and three-dimensional quantitative structure-activity relationship studies for inhibitors of Trypanosoma cruzi dihydrofolate reductase function

    SciTech Connect

    Schormann, N.; Senkovich, O.; Walker, K.; Wright, D.L.; Anderson, A.C.; Rosowsky, A.; Ananthan, S.; Shinkre, B.; Velu, S.; Chattopadhyay, D. (UAB); (Connecticut); (Southern Research); (DFCI)

    2009-07-10

    We have employed a structure-based three-dimensional quantitative structure-activity relationship (3D-QSAR) approach to predict the biochemical activity for inhibitors of T. cruzi dihydrofolate reductase-thymidylate synthase (DHFR-TS). Crystal structures of complexes of the enzyme with eight different inhibitors of the DHFR activity together with the structure in the substrate-free state (DHFR domain) were used to validate and refine docking poses of ligands that constitute likely active conformations. Structural information from these complexes formed the basis for the structure-based alignment used as input for the QSAR study. Contrary to indirect ligand-based approaches the strategy described here employs a direct receptor-based approach. The goal is to generate a library of selective lead inhibitors for further development as antiparasitic agents. 3D-QSAR models were obtained for T. cruzi DHFR-TS (30 inhibitors in learning set) and human DHFR (36 inhibitors in learning set) that show a very good agreement between experimental and predicted enzyme inhibition data. For crossvalidation of the QSAR model(s), we have used the 10% leave-one-out method. The derived 3D-QSAR models were tested against a few selected compounds (a small test set of six inhibitors for each enzyme) with known activity, which were not part of the learning set, and the quality of prediction of the initial 3D-QSAR models demonstrated that such studies are feasible. Further refinement of the models through integration of additional activity data and optimization of reliable docking poses is expected to lead to an improved predictive ability.

  5. Structure-activity relationship of dihydroxy-4-methylcoumarins as powerful antioxidants: correlation between experimental & theoretical data and synergistic effect.

    PubMed

    Kancheva, Vessela D; Saso, Luciano; Boranova, Petya V; Khan, Abdullah; Saroj, Manju K; Pandey, Mukesh K; Malhotra, Shashwat; Nechev, Jordan Z; Sharma, Sunil K; Prasad, Ashok K; Georgieva, Maya B; Joseph, Carleta; DePass, Anthony L; Rastogi, Ramesh C; Parmar, Virinder S

    2010-09-01

    The chain-breaking antioxidant activities of eight coumarins [7-hydroxy-4-methylcoumarin (1), 5,7-dihydroxy-4-methylcoumarin (2), 6,7-dihydroxy-4-methylcoumarin (3), 6,7-dihydroxycoumarin (4), 7,8-dihydroxy-4-methylcoumarin (5), ethyl 2-(7,8-dihydroxy-4-methylcoumar-3-yl)-acetate (6), 7,8-diacetoxy-4-methylcoumarin (7) and ethyl 2-(7,8-diacetoxy-4-methylcoumar-3-yl)-acetate (8)] during bulk lipid autoxidation at 37 degrees C and 80 degrees C in concentrations of 0.01-1.0 mM and their radical scavenging activities at 25 degrees C using TLC-DPPH test have been studied and compared. It has been found that the o-dihydroxycoumarins 3-6 demonstrated excellent activity as antioxidants and radical scavengers, much better than the m-dihydroxy analogue 2 and the monohydroxycoumarin 1. The substitution at the C-3 position did not have any effect either on the chain-breaking antioxidant activity or on the radical scavenging activity of the 7,8-dihydroxy- and 7,8-diacetoxy-4-methylcoumarins 6 and 8. The comparison with DL-alpha-tocopherol (TOH), caffeic acid (CA) and p-coumaric acid (p-CumA) showed that antioxidant efficiency decreases in the following sequence: TOH>CA>3>4>6>5>2>1=7=8=p-CumA. Theoretical calculations and the "Lipinski's Rule of Five" were used for explaining the structure-activity relationships and pharmacokinetic behavior. A higher TGSO oxidation stability was observed in the presence of equimolar (1:1) binary mixtures of coumarins with TOH (1+TOH, 3+TOH and 5+TOH). However, the synergism (14%) was observed only for the binary mixture of 5 + TOH. PMID:20600568

  6. Synthesis and quantitative structure activity relationship (QSAR) of arylidene (benzimidazol-1-yl)acetohydrazones as potential antibacterial agents.

    PubMed

    El-Kilany, Yeldez; Nahas, Nariman M; Al-Ghamdi, Mariam A; Badawy, Mohamed E I; El Ashry, El Sayed H

    2015-01-01

    Ethyl (benzimidazol-1-yl)acetate was subjected to hydrazinolysis with hydrazine hydrate to give (benzimidazol-1-yl)acetohydrazide. The latter was reacted with various aromatic aldehydes to give the respective arylidene (1H-benzimidazol-1-yl)acetohydrazones. Solutions of the prepared hydrazones were found to contain two geometric isomers. Similarly (2-methyl-benzimidazol-1-yl)acetohydrazide was reacted with various aldehydes to give the corresponding hydrazones. The antibacterial activity was evaluated in vitro by minimum inhibitory concentration (MIC) against Agrobacterium tumefaciens (A. tumefaciens), Erwinia carotovora (E. carotovora), Corynebacterium fascians (C. fascians) and Pseudomonas solanacearum (P. solanacearum). MIC result demonstrated that salicylaldehyde(1H-benzimidazol-1-yl)acetohydrazone (4) was the most active compound (MIC = 20, 35, 25 and 30 mg/L against A. tumefaciens, C. fascians, E. carotovora and P. solanacearum, respectively). Quantitative structure activity relationship (QSAR) investigation using Hansch analysis was applied to find out the correlation between antibacterial activity and physicochemical properties. Various physicochemical descriptors and experimentally determined MIC values for different microorganisms were used as independent and dependent variables, respectively. pMICs of the compounds exhibited good correlation (r = 0.983, 0.914, 0.960 and 0.958 for A. tumefaciens, C. fascians, E. carotovora and P. solanacearum, respectively) with the prediction made by the model. QSAR study revealed that the hydrophobic parameter (ClogP), the aqueous solubility (LogS), calculated molar refractivity, topological polar surface area and hydrogen bond acceptor were found to have overall significant correlation with antibacterial activity. The statistical results of training set, correlation coefficient (r and r (2)), the ratio between regression and residual variances (f, Fisher's statistic), the standard error of estimates and significant (s) gave reliability to the prediction of molecules with activity using QSAR models. However, QSAR equations derived for the MIC values against the tested bacteria showed negative contribution of molecular mass. PMID:25304024

  7. A structure-activity relationship study on antiosteoclastogenesis effect of triterpenoids from the leaves of loquat (Eriobotrya japonica).

    PubMed

    Tan, Hui; Ashour, Ahmed; Katakura, Yoshinori; Shimizu, Kuniyoshi

    2015-04-15

    Our previous results elucidated that the leaves of Eriobotrya japonica possessed the potential to suppress ovariectomy-induced bone mineral density deterioration, and ursolic acid, the major bioactive component in these leaves, suppressed the osteoclast differentiation. The aim of this study was to discover more candidates for development of novel antiosteoclastogenesis agents from the leaves of E. japonica. Phytochemical analysis following a cell-based osteoclastic tartrate-resistant acid phosphatase (TRAP) activity assay revealed 11 more compounds with a potent antiosteoclastogenesis effect. The potency of ursane-type triterpenoids from the leaves of E. japonica prompted us to investigate the structure-activity relationships underlying their antiosteoclastogenesis. The results revealed that both the hydroxyl group at C-3 and the carboxylic group at C-17 played indispensable roles in the antiosteoclastogenesis activity of ursane-type triterpenoids. The configuration at C-3 (a beta-form of the hydroxyl group) was found to be important for this activity. While introducing a hydroxyl group at C-19 increased the inhibitory activity of ursane-type triterpenoids carrying an alpha-form hydroxyl group at C-3. The bioactivity analyses of ursolic acid and oleanolic acid demonstrated that the antiosteoclastogenesis effect of ursolic acid may be related to different positions of the C-29 and C-30 methyl groups on the E-ring, since oleanolic acid showed limited activity. The addition of a hydroxyl group at C-2 would dramatically improve the inhibition of oleanane-type triterpenoids. Collectively, these findings could provide important clues for the improvement of multi-targeted antiosteoclastogenesis agents from the leaves of E. japonica. PMID:25925972

  8. Synthesis and quantitative structure-activity relationship (QSAR) study of novel isoxazoline and oxime derivatives of podophyllotoxin as insecticidal agents.

    PubMed

    Wang, Yi; Shao, Yonghua; Wang, Yangyang; Fan, Lingling; Yu, Xiang; Zhi, Xiaoyan; Yang, Chun; Qu, Huan; Yao, Xiaojun; Xu, Hui

    2012-08-29

    In continuation of our program aimed at the discovery and development of natural-product-based insecticidal agents, 33 isoxazoline and oxime derivatives of podophyllotoxin modified in the C and D rings were synthesized and their structures were characterized by Proton nuclear magnetic resonance ((1)H NMR), high-resolution mass spectrometry (HRMS), electrospray ionization-mass spectrometry (ESI-MS), optical rotation, melting point (mp), and infrared (IR) spectroscopy. The stereochemical configurations of compounds 5e, 5f, and 9f were unambiguously determined by X-ray crystallography. Their insecticidal activity was evaluated against the pre-third-instar larvae of northern armyworm, Mythimna separata (Walker), in vivo. Compounds 5e, 9c, 11g, and 11h especially exhibited more promising insecticidal activity than toosendanin, a commercial botanical insecticide extracted from Melia azedarach . A genetic algorithm combined with multiple linear regression (GA-MLR) calculation is performed by the MOBY DIGS package. Five selected descriptors are as follows: one two-dimensional (2D) autocorrelation descriptor (GATS4e), one edge adjacency indice (EEig06x), one RDF descriptor (RDF080v), one three-dimensional (3D) MoRSE descriptor (Mor09v), and one atom-centered fragment (H-052) descriptor. Quantitative structure-activity relationship studies demonstrated that the insecticidal activity of these compounds was mainly influenced by many factors, such as electronic distribution, steric factors, etc. For this model, the standard deviation error in prediction (SDEP) is 0.0592, the correlation coefficient (R(2)) is 0.861, and the leave-one-out cross-validation correlation coefficient (Q(2)loo) is 0.797. PMID:22891988

  9. Quantitative Structure-Activity Relationships Predicting the Antioxidant Potency of 17?-Estradiol-Related Polycyclic Phenols to Inhibit Lipid Peroxidation

    PubMed Central

    Prokai, Laszlo; Rivera-Portalatin, Nilka M.; Prokai-Tatrai, Katalin

    2013-01-01

    The antioxidant potency of 17?-estradiol and related polycyclic phenols has been well established. This property is an important component of the complex events by which these types of agents are capable to protect neurons against the detrimental consequences of oxidative stress. In order to relate their molecular structure and properties with their capacity to inhibit lipid peroxidation, a marker of oxidative stress, quantitative structure-activity relationship (QSAR) studies were conducted. The inhibition of Fe3+-induced lipid peroxidation in rat brain homogenate, measured through an assay detecting thiobarbituric acid reactive substances for about seventy compounds were correlated with various molecular descriptors. We found that lipophilicity (modeled by the logarithm of the n-octanol/water partition coefficient, logP) was the property that influenced most profoundly the potency of these compounds to inhibit lipid peroxidation in the biological medium studied. Additionally, the important contribution of the bond dissociation enthalpy of the phenolic O–H group, a shape index, the solvent-accessible surface area and the energy required to remove an electron from the highest occupied molecular orbital were also confirmed. Several QSAR equations were validated as potentially useful exploratory tools for identifying or designing novel phenolic antioxidants incorporating the structural backbone of 17?-estradiol to assist therapy development against oxidative stress-associated neurodegeneration. PMID:23344051

  10. Potential of 2-Hydroxy-3-Phenylsulfanylmethyl-[1,4]-Naphthoquinones against Leishmania (L.) infantum: Biological Activity and Structure-Activity Relationships

    PubMed Central

    Schmidt, Thomas J.; Borborema, Samanta E. T.; Ferreira, Vitor F.; Rocha, David R.; Tempone, Andre G.

    2014-01-01

    Naphtoquinones have been used as promising scaffolds for drug design studies against protozoan parasites. Considering the highly toxic and limited therapeutic arsenal, the global negligence with tropical diseases and the elevated prevalence of co-morbidities especially in developing countries, the parasitic diseases caused by various Leishmania species (leishmaniasis) became a significant public health threat in 98 countries. The aim of this work was the evaluation of antileishmanial in vitro potential of thirty-six 2-hydroxy-3-phenylsulfanylmethyl-[1,4]-naphthoquinones obtained by a three component reaction of lawsone, the appropriate aldehyde and thiols adequately substituted, exploiting the in situ generation of o-quinonemethides (o-QM) via the Knoevenagel condensation. The antileishmanial activity of the naphthoquinone derivatives was evaluated against promastigotes and intracellular amastigotes of Leishmania (Leishmania) infantum and their cytotoxicity was verified in mammalian cells. Among the thirty-six compounds, twenty-seven were effective against promastigotes, with IC50 values ranging from 8 to 189 µM; fourteen compounds eliminated the intracellular amastigotes, with IC50 values ranging from 12 to 65 µM. The compounds containing the phenyl groups at R1 and R2 and with the fluorine substituent at the phenyl ring at R2, rendered the most promising activity, demonstrating a selectivity index higher than 15 against amastigotes. A QSAR (quantitative structure activity relationship) analysis yielded insights into general structural requirements for activity of most compounds in the series. Considering the in vitro antileishmanial potential of 2-hydroxy-3-phenylsulfanylmethyl-[1,4]-naphthoquinones and their structure-activity relationships, novel lead candidates could be exploited in future drug design studies for leishmaniasis. PMID:25171058

  11. Structure-Activity Relationships of (+)-Naltrexone-Inspired Toll-like Receptor 4 (TLR4) Antagonists.

    PubMed

    Selfridge, Brandon R; Wang, Xiaohui; Zhang, Yingning; Yin, Hang; Grace, Peter M; Watkins, Linda R; Jacobson, Arthur E; Rice, Kenner C

    2015-06-25

    Activation of Toll-like receptors has been linked to neuropathic pain and opioid dependence. (+)-Naltrexone acts as a Toll-like receptor 4 (TLR4) antagonist and has been shown to reverse neuropathic pain in rat studies. We designed and synthesized compounds based on (+)-naltrexone and (+)-noroxymorphone and evaluated their TLR4 antagonist activities by their effects on inhibiting lipopolysaccharide (LPS) induced TLR4 downstream nitric oxide (NO) production in microglia BV-2 cells. Alteration of the N-substituent in (+)-noroxymorphone gave us a potent TLR4 antagonist. The most promising analog, (+)-N-phenethylnoroxymorphone ((4S,4aR,7aS,12bR)-4a,9-dihydroxy-3-phenethyl-2,3,4,4a,5,6-hexahydro-1H-4,12-methanobenzofuro[3,2-e]isoquinolin-7(7aH)-one, 1j) showed ?75 times better TLR-4 antagonist activity than (+)-naltrexone, and the ratio of its cell viability IC50, a measure of its toxicity, to TLR-4 antagonist activity (140 ?M/1.4 ?M) was among the best of the new analogs. This compound (1j) was active in vivo; it significantly increased and prolonged morphine analgesia. PMID:26010811

  12. Biomolecular recognition of antagonists by ?7 nicotinic acetylcholine receptor: Antagonistic mechanism and structure-activity relationships studies.

    PubMed

    Peng, Wei; Ding, Fei

    2015-08-30

    As the key constituent of ligand-gated ion channels in the central nervous system, nicotinic acetylcholine receptors (nAChRs) and neurodegenerative diseases are strongly coupled in the human species. In recently years the developments of selective agonists by using nAChRs as the drug target have made a large progress, but the studies of selective antagonists are severely lacked. Currently these antagonists rest mainly on the extraction of partly natural products from some animals and plants; however, the production of these crude substances is quite restricted, and artificial synthesis of nAChR antagonists is still one of the completely new research fields. In the context of this manuscript, our primary objective was to comprehensively analyze the recognition patterns and the critical interaction descriptors between target ?7 nAChR and a series of the novel compounds with potentially antagonistic activity by means of virtual screening, molecular docking and molecular dynamics simulation, and meanwhile these recognition reactions were also compared with the biointeraction of ?7 nAChR with a commercially natural antagonist - methyllycaconitine. The results suggested clearly that there are relatively obvious differences of molecular structures between synthetic antagonists and methyllycaconitine, while the two systems have similar recognition modes on the whole. The interaction energy and the crucially noncovalent forces of the ?7 nAChR-antagonists are ascertained according to the method of Molecular Mechanics/Generalized Born Surface Area. Several amino acid residues, such as B/Tyr-93, B/Lys-143, B/Trp-147, B/Tyr-188, B/Tyr-195, A/Trp-55 and A/Leu-118 played a major role in the ?7 nAChR-antagonist recognition processes, in particular, residues B/Tyr-93, B/Trp-147 and B/Tyr-188 are the most important. These outcomes tally satisfactorily with the discussions of amino acid mutations. Based on the explorations of three-dimensional quantitative structure-activity relationships, the structure-antagonistic activity relationships of antagonists and the characteristics of ?7 nAChR-ligand recognitions were received a reasonable summary as well. These attempts emerged herein would not only provide helpful guidance for the design of ?7 nAChR antagonists, but shed new light on the subsequent researches in antagonistic mechanism. PMID:25963024

  13. Structure-Activity Relationship Exploration of Kv1.3 Blockers Based on Diphenoxylate

    PubMed Central

    Nguyen, William; Howard, Brittany L.; Jenkins, David P.; Wulff, Heike; Thompson, Philip E.; Manallack, David T.

    2013-01-01

    Diphenoxylate, a well-known opioid agonist and anti-diarrhoeal agent, was recently found to block Kv1.3 potassium channels, which have been proposed as potential therapeutic targets for a range of autoimmune diseases. The molecular basis for this Kv1.3 blockade was assessed by the selective removal of functional groups from the structure of diphenoxylate as well as a number of other structural variations. Removal of the nitrile functional group and replacement of the C-4 piperidinyl substituents resulted in several compounds with submicromolar IC50 values. PMID:23084278

  14. Structure-activity relationship for quaternary ammonium compounds hybridized with poly(methyl methacrylate).

    PubMed

    Melo, Leticia D; Palombo, Renata R; Petri, Denise F S; Bruns, Michael; Pereira, Edla M A; Carmona-Ribeiro, Ana M

    2011-06-01

    Hybrid films from poly (methylmethacrylate) (PMMA) and dioctadecyldimethylammonium bromide (DODAB), cetyltrimethylammonium bromide (CTAB), or tetrapropylammonium bromide (TPAB) were characterized by determination of wettability, ellipsometry, atomic force microscopy, active compounds diffusion to water, X-ray photoelectron spectroscopy (XPS) with determination of atomic composition on the films surface, and biocidal activity against Pseudomonas aeruginosa or Staphylococcus aureus. QAC mobility in the films increased from DODAB to CTAB to TPAB. Diffusion and optimal hydrophobic-hydrophilic balance imparted the highest bioactivity to CTAB. DODAB sustained immobilization at the film surface killed bacteria upon contact. TPAB ability to diffuse was useless because of its unfavorable hydrophobic-hydrophilic balance for bioactivity. PMID:21591705

  15. Toxicity of substituted anilines to Pseudokirchneriella subcapitata and quantitative structure-activity relationship analysis for polar narcotics.

    PubMed

    Chen, Chung-Yuan; Ko, Chia-Wen; Lee, Po-I

    2007-06-01

    This study evaluated the toxic effects of substituted anilines on Pseudokirchneriella subcapitata with the use of a closed algal toxicity testing technique with no headspace. Two response endpoints (i.e., dissolved oxygen production [DO] and algal growth rate) were used to evaluate the toxicity of anilines. Both DO and growth rate endpoints revealed similar sensitivity to the effects of anilines. However, trichloroanilines showed stronger inhibitory effects on microalgal photosynthetic reactions than that on algal growth. For various aquatic organisms, the relative sensitivity relationship for anilines is Daphnia magna > luminescent bacteria (Microtox) > or = Pocelia reticulata > or = Pseudokirchneriella subcapitata > or = fathead minnow > Tetrahymena pyriformis. The susceptibility of P. subcapitata to anilines is similar to fish, but P. subcapitata is apparently less sensitive than the water flea. The lack of correlation between the toxicity revealed by different aquatic organisms (microalgae, D. magna, luminescent bacteria, and P. reticulata) suggests that anilines might have different metabolic routes in these organisms. Both hydrogen bonding donor capacity (the lowest unoccupied molecular orbital energy, Elumo) and hydrophobicity (1-octanol:water partition coefficient, Kow) were found to provide satisfactory descriptions for the toxicity of polar narcotics (substituted anilines and chlorophenols). Quantitative structure-activity relationships (QSARs) based on Elumo, log Kow, or both values were established with r2 values varying from 0.75 to 0.92. The predictive power for the QSAR models were found to be satisfactory through leave-one-out cross-validation. Such relationships could provide useful information for the estimation of toxicity for other polar narcotic compounds. PMID:17571680

  16. Structure Property Relationships for Dirhodium Antitumor Active Compounds: Reactions with Biomolecules and In Cellulo Studies

    E-print Network

    Aguirre-Flores, Jessica Dafhne

    2011-02-22

    Schematic representation of inorganic complexes that exhibit anticancer activity ................................................. 16 I-10 Scheme that depicts the proposed mechanism of cisplatin action... .......................................................................................... 19 I-11 Adducts formed after binding of cisplatin to DNA ................... 20 I-12 Schematic representation of dirhodium tetracarboxylate (Top). Bridging ligands of compounds studied as anticancer agents (Bottom...

  17. Application of data mining to quantitative structure-activity relationship using rough set theory

    Microsoft Academic Search

    Kiyoshi Hasegawa; Michio Koyama; Masamoto Arakawa; Kimito Funatsu

    2009-01-01

    Rough set theory (RST) is a new data mining method originally proposed in chemometrics. RST selects the least descriptor sets for discriminating one sample from the others. These descriptor sets are called reducts. RST constructs any possible rules for high activity using the specific reduct. We have used dihydrofolate reductase (DHFR) inhibitors as a validation set of RST. This data

  18. Inuloxins A-D and derivatives as antileishmanial agents: structure-activity relationship study

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Inuloxins A-D (1-4) and a-costic acid (5), the phytotoxic compounds previously isolated from Inula viscosa, as well as synthetic derivatives of inuloxin A (compounds 6-10), inuloxin C (compound 11) and inuloxin D (compound 12) were tested in vitro for their activity against Leishmania donovani, the ...

  19. Antitumor sulfonylhydrazines: design, structure-activity relationships, resistance mechanisms, and strategies for improving therapeutic utility.

    PubMed

    Shyam, Krishnamurthy; Penketh, Philip G; Baumann, Raymond P; Finch, Rick A; Zhu, Rui; Zhu, Yong-Lian; Sartorelli, Alan C

    2015-05-14

    1,2-Bis(sulfonyl)-1-alkylhydrazines (BSHs) were conceived as more specific DNA guanine O-6 methylating and chloroethylating agents lacking many of the undesirable toxicophores contained in antitumor nitrosoureas. O(6)-Alkylguanine-DNA alkyltransferase (MGMT) is the sole repair protein for O(6)-alkylguanine lesions in DNA and has been reported to be absent in 5-20% of most tumor types. Many BSHs exhibit highly selective cytotoxicity toward cells deficient in MGMT activity. The development of clinically useful MGMT assays should permit the identification of tumors with this vulnerability and allow for the preselection of patient subpopulations with a high probability of responding. The BSH system is highly versatile, permitting the synthesis of many prodrug types with the ability to incorporate an additional level of tumor-targeting due to preferential activation by tumor cells. Furthermore, it may be possible to expand the spectrum of activity of these agents to include tumors with MGMT activity by combining them with tumor-targeted MGMT inhibitors. PMID:25612194

  20. Structure activity relationships of N-linked and diglycosylated glucosamine-based antitumor glycerolipids.

    PubMed

    Ogunsina, Makanjuola; Pan, Hangyi; Samadder, Pranati; Arthur, Gilbert; Schweizer, Frank

    2013-01-01

    1-O-Hexadecyl-2-O-methyl-3-O-(2'-amino-2'-deoxy-?-D-glucopyranosyl)-sn-glycerol (1) was previously reported to show potent in vitro antitumor activity on a range of cancer cell lines derived from breast, pancreas and prostate cancer. This compound was not toxic to mice and was inactive against breast tumor xenografts in mice. This inactivity was attributed to hydrolysis of the glycosidic linkage by glycosidases. Here three N-linked (glycosylamide) analogs 2-4, one triazole-linked analog 5 of 1 as well as two diglycosylated analogs 6 and 7 with different stereochemistry at the C2-position of the glycerol moiety were synthesized and their antitumor activity against breast (JIMT-1, BT-474, MDA-MB-231), pancreas (MiaPaCa2) and prostrate (DU145, PC3) cancer cell lines was determined. The diglycosylated analogs 1-O-hexadecyl-2(R)-, 3-O-di-(2'-amino-2'-deoxy-?-D-glucopyranosyl)-sn-glycerol (7) and the 1:1 diastereomeric mixture of 1-O-hexadecyl-2(R/S), 3-O-di-(2'-amino-2'-deoxy-?-D-glucopyranosyl)-sn-glycerol (6) showed the most potent cytotoxic activity at CC50 values of 17.5 µM against PC3 cell lines. The replacement of the O-glycosidic linkage by a glycosylamide or a glycosyltriazole linkage showed little or no activity at highest concentration tested (30 µM), whereas the replacement of the glycerol moiety by triazole resulted in CC50 values in the range of 20 to 30 µM. In conclusion, the replacement of the O-glycosidic linkage by an N-glycosidic linkage or triazole-linkage resulted in about a two to three fold loss in activity, whereas the replacement of the methoxy group on the glycerol backbone by a second glucosamine moiety did not improve the activity. The stereochemistry at the C2-position of the glycero backbone has minimal effect on the anticancer activities of these diglycosylated analogs. PMID:24335578

  1. Inhibition of calcium phosphate precipitation by human salivary statherin: structure-activity relationships.

    PubMed

    Schwartz, S S; Hay, D I; Schluckebier, S K

    1992-06-01

    Previous studies of human statherin showed the active region for inhibition of secondary calcium phosphate precipitation (crystal growth) to reside in the highly charged amino-terminal one-third of this molecule, and the neutral tyrosine-, glutamine- and proline-rich carboxy-terminal two-thirds of the molecule is required for maximal inhibition of primary (spontaneous) precipitation. The purpose of the present study was to define more clearly the activities of these different molecular segments of statherin with respect to the two kinds of inhibitory activities. Peptides from statherin were prepared by specific proteolysis using trypsin, endoproteinase Arg-C, and activated factor X to produce the amino-terminal hexa-, nona- and decapeptides, respectively, and carboxypeptidase-A was used to obtain a peptide extending from residue 1 to about residues 32-37. The peptides were purified by anion exchange and gel filtration chromatography, and characterized and quantified by amino-acid analysis. Serially diluted samples of statherin and derived peptides were assayed to determine the concentrations, giving a standard 50% inhibition of precipitation (C50%) in assay systems designed for this purpose using polyaspartate as a standard. Results are expressed as (C50% statherin)/(C50% peptide). For inhibition of primary precipitation, these values were peptide(1-6), 0.20; peptide(1-9), 0.15; peptide(1-31/35), 0.24. For inhibition of secondary precipitation, the values were peptide(1-6), 3.8; peptide(1-9), 2.8; peptide(1-10), 1.9; peptide(1-32/37), 1.5. These quantitative findings show that maximum inhibition of primary precipitation by statherin requires the entire molecule. Thus, removal of a relatively small segment of its carboxy-terminal region results in a substantial reduction in inhibitory activity.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:1525706

  2. Cytotoxicity and Structure-activity Relationships of Naphthyridine Derivatives in Human Cervical Cancer, Leukemia, and Prostate Cancer

    PubMed Central

    Hwang, Yu Jin; Chung, Mi Lyang; Sohn, Uy Dong

    2013-01-01

    Naphthyridine compounds are important, because they exhibit various biological activities including anticancer, antimicrobial, and anti-inflammatory activity. Some naphthyridines have antimitotic effects or demonstrate anticancer activity by inhibiting topoisomerase II. These compounds have been investigated as potential anticancer agents, and several compounds are now part of clinical trials. A series of naphthyridine derivatives were evaluated for their in vitro cytotoxic activities against human cervical cancer (HeLa), leukemia (HL-60), and prostate cancer (PC-3) cell lines using an MTT assay. Some compounds (14, 15, and 16) were more potent than colchicine against all three human cancer cell lines and compound (16) demonstrated potency with IC50 values of 0.7, 0.1, and 5.1 µM, respectively. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were used for quantitative structure-activity relationship (QSAR) molecular modeling of these compounds. We obtained accurate and predictive three-dimensional QSAR (3D-QSAR) models as indicated by the high PLS parameters of the HeLa (q2, 0.857; r2, 0.984; r2pred, 0.966), HL-60 (q2, 0.777; r2, 0.937; r2pred, 0.913), and PC-3 (q2, 0.702; r2, 0.983; r2pred, 0.974) cell lines. The 3D-QSAR contour maps suggested that the C-1 NH and C-4 carbonyl group of the naphthyridine ring and the C-2 naphthyl ring were important for cytotoxicity in all three human cancer cell lines. PMID:24381501

  3. Key structure-activity relationships in the vanadium phosphorus oxide catalyst system

    SciTech Connect

    Thompson, M.R. (Pacific Northwest Lab., Richland, WA (USA)); Ebner, J.R. (Monsanto Co., St. Louis, MO (USA))

    1990-04-01

    The crystal structure of vanadyl pyrophosphate has been redetermined using single crystals obtained from a near solidified melt of a microcrystalline catalyst sample. Crystals that index as vanadyl pyrophosphate obtained from this melt are variable in color. Crystallographic refinement of the single crystal x-ray diffraction data indicates that structural differences among these materials can be described in terms of crystal defects associated with linear disorder of the vanadium atoms. The importance of the disorder is outlined in the context of its effect on the proposed surface topology parallel to (1,0,0). Models of the surface topology simply and intuitively account for the non-stoichometric surface atomic P/V ratio exhibited by selective catalysts of this phase. These models also point to the possible role of the excess phosphorus in providing site isolation of reactive centers at the surface. 33 refs., 7 figs.

  4. Chemical modification, characterization and structure-anticoagulant activity relationships of Chinese lacquer polysaccharides

    Microsoft Academic Search

    Jianhong Yang; Yumin Du; Ronghua Huang; Yunyang Wan; Tianyu Li

    2002-01-01

    A natural lacquer polysaccharide with complex branches was separated into two fractions, LPH (MW 16.9×104) and LPL (MW 6.85×104). Results of 13C NMR and FT-IR indicated they had the same structure. The treatment of LPL with sodium periodate led to a partial cut-off of side chains with 4-O-methyl--d-glucuronic acid in the terminal. These polysaccharides were sulfated in the presence of

  5. Some aspects of the in vivo neuroprotective capacity of flavonoids: Bioavailability and structure-activity relationship

    Microsoft Academic Search

    Felicia Rivera; Jessika Urbanavicius; Elena Gervaz; Andrea Morquio; Federico Dajas

    2004-01-01

    On the basis of previous work showing that flavonoids structurally related to quercetin are neuroprotective for cells in culture,\\u000a this work was directed towards determining if several flavonoids (quercetin, fisetin and catechin) could acutely and by an\\u000a intraperitoneal (IP) route reach significant cerebral concentrations and either prevent or facilitate recovery from a brain\\u000a lesion induced by focal ischemia in rats.

  6. Structure-activity relationships of two Rhodnius prolixus calcitonin-like diuretic hormone analogs.

    PubMed

    Zandawala, Meet; Poulos, Constantine; Orchard, Ian

    2015-06-01

    The calcitonin-like diuretic hormone (CT/DH) in Rhodnius prolixus influences various tissues associated with feeding-related physiological events. The receptors for this peptide have also been identified and shown to be expressed in these tissues. In the present study, we have investigated the effects of two R. prolixus CT/DH analogs (full-length form and N-terminal truncated form) on hindgut contractions and in a heterologous receptor expression system. The analogs contained the amino acid methyl-homoserine in place of methionine in order to prevent them from being oxidized and thus increase their stability. The full-length form of the analog retained all of its activity in our assays when compared to the endogenous peptide. Truncated analog displayed no activity in our assays. PMID:24703964

  7. Cytotoxic constituents from Brazilian red propolis and their structure–activity relationship

    Microsoft Academic Search

    Feng Li; Suresh Awale; Yasuhiro Tezuka; Shigetoshi Kadota

    2008-01-01

    Several classes of flavonoids [flavanoids (1–10), flavonol (11), isoflavones (12–18), isoflavanones (19–22), isoflavans (23–26), chalcones (27–30), auronol (31), pterocarpans (32–37), 2-arylbenzofuran (38), and neoflavonoid (39)] and lignans (40–42) isolated from the MeOH extract of Brazilian red propolis were investigated for their cytotoxic activity against a panel of six different cancer cell lines including murine colon 26-L5 carcinoma, murine B16-BL6 melanoma,

  8. Structure-Activity Relationships of Orotidine-5?-Monophosphate Decarboxylase Inhibitors as Anticancer Agents

    SciTech Connect

    Bello, A.; Konforte, D; Poduch, E; Furlonger, C; Wei, L; Liu, Y; Lewis, M; Pai, E; Paige, C; Kotra, L

    2009-01-01

    A series of 6-substituted and 5-fluoro-6-substituted uridine derivatives were synthesized and evaluated for their potential as anticancer agents. The designed molecules were synthesized from either fully protected uridine or the corresponding 5-fluorouridine derivatives. The mononucleotide derivatives were used for enzyme inhibition investigations against ODCase. Anticancer activities of all the synthesized derivatives were evaluated using the nucleoside forms of the inhibitors. 5-Fluoro-UMP was a very weak inhibitor of ODCase. 6-Azido-5-fluoro and 5-fluoro-6-iodo derivatives are covalent inhibitors of ODCase, and the active site Lys145 residue covalently binds to the ligand after the elimination of the 6-substitution. Among the synthesized nucleoside derivatives, 6-azido-5-fluoro, 6-amino-5-fluoro, and 6-carbaldehyde-5-fluoro derivatives showed potent anticancer activities in cell-based assays against various leukemia cell lines. On the basis of the overall profile, 6-azido-5-fluoro and 6-amino-5-fluoro uridine derivatives exhibited potential for further investigations.

  9. Structure-activity relationship studies of benzoxazinones and related compounds. Phytotoxicity on Echinochloa crus-galli (L.) P. Beauv.

    PubMed

    Macías, Francisco A; Chinchilla, Nuria; Varela, Rosa M; Oliveros-Bastidas, Alberto; Marín, David; Molinillo, José M G

    2005-06-01

    Echinochloa crus-galli (E. crus-galli; barnyardgrass) is a weed widely distributed. It constitutes a serious weed problem in 42 countries and has been found in at least 27 more. It is the world's main weed of rice affecting up to 36 crops worldwide. Several biotypes of this plant, with resistance to herbicides with different modes of action have evolved. In our ongoing studies regarding the potential application of benzoxazinones and their soil degradation products for weed control, a complete structure-activity relationships (SARs) study was made by using barnyardgrass as the target plant. Compounds used in this study were previously tested on a wide variety of standard target species (STS), and they include natural allelochemicals 2-O-beta-D-glucopyranosyl-4-hydroxy-(2H)-1,4-benzoxazin-3(4H)-one (DIBOA-Glc), 2,4-dihydroxy-7-methoxy-(2H)-1,4-benzoxazin-3(4H)-one (DIMBOA), and 2,4-dihydroxy-(2H)-1,4-benzoxazin-3(4H)-one (DIBOA), together with some degradation derivatives found in wheat crop soil and some synthetic analogues. Their phytotoxicity on E. crus-galli is discussed and compared with the results obtained from previous screening. This work constitutes the next step in the search for natural herbicide models based on benzoxazinones and their degradation products. The most active compounds were the degradation product 2-aminophenol (APH) and the synthetic analogue 4-hydroxy-(2H)-1,4-benzoxazin-3(4H)-one (D-DIBOA). Their activities confirm the direction proposed in our previous SAR study, which establishes D-DIBOA to be the best lead for natural herbicide model development with benzoxazinone structure. PMID:15913298

  10. Structure-activity relationships of tea compounds against human cancer cells.

    PubMed

    Friedman, Mendel; Mackey, Bruce E; Kim, Hyun-Jeong; Lee, In-Seon; Lee, Kap-Rang; Lee, Seung-Un; Kozukue, Etsuko; Kozukue, Nobuyuki

    2007-01-24

    The content of the biologically active amino acid theanine in 15 commercial black, green, specialty, and herbal tea leaves was determined as the 2,4-dinitrophenyltheanine derivative (DNP-theanine) by a validated HPLC method. To define relative anticarcinogenic potencies of tea compounds and teas, nine green tea catechins, three black tea theaflavins, and theanine as well as aqueous and 80% ethanol/water extracts of the same tea leaves were evaluated for their ability to induce cell death in human cancer and normal cells using a tetrazolium microculture (MTT) assay. Compared to untreated controls, most catechins, theaflavins, theanine, and all tea extracts reduced the numbers of the following human cancer cell lines: breast (MCF-7), colon (HT-29), hepatoma (liver) (HepG2), and prostate (PC-3) as well as normal human liver cells (Chang). The growth of normal human lung (HEL299) cells was not inhibited. The destruction of cancer cells was also observed visually by reverse phase microscopy. Statistical analysis of the data showed that (a) the anticarcinogenic effects of tea compounds and of tea leaf extracts varied widely and were concentration dependent over the ranges from 50 to 400 microg/mL of tea compound and from 50 to 400 microg/g of tea solids; (b) the different cancer cells varied in their susceptibilities to destruction; (c) 80% ethanol/water extracts with higher levels of flavonoids determined by HPLC were in most cases more active than the corresponding water extracts; and (d) flavonoid levels of the teas did not directly correlate with anticarcinogenic activities. The findings extend related observations on the anticarcinogenic potential of tea ingredients and suggest that consumers may benefit more by drinking both green and black teas. PMID:17227049

  11. HLA-A3 supermotif defined by quantitative structure-activity relationship analysis.

    PubMed

    Guan, Pingping; Doytchinova, Irini A; Flower, Darren R

    2003-01-01

    Activation of a cytotoxic T cell requires specific binding of antigenic peptides to major histocompatibility complex (MHC) molecules. This paper reports a study of peptides binding to members of the HLA-A3 superfamily using a recently developed 2D-QSAR method, called the additive method. Four alleles with high phenotype frequency were included in the study: A*0301, A*1101, A*3101 and A*6801. The influence of each of the 20 amino acids at each position of the peptide on binding was studied. A refined A3 supertype motif was defined in the study. PMID:12646688

  12. Cationic dendron-bearing lipids: investigating structure-activity relationships for small interfering RNA delivery.

    PubMed

    Zhang, Yu; Chen, Jie; Xiao, Chunsheng; Li, Mingqiang; Tian, Huayu; Chen, Xuesi

    2013-12-01

    A new family of cationic dendron-bearing lipids (CDLs) with poly(amidoamine) dendrons of first to third generation (named as A1, A2, and A3, respectively) was synthesized through a synthesis approach that permits facile variation of chemical structures. All CDLs could effectively bind small interfering RNA (siRNA) to form complexes confirmed by gel retardation analysis. In in vitro transfection experiments, A1/siRNA complexes exhibited significant gene silencing efficiency close to Lipofectamine 2000/siRNA complexes and much higher than A2/siRNA and A3/siRNA complexes. To reveal the underlying reason, we performed a series of experimental methods. The results suggested that the CDLs with smaller dendron sizes and higher proportion of hydrophobic segments could bind siRNA to form dendriplex aggregates with more compact structures and higher surface potentials. Therefore, they could be internalized via endocytosis more easily, which was believed to be the main reason for higher gene silencing efficiency. This paper provides an efficient CDL (A1) for siRNA delivery and indicates great potential for gene therapy. PMID:24144000

  13. Structure-activity relationship of quaternary acetylcholinesterase inhibitors - outlook for early myasthenia gravis treatment.

    PubMed

    Komloova, M; Musilek, K; Dolezal, M; Gunn-Moore, F; Kuca, K

    2010-01-01

    Myasthenia gravis is a rare autoimmune neuromuscular junction disorder mainly caused by antibodies being targeted against the muscle acetylcholine receptors (AChRs). The loss of AChRs leads to a defect in neuromuscular transmission resulting in muscle weakness and fatigue. Although once an often fatal illness, Myasthenia gravis can now be well managed with relatively safe and effective treatments. However, the severe myasthenic cases associated with thymus tumors remain often fatal exception in the management of the disease. The early treatment includes the use of acetylcholinesterase inhibitors (AChEI) which enhance neuromuscular transmission. To ensure a peripheral effect, charged molecules are used, particularly quaternary ammonium salts. The structure of AChEIs has been continuously modified to obtain the optimal ratio between AChE inhibition and potential side-effects. This review summarizes progress in the use of quaternary compounds as AChE inhibitors in vitro with respect to their structure and inhibitory ability. Namely, carbamic acid esters, piperidinium and pyridinium salts, bisquaternary pyridinium salts and heterogeneous quaternary inhibitors are all discussed. Among data found in the literature, many compounds have shown promising inhibition of AChE when compared to commercial standards (pyridostigmine, neostigmine). Besides a promising inhibitory ability, selectivity for AChE versus butyrylcholinesterase (BChE) for the most potent compounds (sub-nanomolar IC(50)) was also identified. PMID:20345342

  14. Structure-activity relationship of ibogaine analogs interacting with nicotinic acetylcholine receptors in different conformational states.

    PubMed

    Arias, Hugo R; Feuerbach, Dominik; Targowska-Duda, Katarzyna M; Jozwiak, Krzysztof

    2011-09-01

    The interaction of ibogaine analogs with nicotinic acetylcholine receptors (AChRs) in different conformational states was studied by functional and structural approaches. The results established that ibogaine analogs: (a) inhibit (±)-epibatidine-induced Ca²? influx in human embryonic muscle AChRs with the following potency sequence (IC(50) in ?M): (±)-18-methylaminocoronaridine (5.9±0.3)?(±)-18-methoxycoronaridine (18-MC) (6.8±0.8)>(-)-ibogaine (17±3)?(+)-catharanthine (20±1)>(±)-albifloranine (46±13), (b) bind to the [³H]TCP binding site with higher affinity when the Torpedo AChR is in the desensitized state compared to that in the resting state. Similar results were obtained using [³H]18-MC. These and docking results suggest a steric interaction between TCP and ibogaine analogs for the same site, (c) enhance [³H]cytisine binding to resting but not to desensitized AChRs, with desensitizing potencies (apparent EC??) that correlate very well with the pK(i) values in the desensitized state, and (d) there are good bilinear correlations between the ligand molecular volumes and their affinities in the desensitized and resting states, with an optimal volume of ?345 ?³ for the ibogaine site. These results indicate that the size of the binding sites for ibogaine analogs, located between the serine and nonpolar rings and shared with TCP, is an important structural feature for binding and for inducing desensitization. PMID:21642011

  15. Structure-property-composition relationships in doped zinc oxides: enhanced photocatalytic activity with rare Earth dopants.

    PubMed

    Goodall, Josephine B M; Illsley, Derek; Lines, Robert; Makwana, Neel M; Darr, Jawwad A

    2015-02-01

    In this paper, we demonstrate the use of continuous hydrothermal flow synthesis (CHFS) technology to rapidly produce a library of 56 crystalline (doped) zinc oxide nanopowders and two undoped samples, each with different particle properties. Each sample was produced in series from the mixing of an aqueous stream of basic zinc nitrate (and dopant ion or modifier) solution with a flow of superheated water (at 450 °C and 24.1 MPa), whereupon a crystalline nanoparticle slurry was rapidly formed. Each composition was collected in series, cleaned, freeze-dried, and then characterized using analytical methods, including powder X-ray diffraction, transmission electron microscopy, Brunauer-Emmett-Teller surface area measurement, X-ray photoelectron spectroscopy, and UV-vis spectrophotometry. Photocatalytic activity of the samples toward the decolorization of methylene blue dye was assessed, and the results revealed that transition metal dopants tended to reduce the photoactivity while rare earth ions, in general, increased the photocatalytic activity. In general, low dopant concentrations were more beneficial to having greater photodecolorization in all cases. PMID:25602735

  16. Effects of taurine analogues on chloride channel conductance of rat skeletal muscle fibers: a structure-activity relationship investigation.

    PubMed

    Pierno, S; Tricarico, D; De Luca, A; Campagna, F; Carotti, A; Casini, G; Conte Camerino, D C

    1994-04-01

    In rat skeletal muscle, taurine was proposed to interact with a low affinity binding site on sarcolemmal phospholipids near chloride channel, increasing chloride conductance (GCl). In an attempt to evaluate the structure-activity relationship between taurine and its binding site, a series of N-azacycloalkenyl analogues of taurine (A: N-(1'aza-cyclohepten-2'yl)-2-aminoethane sulfonic acid; B: N-(1'-aza-cyclopenten-2'-yl)-2-aminoethane sulfonic acid; C: N-(1'-aza-cyclohepten-2'-yl)-3-amino-propane sulfonic acid; D: N-(1'aza-cyclopenten-2'-yl)-3-aminopropane sulfonic acid) have been synthetized and tested in vitro on rat extensor digitorum longus (EDL) muscle. In spite of the presence of a bulky and lipophilic 5 or 7 membered heterocycle linked to the taurine amino group, analogues A and B determined an increase of GCl, although less potently than taurine. Also 3-amino-propane sulfonic acid (homotaurine), tested in comparison, showed less activity in increasing GCl with respect to taurine, probably for the increased distance between charged groups. Taurine analogues C and D, which differ from compounds A and B for an additional methylene group, showed much lower activity in increasing GCl. It has been reported that guanidinoethane sulfonate (GES) displaces taurine from the low affinity site on sarcolemma by only 7%. This compound, characterized by lower charge density on the guanidinium cationic head, applied in vitro on EDL muscle, show reduced taurine-like activity in increasing GCl.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:8058113

  17. Design, synthesis, and structure--activity-relationship of tetrahydrothiazolopyridine derivatives as potent smoothened antagonists.

    PubMed

    Ma, Haikuo; Lu, Wenfeng; Sun, Zhijian; Luo, Lusong; Geng, Delong; Yang, Zhaohui; Li, Enqin; Zheng, Jiyue; Wang, Meiyu; Zhang, Hongjian; Yang, Shilin; Zhang, Xiaohu

    2015-01-01

    The Smoothened (Smo) receptor is an important component of the hedgehog (Hh) signaling pathway, which plays a critical role during embryonic development. In adults, Hh signaling is curtailed and has limited functions such as stem cell maintenance and tissue repair. However, aberrant activity of the Hh signaling in adults has been linked to numerous human cancers. Inhibition of Smo leads to the blockade of Hh signaling, and therefore represents a promising approach toward novel anticancer therapy. Through scaffold morphing of a few known Smo antagonists, a series of novel tetrahydrothiazolopyridine derivatives were developed. Compounds from this new scaffold demonstrated excellent Hh signaling inhibition which was comparable to or better than that of Vismodegib. Further, compound 30 exhibited a lower melting point and a moderately improved solubility compared with those of Vismodegib; compounds 11 and 30 showed good pharmacokinetic profiles with 34% and 77% oral bioavailability in rat, respectively. Collectively, these results strongly support further optimization of this novel scaffold to develop better Smo antagonists. PMID:25462278

  18. Design, synthesis, and structure-activity relationships of a series of novel N-aryl-2-phenylcyclopropanecarboxamide that are potent and orally active orexin receptor antagonists.

    PubMed

    Yoshida, Yu; Terauchi, Taro; Naoe, Yoshimitsu; Kazuta, Yuji; Ozaki, Fumihiro; Beuckmann, Carsten T; Nakagawa, Makoto; Suzuki, Michiyuki; Kushida, Ikuo; Takenaka, Osamu; Ueno, Takashi; Yonaga, Masahiro

    2014-11-01

    Herein we describe the design, synthesis, and structure-activity relationships (SARs) of a novel phenylcyclopropane series represented by 7 and 33 b as antagonists of orexin 1 and orexin 2 receptors. With 4 serving as the initial lead for the development of orexin antagonists, exploration of SAR resulted in improved binding affinity for orexin 1 and orexin 2 receptors. Among the synthesized compounds, 33 b ((-)-N-(5-cyanopyridin-2-yl)-2-[(3,4-dimethoxyphenyl)oxymethyl]-2-phenylcyclopropanecarboxamide) exhibited potent in vitro activity and oral efficacy in animal sleep measurement experiments. The results of our study suggest that compound 33 b may serve as a valuable template for the development of new orexin receptor antagonists. PMID:25267004

  19. Multi-Site ?-dynamics for simulated Structure-Activity Relationship studies

    PubMed Central

    Knight, Jennifer L.; Brooks, Charles L.

    2011-01-01

    Multi-Site ?-dynamics (MS?D) is a new free energy simulation method that is based on ?-dynamics. It has been developed to enable multiple substituents at multiple sites on a common ligand core to be modeled simultaneously and their free energies assessed. The efficacy of MS?D for estimating relative hydration free energies and relative binding affinties is demonstrated using three test systems. Model compounds representing multiple identical benzene, dihydroxybenzene and dimethoxybenzene molecules show total combined MS?D trajectory lengths of ~1.5 ns are sufficient to reliably achieve relative hydration free energy estimates within 0.2 kcal/mol and are less sensitive to the number of trajectories that are used to generate these estimates for hybrid ligands that contain up to ten substituents modeled at a single site or five substituents modeled at each of two sites. Relative hydration free energies among six benzene derivatives calculated from MS?D simulations are in very good agreement with those from alchemical free energy simulations (with average unsigned differences of 0.23 kcal/mol and R2=0.991) and experiment (with average unsigned errors of 1.8 kcal/mol and R2=0.959). Estimates of the relative binding affinities among 14 inhibitors of HIV-1 reverse transcriptase obtained from MS?D simulations are in reasonable agreement with those from traditional free energy simulations and experiment (average unsigned errors of 0.9 kcal/mol and R2=0.402). For the same level of accuracy and precision MS?D simulations are achieved ~20–50 times faster than traditional free energy simulations and thus with reliable force field parameters can be used effectively to screen tens to hundreds of compounds in structure-based drug design applications. PMID:22125476

  20. Structure-activity relationships of cyclosporines. Toxicity in cultured renal tubular epithelial cells.

    PubMed

    Walker, R J; Lazzaro, V A; Duggin, G G; Horvath, J S; Tiller, D J

    1989-08-01

    Proximal (LLC-PK1) and distal (MDCK) renal epithelial cell cultures were used to investigate early biochemical changes in cellular metabolism following exposure to cyclosporine A (CsA). 3H-thymidine and 3H-leucine incorporation into the cells were used as indices of DNA and protein synthesis. The cells were exposed to concentrations of CsA ranging from 0.2 microgram/ml to 20 micrograms/ml. By 20 hr there was a decrease in the total cell count at concentrations of 10 and 20 micrograms/ml that was more pronounced by 5 days of exposure. At 5 days there was also a reduction in cell count at the lower concentrations of CsA. There was an initial increase in DNA and protein synthesis at 2 hr with inhibition of DNA synthesis evident by 20 hr. Protein synthesis was increased in the LLC-PK1 cells and decreased in the MDCK cells. At 5 days there was evidence of increased DNA and protein synthesis, most marked in the remaining viable cells exposed to the higher concentrations of CsA. Similar alterations in cellular metabolism were evident when the cells were exposed to the immunologically inert cyclosporine H (D-N-MeVal11-Cs). These studies demonstrate that cyclosporine produces alterations in cellular function as early as 2 hr after exposure to the drug. At the lower concentrations there is evidence of sublethal cellular toxicity and cellular regeneration. The toxicity appears to be related to the molecular structure of cyclosporine and its incorporation into cell membranes. We postulate that cyclosporine nephrotoxicity is the summation of several subtoxic alterations in cellular function the final expression of which is modified by other factors affecting renal function. PMID:2756558

  1. Development of quantitative structure-activity relationship (QSAR) models to predict the carcinogenic potency of chemicals

    SciTech Connect

    Venkatapathy, Raghuraman [Pegasus Technical Services, Inc., 46 E. Hollister St., Cincinnati, OH 45219 (United States)], E-mail: venkatapathy.raghuraman@epa.gov; Wang Chingyi; Bruce, Robert Mark [National Center for Environmental Assessment, U.S. Environmental Protection Agency, 26 W Martin Luther King Drive, Cincinnati, OH 45268 (United States); Moudgal, Chandrika [National Homeland Security Research Center, U.S. Environmental Protection Agency, Region 7, ENSV/IO, 901 N 5th Street, Kansas City, KS 66101 (United States)

    2009-01-15

    Determining the carcinogenicity and carcinogenic potency of new chemicals is both a labor-intensive and time-consuming process. In order to expedite the screening process, there is a need to identify alternative toxicity measures that may be used as surrogates for carcinogenic potency. Alternative toxicity measures for carcinogenic potency currently being used in the literature include lethal dose (dose that kills 50% of a study population [LD{sub 50}]), lowest-observed-adverse-effect-level (LOAEL) and maximum tolerated dose (MTD). The purpose of this study was to investigate the correlation between tumor dose (TD{sub 50}) and three alternative toxicity measures as an estimator of carcinogenic potency. A second aim of this study was to develop a Classification and Regression Tree (CART) between TD{sub 50} and estimated/experimental predictor variables to predict the carcinogenic potency of new chemicals. Rat TD{sub 50}s of 590 structurally diverse chemicals were obtained from the Cancer Potency Database, and the three alternative toxicity measures considered in this study were estimated using TOPKAT, a toxicity estimation software. Though poor correlations were obtained between carcinogenic potency and the three alternative toxicity (both experimental and TOPKAT) measures for the CPDB chemicals, a CART developed using experimental data with no missing values as predictor variables provided reasonable estimates of TD{sub 50} for nine chemicals that were part of an external validation set. However, if experimental values for the three alternative measures, mutagenicity and logP are not available in the literature, then either the CART developed using missing experimental values or estimated values may be used for making a prediction.

  2. Suicidal inactivation of haemoproteins by reductive metabolites of halomethanes: a structure-activity relationship study.

    PubMed

    Manno, M; Tolando, R; Ferrara, R; Rezzadore, M; Cazzaro, S

    1995-06-26

    Human haemoglobin (Hb), methaemalbumin (MHA) or rat liver microsomal cytochrome P-450 (P-450) were incubated anaerobically at microM concentrations with 1 mM carbon tetrachloride (CCl4), trichlorobromomethane (CCl3Br), chloroform (CHCl3) or methylene chloride (CH2Cl2) in presence of 1 mM sodium dithionite as the reducing agent. At the end of a 5-min incubation, haem was measured by various methods, i.e. binding spectrum with CO, pyridine-haemochromogen haem assay and porphyrin fluorescence, and compared for the four analogues. Statistically significant losses were observed, with all three haemo-protein systems, for CCi3Br, CCl4 and CHCl3, but not CH2Cl2. For Hb, the loss was greater with CCl3Br (haem assay, 63%; porphyrin fluorescence, 48%; CO binding, 24%) than with CCl4 (haem assay, 31%) or CHCl3 (haem assay, 13%). On the other hand, with MHA, CCl4 gave a dramatic loss (haem assay, 88%; porphyrin fluorescence, 83%; CO binding, 67%), which was greater than that observed with CCl3Br (haem assay, 49%; porphyrin fluorescence, 38%; CO binding, 25%). No loss was found with CHCl3. Finally, with microsomes, the inactivation was larger with CCl4 (CO binding, 58%; haem assay, 50%; porphyrin fluorescence, 33%) than with CCl3Br (CO binding, 33%; haem assay, 10%) or CHCl3 (haem assay, 9%; CO binding, 6%). In a separate set of similar experiments, an ion-pairing reverse phase HPLC method showed the formation of substrate-dependent hae-derived products during incubation of CCl3Br with Hb or microsomes, and of CCl4 with Hb. A correlation between potential for free radical formation (CCl3Br > CCl4 > CHCl3 > CH2Cl2) and extent of haem inactivation was observed with all methods for Hb, but not for microsomal P-450 or MHA. The results indicate that these halomethanes may be activated differently by different haemoproteins and suggest that their potential ability to undergo reductive metabolism may not be the only critical factor involved in P-450 haem inactivation by these chemicals. PMID:7624875

  3. Nociceptin receptor binding in mouse forebrain membranes: thermodynamic characteristics and structure activity relationships

    PubMed Central

    Varani, K; Calo', G; Rizzi, A; Merighi, S; Toth, G; Guerrini, R; Salvadori, S; Borea, P A; Regoli, D

    1998-01-01

    The present study describes the labelling of the nociceptin (NC) receptor, ORL1, in mouse forebrain membranes with a new ligand partially protected from metabolic degradation at the C-terminal; the ligand, [3H]-NC-NH2, has a specific activity of 24.5?Ci?mmol?1Saturation experiments revealed a single class of binding sites with a KD value of 0.55?nM and Bmax of 94?fmol?mg?1 of protein. Non specific binding was 30% of total binding. Kinetic binding studies yielded the following rate constants: Kobs=0.104?min?1; K1=0.034?min?1; T1/2=20?min; K+1=0.07?min?nM?1.Thermodynamic analyses indicated that [3H]-NC-NH2 binding to the mouse ORL1 is totally entropy driven, similar to what has been observed for the labelled agonists to the opioid receptors OP1(?), OP2(?) and OP3(?).Receptor affinities of several NC fragments and analogues, including the newly discovered ORL-1 receptor antagonist [Phe1?(CH2-NH)Gly2]NC(1–13)-NH2 ([F/G]NC(1–13)-NH2), were also evaluated in displacement experiments. The competition curves for these compounds were found to be parallel to that of NC and the following order of potency was determined for NC fragments: NC-OH=NC-NH2=NC(1–13)-NH2 >> NC(1–12)-NH2 > NC(1–13)-OH >> NC(1–11)-NH2, and for NC and NC(1–13)-NH2 analogues: [Tyr1]NC-NH2 ? [Leu1]NC(1–13)-NH2 ? [Tyr1]NC(1–13)-NH2 ? [F/G]NC(1–13)-NH2 >> [Phe3]NC(1–13)-NH2 > [DF/G]NC(1–13)-NH2.Standard opioid receptor ligands (either agonists or antagonists) were unable to displace [3H]-NC-NH2 binding when applied at concentrations up to 10??M indicating that this new radioligand interacts with a non opioid site, probably the ORL1 receptor. PMID:9884077

  4. Exploring the anti-cancer activity of novel thiosemicarbazones generated through the combination of retro-fragments: dissection of critical structure-activity relationships.

    PubMed

    Serda, Maciej; Kalinowski, Danuta S; Rasko, Nathalie; Pot??ková, Eliška; Mrozek-Wilczkiewicz, Anna; Musiol, Robert; Ma?ecki, Jan G; Sajewicz, Mieczys?aw; Ratuszna, Alicja; Muchowicz, Angelika; Go??b, Jakub; Sim?nek, Tomáš; Richardson, Des R; Polanski, Jaroslaw

    2014-01-01

    Thiosemicarbazones (TSCs) are an interesting class of ligands that show a diverse range of biological activity, including anti-fungal, anti-viral and anti-cancer effects. Our previous studies have demonstrated the potent in vivo anti-tumor activity of novel TSCs and their ability to overcome resistance to clinically used chemotherapeutics. In the current study, 35 novel TSCs of 6 different classes were designed using a combination of retro-fragments that appear in other TSCs. Additionally, di-substitution at the terminal N4 atom, which was previously identified to be critical for potent anti-cancer activity, was preserved through the incorporation of an N4-based piperazine or morpholine ring. The anti-proliferative activity of the novel TSCs were examined in a variety of cancer and normal cell-types. In particular, compounds 1d and 3c demonstrated the greatest promise as anti-cancer agents with potent and selective anti-proliferative activity. Structure-activity relationship studies revealed that the chelators that utilized "soft" donor atoms, such as nitrogen and sulfur, resulted in potent anti-cancer activity. Indeed, the N,N,S donor atom set was crucial for the formation of redox active iron complexes that were able to mediate the oxidation of ascorbate. This further highlights the important role of reactive oxygen species generation in mediating potent anti-cancer activity. Significantly, this study identified the potent and selective anti-cancer activity of 1d and 3c that warrants further examination. PMID:25329549

  5. Anti-listerial activity and structure–activity relationships of the six major tyrocidines, cyclic decapeptides from Bacillus aneurinolyticus

    Microsoft Academic Search

    Barbara M. Spathelf; Marina Rautenbach

    2009-01-01

    Six major tyrocidines, purified from the antibiotic tyrothricin complex produced by Bacillus aneurinolyticus, showed significant lytic and growth inhibitory activity towards the Gram+ bacteria, Micrococcus luteus and Listeria monocytogenes, but not against the Gram? bacterium, Escherichia coli. The isolated natural tyrocidines were in particular more active against the leucocin A (antimicrobial peptide) resistant strain, L. monocytogenes B73-MR1, than the sensitive

  6. Three-dimensional quantitative structure-activity relationships and docking studies of some structurally diverse flavonoids and design of new aldose reductase inhibitors

    PubMed Central

    Chandra De, Utpal; Debnath, Tanusree; Sen, Debanjan; Debnath, Sudhan

    2015-01-01

    Aldose reductase (AR) plays an important role in the development of several long-term diabetic complications. Inhibition of AR activities is a strategy for controlling complications arising from chronic diabetes. Several AR inhibitors have been reported in the literature. Flavonoid type compounds are shown to have significant AR inhibition. The objective of this study was to perform a computational work to get an idea about structural insight of flavonoid type compounds for developing as well as for searching new flavonoid based AR inhibitors. The data-set comprising 68 flavones along with their pIC50 values ranging from 0.44 to 4.59 have been collected from literature. Structure of all the flavonoids were drawn in Chembiodraw Ultra 11.0, converted into corresponding three-dimensional structure, saved as mole file and then imported to maestro project table. Imported ligands were prepared using LigPrep option of maestro 9.6 version. Three-dimensional quantitative structure-activity relationships and docking studies were performed with appropriate options of maestro 9.6 version installed in HP Z820 workstation with CentOS 6.3 (Linux). A model with partial least squares factor 5, standard deviation 0.2482, R2 = 0.9502 and variance ratio of regression 122 has been found as the best statistical model. PMID:25709964

  7. Synthesis, structure-activity, and structure-stability relationships of 2-substituted-N-(4-oxo-3-oxetanyl) N-acylethanolamine acid amidase (NAAA) inhibitors.

    PubMed

    Vitale, Romina; Ottonello, Giuliana; Petracca, Rita; Bertozzi, Sine Mandrup; Ponzano, Stefano; Armirotti, Andrea; Berteotti, Anna; Dionisi, Mauro; Cavalli, Andrea; Piomelli, Daniele; Bandiera, Tiziano; Bertozzi, Fabio

    2014-02-01

    N-Acylethanolamine acid amidase (NAAA) is a cysteine amidase that preferentially hydrolyzes saturated or monounsaturated fatty acid ethanolamides (FAEs), such as palmitoylethanolamide (PEA) and oleoylethanolamide (OEA), which are endogenous agonists of nuclear peroxisome proliferator-activated receptor-? (PPAR-?). Compounds that feature an ?-amino-?-lactone ring have been identified as potent and selective NAAA inhibitors and have been shown to exert marked anti-inflammatory effects that are mediated through FAE-dependent activation of PPAR-?. We synthesized and tested a series of racemic, diastereomerically pure ?-substituted ?-amino-?-lactones, as either carbamate or amide derivatives, investigating the structure-activity and structure-stability relationships (SAR and SSR) following changes in ?-substituent size, relative stereochemistry at the ?- and ?-positions, and ?-amino functionality. Substituted carbamate derivatives emerged as more active and stable than amide analogues, with the cis configuration being generally preferred for stability. Increased steric bulk at the ?-position negatively affected NAAA inhibitory potency, while improving both chemical and plasma stability. PMID:24403170

  8. Structure-activity relationships in new polycationic molecules based on two 1,4-diazabicyclo[2.2.2]octanes as artificial ribonucleases.

    PubMed

    Burakova, E; Kovalev, N; Zenkova, M; Vlassov, V; Silnikov, V

    2014-12-01

    In the present study, we designed and synthesised new polycationic molecules based on two 1,4-diazabicyclo[2.2.2]octane (DABCO) moieties with hydrophobic groups connected by different linkers. The structure and the RNA-cleavage activity relationships of this novel series of artificial ribonucleases (aRNases) were investigated. PMID:25462988

  9. STRUCTURE-ACTIVITY RELATIONSHIPS FOR INSECT KININS ON EXPRESSED RECEPTORS FROM A TICK (ACARI:IXODIDAE) AND A MOSQUITO (DIPTERA:CULICIDAE)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The systematic analysis of structure-activity relationships of insect kinins on two heterologous receptor-expressing systems is described. Previously, kinin receptors from the southern cattle tick, Boophilus microplus (Canestrini, 1888) [1; 2] and the dengue vector, the mosquito Aedes aegypti (L.) ...

  10. Data mining and machine learning techniques for the identification of mutagenicity inducing substructures and structure activity relationships of noncongeneric compounds.

    PubMed

    Helma, Christoph; Cramer, Tobias; Kramer, Stefan; De Raedt, Luc

    2004-01-01

    This paper explores the utility of data mining and machine learning algorithms for the induction of mutagenicity structure-activity relationships (SARs) from noncongeneric data sets. We compare (i) a newly developed algorithm (MOLFEA) for the generation of descriptors (molecular fragments) for noncongeneric compounds with traditional SAR approaches (molecular properties) and (ii) different machine learning algorithms for the induction of SARs from these descriptors. In addition we investigate the optimal parameter settings for these programs and give an exemplary interpretation of the derived models. The predictive accuracies of models using MOLFEA derived descriptors is approximately 10-15%age points higher than those using molecular properties alone. Using both types of descriptors together does not improve the derived models. From the applied machine learning techniques the rule learner PART and support vector machines gave the best results, although the differences between the learning algorithms are only marginal. We were able to achieve predictive accuracies up to 78% for 10-fold cross-validation. The resulting models are relatively easy to interpret and usable for predictive as well as for explanatory purposes. PMID:15272848

  11. Determination of boiling point of petrochemicals by gas chromatography-mass spectrometry and multivariate regression analysis of structural activity relationship.

    PubMed

    Fakayode, Sayo O; Mitchell, Breanna S; Pollard, David A

    2014-08-01

    Accurate understanding of analyte boiling points (BP) is of critical importance in gas chromatographic (GC) separation and crude oil refinery operation in petrochemical industries. This study reported the first combined use of GC separation and partial-least-square (PLS1) multivariate regression analysis of petrochemical structural activity relationship (SAR) for accurate BP determination of two commercially available (D3710 and MA VHP) calibration gas mix samples. The results of the BP determination using PLS1 multivariate regression were further compared with the results of traditional simulated distillation method of BP determination. The developed PLS1 regression was able to correctly predict analytes BP in D3710 and MA VHP calibration gas mix samples, with a root-mean-square-%-relative-error (RMS%RE) of 6.4%, and 10.8% respectively. In contrast, the overall RMS%RE of 32.9% and 40.4%, respectively obtained for BP determination in D3710 and MA VHP using a traditional simulated distillation method were approximately four times larger than the corresponding RMS%RE of BP prediction using MRA, demonstrating the better predictive ability of MRA. The reported method is rapid, robust, and promising, and can be potentially used routinely for fast analysis, pattern recognition, and analyte BP determination in petrochemical industries. PMID:24881546

  12. Structure-activity relationship for the estimation of OH-oxidation rate constants of carbonyl compounds in the aqueous phase

    NASA Astrophysics Data System (ADS)

    Doussin, J. F.; Monod, A.

    2013-06-01

    In the atmosphere, one important class of reactions occurs in the aqueous phase in which organic compounds are known to undertake oxidation towards a number of radicals, among which OH radicals are the most reactive oxidants. In 2008, Monod and Doussin have proposed a new structure activity relationship (SAR) to calculate OH-oxidation rate constants in the aqueous phase. This estimation method is based on the group-additivity principle and was until now limited to alkanes, alcohols, acids, bases and related polyfunctional compounds. In this work, the initial SAR is extended to carbonyl compounds, including aldehydes, ketones, dicarbonyls, hydroxy-carbonyls, acidic carbonyls, their conjugated bases, and the hydrated form of all these compounds. To do so, only five descriptors have been added and none of the previously attributed descriptors were modified. This extension leads now to a SAR which is based on a database of 102 distinct compounds for which 252 experimental kinetic rate constants have been gathered and reviewed. The efficiency of this updated SAR is such that 58% of the rate constants could be calculated within ±20% of the experimental data and 76% within ±40%.

  13. Structure-activity relationship for the estimation of OH-oxidation rate constants of carbonyl compounds in the aqueous phase

    NASA Astrophysics Data System (ADS)

    Doussin, J.-F.; Monod, A.

    2013-12-01

    In the atmosphere, one important class of reactions occurs in the aqueous phase in which organic compounds are known to undergo oxidation towards a number of radicals, among which OH radicals are the most reactive oxidants. In 2008, Monod and Doussin have proposed a new structure-activity relationship (SAR) to calculate OH-oxidation rate constants in the aqueous phase. This estimation method is based on the group-additivity principle and was until now limited to alkanes, alcohols, acids, bases and related polyfunctional compounds. In this work, the initial SAR is extended to carbonyl compounds, including aldehydes, ketones, dicarbonyls, hydroxy carbonyls, acidic carbonyls, their conjugated bases, and the hydrated form of all these compounds. To do so, only five descriptors have been added and none of the previously attributed descriptors were modified. This extension leads now to a SAR which is based on a database of 102 distinct compounds for which 252 experimental kinetic rate constants have been gathered and reviewed. The efficiency of this updated SAR is such that 58% of the rate constants could be calculated within ±20% of the experimental data and 76% within ±40% (respectively 41 and 72% for the carbonyl compounds alone).

  14. Structure–activity relationships of a caged thrombin binding DNA aptamer: Insight gained from molecular dynamics simulation studies

    Microsoft Academic Search

    Prabha Jayapal; Günter Mayer; Alexander Heckel; Frank Wennmohs

    2009-01-01

    15-mer ssDNA aptamers play a vital role in the inhibition of ?-thrombin in the blood clotting mechanism. It is of high importance to explore the structural factors controlling the inhibitory nature of the aptamer. Here we investigated the structure–function relationship of the anti-thrombin aptamer, as well as its ‘caged’ variant (2-(2-nitrophenyl)-propyl group (NPP)) by molecular dynamics simulations. The stability of

  15. Derivation of structure-activity relationships from the anticancer properties of ruthenium(II) arene complexes with 2-aryldiazole ligands.

    PubMed

    Martínez-Alonso, Marta; Busto, Natalia; Jalón, Félix A; Manzano, Blanca R; Leal, José M; Rodríguez, Ana M; García, Begoña; Espino, Gustavo

    2014-10-20

    The ligands 2-pyridin-2-yl-1H-benzimidazole (HL(1)), 1-methyl-2-pyridin-2-ylbenzimidazole (HL(2)), and 2-(1H-imidazol-2-yl)pyridine (HL(3)) and the proligand 2-phenyl-1H-benzimidazole (HL(4)) have been used to prepare five different types of new ruthenium(II) arene compounds: (i) monocationic complexes with the general formula [(?(6)-arene)RuCl(?(2)-N,N-HL)]Y [HL = HL(1), HL(2), or HL(3); Y = Cl or BF4; arene = 2-phenoxyethanol (phoxet), benzene (bz), or p-cymene (p-cym)]; (ii) dicationic aqua complexes of the formula [(?(6)-arene)Ru(OH2)(?(2)-N,N-HL(1))](Y)2 (Y = Cl or TfO; arene = phoxet, bz, or p-cym); (iii) the nucleobase derivative [(?(6)-arene)Ru(9-MeG)(?(2)-N,N-HL(1))](PF6)2 (9-MeG = 9-methylguanine); (iv) neutral complexes consistent with the formulation [(?(6)-arene)RuCl(?(2)-N,N-L(1))] (arene = bz or p-cym); (v) the neutral cyclometalated complex [(?(6)-p-cym)RuCl(?(2)-N,C-L(4))]. The cytototoxic activity of the new ruthenium(II) arene compounds has been evaluated in several cell lines (MCR-5, MCF-7, A2780, and A2780cis) in order to establish structure-activity relationships. Three of the compounds with the general formula [(?(6)-arene)RuCl(?(2)-N,N-HL(1))]Cl differing in the arene moiety have been studied in depth in terms of thermodynamic dissociation constants, aquation kinetic constants, and DNA binding measurements. The biologically most active compound is the p-cym derivative, which strongly destabilizes the DNA double helix, whereas those with bz and phoxet have only a small effect on the stability of the DNA double helix. Moreover, the inhibitory activity of several compounds toward CDK1 has also been evaluated. The DNA binding ability of some of the studied compounds and their CDK1 inhibitory effect suggest a multitarget mechanism for their biological activity. PMID:25302401

  16. A novel quantitative structure-activity relationship model for prediction of biomagnification factor of some organochlorine pollutants.

    PubMed

    Fatemi, Mohammad Hossein; Baher, Elham

    2009-08-01

    The biomagnification factor (BMF) is an important property for toxicology and environmental chemistry. In this work, quantitative structure-activity relationship (QSAR) models were used for the prediction of BMF for a data set including 30 polychlorinated biphenyls and 12 organochlorine pollutants. This set was divided into training and prediction sets. The result of diversity test reveals that the structure of the training and test sets can represent those of the whole ones. After calculation and screening of a large number of molecular descriptors, the methods of stepwise multiple linear regression and genetic algorithm (GA) were used for the selection of most important and significant descriptors which were related to BMF. Then multiple linear regression and artificial neural network (ANN) techniques were applied as linear and non-linear feature mapping techniques, respectively. By comparison between statistical parameters of these methods it was concluded that an ANN model, which used GA selected descriptors, was superior over constructed models. Descriptors which were used by this model are: topographic electronic index, complementary information content, XY shadow/XY rectangle and difference between partial positively and negatively charge surface area. The standard errors for training and test sets of this model are 0.03 and 0.20, respectively. The degree of importance of each descriptor was evaluated by sensitivity analysis approach for the nonlinear model. A good results (Q (2) = 0.97 and SPRESS = 0.084) is obtained by applying cross-validation test that indicating the validation of descriptors in the obtained model in prediction of BMF for these compounds. PMID:19219557

  17. Structure-activity relationships in a new series of insecticidally active dioxatricycloalkenes derived by structural comparison of the GABA (. gamma. -aminobutyric acid) antagonists bicycloorthocarboxylates and endosulfan

    SciTech Connect

    Ozoe, Yoshihisa; Sawada, Yoshihiro; Mochida, Kazuo; Nakamura, Toshiie (Shimane Univ. (Japan)); Matsumura, Fumio (Univ. of California, Davis (USA))

    1990-05-01

    To study structural requirements for picrotoxinin-type GABA ({gamma}-aminobutyric acid) antagonists to interact with the receptor site, 5-substituted 4,6-dioxatricyclo(7.2.1.0{sup 2,8})dodec-10-enes and related compounds were prepared and examined for their insecticidal activity and potency in displacing ({sup 35}S)tert-butylbicyclophosphorothionate (TBPS) binding. Compounds with high insecticidal activity possessed a phenyl group with an electron-withdrawing para substituent, a cycloalkyl group, or a C{sub 3}-C{sub 5} straight-chain alkyl group at the 5-position. The effect of the 5-substituents on insecticidal activity was very similar to that of the 1-substituents of the bicyloorthocarboxylate GABA antagonists. Representative dioxatricycloalkenes displaced the binding of the GABA antagonist ({sup 35}S)TBPS to housefly head membranes by 29-53% at 10 {mu}M. X-ray crystal structure analysis demonstrated that this class of compounds had structures superimposable on those of 4-tert-butylbicycloorthocarboxylates. These findings indicate that the dioxatricycloalkenes and some other analogues occupy the picrotoxinin binding site in such a way that the fourth interacting subsite of the receptor site accommodates the 5-substituent.

  18. SOD Therapeutics: Latest Insights into Their Structure-Activity Relationships and Impact on the Cellular Redox-Based Signaling Pathways

    PubMed Central

    Tovmasyan, Artak; Roberts, Emily R. H.; Vujaskovic, Zeljko; Leong, Kam W.; Spasojevic, Ivan

    2014-01-01

    Abstract Significance: Superoxide dismutase (SOD) enzymes are indispensable and ubiquitous antioxidant defenses maintaining the steady-state levels of O2·?; no wonder, thus, that their mimics are remarkably efficacious in essentially any animal model of oxidative stress injuries thus far explored. Recent Advances: Structure-activity relationship (half-wave reduction potential [E1/2] versus log kcat), originally reported for Mn porphyrins (MnPs), is valid for any other class of SOD mimics, as it is dominated by the superoxide reduction and oxidation potential. The biocompatible E1/2 of ?+300?mV versus normal hydrogen electrode (NHE) allows powerful SOD mimics as mild oxidants and antioxidants (alike O2·?) to readily traffic electrons among reactive species and signaling proteins, serving as fine mediators of redox-based signaling pathways. Based on similar thermodynamics, both SOD enzymes and their mimics undergo similar reactions, however, due to vastly different sterics, with different rate constants. Critical Issues: Although log kcat(O2·?) is a good measure of therapeutic potential of SOD mimics, discussions of their in vivo mechanisms of actions remain mostly of speculative character. Most recently, the therapeutic and mechanistic relevance of oxidation of ascorbate and glutathionylation and oxidation of protein thiols by MnP-based SOD mimics and subsequent inactivation of nuclear factor ?B has been substantiated in rescuing normal and killing cancer cells. Interaction of MnPs with thiols seems to be, at least in part, involved in up-regulation of endogenous antioxidative defenses, leading to the healing of diseased cells. Future Directions: Mechanistic explorations of single and combined therapeutic strategies, along with studies of bioavailability and translational aspects, will comprise future work in optimizing redox-active drugs. Antioxid. Redox Signal. 20, 2372–2415. PMID:23875805

  19. Activation by sintering of Pt-beta catalysts in deNO x HC-SCR. Structure–activity relationships

    Microsoft Academic Search

    J. M Garc??a-Cortés; J Pérez-Ram??rez; M. J Illán-Gómez; C Salinas-Mart??nez de Lecea

    2003-01-01

    The effect of the platinum particle size on the selective catalytic reduction of NOx with C3H6 over Pt-beta has been investigated. The structure sensitivity of the lean deNOx reaction towards the platinum phase has been confirmed and a linear correlation between the TOF and the platinum particle size has been derived. Based on our results, it seems that key elements

  20. TRANSFORMATION OF DEVELOPMENTAL NEUROTOXICITY DATA INTO STRUCTURE-SEARCHABLE TOXML DATABASE IN SUPPORT OF STRUCTURE-ACTIVITY RELATIONSHIP (SAR) WORKFLOW.

    EPA Science Inventory

    Early hazard identification of new chemicals is often difficult due to lack of data on the novel material for toxicity endpoints, including neurotoxicity. At present, there are no structure searchable neurotoxicity databases. A working group was formed to construct a database to...

  1. Design, Synthesis, and Structure-Activity Relationship Studies of Thiophene- 3-carboxamide Derivatives as Dual Inhibitors of the c-Jun N-Terminal Kinase

    PubMed Central

    De, Surya K.; Barile, Elisa; Chen, Vida; Stebbins, John L.; Cellitti, Jason F.; Machleidt, Thomas; Carlson, Coby B.; Yang, Li; Dahl, Russell; Pellecchia, Maurizio

    2011-01-01

    We report comprehensive structure activity relationship studies on a novel series of c-Jun N-terminal kinase (JNK) inhibitors. Intriguingly, the compounds have a dual inhibitory activity by functioning as both ATP and JIP mimetics, possibly by binding to both the ATP binding site and to the docking site of the kinase. Several of such novel compounds display potent JNK inhibitory profiles both in vitro and in cell. PMID:21458276

  2. Structure-activity relationships of analogs of 3,4,5-trimethylfuran-2(5H)-one with germination inhibitory activities.

    PubMed

    Pošta, Martin; Light, Marnie E; Papenfus, Heino B; Van Staden, Johannes; Kohout, Ladislav

    2013-09-15

    Smoke-derived butenolide compounds have, in recent years, been shown to be important germination signaling molecules, which also affect seedling growth. The butenolide 3,4,5-trimethylfuran-2(5H)-one was previously isolated from plant-derived smoke and was found to significantly reduce the effect on germination by the highly active promotor karrikinolide (KAR1, 3-methyl-2H-furo[2,3-c]pyran-2-one), another smoke-derived compound. In this study, 11 analogs of 3,4,5-trimethylfuran-2(5H)-one were synthesized and their effect on the germination of light-sensitive 'Grand Rapids' lettuce seeds (Lactua sativa cv. 'Grand Rapids') were evaluated. A concentration series (1mM-1?M) of the analogs were tested alone, or in combination with 0.01?M KAR1. Only two compounds were found to reduce the germination promotory effect of 0.01?M KAR1 in a similar manner as observed with 3,4,5-trimethylfuran-2(5H)-one, with activity ranging from 1mM to 10?M. Four compounds were found to have inhibitory activity at 1mM and 100?M. The retention of activity by some of the analogs may be useful for designing novel compounds with improved activity. Furthermore, understanding the structure-activity relationships of these compounds may be helpful in synthesizing molecular probes that can be used to further investigate the mechanism of action of these compounds in regulating seed germination. PMID:23648109

  3. Pseudocyanides of sanguinarine and chelerythrine and their series of structurally simple analogues as new anticancer lead compounds: Cytotoxic activity, structure-activity relationship and apoptosis induction.

    PubMed

    Cao, Fang-Jun; Yang, Rui; Lv, Chao; Ma, Qun; Lei, Ming; Geng, Hui-Ling; Zhou, Le

    2015-01-25

    6-Cyano dihydrosanguinarine (CNS) and 6-cyano dihydrochelerythrine (CNC) are respectively artificial derivatives of sanguinarine and chelerythrine, two anticancer quaternary benzo[c]phenanthridine alkaloids (QBAs) while 1-cyano-2-aryl-1,2,3,4-tetrahydroisoquinolines (CATHIQs) are a class of structurally simple analogues of CNS or CNC. This study investigated the inhibition activity of CNS, CNC and CATHIQs on cancer cells, apoptosis induction as well as their preliminary SAR. The results showed that CNS and 18 out of CATHIQs showed IC50 values of 0.53 and 0.62-2.24?M against NB4 and 1.53 and 2.99-11.17?M against MKN-45 cells, respectively, superior to a standard anticancer drug cis-platinum with IC50 of 2.39 and 11.36?M. CNC showed a higher activity against NB4 cells (IC50=1.85?M) and a moderate activity against MKN-45 cells (IC50=12.72?M). Among all CATHIQs, 2 and 17 gave the highest activity against NB4 cells and MKN-45 cells (IC50=0.62 and 2.99?M), respectively. DAPI staining, AO/EB staining and ultrastructure analysis of cells demonstrated that CATHIQs were able to induce apoptosis of the cells in a concentration-dependent manner. SAR showed that substitution patterns on the N-aromatic ring significantly influenced the activity of CATHIQs. The general trend was that the introduction of electron-withdrawing substituents like halogen atom, nitro, trifluoromethyl led to a significant improvement of the activity, while the presence of electron-donating groups like methyl, methoxyl caused a reduction of the activity. In most cases, the 2' site was the most favorable substitution position for the improvement of the activity. Thus, the present results strongly suggested that QBA-type pseudocyanides may serve as potential alternatives of anticancer QBAs while CATHIQs should be a class of promising lead compounds for the development of new QBA-like-type anticancer drugs. CNS exhibited the highest cytotoxicities with IC50 values of 0.53?M on NB4 cells and 1.53?M on MKN-45 cells. PMID:25444843

  4. Noncompetitive Antagonist Binding Sites in the Torpedo Nicotinic Acetylcholine Receptor Ion Channel. Structure?Activity Relationship Studies Using Adamantane Derivatives †

    Microsoft Academic Search

    Hugo R. Arias; James R. Trudell; Erin Z. Bayer; Brent Hester; Elizabeth A. McCardy; Michael P. Blanton

    2003-01-01

    We used a series of adamantane derivatives to probe the structure of the phencyclidine locus in either the resting or desensitized state of the nicotinic acetylcholine receptor (AChR). Competitive radioligand binding and photolabeling experiments using well-characterized noncompetitive antagonists such as the phencyclidine analogue (piperidyl-3,4-3H(N))-N-(1-(2-thienyl)cyclohexyl)-3,4-piperidine (( 3H)- TCP), (3H)ethidium, (3H)tetracaine, (14C)amobarbital, and 3-(trifluoromethyl)-3-(m-(125I)iodophenyl)- diazirine ((125I)TID) were performed. Thermodynamic and structure-function relationship

  5. Anticancer and antiangiogenic activity of surfactant-free nanoparticles based on self-assembled polymeric derivatives of vitamin e: structure-activity relationship.

    PubMed

    Palao-Suay, Raquel; Aguilar, María Rosa; Parra-Ruiz, Francisco J; Fernández-Gutiérrez, Mar; Parra, Juan; Sánchez-Rodríguez, Carolina; Sanz-Fernández, Ricardo; Rodrigáñez, Laura; Román, Julio San

    2015-05-11

    ?-Tocopheryl succinate (?-TOS) is a well-known mitochondrially targeted anticancer compound, however, it is highly hydrophobic and toxic. In order to improve its activity and reduce its toxicity, new surfactant-free biologically active nanoparticles (NP) were synthesized. A methacrylic derivative of ?-TOS (MTOS) was prepared and incorporated in amphiphilic pseudoblock copolymers when copolymerized with N-vinylpyrrolidone (VP) by free radical polymerization (poly(VP-co-MTOS)). The selected poly(VP-co-MTOS) copolymers formed surfactant-free NP by nanoprecipitation with sizes between 96 and 220 nm and narrow size distribution, and the in vitro biological activity was tested. In order to understand the structure-activity relationship three other methacrylic monomers were synthesized and characterized: MVE did not have the succinate group, SPHY did not have the chromanol ring, and MPHY did not have both the succinate group and the chromanol ring. The corresponding families of copolymers (poly(VP-co-MVE), poly(VP-co-SPHY), and poly(VP-co-MPHY)) were synthesized and characterized, and their biological activity was compared to poly(VP-co-MTOS). Both poly(VP-co-MTOS) and poly(VP-co-MVE) presented triple action: reduced cell viability of cancer cells with little or no harm to normal cells (anticancer), reduced viability of proliferating endothelial cells with little or no harm to quiescent endothelial cells (antiangiogenic), and efficiently encapsulated hydrophobic molecules (nanocarrier). The anticancer and antiangiogenic activity of the synthesized copolymers is demonstrated as the active compound (vitamin E or ?-tocopheryl succinate) do not need to be cleaved to trigger the biological action targeting ubiquinone binding sites of complex II. Poly(VP-co-SPHY) and poly(VP-co-MPHY) also formed surfactant-free NP that were also endocyted by the assayed cells; however, these NP did not selectively reduce cell viability of cancer cells. Therefore, the chromanol ring of the vitamin E analogues has an important role in the biological activity of the copolymers. Moreover, when succinate moiety is substituted and vitamin E is directly linked to the macromolecular chain through an ester bond, the biological activity is maintained. PMID:25848887

  6. Structure-Activity Relationship and Substrate-Dependent Phenomena in Effects of Ginsenosides on Activities of Drug-Metabolizing P450 Enzymes

    PubMed Central

    Hao, Miao; Zhao, Yuqing; Chen, Peizhan; Huang, He; Liu, Hong; Jiang, Hualiang; Zhang, Ruiwen; Wang, Hui

    2008-01-01

    Ginseng, a traditional herbal medicine, may interact with several co-administered drugs in clinical settings, and ginsenosides, the major active components of ginseng, may be responsible for these ginseng-drug interactions (GDIs). Results from previous studies on ginsenosides' effects on human drug-metabolizing P450 enzymes are inconsistent and confusing. Herein, we first evaluated the inhibitory effects of fifteen ginsenosides and sapogenins on human CYP1A2, CYP2C9, CYP2C19, CYP2D6 and CYP3A4 enzymes by using commercially available fluorescent probes. The structure-activity relationship of their effects on the P450s was also explored and a pharmacophore model was established for CYP3A4. Moreover, substrate-dependent phenomena were found in ginsenosides' effects on CYP3A4 when another fluorescent probe was used, and were further confirmed in tests with conventional drug probes and human liver microsomes. These substrate-dependent effects of the ginsenosides may provide an explanation for the inconsistent results obtained in previous GDI reports. PMID:18628990

  7. Toxic and antifeedant activities of prenylated flavonoids isolated from Tephrosia apollinea L. against three major coleopteran pests of stored grains with reference to their structure-activity relationship.

    PubMed

    Nenaah, Gomah E

    2014-01-01

    Four prenylated flavonoids, isoglabratephrin, (+)-glabratephrin, tephroapollin-F and lanceolatin-A, were isolated from Tephrosia apollinea L. and tested against three stored grain insects. Using the filter paper bioassay, compounds showed adulticidal activity against Sitophilus oryzae (L), Rhyzopertha dominica (F) and Tribolium castaneum (Herbst) at concentrations of 0.875, 1.75 and 3.5 mg mL(- 1). At 3.5 mg mL(- 1), tephroapollin-F was the most toxic (78.6%, 64.6% and 60.7% mortality was recorded after 10 days exposure of S. oryzae, R. dominica and T. castaneum, respectively). The F1 progeny production of insects was affected after parental exposure to flavonoids, where S. oryzae was the most susceptible. A nutritional bioassay, employing a flour disc and test concentrations of 0.65, 1.3 and 2.6 mg g(- 1), revealed a significant reduction in the relative growth rate, relative consumption rate and efficiency of conversion of ingested food by all insects. The structure-activity relationship among the tested flavonoids was discussed. PMID:24980754

  8. Structure-activity relationships in the haemolytic activity and nephrotoxicity of derivatives of 1,2- and 1,4-naphthoquinone.

    PubMed

    Munday, Rex; Smith, Barry L; Munday, Christine M

    2007-01-01

    Naphthoquinone derivatives are under investigation as potential therapeutic agents. Some such compounds are known, however, to be toxic to both animals and humans. Many naphthoquinone derivatives are haemolytic agents, while others cause necrosis of tubular epithelial cells. In the present study, the short-term toxicity of 16 derivatives of 1,2- and 1,4-naphthoquinone has been examined in rats in order to give information on structure-activity relationships. All the naphthoquinones except one caused haemolytic anaemia, but only hydroxy and amino derivatives were nephrotoxic. Among derivatives of 2-amino-1,4-naphthoquinone, substitution in the 3-position decreased haemolytic activity and abolished nephrotoxicity. Methylation of the hydroxyl group of 2-hydroxy-1,4-naphthoquinone had a similar effect. In contrast, methylation of the amino group of 2-amino-1,4-naphthoquinone increased the severity of both haemolysis and renal damage. Among the 1,2-naphthoquinones tested, the 4-methoxy and 4-amino derivatives were more toxic than the corresponding 1,4-isomers, although 4-methyl-1,2-naphthoquinone was less toxic than 2-methyl-1,4-naphthoquinone. At present, the toxicity of naphthoquinone derivatives cannot accurately be predicted on the basis of their chemical structure. In developing naphthoquinone derivatives for use in humans, toxicological studies in animals should be conducted at an early stage, bearing in mind that clinical studies have shown that humans appear to be particularly vulnerable to the nephrotoxic action of these compounds, and that certain individuals are unusually susceptible to their haemolytic action. PMID:17265417

  9. Modeling chemical interaction profiles: I. Spectral data-activity relationship and structure-activity relationship models for inhibitors and non-inhibitors of cytochrome P450 CYP3A4 and CYP2D6 isozymes.

    PubMed

    McPhail, Brooks; Tie, Yunfeng; Hong, Huixiao; Pearce, Bruce A; Schnackenberg, Laura K; Ge, Weigong; Valerio, Luis G; Fuscoe, James C; Tong, Weida; Buzatu, Dan A; Wilkes, Jon G; Fowler, Bruce A; Demchuk, Eugene; Beger, Richard D

    2012-01-01

    An interagency collaboration was established to model chemical interactions that may cause adverse health effects when an exposure to a mixture of chemicals occurs. Many of these chemicals--drugs, pesticides, and environmental pollutants--interact at the level of metabolic biotransformations mediated by cytochrome P450 (CYP) enzymes. In the present work, spectral data-activity relationship (SDAR) and structure-activity relationship (SAR) approaches were used to develop machine-learning classifiers of inhibitors and non-inhibitors of the CYP3A4 and CYP2D6 isozymes. The models were built upon 602 reference pharmaceutical compounds whose interactions have been deduced from clinical data, and 100 additional chemicals that were used to evaluate model performance in an external validation (EV) test. SDAR is an innovative modeling approach that relies on discriminant analysis applied to binned nuclear magnetic resonance (NMR) spectral descriptors. In the present work, both 1D ¹³C and 1D ¹?N-NMR spectra were used together in a novel implementation of the SDAR technique. It was found that increasing the binning size of 1D ¹³C-NMR and ¹?N-NMR spectra caused an increase in the tenfold cross-validation (CV) performance in terms of both the rate of correct classification and sensitivity. The results of SDAR modeling were verified using SAR. For SAR modeling, a decision forest approach involving from 6 to 17 Mold2 descriptors in a tree was used. Average rates of correct classification of SDAR and SAR models in a hundred CV tests were 60% and 61% for CYP3A4, and 62% and 70% for CYP2D6, respectively. The rates of correct classification of SDAR and SAR models in the EV test were 73% and 86% for CYP3A4, and 76% and 90% for CYP2D6, respectively. Thus, both SDAR and SAR methods demonstrated a comparable performance in modeling a large set of structurally diverse data. Based on unique NMR structural descriptors, the new SDAR modeling method complements the existing SAR techniques, providing an independent estimator that can increase confidence in a structure-activity assessment. When modeling was applied to hazardous environmental chemicals, it was found that up to 20% of them may be substrates and up to 10% of them may be inhibitors of the CYP3A4 and CYP2D6 isoforms. The developed models provide a rare opportunity for the environmental health branch of the public health service to extrapolate to hazardous chemicals directly from human clinical data. Therefore, the pharmacological and environmental health branches are both expected to benefit from these reported models. PMID:22421792

  10. N-Benzoyl amino acids as ICAM\\/LFA-1 inhibitors. Part 2: Structure–activity relationship of the benzoyl moiety

    Microsoft Academic Search

    Daniel J Burdick; James C Marsters Jr.; Ignacio Aliagas-Martin; Mark Stanley; Maureen Beresini; Kevin Clark; Robert S McDowell; Thomas R Gadek

    2004-01-01

    o-Bromobenzoyl l-tryptophan 1 inhibits the association of LFA-1 with ICAM-1 with an IC50 of 1.7?M. Evaluation of the structure–activity relationship of the benzoyl moiety shows that 2,6-di-substitutions greatly enhance potency of this class of inhibitors. Electronegative substitutions that favor a 90° angle between the benzoyl ring and the amide bond yield the most potent compounds. There is a strong correlation

  11. Polynomial Neural Network for Linear and Non-linear Model Selection in Quantitative-Structure Activity Relationship Studies on the Internet

    Microsoft Academic Search

    Igor V. Tetko; Tetyana I. Aksenova; Vladimir V. Volkovich; Tamara N. Kasheva; D. V. Filipov; William J. Welsh; David J. Livingstone; A. E. P. Villa

    2000-01-01

    This article presents a self-organising multilayered iterative algorithm that provides linear and non-linear polynomial regression models thus allowing the user to control the number and the power of the terms in the models. The accuracy of the algorithm is compared to the partial least squares (PLS) algorithm using fourteen data sets in quantitative-structure activity relationship studies. The calculated data show

  12. Kinetics of nonpeptide antagonist binding to the human gonadotropin-releasing hormone receptor: Implications for structure–activity relationships and insurmountable antagonism

    Microsoft Academic Search

    Susan K. Sullivan; Sam R. J. Hoare; Beth A. Fleck; Yun-Fei Zhu; Christopher E. Heise; R. Scott Struthers; Paul D. Crowe

    2006-01-01

    Numerous nonpeptide ligands have been developed for the human gonadotropin-releasing hormone (GnRH) receptor as potential agents for treatment of disorders of the reproductive-endocrine axis. While the equilibrium binding of these ligands has been studied in detail, little is known of the kinetics of their receptor interaction. In this study we evaluated the kinetic structure–activity relationships (SAR) of uracil-series antagonists by

  13. STRUCTURE-GENOTOXIC ACTIVITY RELATIONSHIPS OF PESTICIDES: COMPARISON OF THE RESULTS FROM SEVERAL SHORT-TERM ASSAYS

    EPA Science Inventory

    The Computer-Automated Structure Evaluation (CASE) program has been applied to the analysis of the genotoxic activity of 54 pesticides (31 insecticides, 15 herbicides and 8 fungicides), in 5 different short-term test systems measuring point-gene mutation and DNA damage. The datab...

  14. Structure-plant phytotoxic activity relationship of 7,7'-epoxylignanes, (+)- and (-)-verrucosin: simplification on the aromatic ring substituents.

    PubMed

    Yamauchi, Satoshi; Nakayama, Kumiko; Nishiwaki, Hisashi; Shuto, Yoshihiro

    2014-10-15

    The synthesized 7-aryl derivatives of (7R,7'S,8S,8'S)-(+)-verrucosin were applied to growth inhibitory activity test against ryegrass at 1mM. 7-(3-Ethoxy-4-hydroxyphenyl) derivative 12 and 7-(2-hydroxyphenyl) derivative 4 showed comparable activity to those of (+)-verrucosin against the root (-95%) and the shoot (-60%), respectively. The growth inhibitory activity test against lettuce using synthesized 7-aryl derivatives of (7S,7'R,8R,8'R)-(-)-verrucosin at 1mM showed that the activities of 7-(3-hydroxyphenyl) derivative 20 and 7-(3-ethoxy-4-hydroxyphenyl) derivative 28 are similar to that of (-)-verrucosin against the root (-95%). Against the shoot, 7-(3-hydroxyphenyl) derivative 20 showed higher activity (-80%) than that of (-)-verrucosin (-60%). As the next step, (7S,7'R,8R,8'R)-7-(3-hydroxyphenyl)-7'-aryl-(-)-verrucosin derivatives, in which the most effective 3-hydroxyphenyl group is employed as 7-aromatic ring, were synthesized for the assay against lettuce. In this experiment, 7'-(2-hydroxyphenyl) derivative 37 and 7'-(3-hydroxyphenyl) derivative 38 showed similar activity to that of derivative 20. The effect of 7- and 7'-aryl structures of 7,7'-epoxylignanes on the plant growth inhibitory activity was clarified. The 7- and 7'-aryl structures were simplified to show comparable activity to or higher activity than that of (-)-verrucosin. The plant growth inhibitory activity of a nutmeg component, (+)-fragransin C3b, was estimated as -80% inhibition at 1mM against ryegrass roots. PMID:25248684

  15. Insights into StructureActivity Relationships in the C-Terminal Region of Divercin V41, a Class IIa Bacteriocin with High-Level Antilisterial Activity

    Microsoft Academic Search

    Jitka Rihakova; Vanessa W. Petit; Katerina Demnerova; H. Prevost; S. Rebuffat; D. Drider

    2009-01-01

    Divercin V41 (DvnV41) is a class IIa bacteriocin with potent antilisterial activity isolated from Carnobac- terium divergens V41. Previously, we expressed from a synthetic gene, in Escherichia coli Origami, a recombinant DvnV41 designated DvnRV41, which possesses four additional amino acids (AMDP) in the N-terminal region that result from enzymatic cleavage and retains the initial DvnV41 activity. To unravel the relationship

  16. Discovery of substituted 1,4-dihydroquinolines as novel promising class of P-glycoprotein inhibitors: First structure-activity relationships and bioanalytical studies.

    PubMed

    Hemmer, Marc; Krawczyk, Sören; Simon, Ina; Hilgeroth, Andreas

    2015-08-01

    Multidrug resistance (mdr) is the most important problem in the therapeutical treatment of cancer. One central problem in the resistance proceeding is the expression of transmembrane efflux pumps which transport drugs out of the cells. We developed novel substituted 1,4-dihydroquinolines as inhibitors of the transmembrane efflux pump P-glycoprotein. Structure-activity relationships are discussed for this first series. Promising active inhibitors have been identified and first bioanalytical studies have been carried out to address questions of cellular toxicity, P-gp substrate as well as mdr reversal properties. PMID:26048803

  17. Anti-enterovirus activity and structure–activity relationship of a series of 2,6-dihalophenyl-substituted 1 H,3 H-thiazolo[3,4- a]benzimidazoles

    Microsoft Academic Search

    Armando M. De Palma; Ward Heggermont; Pieter Leyssen; Gerhard Pürstinger; Eva Wimmer; Erik De Clercq; Angela Rao; Anna-Maria Monforte; Alba Chimirri; Johan Neyts

    2007-01-01

    Despite the fact that enteroviruses are implicated in a variety of human diseases, there is no approved therapy for the treatment of enteroviral infections. Here, a series of 2,6-dihalophenyl-substituted 1H,3H-thiazolo[3,4-a]benzimidazoles with anti-enterovirus activity is reported. The compounds elicit potent activity against coxsackievirus A9, echovirus 9 and 11 and all six strains of coxsackievirus B. A structure–activity relationship analysis revealed that

  18. A quantitative structure-activity relationship study of herbicidal analogues of alpha-hydroxy-substituted 3-benzylidenepyrrolidene-2,4-diones.

    PubMed

    Zhu, You-Quan; Liu, Pei; Si, Xue-Kai; Zou, Xiao-Mao; Liu, Bin; Song, Hai-Bin; Yang, Hua-Zheng

    2006-09-20

    A series of pyrrolidine-2,4-dione and piperidine-2,4-dione derivatives were prepared and evaluated for their herbicidal activities where some of these compounds exhibited good bioactivity against Echinochloa crus-galli in comparison with sulcotrione. Quantitative structure-activity relationship studies were performed on these compounds using physicochemical parameters (hydrophobic, electronic, and Taft) as independent parameters and herbicidal activity as a dependent parameter, where herbicidal activity correlated best (r > 0.8) with hydrophobic (pi(o) + pi(p)), steric (Es), STERIMOL (B4), indicator (H(M)), van der Waals volume (V), and electronic parameter (sigma(m) + sigma(p)) in this set of molecules; the optimum van der Waals volume for R(2) is about 41.8 A3; when B4 is equal to 3, the target molecule possessed the lowest herbicidal activity. PMID:16968083

  19. Structure determination of glycogen synthase kinase-3 from Leishmania major and comparative inhibitor structure?activity relationships with Trypanosoma brucei GSK-3

    SciTech Connect

    Ojo, Kayode K.; Arakaki, Tracy L.; Napuli, Alberto J.; Inampudi, Krishna K.; Keyloun, Katelyn R.; Zhang, Li; Hol, Wim G.J.; Verlind, Christophe L.M.J.; Merritt, Ethan A.; Van Voorhis, Wesley C. (UWASH)

    2012-04-24

    Glycogen synthase kinase-3 (GSK-3) is a drug target under intense investigation in pharmaceutical companies and constitutes an attractive piggyback target for eukaryotic pathogens. Two different GSKs are found in trypanosomatids, one about 150 residues shorter than the other. GSK-3 short (GeneDB: Tb927.10.13780) has previously been validated genetically as a drug target in Trypanosoma brucei by RNAi induced growth retardation; and chemically by correlation between enzyme and in vitro growth inhibition. Here, we report investigation of the equivalent GSK-3 short enzymes of L. major (LmjF18.0270) and L. infantum (LinJ18{_}V3.0270, identical in amino acid sequences to LdonGSK-3 short) and a crystal structure of LmajGSK-3 short at 2 {angstrom} resolution. The inhibitor structure-activity relationships (SARs) of L. major and L. infantum are virtually identical, suggesting that inhibitors could be useful for both cutaneous and visceral leishmaniasis. Leishmania spp. GSK-3 short has different inhibitor SARs than TbruGSK-3 short, which can be explained mostly by two variant residues in the ATP-binding pocket. Indeed, mutating these residues in the ATP-binding site of LmajGSK-3 short to the TbruGSK-3 short equivalents results in a mutant LmajGSK-3 short enzyme with SAR more similar to that of TbruGSK-3 short. The differences between human GSK-3{beta} (HsGSK-3{beta}) and LmajGSK-3 short SAR suggest that compounds which selectively inhibit LmajGSK-3 short may be found.

  20. The inhibitory effects of a rhamnogalacturonan I (RG-I) domain from ginseng pectin on galectin-3 and its structure-activity relationship.

    PubMed

    Gao, Xiaoge; Zhi, Yuan; Sun, Lin; Peng, Xiaoxia; Zhang, Tao; Xue, Huiting; Tai, Guihua; Zhou, Yifa

    2013-11-22

    Pectin has been shown to inhibit the actions of galectin-3, a ?-galactoside-binding protein associated with cancer progression. The structural features of pectin involved in this activity remain unclear. We investigated the effects of different ginseng pectins on galectin-3 action. The rhamnogalacturonan I-rich pectin fragment, RG-I-4, potently inhibited galectin-3-mediated hemagglutination, cancer cell adhesion and homotypic aggregation, and binding of galectin-3 to T-cells. RG-I-4 specifically bound to the carbohydrate recognition domain of galectin-3 with a dissociation constant of 22.2 nm, which was determined by surface plasmon resonance analysis. The structure-activity relationship of RG-I-4 was investigated by modifying the structure through various enzymatic and chemical methods followed by activity tests. The results showed that (a) galactan side chains were essential to the activity of RG-I-4, whereas arabinan side chains positively or negatively regulated the activity depending on their location within the RG-I-4 molecule. (b) The activity of galactan chain was proportional to its length up to 4 Gal residues and largely unchanged thereafter. (c) The majority of galactan side chains in RG-I-4 were short with low activities. (d) The high activity of RG-I-4 resulted from the cooperative action of these side chains. (e) The backbone of the molecule was very important to RG-I-4 activity, possibly by maintaining a structural conformation of the whole molecule. (f) The isolated backbone could bind galectin-3, which was insensitive to lactose treatment. The novel discovery that the side chains and backbone play distinct roles in regulating RG-I-4 activity is valuable for producing highly active pectin-based galectin-3 inhibitors. PMID:24100038

  1. Molecular dynamics investigation of psalmopeotoxin I. Probing the relationship between 3D structure, anti-malarial activity and thermal stability.

    PubMed

    Gleeson, Matthew Paul; Deechongkit, Songpon; Ruchirawat, Somsak

    2011-04-01

    PcFK1 is a member of the cysteine knot inhibitor family that displays anti-malarial properties. The naturally occurring molecule is ? 40 amino acids in length and forms a highly constrained 3D structure due to the presence of 3 disulfide and multiple intra-molecular H-bonds. Recent experimental studies on PcFK1 wild-type and mutants, where the cystiene residues of each disulfide bond were mutated into serine residues, suggest that alterations to these structural constraints can give rise to sizeable differences in SAR. To better understand the relationship between the dynamic inhibitor 3D structure, biophysical and biological properties we have performed solution based molecular dynamics calculations over 150 ns using the CHARMM forcefield. We have analyzed the theoretical trajectory in a systematic way using principal components analysis, which allows us to identify the correlated nature of the protein loop, turn and sheet movements. We have identified the key molecular motions that give rise to the differing SAR which has helped to more precisely direct our ongoing SAR studies in this important therapeutic area. PMID:20544240

  2. Physiological and Biochemical Role of Brassinosteroids and Their StructureActivity Relationship in the Green Alga Chlorella vulgaris Beijerinck ( Chlorophyceae )

    Microsoft Academic Search

    A. Bajguz; R. Czerpak

    1998-01-01

    .   This paper studies the influence of the 7-oxalactone type of brassinosteroids (BRs) and 6-ketone upon the biological activity\\u000a of the alga Chlorella vulgaris (Chlorophyceae). The results of the study indicate significant differences in the growth and metabolism of C. vulgaris cells caused by the different chemical structures of the BRs used. The most significant differences in the stimulation of

  3. Biological implications of the structural, antithrombin affinity and anticoagulant activity relationships among vertebrate heparins and heparan sulphates.

    PubMed Central

    Hovingh, P; Piepkorn, M; Linker, A

    1986-01-01

    We analysed the distribution, structural characteristics, antithrombin-III-binding properties and anticoagulant activities of heparins and heparan sulphates isolated from the tissues of a wide range of vertebrates. Heparin has a curiously limited distribution, since it was absent from lower aquatic vertebrate species, present in only certain organs such as intestine in many higher vertebrates, and completely absent from the rabbit among mammals examined. The heparins were structurally diverse, and they exhibited a broad range of anticoagulant activities, from approx. 50% to 150% of average commercial heparins. Although there was a rough correlation between the anticoagulant potency of the starting isolate and the proportional content of material exhibiting high-affinity binding to the proteinase inhibitor antithrombin III, activities of high-affinity fractions from heparins low in activity overlapped those of low-affinity fractions from highly active heparins. Heparan sulphates, which in contrast were isolated from nearly all vertebrate organs, contained high-affinity subfractions constituting up to 5% of the starting material and possessing anticoagulant potencies of 2-30 units/mg. In consideration of the heparin data, we infer that its biological function is either species-specific or may be served by other molecular elements, and that there exists considerable diversity in the antithrombin-III-binding sequence of heparin. The more-generally distributed glycosaminoglycan heparan sulphate possesses within its variable structure a small high-affinity subfraction with low anticoagulant potency, whether isolated from aorta or other tissues. Although heparan sulphate appears to have an essential function at the cellular level, we suggest that this is probably not that of providing heparin-like antithrombotic effects on vascular surfaces. PMID:2948492

  4. Bordetella pertussis tracheal cytotoxin and other muramyl peptides: distinct structure-activity relationships for respiratory epithelial cytopathology.

    PubMed Central

    Luker, K E; Collier, J L; Kolodziej, E W; Marshall, G R; Goldman, W E

    1993-01-01

    Tracheal cytotoxin (TCT) is a disaccharide-tetrapeptide released by Bordetella pertussis, the causative agent of pertussis (whooping cough). We have previously determined the structure of TCT to be GlcNAc-1,6-anhydro-MurNAc-L-Ala-gamma-D-Glu-meso-A2pm-D-Ala, where MurNAc = N-acetylmuramic acid and A2pm = diaminopimelic acid. Purified TCT reproduces the respiratory cytopathology observed during pertussis, including ciliostasis and extrusion of ciliated cells. We have tested structural analogs of TCT for their ability to reproduce native TCT toxicity in explanted hamster tracheal tissue and hamster trachea epithelial (HTE) cell cultures. Other investigators have evaluated many of these analogs, which are muramyl or desmuramyl peptides, for muramyl peptide activities such as immunopotentiation, induction of slow-wave sleep, and pyrogenicity. Four desmuramyl peptides were produced in our laboratory from B. pertussis peptidoglycan or by chemical synthesis, including unusual peptides containing alpha-aminopimelic acid in place of A2pm. Based on the relative ability of compounds to inhibit DNA synthesis in HTE cells, truncated analogs lacking A2pm entirely or lacking only the side-chain amine or carboxyl group of A2pm were less active than TCT by a factor of at least 1000. All active analogs included a native or near-native peptide moiety, independent of the presence, absence, or substitution of the sugar moiety. We conclude that the structural requirements for TCT toxicity differ considerably from those for most other muramyl peptide activities, in that the disaccharide moiety is irrelevant for toxicity and both the free amino and carboxyl groups of the A2pm side chain are required for activity. PMID:8460147

  5. Bordetella pertussis tracheal cytotoxin and other muramyl peptides: distinct structure-activity relationships for respiratory epithelial cytopathology.

    PubMed

    Luker, K E; Collier, J L; Kolodziej, E W; Marshall, G R; Goldman, W E

    1993-03-15

    Tracheal cytotoxin (TCT) is a disaccharide-tetrapeptide released by Bordetella pertussis, the causative agent of pertussis (whooping cough). We have previously determined the structure of TCT to be GlcNAc-1,6-anhydro-MurNAc-L-Ala-gamma-D-Glu-meso-A2pm-D-Ala, where MurNAc = N-acetylmuramic acid and A2pm = diaminopimelic acid. Purified TCT reproduces the respiratory cytopathology observed during pertussis, including ciliostasis and extrusion of ciliated cells. We have tested structural analogs of TCT for their ability to reproduce native TCT toxicity in explanted hamster tracheal tissue and hamster trachea epithelial (HTE) cell cultures. Other investigators have evaluated many of these analogs, which are muramyl or desmuramyl peptides, for muramyl peptide activities such as immunopotentiation, induction of slow-wave sleep, and pyrogenicity. Four desmuramyl peptides were produced in our laboratory from B. pertussis peptidoglycan or by chemical synthesis, including unusual peptides containing alpha-aminopimelic acid in place of A2pm. Based on the relative ability of compounds to inhibit DNA synthesis in HTE cells, truncated analogs lacking A2pm entirely or lacking only the side-chain amine or carboxyl group of A2pm were less active than TCT by a factor of at least 1000. All active analogs included a native or near-native peptide moiety, independent of the presence, absence, or substitution of the sugar moiety. We conclude that the structural requirements for TCT toxicity differ considerably from those for most other muramyl peptide activities, in that the disaccharide moiety is irrelevant for toxicity and both the free amino and carboxyl groups of the A2pm side chain are required for activity. PMID:8460147

  6. Cyclopaldic acid, seiridin, and sphaeropsidin A as fungal phytotoxins, and larvicidal and biting deterrents against Aedes aegypti (Diptera: Culicidae): structure-activity relationships.

    PubMed

    Cimmino, Alessio; Andolfi, Anna; Avolio, Fabiana; Ali, Abbas; Tabanca, Nurhayat; Khan, Ikhlas A; Evidente, Antonio

    2013-07-01

    Aedes aegypti L. is the major vector of the arboviruses responsible for dengue fever, one of the most devastating human diseases. From a preliminary screening of fungal phytotoxins, cyclopaldic acid (1), seiridin (2), sphaeropsidin A (4), and papyracillic acid (5) were evaluated for their biting deterrent and larvicidal activities against Ae. aegypti L. Because compounds 1, 2, 4, and 5 exhibited mosquito biting deterrent activities and 1 and 4 demonstrated larvicidal activities, further structure?activity relationship studies were initiated on these toxins. In biting-deterrence bioassays, 1, 2, 4, and 5, 3,8-didansylhydrazone of cyclopaldic acid, 1F, 5-azidopentanoate of cyclopaldic acid A, 1G, the reduced derivative of cyclopaldic acid, 1?H, isoseiridin (3), 2'-O-acetylseiridin (2A), 2'-oxoseiridin (2C), 6-O-acetylsphaeropsidin A (4A), 8,14-methylensphaeropsidin A methyl ester (4B), and sphaeropsidin B (4C) showed activities higher than the solvent control. Sphaeropsidin B (4C) was the most active compound followed by 2A, while the other compounds were less active. Biting-deterrence activity of compound 4C was statistically similar to DEET. In the larvicidal screening bioassays, only compounds 1 and 4 demonstrated larvicidal activities. Based on LD50 values, compound 4 (LD50 36.8?ppm) was significantly more active than compound 1 (LD50 58.2?ppm). However, the activity of these compounds was significantly lower than permethrin. PMID:23847068

  7. DNA interaction studies and evaluation of biological activity of homo- and hetero-trihalide mononuclear Cu(II) Schiff base complexes. Quantitative structure-activity relationships.

    PubMed

    Chaviara, A T; Kioseoglou, E E; Pantazaki, A A; Tsipis, A C; Karipidis, P A; Kyriakidis, D A; Bolos, C A

    2008-09-01

    A new series of mixed-ligand mono- or hetero-trihalide Cu(II) complexes of the type [Cu(dienXX)Y(YZ(2))], where dienXX=Schiff dibase of diethylenetriamine with 2-thiophene-carboxaldehyde (dienSS), 2-furaldehyde (dienOO) or 2-pyrrole-2-carboxaldehyde (dienNN), Y=Cl, Br and Z=Br, I was synthesized by the reaction of the precursors of the type [Cu(dienXX)Y]Y with iodine or bromine in 1:1 molar ratio. The distorted square pyramidal configuration of the new homo- and hetero-trihalide Cu(II) mononuclear complexes was identified by C, H, N, Cu analysis, spectroscopic methods (IR, UV-visible), molar conductivity and magnetic measurements. The basal plane consists of three nitrogen atoms of the Schiff base and one halogen (terminal) atom while another axially located trihalogen moiety occupies the fifth side of the square pyramid as a YZ(2) entity, adopting an almost linear configuration. The equilibrium geometry of these complexes was further corroborated by theoretical studies at the B3LYP/DGDZVP level. A series of quantum chemical descriptors (e.g. SOMO (singly occupied molecular orbital) LUMO (lowest occupied molecular orbital), SOMO and LUMO energies, SOMO-LUMO gap, dipole moment, polarizability, molar volume, etc.) have been utilized in order to deduce quantitative structure-activity relationships (QSARs). The effect of the new compounds on the single stranded (ss), double stranded (ds) and pDNA led either to the formation of a DNA-complex cationic adduct, or to its degradation, evidenced by DNA electrophoretic mobility and DNA interaction spectroscopic titration studies. Moreover, the antimicrobial activity of Cu(II) complexes against Gram(+) and Gram(-) bacteria can be attributed to the synergistic action of the dissociation species, namely the cationic [Cu(dienXX)Y](+) and anionic [YZ(2)](-) ones. Finally, de Novo linear regression analysis correlating the bioactivity of these complexes with their structural substituents has been carried out, leading to some interesting qualitative observations/conclusions. PMID:18584877

  8. Identification of Lilial as a fragrance sensitizer in a perfume by bioassay-guided chemical fractionation and structure-activity relationships.

    PubMed

    Arnau, E G; Andersen, K E; Bruze, M; Frosch, P J; Johansen, J D; Menné, T; Rastogi, S C; White, I R; Lepoittevin, J P

    2000-12-01

    Fragrance materials are among the most common causes of allergic contact dermatitis. The aim of this study was to identify in a perfume fragrance allergens not included in the fragrance mix, by use of bioassay-guided chemical fractionation and chemical analysis/structure-activity relationships (SARs). The basis for the investigation was a 45-year-old woman allergic to her own perfume. She had a negative patch test to the fragrance mix and agreed to participate in the study. Chemical fractionation of the perfume concentrate was used for repeated patch testing and/or repeated open application test on the pre-sensitized patient. The chemical composition of the fractions giving a positive patch-test response and repeated open application test reactions was obtained by gas chromatography-mass spectrometry. From the compounds identified, those that contained a "structural alert" in their chemical structure, indicating an ability to modify skin proteins and thus behave as a skin sensitizer, were tested on the patient. The patient reacted positively to the synthetic fragrance p-t-butyl-alpha-methylhydrocinnamic aldehyde (Lilial), a widely used fragrance compound not present in the fragrance mix. The combination of bioassay-guided chemical fractionation and chemical analysis/structure-activity relationships seems to be a valuable tool for the investigation of contact allergy to fragrance materials. PMID:11140386

  9. Structure-Function Relationship of the Chloroplastic Glutaredoxin S12 with an Atypical WCSYS Active Site*S?

    PubMed Central

    Couturier, Jeremy; Koh, Cha San; Zaffagnini, Mirko; Winger, Alison M.; Gualberto, Jose Manuel; Corbier, Catherine; Decottignies, Paulette; Jacquot, Jean-Pierre; Lemaire, Stéphane D.; Didierjean, Claude; Rouhier, Nicolas

    2009-01-01

    Glutaredoxins (Grxs) are efficient catalysts for the reduction of mixed disulfides in glutathionylated proteins, using glutathione or thioredoxin reductases for their regeneration. Using GFP fusion, we have shown that poplar GrxS12, which possesses a monothiol 28WCSYS32 active site, is localized in chloroplasts. In the presence of reduced glutathione, the recombinant protein is able to reduce in vitro substrates, such as hydroxyethyldisulfide and dehydroascorbate, and to regenerate the glutathionylated glyceraldehyde-3-phosphate dehydrogenase. Although the protein possesses two conserved cysteines, it is functioning through a monothiol mechanism, the conserved C terminus cysteine (Cys87) being dispensable, since the C87S variant is fully active in all activity assays. Biochemical and crystallographic studies revealed that Cys87 exhibits a certain reactivity, since its pKa is around 5.6. Coupled with thiol titration, fluorescence, and mass spectrometry analyses, the resolution of poplar GrxS12 x-ray crystal structure shows that the only oxidation state is a glutathionylated derivative of the active site cysteine (Cys29) and that the enzyme does not form inter- or intramolecular disulfides. Contrary to some plant Grxs, GrxS12 does not incorporate an iron-sulfur cluster in its wild-type form, but when the active site is mutated into YCSYS, it binds a [2Fe-2S] cluster, indicating that the single Trp residue prevents this incorporation. PMID:19158074

  10. Structural analysis of Canavalia maritima and Canavalia gladiata lectins complexed with different dimannosides: New insights into the understanding of the structure–biological activity relationship in legume lectins

    Microsoft Academic Search

    Gustavo Arruda Bezerra; Taianá Maia Oliveira; Frederico Bruno Mendes Batista Moreno; Emmanuel Prata de Souza; Bruno Anderson Matias da Rocha; Raquel Guimarães Benevides; Plínio Delatorre; Walter Filgueira de Azevedo; Benildo Sousa Cavada

    2007-01-01

    Plant lectins, especially those purified from species of the Leguminosae family, represent the best studied group of carbohydrate-binding proteins. The legume lectins from Diocleinae subtribe are highly similar proteins that present significant differences in the potency\\/efficacy of their biological activities. The structural studies of the interactions between lectins and sugars may clarify the origin of the distinct biological activities observed

  11. Structure–activity relationship study between Ornithyl-Proline and Lysyl-Proline based tripeptidomimics as angiotensin-converting enzyme inhibitors

    Microsoft Academic Search

    Mahesh Chand Pavar; Kashif Hanif; Amir Azam; Sneh lata; M. A. Qadar Pasha; Santosh Pasha

    2006-01-01

    A designed library of tripeptidomimics of Ornithyl-Proline (Orn-Pro) and Lysyl-Proline (Lys-Pro) conjugated with various unnatural amino acids and carboxylic acid derived heterocyclics was synthesized and screened for possible inhibitors of angiotensin-converting enzyme (ACE). Among the tripeptidomimics 10[MTP-Orn-Pro], 11[HTP-Orn-Pro], 14[TA-Orn-Pro] and 20[BPA-Orn-Pro] showed prominent inhibition with IC50 values in micromolar concentrations. Structure–activity relationship study indicated that C3 side chain of Orn

  12. Mode of action and the assessment of chemical hazards in the presence of limited data: use of structure-activity relationships (SAR) under TSCA, Section 5.

    PubMed Central

    Auer, C M; Nabholz, J V; Baetcke, K P

    1990-01-01

    Section 5 of the Toxic Substances Control Act (TSCA) requires that manufacturers and importers of new chemicals must submit a Premanufacture Notification (PMN) to the U.S. Environmental Protection Agency 90 days before they intend to commence manufacture or import. Certain information such as chemical identity, uses, etc., must be included in the notification. The submission of test data on the new substance, however, is not required, although any available health and environmental information must be provided. Nonetheless, over half of all PMNs submitted to the agency do not contain any test data; because PMN chemicals are new, no test data is generally available in the scientific literature. Given this situation, EPA has had to develop techniques for hazard assessment that can be used in the presence of limited test data. EPA's approach has been termed "structure-activity relationships" (SAR) and involves three major components: the first is critical evaluation and interpretation of available toxicity data on the chemical; the second component involves evaluation of test data available on analogous substances and/or potential metabolites; and the third component involves the use of mathematical expressions for biological activity known as "quantitative structure-activity relationships" (QSARs). At present, the use of QSARs is limited to estimating physical chemical properties, environmental toxicity, and bioconcentration factors. An important overarching element in EPA's approach is the experience and judgment of scientific assessors in interpreting and integrating the available data and information. Examples are provided that illustrate EPA's approach to hazard assessment for PMN chemicals. PMID:2269224

  13. Structure–Activity Relationship of Adenosine 5?-diphosphoribose at the Transient Receptor Potential Melastatin 2 (TRPM2) Channel: Rational Design of Antagonists

    PubMed Central

    2013-01-01

    Adenosine 5?-diphosphoribose (ADPR) activates TRPM2, a Ca2+, Na+, and K+ permeable cation channel. Activation is induced by ADPR binding to the cytosolic C-terminal NudT9-homology domain. To generate the first structure–activity relationship, systematically modified ADPR analogues were designed, synthesized, and evaluated as antagonists using patch-clamp experiments in HEK293 cells overexpressing human TRPM2. Compounds with a purine C8 substituent show antagonist activity, and an 8-phenyl substitution (8-Ph-ADPR, 5) is very effective. Modification of the terminal ribose results in a weak antagonist, whereas its removal abolishes activity. An antagonist based upon a hybrid structure, 8-phenyl-2?-deoxy-ADPR (86, IC50 = 3 ?M), is more potent than 8-Ph-ADPR (5). Initial bioisosteric replacement of the pyrophosphate linkage abolishes activity, but replacement of the pyrophosphate and the terminal ribose by a sulfamate-based group leads to a weak antagonist, a lead to more drug-like analogues. 8-Ph-ADPR (5) inhibits Ca2+ signalling and chemotaxis in human neutrophils, illustrating the potential for pharmacological intervention at TRPM2. PMID:24304219

  14. Structure activity relationship of substituted 1,5-naphthyridine analogs of oxabicyclooctane-linked novel bacterial topoisomerase inhibitors as broad-spectrum antibacterial agents (Part-4).

    PubMed

    Singh, Sheo B; Kaelin, David E; Wu, Jin; Miesel, Lynn; Tan, Christopher M; Meinke, Peter T; Olsen, David B; Lagrutta, Armando; Wei, Changqing; Peng, Xuanjia; Wang, Xiu; Fukuda, Hideyuki; Kishii, Ryuta; Takei, Masaya; Shibata, Takeshi; Ohata, Kohei; Takano, Hisashi; Kurasaki, Haruaki; Takeuchi, Tomoko; Nishimura, Akinori; Fukuda, Yasumichi

    2015-06-01

    Bacterial resistance is rapidly growing, necessitating the need to discover new agents. Novel bacterial topoisomerase inhibitors (NBTIs) are new class of broad-spectrum antibacterial agents targeting bacterial DNA gyrase and topoisomerase IV. This class of inhibitors binds to an alternative binding site relative to fluoroquinolones and shows no cross-resistance to quinolones. NBTIs consist of three structural motifs. A structure activity relationship of the left hand motif 1,5-naphthyridine of oxabicyclooctane-linked NBTIs is described. Fifty five compounds were evaluated against a panel of key Gram-positive and Gram-negative strains of bacteria, as well as for hERG activity and five compounds were tested for in vivo efficacy in murine model of Staphylococcus aureus infection. These studies suggest that only a narrow range (activating and deactivating) of substitutions at C-2 and C-7 are tolerated for optimal antibacterial activity and spectrum. An alkoxy (methoxy) and CN at C-2, and a halogen and hydroxyl at C-7, appeared to be preferred in this series. Substitutions on the other three carbons generally have detrimental effect on the activity. No clear hERG activity SAR emerged from these substitutions. PMID:25911300

  15. Unraveling the structure-activity relationship of tomatidine, a steroid alkaloid with unique antibiotic properties against persistent forms of Staphylococcus aureus.

    PubMed

    Chagnon, Félix; Guay, Isabelle; Bonin, Marc-André; Mitchell, Gabriel; Bouarab, Kamal; Malouin, François; Marsault, Éric

    2014-06-10

    Staphylococcus aureus (S. aureus) is responsible for difficult-to-treat and relapsing infections and constitutes one of the most problematic pathogens due to its multiple resistances to clinically available antibiotics. Additionally, the ability of S. aureus to develop small-colony variants is associated with a reduced susceptibility to aminoglycoside antibiotics and in vivo persistence. We have recently demonstrated that tomatidine, a steroid alkaloid isolated from tomato plants, possesses anti-virulence activity against normal strains of S. aureus as well as the ability to potentiate the effect of aminoglycoside antibiotics. In addition, tomatidine has shown antibiotic activity against small-colony variants of S. aureus. We herein report the first study of the structure-activity relationship of tomatidine against S. aureus. PMID:24877760

  16. Structure-Activity Relationship of Au/ZrO2 Catalyst on Formation of Hydroxyl Groups and Its Influence on CO Oxidation

    SciTech Connect

    Karwacki, Christopher J [US Army Aberdeen Proving Ground; Ganesh, Panchapakesan [ORNL; Gordon, Wesley O [ORNL; Peterson, Gregory W [US Army Aberdeen Proving Ground; Niu, Jun Jie [Drexel University; Gogotsi, Yury G. [Drexel University

    2013-01-01

    The effect of changes in morphology and surface hydroxyl species upon thermal treatment of zirconia on the oxidation activity of Au/ZrO2 catalyst was studied. We observed using transmission fourier transform infrared (FTIR) spectroscopy progressive changes in the presence of monodentate (type I), bidentate (type II) and hydrogen bridged species (type III) for each of the thermally treated (85 to 500 C) supports consisting of bare zirconia and Au/ZrO2 catalysts. Furthermore, structural changes in zirconia were accompanied by an increase in crystal size (7 to 58 nm) and contraction of the supports porosity (SSA 532 to 7 m2/g) with increasing thermal treatment. Deposition of gold nanoparticles under similar preparation conditions on different thermally treated zirconia resulted in changes in the mean gold cluster size, ranging from 3.7 to 5.6 nm. Changes in the surface hydroxyl species, support structure and size of the gold centers are important parameters responsible for the observed decrease (> 90 %) in CO conversion activity for the Au/ZrO2 catalysts. Density functional theory calculations provide evidence of increased CO binding to Au nanoclusters in the presence of surface hydroxyls on zirconia, which increases charge transfer at the perimeter of the gold nanocluster on zirconia support. This further helps in reducing a model CO-oxidation reaction barrier in the presence of surface hydroxyls. This work demonstrates the need to understand the structure-activity relationship of both the support and active particles for the design of catalytic materials.

  17. Structure-activity relationship of Au-ZrO2 catalyst on formation of hydroxyl groups and its influence on CO oxidation

    SciTech Connect

    Karwacki, Christopher J [US Army Aberdeen Proving Ground; Ganesh, Panchapakesan [ORNL; Kent, P. R. C. [University of Tennessee, Knoxville (UTK); Gordon, Wesley O [ORNL; Peterson, Gregory W [US Army Aberdeen Proving Ground; Niu, Jun Jie [Drexel University; Gogotsi, Yury G. [Drexel University

    2013-01-01

    The effect of changes in morphology and surface hydroxyl species upon thermal treatment of zirconia on the oxidation activity of Au/ZrO2 catalyst was studied. We observed using transmission Fourier transform infrared (FTIR) spectroscopy progressive changes in the presence of monodentate (type I), bidentate (type II) and hydrogen bridged species (type III) for each of the thermally treated (85 to 500 C) supports consisting of bare zirconia and Au/ZrO2 catalysts. Furthermore, structural changes in zirconia were accompanied by an increase in crystal size (7 to 58 nm) and contraction of the supports porosity (SSA 532 to 7 m2 g 1) with increasing thermal treatment. Deposition of gold nanoparticles under similar preparation conditions on different thermally treated zirconia resulted in changes in the mean gold cluster size, ranging from 3.7 to 5.6 nm. Changes in the surface hydroxyl species, support structure and size of the gold centers are important parameters responsible for the observed decrease (>90%) in CO conversion activity for the Au/ZrO2 catalysts. Density functional theory calculations provide evidence of increased CO binding to Au nanoclusters in the presence of surface hydroxyls on zirconia, which increases charge transfer at the perimeter of the gold nanocluster on zirconia support. This further helps in reducing a model CO-oxidation reaction barrier in the presence of surface hydroxyls. This work demonstrates the need to understand the structure activity relationship of both the support and active particles for the design of catalytic materials.

  18. Structure-activity relationships of the intramolecular disulfide bonds in coprisin, a defensin from the dung beetle.

    PubMed

    Lee, Jaeho; Lee, Daeun; Choi, Hyemin; Kim, Ha Hyung; Kim, Ho; Hwang, Jae Sam; Lee, Dong Gun; Kim, Jae Il

    2014-11-01

    Defensins, which are small cationic molecules produced by organisms as part of their innate immune response, share a common structural scaffold that is stabilized by three disulfide bridges. Coprisin is a 43-amino acid defensin-like peptide from Copris tripartitus. Here, we report the intramolecular disulfide connectivity of cysteine-rich coprisin, and show that it is the same as in other insect defensins. The disulfide bond pairings of coprisin were determined by combining the enzymatic cleavage and mass analysis. We found that the loss of any single disulfide bond in coprisin eliminated all antibacterial, but not antifungal, activity. Circular dichroism (CD) analysis showed that two disulfide bonds, Cys20-Cys39 and Cys24-Cys41, stabilize coprisin's ?-helical region. Moreover, a BLAST search against UniProtKB database revealed that coprisin's ?-helical region is highly homologous to those of other insect defensins. PMID:24393527

  19. Synthesis and quantitative structure-activity relationship of hydrazones of N-amino-N'-hydroxyguanidine as electron acceptors for xanthine oxidase.

    PubMed

    Prusis, Peteris; Dambrova, Maija; Andrianov, Victor; Rozhkov, Eugene; Semenikhina, Valentina; Piskunova, Irena; Ongwae, Enock; Lundstedt, Torbjörn; Kalvinsh, Ivars; Wikberg, Jarl E S

    2004-06-01

    A series of new N-hydroxyguanidines were synthesized and tested for electron acceptor activity on bovine milk xanthine oxidase using xanthine as reducing substrate. Manual inspection of the structure-activity data revealed that molecules containing nitro groups ("set A") show a different structure-activity relationship pattern compared to non-nitro compounds ("set B"). Accordingly separate QSAR models were built and validated for the two sets. Substantial differences were found in properties governing acceptor activity for the models, the only common property being sterical access to the imino nitrogen atom of the hydroxyguanidinimines. For set A molecules the presence of a nitro substituent at a certain distance range from the hydroxuguanidino group was most important. In addition, the presence of a nitro group in the ortho position interacting with NH(2) of the hydroxyguanidino group, and the mutual geometry of the phenyl ring, hydroxyguanidine, and imine groups was important for this set. By contrast, for set B molecules the acceptor activity was most influenced by the geometry of methoxy groups and the size and geometry of meta and para substituents of the phenyl ring. PMID:15163191

  20. Determinants of activity at human Toll-like receptors 7 and 8: quantitative structure-activity relationship (QSAR) of diverse heterocyclic scaffolds.

    PubMed

    Yoo, Euna; Salunke, Deepak B; Sil, Diptesh; Guo, Xiaoqiang; Salyer, Alex C D; Hermanson, Alec R; Kumar, Manoj; Malladi, Subbalakshmi S; Balakrishna, Rajalakshmi; Thompson, Ward H; Tanji, Hiromi; Ohto, Umeharu; Shimizu, Toshiyuki; David, Sunil A

    2014-10-01

    Toll-like receptor (TLR) 7 and 8 agonists are potential vaccine adjuvants, since they directly activate APCs and enhance Th1-driven immune responses. Previous SAR investigations in several scaffolds of small molecule TLR7/8 activators pointed to the strict dependence of the selectivity for TLR7 vis-à-vis TLR8 on the electronic configurations of the heterocyclic systems, which we sought to examine quantitatively with the goal of developing "heuristics" to define structural requisites governing activity at TLR7 and/or TLR8. We undertook a scaffold-hopping approach, entailing the syntheses and biological evaluations of 13 different chemotypes. Crystal structures of TLR8 in complex with the two most active compounds confirmed important binding interactions playing a key role in ligand occupancy and biological activity. Density functional theory based quantum chemical calculations on these compounds followed by linear discriminant analyses permitted the classification of inactive, TLR8-active, and TLR7/8 dual-active compounds, confirming the critical role of partial charges in determining biological activity. PMID:25192394

  1. Three-dimensional quantitative structure-activity relationships of dioxins and dioxin-like compounds: model validation and Ah receptor characterization.

    PubMed

    Waller, C L; McKinney, J D

    1995-09-01

    In the present study we have utilized comparative molecular field analysis (CoMFA), a three-dimensional quantitative structure-activity relationship paradigm, to explore the physico-chemical requirements for binding to the Ah (dioxin) receptor. Recent developments by Gillner et al. [(1993) Mol. Pharmacol. 44, 336-345] prompted us to review and revise our previous CoMFA/QSAR model [Waller, C. L., and McKinney, J. D. (1992) J. Med. Chem. 36, 3660-3666] to include a structurally-diverse training set of Ah receptor ligands ranging in size from naphthalene to indolo[3,2-b]carbazole nuclei. An exhaustive validation process utilizing external test sets and hierarchical cluster analysis routines was employed during model construction and is discussed herein. The limitations of the approach presented herein are discussed with respect to predictive ability of the CoMFA/QSAR models, which is demonstrated to be dependent on a balance between structural diversity and redundancy in the molecules comprising the training set. The results of our modified CoMFA/QSAR model are consistent with and unify all previously established structure-activity relationships established for less structurally-diverse training sets of Ah receptor ligands. As a result of the more complete nature of the series of molecules under examination in the present study, the CoMFA/QSAR steric and electrostatic field contour plots as well as the essential and excluded volume plots provide for a more detailed characterization of the molecular binding domain of the Ah receptor. The implications of the CoMFA/QSAR model presented herein are explored with respect to quantitative hazard identification of potential toxicants. PMID:7492734

  2. Structure-Activity Relationships for Some Diamine, Triamine and Schiff Base Derivatives and Their Copper(II) Complexes

    PubMed Central

    Bolos, C. A.; Nikolov, G. St.; Ekateriniadou, L.; Kortsaris, A.; Kyriakidis, D. A.

    1998-01-01

    Ethylenediamine (en), putrescine (pu), diethylenetriamine (dien), dipropylenetriamine (dpta), spermidine (spmd) and their CuII compounds as well as the Schiff bases with 2-furaldehyde (dienOO), 2- thiophenecarboxaldehyde (dienSS) and pyrrole-2-carboxaldehyde (dienNN) of dien and that of dpta with 2- thiophenecarboxaldehyde (dptaSS), were prepared and characterised. They were tested against Bacillus substilis, Bacillus cereus, Staphylococcus aureus, Escherichia coli, Proteus vulgaris and Xanthomonas campestris as antibacterial reagents, the highest activity being exhibited by Cu(dptaSS)(NO3)2 complex, which acts as antibiotic. In the antiproliferative tests (vs. T47D,L929 and BHK21/c13 cell lines) the best results were obtained with Cu(dptaSS)2+ and Cu(dienSS)2+. Electronic structure calculations gave for dptaSS and dienSS the higher negative charges on the N atoms. The counter-ions (Br-, NO3- and SO42-) play an important role by modulating the reagent's selectivity versus the bacteria [Gram(+) or Gram(-)], but they have no effect on the antiproliferative activity. PMID:18475868

  3. Design, Synthesis and Structure-Activity Relationship Studies of Novel Survivin Inhibitors with Potent Anti-Proliferative Properties

    PubMed Central

    Xiao, Min; Wang, Jin; Lin, Zongtao; Lu, Yan; Li, Zhenmei; White, Stephen W.; Miller, Duane D.; Li, Wei

    2015-01-01

    The anti-apoptotic protein survivin is highly expressed in most human cancer cells, but has very low expression in normal differentiated cells. Thus survivin is considered as an attractive cancer drug target. Herein we report the design and synthesis of a series of novel survivin inhibitors based on the oxyquinoline scaffold from our recently identified hit compound UC-112. These new analogs were tested against a panel of cancer cell lines including one with multidrug-resistant phenotype. Eight of these new UC-112 analogs showed IC50 values in the nanomole range in anti-proliferative assays. The best three compounds among them along with UC-112 were submitted for NCI-60 cancer cell line screening. The results indicated that structural modification from UC-112 to our best compound 4g has improved activity by four folds (2.2 ?M for UC-112 vs. 0.5 ?M for 4g, average GI50 values over all cancer cell lines in the NCI-60 panel).Western blot analyses demonstrated the new compounds maintained high selectivity for survivin inhibition over other members in the inhibition of apoptosis protein family. When tested in an A375 human melanoma xenograft model, the most active compound 4g effectively suppressed tumor growth and strongly induced cancer cell apoptosis in tumor tissues. This novel scaffold is promising for the development of selective survivin inhibitors as potential anticancer agents. PMID:26070194

  4. Dynamic relationships among type IIa bacteriocins: temperature effects on antimicrobial activity and on structure of the C-terminal amphipathic alpha helix as a receptor-binding region.

    PubMed

    Kaur, Kamaljit; Andrew, Lena C; Wishart, David S; Vederas, John C

    2004-07-20

    Dynamic aspects of structural relationships among class IIa bacteriocins, which are antimicrobial peptides from lactic acid bacteria (LAB), have been examined by use of circular dichroism (CD), molecular dynamics (MD) simulations, and activity testing. Pediocin PA-1 is a potent class IIa bacteriocin, which contains a second C-terminal disulfide bond in addition to the highly conserved N-terminal disulfide bond. A mutant of pediocin PA-1, ped[M31Nle], wherein the replacement of methionine by norleucine (Nle) gives enhanced stability toward aerobic oxidation, was synthesized by solid-phase peptide synthesis to study the activity of the peptide in relation to its structure. The secondary structural analysis from CD spectra of ped[M31Nle], carnobacteriocin B2 (cbn B2), and leucocin A (leuA) at different temperatures suggests that the alpha-helical region of these peptides is important for target recognition and activity. Using molecular modeling and dynamic simulations, complete models of pediocin PA-1, enterocin P, sakacin P, and curvacin A in 2,2,2-trifluoroethanol (TFE) were generated to compare structural relationships among this class of bacteriocins. Their high sequence similarity allows for the use of homology modeling techniques. Starting from homology models based on solution structures of leuA (PDB code 1CW6) and cbnB2 (PDB code 1CW5), results of 2-4 ns MD simulations in TFE and water at 298 and 313 K are reported. The results indicate that these peptides have a common helical C-terminal domain in TFE but a more variable beta sheet or coiled N terminus. At elevated temperatures, pediocin PA-1 maintains its overall structure, whereas peptides without the second C-terminal disulfide bond, such as enterocin P, sakacin P, curvacin A, leuA, and cbnB2 experience partial disruption of the helical section. Pediocin PA-1 and ped[M31Nle] were found to be equally active at different temperatures, whereas the other peptides that lack the second C-terminal disulfide bond are 30-50 times less antimicrobially potent at 310 K (37 degrees C) than at 298 K (25 degrees C). These results indicate that the structural changes in the helical region observed at elevated temperatures account for the loss of activity of these peptides. The presence of C-terminal hydrophobic residues on one side of the amphipathic helix in class IIa bacteriocins is an important feature for receptor recognition and specificity toward particular organisms. This study assists in the understanding of structure-activity relationships in type IIa bacteriocins and demonstrates the importance of the conserved C-terminal amphipathic alpha helix for activity. PMID:15248758

  5. Sharing chemical relationships does not reveal structures.

    PubMed

    Matlock, Matthew; Swamidass, S Joshua

    2014-01-27

    In this study, we propose a new, secure method of sharing useful chemical information from small-molecule libraries, without revealing the structures of the libraries' molecules. Our method shares the relationship between molecules rather than structural descriptors. This is an important advance because, over the past few years, several groups have developed and published new methods of analyzing small-molecule screening data. These methods include advanced hit-picking protocols, promiscuous active filters, economic optimization algorithms, and screening visualizations, which can identify patterns in the data that might otherwise be overlooked. Application of these methods to private data requires finding strategies for sharing useful chemical data without revealing chemical structures. This problem has been examined in the context of ADME prediction models, with results from information theory suggesting it is impossible to share useful chemical information without revealing structures. In contrast, we present a new strategy for encoding the relationships between molecules instead of their structures, based on anonymized scaffold networks and trees, that safely shares enough chemical information to be useful in analyzing chemical data, while also sufficiently blinding structures from discovery. We present the details of this encoding, an analysis of the usefulness of the information it conveys, and the security of the structures it encodes. This approach makes it possible to share data across institutions, and may securely enable collaborative analysis that can yield insight into both specific projects and screening technology as a whole. PMID:24289228

  6. Synthesis and Structure-Activity Relationship Studies on Tryprostatin A, A Potent Inhibitor of Breast Cancer Resistance Protein

    PubMed Central

    Jain, Hiteshkumar D.; Zhang, Chunchun; Zhou, Shuo; Zhou, Hao; Ma, Jun; Liu, Xiaoxiang; Liao, Xuebin; Deveau, Amy M.; Dieckhaus, Christine M.; Johnson, Michael A.; Smith, Kirsten S.; Macdonald, Timothy L.; Kakeya, Hideaki; Osada, Hiroyuki; Cook, James M.

    2008-01-01

    Tryprostatin A is a potent inhibitor of breast cancer resistance protein, consequently a series of structure-activity studies on the cell cycle inhibitory effects of tryprostatin A analogues as potential antitumor antimitotic agents have been carried out. These analogues were assayed for their growth inhibition properties and their ability to perturb the cell cycle in tsFT210 cells. SAR studies resulted in the identification of the essential structural features required for cytotoxic activity. The absolute configuration L-Tyr-L-pro in the diketopiperazine ring along with the presence of the 6-methoxy substituent on the indole moiety of 1 was shown to be essential for dual inhibition of topoisomerase II and tubulin polymerization. Biological evaluation also indicated the presence of the 2-isoprenyl moiety on the indole scaffold of 1 was essential for potent inhibition of cell proliferation. Substitution of the indole Na-H in 1 with various alkyl or aryl groups, incorporation of various L-amino acids into the diketopiperazine ring in place of L-proline, and substitution of the 6-methoxy group in 1 with other functionality provided active analogues. The nature of the substituents present on the indole Na-H or the indole C-2 position influenced the mechanism of action of these analogues. nalogues 68 (IC50 = 10 ?M) and 67 (IC50 = 19 ?M) were 7-fold and 3.5-fold more potent, respectively than 1 (IC50 = 68 ?M) in the inhibition of the growth of tsFT210 cells. Diastereomer-2 of tryprostatin B 8 was a potent inhibitor of the growth of three human carcinoma cell lines: H520 (IC50 = 11.9 ?M), MCF7 (IC50 = 17.0 ?M) and PC3 (IC50 = 11.1 ?M) and was equipotent with etoposide, a clinically used anticancer agent. Isothiocyanate analogue 71 and 6-azido analogue 72 were as potent as 1 in the tsFT210 cell proliferation and may be useful tools in labeling BCRP. PMID:18321710

  7. Benzaldehyde Schiff bases regulation to the metabolism, hemolysis, and virulence genes expression in vitro and their structure-microbicidal activity relationship.

    PubMed

    Xia, Lei; Xia, Yu-Fen; Huang, Li-Rong; Xiao, Xiao; Lou, Hua-Yong; Liu, Tang-Jingjun; Pan, Wei-Dong; Luo, Heng

    2015-06-01

    There is an urgent need to develop new antibacterial agents because of multidrug resistance by bacteria and fungi. Schiff bases (aldehyde or ketone-like compounds) exhibit intense antibacterial characteristics, and are therefore, promising candidates as antibacterial agents. To investigate the mechanism of action of newly designed benzaldehyde Schiff bases, a series of high-yielding benzaldehyde Schiff bases were synthesized, and their structures were determined by NMR and MS spectra data. The structure-microbicidal activity relationship of derivatives was investigated, and the antibacterial mechanisms were investigated by gene assays for the expression of functional genes in vitro using Escherichia coli, Staphylococcus aureus, and Bacillus subtilis. The active compounds were selective for certain active groups. The polar substitution of the R2 group of the amino acids in the Schiff bases, affected the antibacterial activity against E. coli and S. aureus; specific active group at the R3 or R4 groups of the acylhydrazone Schiff bases could improve their inhibitory activity against these three tested organisms. The antibacterial mechanism of the active benzaldehyde Schiff bases appeared to regulate the expression of metabolism-associated genes in E. coli, hemolysis-associated genes in B. subtilis, and key virulence genes in S. aureus. Some benzaldehyde Schiff bases were bactericidal to all the three strains and appeared to regulate gene expression associated with metabolism, hemolysis, and virulence, in vitro. The newly designed benzaldehyde Schiff bases possessed unique antibacterial activity and might be potentially useful for prophylactic or therapeutic intervention of bacterial infections. PMID:25982329

  8. Structure-activity relationships derived by machine learning: the use of atoms and their bond connectivities to predict mutagenicity by inductive logic programming.

    PubMed Central

    King, R D; Muggleton, S H; Srinivasan, A; Sternberg, M J

    1996-01-01

    We present a general approach to forming structure-activity relationships (SARs). This approach is based on representing chemical structure by atoms and their bond connectivities in combination with the inductive logic programming (ILP) algorithm PROGOL. Existing SAR methods describe chemical structure by using attributes which are general properties of an object. It is not possible to map chemical structure directly to attribute-based descriptions, as such descriptions have no internal organization. A more natural and general way to describe chemical structure is to use a relational description, where the internal construction of the description maps that of the object described. Our atom and bond connectivities representation is a relational description. ILP algorithms can form SARs with relational descriptions. We have tested the relational approach by investigating the SARs of 230 aromatic and heteroaromatic nitro compounds. These compounds had been split previously into two subsets, 188 compounds that were amenable to regression and 42 that were not. For the 188 compounds, a SAR was found that was as accurate as the best statistical or neural network-generated SARs. The PROGOL SAR has the advantages that it did not need the use of any indicator variables handcrafted by an expert, and the generated rules were easily comprehensible. For the 42 compounds, PROGOL formed a SAR that was significantly (P < 0.025) more accurate than linear regression, quadratic regression, and back-propagation. This SAR is based on an automatically generated structural alert for mutagenicity. PMID:8552655

  9. Using quantitative structure activity relationship models to predict an appropriate solvent system from a common solvent system family for countercurrent chromatography separation.

    PubMed

    Marsden-Jones, Siân; Colclough, Nicola; Garrard, Ian; Sumner, Neil; Ignatova, Svetlana

    2015-06-12

    Countercurrent chromatography (CCC) is a form of liquid-liquid chromatography. It works by running one immiscible solvent (mobile phase) over another solvent (stationary phase) being held in a CCC column using centrifugal force. The concentration of compound in each phase is characterised by the partition coefficient (Kd), which is the concentration in the stationary phase divided by the concentration in the mobile phase. When Kd is between approximately 0.2 and 2, it is most likely that optimal separation will be achieved. Having the Kd in this range allows the compound enough time in the column to be separated without resulting in a broad peak and long run time. In this paper we report the development of quantitative structure activity relationship (QSAR) models to predict logKd. The QSAR models use only the molecule's 2D structure to predict the molecular property logKd. PMID:25931379

  10. Further structure-activity relationship studies on 8-substituted-3-[2-(diarylmethoxyethylidenyl)]-8-azabicyclo[3.2.1]octane derivatives at monoamine transporters.

    PubMed

    Cararas, Shaine A; Izenwasser, Sari; Wade, Dean; Housman, Amy; Verma, Abha; Lomenzo, Stacey A; Trudell, Mark L

    2011-12-15

    The synthesis and structure-activity relationships of 8-substituted-3-[2-(diarylmethoxyethylidenyl)]-8-azabicyclo[3.2.1]octane derivatives were investigated at the dopamine transporter (DAT), the serotonin transporter (SERT) and norepinephrine transporter (NET). The rigid ethylidenyl-8-azabicyclic[3.2.1]octane skeleton imparted modestly stereoselective binding and uptake inhibition at the DAT. Additional structure-activity studies provided a transporter affinity profile that was reminiscent of the structure-activity of GBR 12909. From these studies, the 8-cyclopropylmethyl group has been identified as a unique moiety that imparts high SERT/DAT selectivity. In this study the 8-cyclopropylmethyl derivative 22e (DAT K(i) of 4.0 nM) was among the most potent compounds of the series at the DAT and was the most DAT selective ligand of the series (SERT/DAT: 1060). Similarly, the 8-chlorobenzyl derivative 22g (DAT K(i) of 3.9 nM) was found to be highly selective for the DAT over the NET (NET/DAT: 1358). PMID:22055716

  11. Structure-activity relationship study of oxindole-based inhibitors of cyclin-dependent kinases based on least-squares support vector machines.

    PubMed

    Li, Jiazhong; Liu, Huanxiang; Yao, Xiaojun; Liu, Mancang; Hu, Zhide; Fan, Botao

    2007-01-01

    The least-squares support vector machines (LS-SVMs), as an effective modified algorithm of support vector machine, was used to build structure-activity relationship (SAR) models to classify the oxindole-based inhibitors of cyclin-dependent kinases (CDKs) based on their activity. Each compound was depicted by the structural descriptors that encode constitutional, topological, geometrical, electrostatic and quantum-chemical features. The forward-step-wise linear discriminate analysis method was used to search the descriptor space and select the structural descriptors responsible for activity. The linear discriminant analysis (LDA) and nonlinear LS-SVMs method were employed to build classification models, and the best results were obtained by the LS-SVMs method with prediction accuracy of 100% on the test set and 90.91% for CDK1 and CDK2, respectively, as well as that of LDA models 95.45% and 86.36%. This paper provides an effective method to screen CDKs inhibitors. PMID:17386461

  12. Further Structure-Activity Relationship Studies on 8-Substituted-3-[2-(diarylmethoxyethylidenyl)]-8-azabicyclo[3.2.1]octane Derivatives at Monoamine Transporters

    PubMed Central

    Cararas, Shaine A.; Izenwasser, Sari; Wade, Dean; Housman, Amy; Verma, Abha; Lomenzo, Stacey A.; Trudell, Mark L.

    2011-01-01

    The synthesis and structure-activity relationships of 8-substituted-3-[2-(diarylmethoxyethylidenyl)]-8-azabicyclo[3.2.1]octane derivatives were investigated at the dopamine transporter(DAT), the serotonin transporter (SERT) and norepinephrine transporter (NET). The rigid ethylidenyl-8-azabicyclic[3.2.1]octane skeleton imparted modestly stereoselective binding and uptake inhibition at the DAT. Additional structure-activity studies provided a transporter affinity profile that was reminiscent of the structure-activity of GBR 12909. From these studies, the 8-cyclopropylmethyl group has been identified as a unique moiety that imparts high SERT/DAT selectivity. In this study the 8-cyclopropylmethyl derivative 22e (DAT Ki of 4.0 nM) was among the most potent compounds of the series at the DAT and was the most DAT selective ligand of the series (SERT/DAT:1060). Similarly, the 8-chlorobenzyl derivative 22g (DAT Ki of 3.9 nM) was found to be highly selective for the DAT over the NET (NET/DAT: 1358). PMID:22055716

  13. Synthesis and Structure-Activity Relationships of 5,6,7-substituted Pyrazolopyrimidines: Discovery of a novel TSPO PET Ligand for Cancer Imaging

    PubMed Central

    Tang, Dewei; McKinley, Eliot T.; Hight, Matthew R.; Uddin, Md. Imam; Harp, Joel M.; Fu, Allie; Nickels, Michael L.; Buck, Jason R.; Manning, H. Charles

    2013-01-01

    Focused library synthesis and structure-activity relationship development of 5,6,7-substituted pyrazolopyrimidines led to the discovery of 2-(5,7-diethyl-2-(4-(2-fluoroethoxy)phenyl)pyrazolo[1,5-a]pyrimidin-3-yl)-N,N-diethylacetamide (6b), a novel translocator protein (TSPO) ligand exhibiting a 36-fold enhancement in affinity compared to another pyrazolopyrimidine-based TSPO ligand, 6a (DPA-714). Radiolabeling with fluorine-18 (18F) facilitated production of 2-(5,7-diethyl-2-(4-(2-[18F]fluoroethoxy)phenyl)pyrazolo[1,5-a]pyrimidin-3-yl)-N,N-diethylacetamide (18F-6b) in high radiochemical yield and specific activity. In vivo studies of 18F-6b were performed which illuminated this agent as an improved probe for molecular imaging of TSPO-expressing cancers. PMID:23521048

  14. Environmentally-benign catalysts for the selective catalytic reduction of NO(x) from diesel engines: structure-activity relationship and reaction mechanism aspects.

    PubMed

    Liu, Fudong; Yu, Yunbo; He, Hong

    2014-08-11

    Selective catalytic reduction of NOx using NH3 or hydrocarbons (NH3-SCR or HC-SCR) in oxygen-rich exhaust from diesel engines remains a major challenge in environmental catalysis. The development of highly efficient, stable and environmentally-benign catalysts for SCR processes is very important for practical use. In this feature article, the structure-activity relationship of vanadium-free catalysts in the NH3-SCR reaction is discussed in detail, including Fe-, Ce-based oxide catalysts and Fe-, Cu-based zeolite catalysts, which is beneficial for catalyst redesign and activity improvement. Based on our research, a comprehensive mechanism contributing to the performance of Ag/Al2O3 in HC-SCR is provided, giving a clue to the design of a catalytic system with high efficiency. PMID:24819654

  15. Evaluation of Phytocannabinoids from High Potency Cannabis sativa using In Vitro Bioassays to Determine Structure-Activity Relationships for Cannabinoid Receptor 1 and Cannabinoid Receptor 2.

    PubMed

    Husni, Afeef S; McCurdy, Christopher R; Radwan, Mohamed M; Ahmed, Safwat A; Slade, Desmond; Ross, Samir A; ElSohly, Mahmoud A; Cutler, Stephen J

    2014-09-01

    Cannabis has been around for thousands of years and has been used recreationally, medicinally, and for fiber. Over 500 compounds have been isolated from Cannabis sativa with approximately 105 being cannabinoids. Of those 105 compounds, ?(9)-tetrahydrocannabinol has been determined as the primary constituent, which is also responsible for the psychoactivity associated with Cannabis. Cannabinoid receptors belong to the large superfamily of G protein-coupled receptors. Targeting the cannabinoid receptors has the potential to treat a variety of conditions such as pain, neurodegeneration, appetite, immune function, anxiety, cancer, and others. Developing in vitro bioassays to determine binding and functional activity of compounds has the ability to lead researchers to develop a safe and effective drug that may target the cannabinoid receptors. Using radioligand binding and functional bioassays, a structure-activity relationship for major and minor cannabinoids was developed. PMID:25419092

  16. Synthesis and structure-activity relationship of non-phosphorus-based fructose-1,6-bisphosphatase inhibitors: 2,5-Diphenyl-1,3,4-oxadiazoles.

    PubMed

    Liao, Ben-Ren; He, Hai-Bing; Yang, Ling-Ling; Gao, Li-Xin; Chang, Liang; Tang, Jie; Li, Jing-Ya; Li, Jia; Yang, Fan

    2014-08-18

    With the aim of discovering a novel class of non-phosphorus-based fructose-1,6-bisphosphatase (FBPase) inhibitors, a series of 2,5-diphenyl-1,3,4-oxadiazoles were synthesized based on the hit compound (1) resulting from a high-throughput screening (HTS). Structure-activity relationship (SAR) studies led to the identification of several compounds with comparable inhibitory activities to AMP, the natural allosteric inhibitor of FBPase. Notably, compound 22 and 27b, bearing a terminal carboxyl or 1H-tetrazole, demonstrated remarkable inhibition to gluconeogenesis (GNG). In addition, both inhibition and binding mode to the enzyme were investigated by enzymatic kinetics and in silico experiments for representative compounds 16 and 22. PMID:24946215

  17. Structure-activity relationship of 1-desamino-8-D-arginine vasopressin as an antiproliferative agent on human vasopressin V2 receptor-expressing cancer cells.

    PubMed

    Pastrian, María B; Guzmán, Fanny; Garona, Juan; Pifano, Marina; Ripoll, Giselle V; Cascone, Osvaldo; Ciccia, Graciela N; Albericio, Fernando; Gómez, Daniel E; Alonso, Daniel F; Iannucci, Nancy B

    2014-06-01

    The synthetic nonapeptide 1?desamino?8?D?arginine vasopressin (dDAVP) can reduce tumor cell growth through agonist action on the vasopressin V2 receptor. A structure?antiproliferative activity relationship analysis of dDAVP was performed using the alanine scanning technique on the aggressive MDA?MB?231 human breast carcinoma cell line. The results from this analysis demonstrated that the amino acids located at the loop of dDAVP are important for the antiproliferative activity of dDAVP, highlighting the key role of the N?terminal region of the peptide in the interaction with the tumor cell surface receptor. The findings from this study present novel strategies for designing improved compounds with enhanced stability for cancer therapy. PMID:24737067

  18. In vitro anti-plasmodial activity of Dicoma anomala subsp. gerrardii (Asteraceae): identification of its main active constituent, structure-activity relationship studies and gene expression profiling

    PubMed Central

    2011-01-01

    Background Anti-malarial drug resistance threatens to undermine efforts to eliminate this deadly disease. The resulting omnipresent requirement for drugs with novel modes of action prompted a national consortium initiative to discover new anti-plasmodial agents from South African medicinal plants. One of the plants selected for investigation was Dicoma anomala subsp. gerrardii, based on its ethnomedicinal profile. Methods Standard phytochemical analysis techniques, including solvent-solvent extraction, thin-layer- and column chromatography, were used to isolate the main active constituent of Dicoma anomala subsp. gerrardii. The crystallized pure compound was identified using nuclear magnetic resonance spectroscopy, mass spectrometry and X-ray crystallography. The compound was tested in vitro on Plasmodium falciparum cultures using the parasite lactate dehydrogenase (pLDH) assay and was found to have anti-malarial activity. To determine the functional groups responsible for the activity, a small collection of synthetic analogues was generated - the aim being to vary features proposed as likely to be related to the anti-malarial activity and to quantify the effect of the modifications in vitro using the pLDH assay. The effects of the pure compound on the P. falciparum transcriptome were subsequently investigated by treating ring-stage parasites (alongside untreated controls), followed by oligonucleotide microarray- and data analysis. Results The main active constituent was identified as dehydrobrachylaenolide, a eudesmanolide-type sesquiterpene lactone. The compound demonstrated an in vitro IC50 of 1.865 ?M against a chloroquine-sensitive strain (D10) of P. falciparum. Synthetic analogues of the compound confirmed an absolute requirement that the ?-methylene lactone be present in the eudesmanolide before significant anti-malarial activity was observed. This feature is absent in the artemisinins and suggests a different mode of action. Microarray data analysis identified 572 unique genes that were differentially expressed as a result of the treatment and gene ontology analysis identified various biological processes and molecular functions that were significantly affected. Comparison of the dehydrobrachylaenolide treatment transcriptional dataset with a published artesunate (also a sesquiterpene lactone) dataset revealed little overlap. These results strengthen the notion that the isolated compound and the artemisinins have differentiated modes of action. Conclusions The novel mode of action of dehydrobrachylaenolide, detected during these studies, will play an ongoing role in advancing anti-plasmodial drug discovery efforts. PMID:21985233

  19. Hologram quantitative structure–activity relationship and comparative molecular field analysis studies within a series of tricyclic phthalimide HIV-1 integrase inhibitors

    PubMed Central

    de Oliveira Magalhães, Uiaran; de Souza, Alessandra Mendonça Teles; Albuquerque, Magaly Girão; de Brito, Monique Araújo; Bello, Murilo Lamim; Cabral, Lucio Mendes; Rodrigues, Carlos Rangel

    2013-01-01

    Acquired immunodeficiency syndrome is a public health problem worldwide caused by the Human immunodeficiency virus (HIV). Treatment with antiretroviral drugs is the best option for viral suppression, reducing morbidity and mortality. However, viral resistance in HIV-1 therapy has been reported. HIV-1 integrase (IN) is an essential enzyme for effective viral replication and an attractive target for the development of new inhibitors. In the study reported here, two- and three-dimensional quantitative structure–activity relationship (2D/3D-QSAR) studies, applying hologram quantitative structure–activity relationship (HQSAR) and comparative molecular field analysis (CoMFA) methods, respectively, were performed on a series of tricyclic phthalimide HIV-1 IN inhibitors. The best HQSAR model (q2 = 0.802, r2 = 0.972) was obtained using atoms, bonds, and connectivity as the fragment distinction, a fragment size of 2–5 atoms, hologram length of 61 bins, and six components. The best CoMFA model (q2 = 0.748, r2 = 0.974) was obtained with alignment of all atoms of the tricyclic phthalimide moiety (alignment II). The HQSAR contribution map identified that the carbonyl-hydroxy-aromatic nitrogen motif made a positive contribution to the activity of the compounds. Furthermore, CoMFA contour maps suggested that bulky groups in meta and para positions in the phenyl ring would increase the biological activity of this class. The conclusions of this work may lead to a better understanding of HIV-1 IN inhibition and contribute to the design of new and more potent derivatives. PMID:24039405

  20. The structure of marketing channel relationships

    Microsoft Academic Search

    Robert A. Robicheaux; James E. Coleman

    1994-01-01

    Distribution channel research has been advanced in recent years by contributions based on the political economy paradigm,\\u000a transaction cost analysis, and relationship marketing. Drawing on these bodies of thought, we propose a new conceptualization\\u000a of the structure of marketing channel relationships. Relationship structure is defined in terms of decision-making structure\\u000a and operational integration. The proposed model of channel structure antecedents

  1. Research on the structure-surface adsorptive activity relationships of triazolyl glycolipid derivatives for mild steel in HCl.

    PubMed

    Zhang, Hai-Lin; He, Xiao-Peng; Deng, Qiong; Long, Yi-Tao; Chen, Guo-Rong; Chen, Kaixian

    2012-06-01

    Triazolyl glycolipid derivatives constructed via Cu(I)-catalyzed azide-alkyne 1,3-dipolar cycloaddition reaction (Cue-AAC) represent a new range of carbohydrate-based scaffolds for use in many fields of the chemical research. Here the surface adsorptive ability of series of our previously prepared C1- or C6-triazole linked gluco- and galactolipid derivatives for mild steel in 1 M HCl was studied via electrochemical impedance spectroscopy (EIS). Results indicated that these monosaccharide-fatty acid conjugates are weak inhibitors against HCl corrosion for mild steel. Moreover, some newly synthesized triazolyl disaccharide (maltose)-fatty alcohol conjugates failed to display enhanced activity, meaning that the structural enlargement of the sugar moiety does not favor the iron surface adsorption. However, a bis-triazolyl glycolipid derivative, which was realized by introducing a benzenesulfonamide group via Cue-AAC to the C6-position of a C1-triazolyl glucolipid analog, eventually showed significantly improved adsorptive potency compared to that of its former counterparts. The corrosion inhibitive modality of this compound for mild steel in HCl was subsequently studied via potentiodynamic polarization and thermodynamic calculations. PMID:22537861

  2. A relationship between the solar rotation and activity in the period 1998-2006 analysed by tracing small bright coronal structures in SOHO-EIT images

    NASA Astrophysics Data System (ADS)

    Jurdana-Šepi?, R.; Brajša, R.; Wöhl, H.; Hanslmeier, A.; Poljan?i?, I.; Svalgaard, L.; Gissot, S. F.

    2011-10-01

    Aims: The study aims to find a relationship between the rotation of the small bright coronal structures (SBCS) described by the solar rotation parameters and indices of solar activity on monthly and yearly temporal scales. Methods: We analyse precise measurements of the solar differential rotation determined by tracing SBCS in SOHO-EIT images and compare the derived solar rotation parameters with the status of solar activity in the period 1998 - 2006. Full-disc solar images obtained with the Extreme ultraviolet Imaging Telescope (EIT) on board the Solar and Heliospheric Observatory (SOHO) were used to analyse solar differential rotation determined by tracing SBCS. An automatic method to identify and track the SBCS in EIT full-disc images with a six hour cadence is applied. We performed a statistical analysis of the monthly and yearly values of solar sidereal rotation velocity parameters A and B (corresponding to the equatorial rotation velocity and the gradient of the solar differential rotation, respectively) as a function of various solar activity indices. Results: The dependence of the solar rotation on the phase of the solar cycle was found. It is clearly visible for the solar rotation parameter A, whilst the results are not conclusive for parameter B. The relationship between the solar rotation and activity, expressed by the monthly relative sunspot number, the smoothed monthly relative sunspot number, the yearly relative sunspot number, and the interdiurnal variability (IDV) index was investigated. The statistically significant correlation was found for the solar rotation parameter A, whilst a very low and insignificant correlation was obtained for the rotation parameter B. Conclusions: During the maximum of the solar cycle 23 and just after it, the equatorial solar rotation velocity was lower than in other phases of the cycle, when there was less activity. This is consistent with other observational findings, obtained by different tracers and methods.

  3. Synthesis and structure-activity relationship (SAR) of 2-methyl-4-oxo-3-oxetanylcarbamic acid esters, a class of potent N-acylethanolamine acid amidase (NAAA) inhibitors.

    PubMed

    Ponzano, Stefano; Bertozzi, Fabio; Mengatto, Luisa; Dionisi, Mauro; Armirotti, Andrea; Romeo, Elisa; Berteotti, Anna; Fiorelli, Claudio; Tarozzo, Glauco; Reggiani, Angelo; Duranti, Andrea; Tarzia, Giorgio; Mor, Marco; Cavalli, Andrea; Piomelli, Daniele; Bandiera, Tiziano

    2013-09-12

    N-Acylethanolamine acid amidase (NAAA) is a lysosomal cysteine hydrolase involved in the degradation of saturated and monounsaturated fatty acid ethanolamides (FAEs), a family of endogenous lipid agonists of peroxisome proliferator-activated receptor-?, which include oleoylethanolamide (OEA) and palmitoylethanolamide (PEA). The ?-lactone derivatives (S)-N-(2-oxo-3-oxetanyl)-3-phenylpropionamide (2) and (S)-N-(2-oxo-3-oxetanyl)-biphenyl-4-carboxamide (3) inhibit NAAA, prevent FAE hydrolysis in activated inflammatory cells, and reduce tissue reactions to pro-inflammatory stimuli. Recently, our group disclosed ARN077 (4), a potent NAAA inhibitor that is active in vivo by topical administration in rodent models of hyperalgesia and allodynia. In the present study, we investigated the structure-activity relationship (SAR) of threonine-derived ?-lactone analogues of compound 4. The main results of this work were an enhancement of the inhibitory potency of ?-lactone carbamate derivatives for NAAA and the identification of (4-phenylphenyl)-methyl-N-[(2S,3R)-2-methyl-4-oxo-oxetan-3-yl]carbamate (14q) as the first single-digit nanomolar inhibitor of intracellular NAAA activity (IC50 = 7 nM on both rat NAAA and human NAAA). PMID:23991897

  4. Structure-activity relationships of 18 endogenous neuropeptides on the motor nervous system of the nematode Ascaris suum.

    PubMed

    Davis, R E; Stretton, A O

    2001-01-01

    Neuropeptides play an important role in all nervous systems and structure-activity studies of related peptides is one approach to understanding this role. This study of the motor nervous system of the parasitic nematode Ascaris suum describes the physiological effects of a family of 18 endogenous Ascaris FMRFamide-like peptides (AF peptides) on the membrane potential and input resistance of the dorsal excitatory type 2 (DE2) and dorsal inhibitory (DI) motor neurons. These motor neurons are part of the final common output pathway from the motor nervous system to the somatic muscle cells responsible for locomotion. AF peptide effects on the frequency of excitatory postsynaptic potentials (EPSPs) in DE2 motor neurons were also measured to infer peptide effects on central presynaptic spiking neurons. AF peptide injections into intact worms were made to assess their qualitative effects on behavior, providing a context for interpreting motor neuron data. One category of AF peptides, N-terminally extended -FIRFa peptides (AF5, AF7 and AF1), has pronounced behavioral effects and qualitatively similar, but quantitatively different effects on DE2 and DI motor neurons. A second category of AF peptides (AF2, AF9, and AF8) also produces dramatic behavioral effects and strong electrophysiological effects on DE2 and/or DI motor neurons. A third category of AF peptides, consisting of six members of the -PGVLRFa group (which are encoded by the same gene and have closely related sequences) and peptide AF11, have pronounced behavioral effects, but relatively weak or negligible effects on DE2 and DI motor neurons. A fourth category of AF peptides, also consisting of structurally unrelated members, has pronounced behavioral effects and, as individual peptides, similar effects on both DE2 and DI motor neurons; AF15 is excitatory, while AF17 and AF19 are inhibitory, on both motor neuron types. Finally, two AF peptides (AF6, AF16) are relatively weak or inactive in producing behavioral or motor neuronal effects. Based on comparisons of the effects of AF peptides on DE2 and DI motor neurons, a tentative list of 5 major response-types is proposed as a working hypothesis to guide the search for AF peptide receptors. The findings attest to the potential complexity of neurosignaling in this comparatively simple nervous system. PMID:11179593

  5. Discovery of benzamide analogs as negative allosteric modulators of human neuronal nicotinic receptors: Pharmacophore modeling and structure-activity relationship studies

    PubMed Central

    Yi, Bitna; Long, Sihui; González-Cestari, Tatiana F.; Henderson, Brandon J.; Pavlovicz, Ryan E.; Werbovetz, Karl; Li, Chenglong; McKay, Dennis B.

    2015-01-01

    The present study describes our ongoing efforts toward the discovery of drugs that selectively target nAChR subtypes. We exploited knowledge on nAChR ligands and their binding site that were previously identified by our laboratory through virtual screenings and identified benzamide analogs as a novel chemical class of neuronal nicotinic receptor (nAChR) ligands. The lead molecule, compound 1 (4-(allyloxy)-N-(6-methylpyridin-2-yl)benzamide) inhibits nAChR activity with an IC50 value of 6.0 (3.4–10.6) µM on human ?4?2 nAChRs with a ~5-fold preference against human ?3?4 nAChRs. Twenty-six analogs of compound 1 were also either synthesized or purchased for structure-activity relationship (SAR) studies and provided information relating the chemical/structural properties of the molecules to their ability to inhibit nAChR activity. The discovery of subtype-selective ligands of nAChRs described here should contribute significantly to our understanding of the involvement of specific nAChR subtypes in normal and pathophysiological states. PMID:23757208

  6. Non-dioxin-like PCBs inhibit [(3)H]WIN-35,428 binding to the dopamine transporter: a structure-activity relationship study.

    PubMed

    Wigestrand, M B; Stenberg, M; Walaas, S I; Fonnum, F; Andersson, P L

    2013-12-01

    Non-dioxin-like polychlorinated biphenyls (NDL-PCBs) are neurotoxic compounds with known effects at the dopaminergic system in the brain. In a previous study we demonstrated that NDL-PCBs inhibit uptake of dopamine into rat brain synaptosomes, an effect most likely mediated by inhibition of the dopamine transporter (DAT). Here, using the cocaine analogue [(3)H]WIN-35,428 binding assay and synaptosomes, we directly investigate whether NDL-PCBs act via DAT and explore the structure-activity relationship of this effect. In total, thirty PCBs were investigated, including a previously selected training set of twenty PCBs covering the structural variation within tri- to hepta-chlorinated NDL-PCBs, and an additional set of ten NDL-PCB congeners selected to validate the structure-activity pattern of neurotoxic PCBs. Since previous work has demonstrated that NDL-PCBs can also inhibit the vesicular monoamine transporter 2 (VMAT2), we additionally examined whether some PCB congeners favour an effect on VMAT2 and others on DAT. Our results show that NDL-PCBs are potent inhibitors of [(3)H]WIN-35,428 binding to DAT. In fact, we identify a PCB congener (PCB 110) with similar potency for [(3)H]WIN-35,428 binding inhibition as cocaine. All active congeners were ortho-chlorinated PCBs, and in particular, tetra- and penta-chlorinated with 2-3 chlorine atoms in the ortho position were potent inhibitors of [(3)H]WIN-35,428 binding. Notably, the most active PCBs are highly prevalent in commercial mixtures of PCBs (Aroclor 1242, 1254 and 1260), which indicates that DAT inhibition could be one of the factors contributing to behavioural effects after Aroclor exposure. Derived data correlated well with the recently derived neurotoxic equivalency factors (NEQs), indicating the generality and applicability of the NEQ scheme in risk assessments of PCBs. PMID:23933243

  7. Stepwise development of structure-activity relationship of diverse PARP-1 inhibitors through comparative and validated in silico modeling techniques and molecular dynamics simulation.

    PubMed

    Halder, Amit K; Saha, Achintya; Saha, Krishna Das; Jha, Tarun

    2015-08-01

    Inhibitors of poly (ADP-ribose) polymerase-1 (PARP-1) enzyme are useful for the treatment of various diseases including cancer. Comparative in silico studies were performed on different ligand-based (2D-QSAR, Kernel-based partial least square (KPLS) analysis, Pharmacophore Search Engine (PHASE) pharmacophore mapping), and structure-based (molecular docking, MM-GBSA analyses, Gaussian-based 3D-QSAR analyses on docked poses) modeling techniques to explore the structure-activity relationship of a diverse set of PARP-1 inhibitors. Two-dimensional (2D)-QSAR highlighted the importance of charge topological index (JGI7), fractional polar surface area (JursFPSA3), and connectivity index (CIC2) along with different molecular fragments. Favorable and unfavorable fingerprints were demonstrated in KPLS analysis, whereas important pharmacophore features (one acceptor, one donor, and two ring aromatic) along with favorable and unfavorable field effects were demonstrated in PHASE-based pharmacophore model. MM-GBSA analyses revealed significance of different polar, non-polar, and solvation energies. Docking-based alignment of ligands was used to perform Gaussian-based 3D-QSAR study that further demonstrated importance of different field effects. Overall, it was found that polar interactions (hydrogen bonding, bridged hydrogen bonding, and pi-cation) play major roles for higher activity. Steric groups increase the total contact surface area but it should have higher fractional polar surface area to adjust solvation energy. Structure-based pharmacophore mapping spotted the positive ionizable feature of ligands as the most important feature for discriminating highly active compounds from inactives. Molecular dynamics simulation, conducted on highly active ligands, described the dynamic behaviors of the protein complexes and supported the interpretations obtained from other modeling analyses. The current study may be useful for designing PARP-1 inhibitors. PMID:25350685

  8. Binary classification of a large collection of environmental chemicals from estrogen receptor assays by quantitative structure-activity relationship and machine learning methods.

    PubMed

    Zang, Qingda; Rotroff, Daniel M; Judson, Richard S

    2013-12-23

    There are thousands of environmental chemicals subject to regulatory decisions for endocrine disrupting potential. The ToxCast and Tox21 programs have tested ?8200 chemicals in a broad screening panel of in vitro high-throughput screening (HTS) assays for estrogen receptor (ER) agonist and antagonist activity. The present work uses this large data set to develop in silico quantitative structure-activity relationship (QSAR) models using machine learning (ML) methods and a novel approach to manage the imbalanced data distribution. Training compounds from the ToxCast project were categorized as active or inactive (binding or nonbinding) classes based on a composite ER Interaction Score derived from a collection of 13 ER in vitro assays. A total of 1537 chemicals from ToxCast were used to derive and optimize the binary classification models while 5073 additional chemicals from the Tox21 project, evaluated in 2 of the 13 in vitro assays, were used to externally validate the model performance. In order to handle the imbalanced distribution of active and inactive chemicals, we developed a cluster-selection strategy to minimize information loss and increase predictive performance and compared this strategy to three currently popular techniques: cost-sensitive learning, oversampling of the minority class, and undersampling of the majority class. QSAR classification models were built to relate the molecular structures of chemicals to their ER activities using linear discriminant analysis (LDA), classification and regression trees (CART), and support vector machines (SVM) with 51 molecular descriptors from QikProp and 4328 bits of structural fingerprints as explanatory variables. A random forest (RF) feature selection method was employed to extract the structural features most relevant to the ER activity. The best model was obtained using SVM in combination with a subset of descriptors identified from a large set via the RF algorithm, which recognized the active and inactive compounds at the accuracies of 76.1% and 82.8% with a total accuracy of 81.6% on the internal test set and 70.8% on the external test set. These results demonstrate that a combination of high-quality experimental data and ML methods can lead to robust models that achieve excellent predictive accuracy, which are potentially useful for facilitating the virtual screening of chemicals for environmental risk assessment. PMID:24279462

  9. The Structure-Activity Relationship of the 3-Oxy Site in the Anticonvulsant (R)-N-Benzyl 2-Acetamido-3-methoxypropionamide

    PubMed Central

    Morieux, Pierre; Salomé, Christophe; Park, Ki Duk; Stables, James P.; Kohn, Harold

    2010-01-01

    Lacosamide ((R)-N-benzyl 2-acetamido-3-methoxypropionamide, (R)-1) is a low molecular weight anticonvulsant recently introduced in the United States and Europe for adjuvant treatment of partial-onset seizures in adults. In this study, we define the structure-activity relationship (SAR) for the compound's 3-oxy site. Placement of small non-polar, non-bulky substituents at the 3-oxy site provided compounds with pronounced seizure protection in the maximal electroshock (MES) seizure test with activities similar to (R)-1. The anticonvulsant activity loss that accompanied introduction of larger moieties at the 3-oxy site in (R)-1 was offset, in part, by including unsaturated groups at this position. Our findings were similar to a recently reported SAR study of the 4?-benzylamide site in (R)-1 (J. Med. Chem.2010, 53, 1288–1305). Together, these results indicate that both the 3-oxy and 4?-benzylamide positions in (R)-1 can accommodate non-bulky, hydrophobic groups and still retain pronounced anticonvulsant activities in rodents in the MES seizure model. PMID:20614888

  10. Structure-activity relationship of Cr/Ti-PILC catalysts using a pre-modification method for NO oxidation and their surface species study.

    PubMed

    Zhong, Lei; Yu, Yang; Cai, Wei; Geng, Xinxin; Zhong, Qin

    2015-05-27

    The performances of Cr/Ti-PILC catalysts, which were prepared by the pre-modification method, are studied for the selective catalytic oxidation of NO. The aim of this paper is to elucidate the detailed relationship between physical nanoparticle structure and chemical properties. The maximum NO conversion over the Cr-HP(3)/TP catalyst reached 71.4% at 280 °C. The catalysts were characterized by powder X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), transmission electron microscopy (TEM), X-ray photoelectron spectroscopy (XPS), temperature-programmed reduction of H2 (H2-TPR), temperature-programmed desorption (TPD) and diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) techniques. The characterization results demonstrated that the enhanced catalytic activity was ascribed to several beneficial effects, which were caused by the pre-modification such as the inhibition of crystallite size, improvement of Cr species dispersion and increase of the amount of active sites. XPS and FTIR experiments indicated that two Cr(vi) species, oxidized state CrO3 and chromate species with the anionic form, were generated via pre-modification, which played different roles in the catalytic reaction. In addition, the TPR and TPD results suggest that the increased active sites (Cr(vi) species) were conducive for the preferential adsorption and activation of NO. Furthermore, DRIFTS results revealed that the intermediates, NO(+) and nitrates, interacted quickly to generate gaseous NO2. PMID:25988234

  11. Structure-Activity Relationships in the Binding of Chemically Derivatized CD4 to gp120 from Human Immunodeficiency Virus

    E-print Network

    Hendrickson, Wayne A.

    , as evidenced by multiple X-ray crystal structures of core gp120 proteins derived from different isolates for structure-based assembly of small molecules targeting gp120-CD4 interaction. Introduction Human antiretroviral drugs that have been approved by FDA for clinical treatment of AIDS,3 nearly all target either

  12. Lathyrol diterpenes as modulators of P-glycoprotein dependent multidrug resistance: structure-activity relationship studies on Euphorbia factor L3 derivatives.

    PubMed

    Jiao, Wei; Wan, Zhongmin; Chen, Shuang; Lu, Runhua; Chen, Xiaozhen; Fang, Dongmei; Wang, Jiufeng; Pu, Shengcai; Huang, Xin; Gao, Haixiang; Shao, Huawu

    2015-05-14

    Five series of 37 new acylate and epoxide derivatives (3-39) of Euphorbia factor L3, a lathyrol diterpene isolated from Euphorbia lathyris, were designed by modifying the hydroxyl moiety of C-3, C-5, or C-15. Chemoreversal effects of the acylates on multidrug resistance (MDR) were evaluated in breast cancer multidrug-resistant MCF-7/ADR cells that overexpress P-glycoprotein (P-gp). Eight derivatives exhibited greater chemoreversal ability than verapamil (VRP) against adriamycin (ADR) resistance. Compounds 19 and 25 exhibited 4.8 and 4.0 times, respectively, more effective reversal ability than VRP against ADR resistance. To determine the key characteristics of Euphorbia factor L3 derivatives that contribute to MDR reversal, we conducted a structure-activity relationship study of these compounds. The simulation studies indicated different possible mechanisms and revealed the important influence of hydrophobic interactions and hydrogen bonds in the flexible cavity of P-gp. PMID:25856545

  13. Seamless integration of dose-response screening and flow chemistry: efficient generation of structure-activity relationship data of ?-secretase (BACE1) inhibitors.

    PubMed

    Werner, Michael; Kuratli, Christoph; Martin, Rainer E; Hochstrasser, Remo; Wechsler, David; Enderle, Thilo; Alanine, Alexander I; Vogel, Horst

    2014-02-01

    Drug discovery is a multifaceted endeavor encompassing as its core element the generation of structure-activity relationship (SAR) data by repeated chemical synthesis and biological testing of tailored molecules. Herein, we report on the development of a flow-based biochemical assay and its seamless integration into a fully automated system comprising flow chemical synthesis, purification and in-line quantification of compound concentration. This novel synthesis-screening platform enables to obtain SAR data on b-secretase (BACE1) inhibitors at an unprecedented cycle time of only 1 h instead of several days. Full integration and automation of industrial processes have always led to productivity gains and cost reductions, and this work demonstrates how applying these concepts to SAR generation may lead to a more efficient drug discovery process. PMID:24458566

  14. Structure-activity relationships for chemical and glutathione S-transferase-catalysed glutathione conjugation reactions of a series of 2-substituted 1-chloro-4-nitrobenzenes.

    PubMed Central

    Van der Aar, E M; Bouwman, T; Commandeur, J N; Vermeulen, N P

    1996-01-01

    Glutathione S-transferases (GSTs) constitute an important class of phase II (de)toxifying enzymes, catalysing the conjugation of glutathione (GSH) with electrophilic compounds. In the present study, Km, kcat and kcat/Km values for the rat GST 1-1-, 3-3-, 4-4- and 7-7-catalysed conjugation reactions between GSH and a series of 10 different 2-substituted 1-chloro-4-nitrobenzenes, and the second-order rate constants (ks) of the corresponding base-catalysed reactions, were correlated with nine classical physicochemical parameters (electronic, steric and lipophilic) of the substituents and with 16 computer-calculated molecular parameters of the substrates and of the corresponding Meisenheimer complexes with MeS- as a model nucleophile for GS- (charge distributions and several energy values), giving structure-activity relationships. On the basis of an identical dependence of the base-catalysed as well as the GST 1-1- and GST 7-7-catalysed reactions on electronic parameters (among others, Hammett substituent constant sigma p and charge on p-nitro substituents), and the finding that the corresponding reactions catalysed by GSTs 3-3 and 4-4 depend to a significantly lesser extent on these parameters, it was concluded that the Mu-class GST isoenzymes have a rate-determining transition state in the conjugation reaction between 2-substituted 1-chloro-4-nitrobenzenes and GSH which is different from that of the other two GSTs. Several alternative rate-limiting transition states for GST 3-3 and 4-4 are discussed. Furthermore, based on the obtained structure-activity relationships, it was possible to predict the kcat/Km values of the four GST isoenzymes and the ks of the base-catalysed GSH conjugation of 1-chloro-4-nitrobenzene. PMID:8973562

  15. Structural analysis of Canavalia maritima and Canavalia gladiata lectins complexed with different dimannosides: new insights into the understanding of the structure-biological activity relationship in legume lectins.

    PubMed

    Bezerra, Gustavo Arruda; Oliveira, Taianá Maia; Moreno, Frederico Bruno Mendes Batista; de Souza, Emmanuel Prata; da Rocha, Bruno Anderson Matias; Benevides, Raquel Guimarães; Delatorre, Plínio; de Azevedo, Walter Filgueira; Cavada, Benildo Sousa

    2007-11-01

    Plant lectins, especially those purified from species of the Leguminosae family, represent the best studied group of carbohydrate-binding proteins. The legume lectins from Diocleinae subtribe are highly similar proteins that present significant differences in the potency/efficacy of their biological activities. The structural studies of the interactions between lectins and sugars may clarify the origin of the distinct biological activities observed in this high similar class of proteins. In this way, this work presents a crystallographic study of the ConM and CGL (agglutinins from Canavalia maritima and Canavalia gladiata, respectively) in the following complexes: ConM/CGL:Man(alpha1-2)Man(alpha1-O)Me, ConM/CGL:Man(alpha1-3)Man(alpha1-O)Me and ConM/CGL:Man(alpha1-4)Man(alpha1-O)Me, which crystallized in different conditions and space group from the native proteins. The structures were solved by molecular replacement, presenting satisfactory values for R(factor) and R(free). Comparisons between ConM, CGL and ConA (Canavalia ensiformis lectin) binding mode with the dimannosides in subject, presented different interactions patterns, which may account for a structural explanation of the distincts biological properties observed in the lectins of Diocleinae subtribe. PMID:17881248

  16. Design, synthesis and structure-activity relationship of oxazolidinone derivatives containing novel S4 ligand as FXa inhibitors.

    PubMed

    Zhao, Yanfang; Jiang, Mingyan; Zhou, Shunguang; Wu, Shasha; Zhang, Xiaolong; Ma, Longsheng; Zhang, Kai; Gong, Ping

    2015-05-26

    A novel series of potent and efficacious factor Xa inhibitors which possesses pyrrole/indole/thiazole moieties as S4 binding element was identified. Compound 7b showed strong human factor Xa inhibitory activity (IC50 = 2.01 nM) and anticoagulant activities in both human (PTCT2 = 0.15 ?M, APPTCT2 = 0.30 ?M) and rabbit plasma (PTCT2 = 0.46 ?M, APPTCT2 = 0.75 ?M). The SARs analyses indicated that the size and water solubility of different alkylamino group at the position of S4 ligand were responsible for the anticoagulant activity. PMID:25911624

  17. Inhibitors of HCV NS5B polymerase: Synthesis and structure–activity relationships of unsymmetrical 1-hydroxy-4,4-dialkyl-3-oxo-3,4-dihydronaphthalene benzothiadiazine derivatives

    Microsoft Academic Search

    A. Chris Krueger; Darold L. Madigan; Brian E. Green; Douglas K. Hutchinson; Wen W. Jiang; Warren M. Kati; Yaya Liu; Clarence J. Maring; Sherie V. Masse; Keith F. McDaniel; Tim R. Middleton; Hongmei Mo; Akhteruzzaman Molla; Debra A. Montgomery; Teresa I. Ng; Dale J. Kempf

    2007-01-01

    Substituted 1-hydroxy-4,4-dialkyl-3-oxo-3,4-dihydronaphthalene benzothiadiazine derivatives were investigated as inhibitors of genotype 1 HCV polymerase. Structure–activity relationship patterns for this class of compounds are discussed. It was found that the saturated alkane dialkyl units provided the most active analogs.

  18. Structure-activity relationships for the impact of selected isothiazol-3-one biocides on glutathione metabolism and glutathione reductase of the human liver cell line Hep G2.

    PubMed

    Arning, Jürgen; Dringen, Ralf; Schmidt, Maike; Thiessen, Anette; Stolte, Stefan; Matzke, Marianne; Bottin-Weber, Ulrike; Caesar-Geertz, Birgit; Jastorff, Bernd; Ranke, Johannes

    2008-04-18

    To investigate the toxic mode of action of isothiazol-3-one biocides the four compounds N-methylisothiazol-3-one (MIT), 5-chloro-N-methylisothiazol-3-one (CIT), N-octylisothiazol-3-one (OIT) and 4,5-dichloro-N-octylisothiazol-3-one (DCOIT) were purified and tested as single chemical entities for their effects on the human hepatoblastoma cell line Hep G2 and on isolated and cellular glutathione reductase GR). The two chlorinated substances CIT and DCOIT significantly decreased the amount of total cellular glutathione (GSx) in a dose and time dependent manner. Concomitantly, an increase in the level of oxidised glutathione (GSSG) was observed. The resulting shift in the GSH/GSSG ratio entailing the breakdown of the cellular thiol reduction potential was accompanied by necrotic morphological changes like swelling of the plasma membrane and subsequent lysis of the cells. Additionally, CIT and DCOIT were found to inhibit cellular GR in the cells in a concentration dependent manner. The T-SAR-based (thinking in terms of structure-activity relationships) comparison of the chlorine-substituted structures CIT and DCOIT with their non-chlorinated and less active analogues MIT and OIT identified the chlorine substituents and the resulting reaction mechanisms to be the key structural mediators of the observed toxic effects. Furthermore, differences in the activity of both chlorinated substances could be explained using the T-SAR approach to link the lipophilicity and the intrinsic glutathione-reactivity of the compounds to the expected target site concentrations inside the cells. PMID:18313196

  19. Structure-activity relationship of non-coplanar polychlorinated biphenyls toward skeletal muscle ryanodine receptors in rainbow trout (Oncorhynchus mykiss)

    PubMed Central

    Fritsch, Erika B.; Pessah, Isaac N.

    2013-01-01

    Research addressing the health impacts of polychlorinated biphenyls (PCBs) has primarily focused on the effects of coplanar, or dioxin-like (DL), congeners, which is especially true for research assessing impacts in fish species. Ortho substituted non-coplanar, termed non-dioxin-like (NDL), PCBs have received less attention. In mammals, NDL PCBs enhance the activity of ryanodine receptors (RyR), calcium release channels necessary for engaging excitation-contraction (EC) coupling in striated muscle. We utilized in vitro receptor binding analysis to determine whether NDL PCB congeners detected in aquatic environments alter the activity of RyR isoform 1 (RyR1) found in the skeletal muscle of rainbow trout. Congeners 52, 95, 136, and 149 were the most efficacious leading to an increase in receptor activity that was approximately 250% greater than that found under solvent control conditions. Other environmentally relevant congeners, namely PCB 153, 151 and 101, which all contain two or more chlorines in the ortho-position, enhanced receptor activity by greater than 160% of baseline. The mono-ortho congeners or the non-ortho PCB 77 had negligible impact on the RyR1. When combined, in binary or environmentally relevant mixtures, congeners shown to enhance receptor activity appeared to display additivity and when the active PCB 95 was present with the non-active congener PCB 77 the impact on receptor activity was reduced from 250% to 230%. The important role of the RyR and the demonstrated additive nature of NDL congeners towards altering channel function calls for further investigation into the ecological implications of altered RyR function in fish with high PCB burdens. PMID:23827775

  20. Synthesis and structure-activity relationship of aminoarylthiazole derivatives as correctors of the chloride transport defect in cystic fibrosis.

    PubMed

    Pesce, Emanuela; Bellotti, Marta; Liessi, Nara; Guariento, Sara; Damonte, Gianluca; Cichero, Elena; Galatini, Andrea; Salis, Annalisa; Gianotti, Ambra; Pedemonte, Nicoletta; Zegarra-Moran, Olga; Fossa, Paola; Galietta, Luis J V; Millo, Enrico

    2015-06-24

    The cystic ?brosis transmembrane conductance regulator (CFTR) is a chloride channel present in the membrane of epithelial cells. Mutations affecting the CFTR gene cause cystic fibrosis (CF), a multi-organ severe disease. The most common CF mutation, F508del, impairs the processing and activity (gating) of CFTR protein. Other mutations, like G551D, only cause a gating defect. Processing and gating defects can be targeted by small molecules called generically correctors and potentiators, respectively. Aminoarylthiazoles (AATs) represent an interesting class of compounds that includes molecules with dual activity, as correctors and potentiators. With the aim to improve the activity profile of AATs, we have now designed and synthesized a library of novel compounds in order to establish an initial SAR that may provide indications about the chemical groups that are beneficial or detrimental for rescue activity. The new compounds were tested as correctors and potentiators in CFBE41o-expressing F508del-CFTR using a functional assay. A dual active compound, AAT-4a, characterized by improved efficacy and marked synergy when combined with the corrector VX-809 has been identified. Moreover, by computational methods, a possible binding site for AATs in nucleotide binding domain NBD1 has been detected. These results will direct the synthesis of new analogues with possibly improved activity. PMID:26041577

  1. Solution structure of carnobacteriocin B2 and implications for structure-activity relationships among type IIa bacteriocins from lactic acid bacteria.

    PubMed

    Wang, Y; Henz, M E; Gallagher, N L; Chai, S; Gibbs, A C; Yan, L Z; Stiles, M E; Wishart, D S; Vederas, J C

    1999-11-23

    Carnobacteriocin B2 (CbnB2), a type IIa bacteriocin, is a 48 residue antimicrobial peptide from the lactic acid bacterium Carnobacterium pisicola LV17B. Type IIa bacteriocins have a conserved YGNGVXC sequence near the N-terminus and usually contain a disulfide bridge. CbnB2 seemed to be unique in that its two cysteines (Cys9 and Cys14) could be isolated as free thiols [Quadri et al. (1994) J. Biol. Chem. 26, 12204-12211]. To establish the structural consequences of the presence or absence of a disulfide bridge and to investigate if the YGNGVXC sequence is a receptor-binding motif [Fleury et al. (1996) J. Biol. Chem. 271, 14421-14429], the three-dimensional solution structure of CbnB2 was determined by two-dimensional (1)H nuclear magnetic resonance (NMR) techniques. Mass spectroscopic and thiol modification experiments on CbnB2 and on model peptides, in conjunction with activity measurements, were used to verify the redox status of CbnB2. The results show that CbnB2 readily forms a disulfide bond and that this peptide has full antimicrobial activity. NMR results indicate that CbnB2 in trifluoroethanol (TFE) has a well-defined central helical structure (residues 18-39) but a disordered N terminus. Comparison of the CbnB2 structure with the refined solution structure of leucocin A (LeuA), another type IIa bacteriocin, indicates that the central helical structure is conserved between the two peptides despite differences in sequence but that the N-terminal structure (a proposed receptor binding site) is not. This is unexpected because LeuA and CbnB2 exhibit >66% sequence identity in the first 24 residues. This suggests that the N-terminus, which had been proposed [Fleury et al. (1996) J. Biol. Chem. 271, 14421-14429] to be a receptor binding site of type IIa bacteriocins, may not be directly involved and that recognition of the amphiphilic helical portion is the critical feature. PMID:10569926

  2. Discovery of a novel COX-2 inhibitor as an orally potent anti-pyretic and anti-inflammatory drug: design, synthesis, and structure-activity relationship.

    PubMed

    Hayashi, Shigeo; Sumi, Yoko; Ueno, Naomi; Murase, Akio; Takada, Junji

    2011-10-01

    Cyclooxygenase (COX) has been considered as a significant pharmacological target because of its pivotal roles in the prostaglandin biosynthesis and following cascades that lead to various (patho)physiological effects. Non-steroidal anti-inflammatory drugs (NSAIDs) that suppress COX activities have been used clinically for the treatment of fever, inflammation, and pain; however, nonselective COX inhibitors exhibit serious side-effects such as gastrointestinal damage because of their inhibitory activities against COX-1. Thus, COX-1 is constitutive and expressed ubiquitously and serves a housekeeping role, while COX-2 is inducible or upregulated by inflammatory/injury stimuli such as interleukin-1?, tumor necrosis factor-?, and lipopolysaccharide in macrophage, monocyte, synovial, liver, and lung, and is associated with prostaglandin E? and prostacyclin production that evokes or sustains systemic/peripheral inflammatory symptoms. Also, hypersensitivity of aspirin is a significant concern clinically. Hence, design, synthesis, and structure-activity relationship of [2-{[(4-substituted)-pyridin-2-yl]carbonyl}-(6- or 5-substituted)-1H-indol-3-yl]acetic acid analogues were investigated to discover novel acid-type COX-2 inhibitor as an orally potent new-class anti-pyretic and anti-inflammatory drug. As significant findings, compounds 1-3 demonstrated potent COX-2 inhibitory activities with high selectivities for COX-2 over COX-1 in human cells or whole-blood in vitro, and demonstrated orally potent anti-pyretic activity against lipopolysaccharide-induced systemic-inflammatory fever model in F344 rats. Also compound 1 demonstrated orally potent anti-inflammatory activity against edema formation and a suppressive effect against PGE? production in carrageenan-induced peripheral-inflammation model on the paw of SD rats. These results suggest that compounds 1-3 are potential agents for the treatment of inflammatory disease and are useful for further pharmacological COX-2 inhibitor investigations. PMID:21741371

  3. Simplified cyclic analogues of bastadin-5. Structure-activity relationships for modulation of the RyR1/FKBP12 Ca2+ channel complex.

    PubMed

    Masuno, Makoto N; Pessah, Isaac N; Olmstead, Marilyn M; Molinski, Tadeusz F

    2006-07-27

    Bastadin-5, a brominated macro-dilactam from the marine sponge Ianthella basta, enhances release of Ca2+ from stores within the sarcoplasmic reticulum (SR) of muscle and nonmuscle cells by modulating RyR1/FKBP12 complex. Analogues of bastadin-5 present desirable targets for SAR studies to shed light on the gating mechanism and locus of bastadin-5 binding on these heteromeric channels that mediate essential steps in early coupling of membrane excitation to Ca2+ signaling cascades. Simple, ring-constrained analogues of bastadin-5 were synthesized from substituted benzaldehydes in a convergent manner, featuring an efficient S(N)Ar macroetherification, and evaluated in an assay that measures [3H]-ryanodine that is known to correlate with the functional open state of the Ca2+ channel. The simplified 14-membered ring, atropisomeric analogue (+/-)-7, like bastadin-5, enhanced ryanodine binding to the RyR1/FKBP12 complex (EC50 11 microM), however, unexpectedly, the corresponding achiral 18-membered ring analogue 14 potently inhibited binding (IC50 6 microM) under the same conditions. Structure-activity relationships of both families of cyclic analogues showed activity in a ryanodine binding assay that varied with substitutions of the Br atom on the trisubstituted aryl ring by various functional groups. The most active analogues were those that conserved the dibromocatechol ether moiety that corresponds to the 'western edge' of the bastadin-5 structure. These data suggest that cyclic analogues of bastadin-5 interact with the channel complex in a complex manner that can either enhance or inhibit channel activity. PMID:16854055

  4. Simplified Cyclic Analogs of Bastadin-5. Structure Activity Relationships for Modulation of the RyR1/FKBP12 Ca2+ Channel Complex

    PubMed Central

    Masuno, Makoto N.; Pessah, Isaac N.; Olmstead, Marilyn M.; Molinski, Tadeusz F.

    2011-01-01

    Bastadin-5, a brominated macro-dilactam from the marine sponge Ianthella basta, enhances release of Ca2+ from stores within the sarcoplasmic reticulum (SR) of muscle and non-muscle cells by modulating RyR1/FKBP12 complex. Analogs of bastadin-5 present desirable targets for SAR studies to shed light on the gating mechanism and locus of bastadin-5 binding on these heteromeric channels that mediate essential steps in early coupling of membrane excitation to Ca2+ signaling cascades. Simple, ring-constrained analogs of bastadin-5 were synthesized from substituted benzaldehydes in a convergent manner, featuring an efficient SNAr macroetherification, and evaluated in an assay that measures [3H]-ryanodine that is known to correlate with the functional open state of the Ca2+ channel. The simplified 14-membered ring, atropisomeric analog (±)-7, like bastadin-5, enhanced ryanodine binding to the RyR1/FKBP12 complex (EC50 11 ?M), however, unexpectedly, the corresponding achiral 18-membered ring analog 14 potently inhibited binding (IC50 6 ?M) under the same conditions. Structure-activity relationships of both families of cyclic analogs showed activity in a ryanodine binding assay that varied with substitutions of the Br atom on the trisubstituted aryl ring by various functional groups. The most active analogs were those that conserved the dibromocatechol ether moiety that corresponds to the ‘western edge’ of the bastadin-5 structure. These data suggest that cyclic analogs of bastadin-5 interact with the channel complex in a complex manner that can either enhance or inhibit channel activity. PMID:16854055

  5. Use of mechanism-based structure-activity relationships analysis in carcinogenic potential ranking for drinking water disinfection by-products.

    PubMed Central

    Woo, Yin-Tak; Lai, David; McLain, Jennifer L; Manibusan, Mary Ko; Dellarco, Vicki

    2002-01-01

    Disinfection by-products (DBPs) are formed when disinfectants such as chlorine, chloramine, and ozone react with organic and inorganic matter in water. The observations that some DBPs such as trihalomethanes (THMs), di-/trichloroacetic acids, and 3-chloro-4-(dichloromethyl)-5-hydroxy-2(5H)-furanone (MX) are carcinogenic in animal studies have raised public concern over the possible adverse health effects of DBPs. To date, several hundred DBPs have been identified. To prioritize research efforts, an in-depth, mechanism-based structure-activity relationship analysis, supplemented by extensive literature search for genotoxicity and other data, was conducted for ranking the carcinogenic potential of DBPs that met the following criteria: a) detected in actual drinking water samples, b) have insufficient cancer bioassay data for risk assessment, and c) have structural features/alerts or short-term predictive assays indicative of carcinogenic potential. A semiquantitative concern rating scale of low, marginal, low-moderate, moderate, high-moderate, and high was used along with delineation of scientific rationale. Of the 209 DBPs analyzed, 20 were of priority concern with a moderate or high-moderate rating. Of these, four were structural analogs of MX and five were haloalkanes that presumably will be controlled by existing and future THM regulations. The other eleven DBPs, which included halonitriles (6), haloketones (2), haloaldehyde (1), halonitroalkane (1), and dialdehyde (1), are suitable priority candidates for future carcinogenicity testing and/or mechanistic studies. PMID:11834465

  6. MS/MS fragmentation-guided search of TMG-chitooligomycins and their structure-activity relationship in specific ?-N-acetylglucosaminidase inhibition.

    PubMed

    Usuki, Hirokazu; Yamamoto, Yukihiro; Kumagai, Yuya; Nitoda, Teruhiko; Kanzaki, Hiroshi; Hatanaka, Tadashi

    2011-04-21

    The reducing tetrasaccharide TMG-chitotriomycin (1) is an inhibitor of ?-N-acetylglucosaminidase (GlcNAcase), produced by the actinomycete Streptomyces anulatus NBRC13369. The inhibitor shows a unique inhibitory spectrum, that is, selectivity toward enzymes from chitin-containing organisms such as insects and fungi. Nevertheless, its structure-selectivity relationship remains to be clarified. In this study, we conducted a structure-guided search of analogues of 1 in order to obtain diverse N,N,N-trimethylglucosaminium (TMG)-containing chitooligosaccharides. In this approach, the specific fragmentation profile of 1 on ESI-MS/MS analysis was used for the selective detection of desired compounds. As a result, two new analogues, named TMG-chitomonomycin (3) and TMG-chitobiomycin (2), were obtained from a culture filtrate of 1-producing Streptomyces. Their enzyme-inhibiting activity revealed that the potency and selectivity depended on the degree of polymerization of the reducing end GlcNAc units. Furthermore, a computational modeling study inspired the inhibitory mechanism of TMG-related compounds as a mimic of the substrate in the Michaelis complex of the GH20 enzyme. This study is an example of the successful application of a MS/MS experiment for structure-guided isolation of natural products. PMID:21373681

  7. Structure-Activity Relationships in Nucleotide Oligomerization Domain-1 (Nod1)-Agonistic ?-Glutamyl-diaminopimelic Acid Derivatives

    PubMed Central

    Agnihotri, Geetanjali; Ukani, Rehman; Malladi, Subbalakshmi S.; Warshakoon, Hemamali J.; Balakrishna, Rajalakshmi; Wang, Xinkun; David, Sunil A.

    2011-01-01

    N-acyl-?-glutamyl-diaminopimelic acid is a prototype ligand for Nod1. We report a detailed SAR of C12-?-D-Glu-DAP. Analogues with glutaric or ?-aminobutyric acid replacing the glutamic acid show greatly attenuated Nod1-agonistic activity. Substitution of the meso-diaminopimelic (DAP) acid component with monoaminopimelic acid, L- or D-lysine, or cadaverine also results in reduced activity. The free amine on DAP is crucial. However, the N-acyl group on the D-glutamyl residue can be substituted with N-alkyl groups with full preservation of activity. The free carboxylates on the DAP and Glu components can also be esterified, resulting in more lipophilic, but active analogues. Transcriptomal profiling showed a dominant upregulation of IL-19, IL-20, IL-22, and IL-24, which may explain the pronounced Th2-polarizing activity of these compounds, and also implicate cell signaling mediated by TREM-1. These results may explain the hitherto unknown mechanism of synergy between Nod1- and TLR-agonists, and are likely to be useful in designing vaccine adjuvants. PMID:21299227

  8. Bordetella pertussis Tracheal Cytotoxin and Other Muramyl Peptides: Distinct StructureActivity Relationships for Respiratory Epithelial Cytopathology

    Microsoft Academic Search

    Kathryn E. Luker; Jayne L. Collier; Eric W. Kolodziej; Garland R. Marshall; William E. Goldman

    1993-01-01

    Tracheal cytotoxin (TCT) is a disaccharide-tetrapeptide released by Bordetella pertussis, the causative agent of pertussis (whooping cough). We have previously determined the structure of TCT to be GlcNAc-1,6-anhydro-MurNAc-L-Ala-gamma-D-Glu-meso-A_2pm-D-Ala, where MurNAc = N-acetylmuramic acid and A_2pm = diaminopimelic acid. Purified TCT reproduces the respiratory cytopathology observed during pertussis, including ciliostasis and extrusion of ciliated cells. We have tested structural analogs of

  9. A Novel Two-Step Hierarchical Quantitative Structure–Activity Relationship Modeling Work Flow for Predicting Acute Toxicity of Chemicals in Rodents

    PubMed Central

    Zhu, Hao; Ye, Lin; Richard, Ann; Golbraikh, Alexander; Wright, Fred A.; Rusyn, Ivan; Tropsha, Alexander

    2009-01-01

    Background Accurate prediction of in vivo toxicity from in vitro testing is a challenging problem. Large public–private consortia have been formed with the goal of improving chemical safety assessment by the means of high-throughput screening. Objective A wealth of available biological data requires new computational approaches to link chemical structure, in vitro data, and potential adverse health effects. Methods and results A database containing experimental cytotoxicity values for in vitro half-maximal inhibitory concentration (IC50) and in vivo rodent median lethal dose (LD50) for more than 300 chemicals was compiled by Zentralstelle zur Erfassung und Bewertung von Ersatz- und Ergaenzungsmethoden zum Tierversuch (ZEBET; National Center for Documentation and Evaluation of Alternative Methods to Animal Experiments). The application of conventional quantitative structure–activity relationship (QSAR) modeling approaches to predict mouse or rat acute LD50 values from chemical descriptors of ZEBET compounds yielded no statistically significant models. The analysis of these data showed no significant correlation between IC50 and LD50. However, a linear IC50 versus LD50 correlation could be established for a fraction of compounds. To capitalize on this observation, we developed a novel two-step modeling approach as follows. First, all chemicals are partitioned into two groups based on the relationship between IC50 and LD50 values: One group comprises compounds with linear IC50 versus LD50 relationships, and another group comprises the remaining compounds. Second, we built conventional binary classification QSAR models to predict the group affiliation based on chemical descriptors only. Third, we developed k-nearest neighbor continuous QSAR models for each subclass to predict LD50 values from chemical descriptors. All models were extensively validated using special protocols. Conclusions The novelty of this modeling approach is that it uses the relationships between in vivo and in vitro data only to inform the initial construction of the hierarchical two-step QSAR models. Models resulting from this approach employ chemical descriptors only for external prediction of acute rodent toxicity. PMID:19672406

  10. Azaindenoisoquinolines as Topoisomerase I Inhibitors and Potential Anticancer Agents: A Systematic Study of Structure-Activity Relationships

    PubMed Central

    Kiselev, Evgeny; Agama, Keli; Pommier, Yves; Cushman, Mark

    2012-01-01

    A comprehensive study of a series of azaindenoisoquinoline topoisomerase I (Top1) inhibitors is reported. The synthetic pathways have been developed to prepare 7-, 8-, 9-, and 10-azaindenoisoquinolines. The present study shows that 7-azaindenoisoquinolines possess the greatest Top1 inhibitory activity and cytotoxicity. Additionally, the introduction of a methoxy group into the D-ring of 7-azaindenoisoquinolines improved their biological activities, leading to new lead molecules for further development. A series of QM calculations were performed on the model “sandwich” complexes of azaindenoisoquinolines with flanking DNA base pairs from the Drug–Top1–DNA ternary complex. The results of these calculations demonstrate how changes in two forces contributing to the ?–? stacking, dispersion and charge-transfer interactions, affect the binding of the drug to the Top1–DNA cleavage complex and thus modulate the drug’s Top1 inhibitory activity. PMID:22329436

  11. DEVELOPMENT OF QUANTITATIVE STRUCTURE ACTIVITY RELATIONSHIPS (QSARS) TO PREDICT TOXICITY FOR A VARIETY OF HUMAN AND ECOLOGICAL ENDPOINTS

    EPA Science Inventory

    A web accessible software tool is being developed to predict the toxicity of unknown chemicals for a wide variety of endpoints. The tool will enable a user to easily predict the toxicity of a query compound by simply entering its structure in a 2-dimensional (2-D) chemical sketc...

  12. Structural relationships of stemona alkaloids: assessment of species-specific accumulation trends for exploiting their biological activities.

    PubMed

    Kongkiatpaiboon, Sumet; Schinnerl, Johann; Felsinger, Susanne; Keeratinijakal, Vichien; Vajrodaya, Srunya; Gritsanapan, Wandee; Brecker, Lothar; Greger, Harald

    2011-09-23

    On the basis of a comparison of 42 Stemona samples, representing eight different species collected and cultivated in Thailand, species-specific accumulation trends of Stemona alkaloids were analyzed. An overview was achieved by comparative HPLC analyses of methanolic crude extracts of underground parts coupled with diode array or evaporative light scattering detectors. All major compounds were isolated and their structures elucidated by NMR and MS analyses. Protostemonine- and stichoneurine-type derivatives dominated, from which the latter characterize S. tuberosa and S. phyllantha accumulating species-specific isomers of tuberostemonine (3). The widespread S. curtisii and S. collinsiae clearly deviate by protostemonine-type derivatives dominated by stemofoline (10) and/or didehydrostemofoline (11). Further diversification within this structural type results from a mutual accumulation of derivatives with a pyrrolo- or pyridoazepine nucleus, leading to chemical variability in S. curtisii and S. aphylla. PMID:21902195

  13. The relationship of pork longissimus muscle pH to mitochondrial respiratory activities, meat quality and muscle structure.

    PubMed

    Popp, J; Wicke, M; Klein, G; Krischek, C

    2015-02-01

    The way the pH falls post-slaughter has an impact on meat quality. Pork longissimus muscles (n=48) were sorted in fast- (FG) (n=15) and normal glycolysing (NG) (n=33) muscles according to the post-slaughter pH 45 min values (FG<6.0; NG>6.0). FG muscles (5.84±0.04) compared with NG muscles (6.27±0.04) were accompanied with higher temperature, electrical conductivity, lightness and yellowness, and reduced grill loss and shear force values (P<0.05), but there were no pH-dependent changes of the drip loss and redness results. FG muscles had higher (P<0.05) percentages of fast-twitch glycolytic and lower proportions of fast-twitch oxidative and slow-twitch oxidative (P<0.05) muscle fibres. The study confirms the relationship of pH value to meat quality and muscle fibre characteristics also showing that pH values have no impact on intrinsic mitochondrial respiratory function. PMID:25245462

  14. Molecular analysis and structure-activity relationship modeling of the substrate/inhibitor interaction site of plasma membrane monoamine transporter.

    PubMed

    Ho, Horace T B; Pan, Yongmei; Cui, Zhiyi; Duan, Haichuan; Swaan, Peter W; Wang, Joanne

    2011-11-01

    Plasma membrane monoamine transporter (PMAT) is a new polyspecific transporter that interacts with a wide range of structurally diverse organic cations. To map the physicochemical descriptors of cationic compounds that allow interaction with PMAT, we systematically analyzed the interactions between PMAT and three series of structural analogs of known organic cation substrates including phenylalkylamines, n-tetraalkylammonium (n-TAA) compounds, and ?-carbolines. Our results showed that phenylalkylamines with a distance between the aromatic ring and the positively charged amine nitrogen atom of ?6.4 ? confer optimal interactions with PMAT, whereas studies with n-TAA compounds revealed an excellent correlation between IC(50) values and hydrophobicity. The five ?-carbolines that we tested, which possess a pyridinium-like structure and are structurally related to the neurotoxin 1-methyl-4-phenylpyridinium, inhibited PMAT with high affinity (IC(50) values of 39.1-65.5 ?M). Cytotoxicity analysis further showed that cells expressing PMAT are 14- to 15-fold more sensitive to harmalan and norharmanium, suggesting that these two ?-carbolines are also transportable substrates of PMAT. We then used computer-aided modeling to generate qualitative and quantitative three-dimensional pharmacophore models on the basis of 23 previously reported and currently identified PMAT inhibitors and noninhibitors. These models are characterized by a hydrogen bond donor and two to three hydrophobic features with distances between the hydrogen bond donor and hydrophobic features ranging between 5.20 and 7.02 ?. The consistency between the mapping results and observed PMAT affinity of a set of test compounds indicates that the models performed well in inhibitor prediction and could be useful for future virtual screening of new PMAT inhibitors. PMID:21816955

  15. Structure-activity relationships for the interaction between cyclosporin A derivatives and the Fab fragment of a monoclonal antibody.

    PubMed

    Rauffer, N; Zeder-Lutz, G; Wenger, R; Van Regenmortel, M H; Altschuh, D

    1994-08-01

    The crystallographic structure of a complex between cyclosporin A and the Fab fragment of monoclonal antibody R45-45-11 has been solved to 2.65 A resolution (Altschuh et al., 1992a, Science 256, 92; Vix et al., 1993, Proteins 15, 339), yielding a precise three-dimensional picture of interacting surfaces. In order to evaluate the contribution of observed contacts to the energy of interaction, we have measured the effect on binding affinity of minor chemical modifications of CS. The equilibrium binding constant of the Fab fragment for a set of cyclosporin analogs was obtained by measuring in a biosensor instrument the dependence of complex formation on Fab concentration, at constant analog concentrations. Data were analysed using Scatchard plots. Differences in binding energy resulting from cyclosporin modifications discriminated between two types of contact areas. The first type displays adaptability to structural modifications of cyclosporin at the cost of a small decrease in binding energy, and contacting residues in the antibody form the periphery of the combining site. The second type does not accommodate structural changes and corresponds in cyclosporin to three residues whose modifications drastically decrease binding energy with the antibody. The corresponding contact residues in the antibody form the core of the antibody combining site. PMID:8065374

  16. Total Synthesis and Structure-Activity Relationship Study of the Potent cAMP Signaling Agonist (-)-Alotaketal A

    PubMed Central

    Huang, Jinhua; Yang, Jessica R.

    2013-01-01

    A detailed account of the first total synthesis of alotaketal A, a tricyclic spiroketal sesterterpenoid that potently activates the cAMP signaling pathway, is provided. The synthesis employs both intra- and intermolecular reductive allylation of esters for assembling one of the fragments and their coupling. A Hg(OAc)2-mediated allylic mercuration is used to introduce the C22-hydroxyl group. The subtle influence of substituents over the course of the spiroketalization process is revealed. The synthesis confirms the relative and absolute stereochemistry of (-)-alotaketal A and allows verification of alotaketal A’s effect over cAMP signaling using reporter-based FRET imaging assays with HEK 293T cells. Our studies also revealed alotaketal A’s unique activity in selectively targeting nuclear PKA signaling in living cells. PMID:23584129

  17. The discovery and structure—activity relationships of nonpeptide, low molecular weight antagonists selective for the endothelin ET B receptor

    Microsoft Academic Search

    Ming Fai Chan; Adam Kois; Erik J. Verner; Bore G. Raju; Rosario S. Castillo; Chengde Wu; Ilya Okun; Fiona D. Stavros; V. N. Balaji

    1998-01-01

    The systematic modification of the ETA selective N-(5-isoxazolyl)benzene-sulfonamide endothelin antagonists to give ETB selective antagonists is reported. The reversal in selectivity was brought about by substitution of the 4-position with aryl and substituted aryl groups. Of all the aromatic substituents studied, the para-tolyl group gave rise to the most active and selective ETB antagonist. Larger substituents caused a decrease in

  18. Structure-activity relationship in the toxicity of some naturally occurring coumarins-chalepin, imperatorin and oxypeucedanine.

    PubMed

    Emerole, G; Thabrew, M I; Anosa, V; Okorie, D A

    1981-01-01

    Imperatorin, oxypeucedanine and chalepin are furanocoumarins isolated from Clausena anisata a medicinal plant common in West Africa. Only chalepin is found to have anticoagulant activity when administered to rats at a single dose. Aniline hydroxylase activity was appreciably depressed by each of the substances. Ethylmorphine demethylase, hepatic DNA, reduced glutathione and glucose-6-phosphatase were unaffected by these compounds when administered at a dose of 50 mg/kg for 3 days prior to sacrifice. Under similar conditions only chalepin treatment resulted in alpha-1-globulin increase and a decrease in beta-globulin content of the serum. Intraperitoneal treatment with chalepin (100 mg/kg) for 2 days resulted in the death of 4 rats out of 10 within a 48 h of treatment. Livers of dead rats showed generalized necrosis of hepatocytes. No deaths were recorded for imperatorin and oxypeucedanine. Rats surviving after 8 weeks showed no changes in hepatic enzyme activity, reduced glutathione and DNA concentrations. However, chalepin and imperatorin induced alterations in the serum protein pattern within this period. Liver lesions were observed in chalepin treated animals and were characterized by very mild necrosis of hepatocytes. No lesions were observed in the livers of rats treated with imperatorin and oxypeucedanine. PMID:7268793

  19. Structure-activity relationships and mechanism of action of Eph-ephrin antagonists: interaction of cholanic acid with the EphA2 receptor

    PubMed Central

    Tognolini, Massimiliano; Incerti, Matteo; Mohamed, Iftiin Hassan; Giorgio, Carmine; Russo, Simonetta; Bruni, Renato; Lelli, Barbara; Bracci, Luisa; Noberini, Roberta; Pasquale, Elena B.; Barocelli, Elisabetta; Vicini, Paola; Mor, Marco

    2012-01-01

    The Eph–ephrin system, including the EphA2 receptor and the ephrin-A1 ligand, plays a critical role in tumor and vascular functions during carcinogenesis. We previously identified (3?,5?)-3-hydroxycholan-24-oic acid (lithocholic acid) as an Eph-ephrin antagonist able to inhibit EphA2 receptor activation and therefore potentially useful as a novel EphA2 receptor targeting agent. Here, we explore the structure-activity relationships of a focused set of lithocholic acid derivatives, based on molecular modelling investigation and displacement binding assays. Our exploration shows that while the 3-?-hydroxyl group of lithocholic acid has a negligible role in the recognition of the EphA2 receptor, its carboxylate group is critical for disrupting the binding of ephrin-A1 to the EphA2. As a result of our investigation, we identified (5?)-cholan-24-oic acid (cholanic acid) as a novel compound that competitively inhibits EphA2-ephrin-A1 interaction with higher potency than lithocholic acid. Surface plasmon resonance analysis indicates that cholanic acid binds specifically and reversibly to the ligand-binding domain of EphA2, with a steady-state dissociation constant (KD) in the low micromolar range. Furthermore, cholanic acid blocks the phosphorylation of EphA2 and cell retraction and rounding in PC3 prostate cancer cells, two effects that depend on EphA2 activation by the ephrin-A1 ligand. These findings suggest that cholanic acid can be used as a template structure to design effective EphA2 antagonists, with potential impact in the elucidation of the role played by this receptor in pathological conditions. PMID:22529030

  20. Quantitative structure activity relationship model for predicting the depletion percentage of skin allergic chemical substances of glutathione.

    PubMed

    Si, Hongzong; Wang, Tao; Zhang, Kejun; Duan, Yun-Bo; Yuan, Shuping; Fu, Aiping; Hu, Zhide

    2007-05-22

    A quantitative model was developed to predict the depletion percentage of glutathione (DPG) compounds by gene expression programming (GEP). Each kind of compound was represented by several calculated structural descriptors involving constitutional, topological, geometrical, electrostatic and quantum-chemical features of compounds. The GEP method produced a nonlinear and five-descriptor quantitative model with a mean error and a correlation coefficient of 10.52 and 0.94 for the training set, 22.80 and 0.85 for the test set, respectively. It is shown that the GEP predicted results are in good agreement with experimental ones, better than those of the heuristic method. PMID:17481417

  1. The structural relationships between the various phases of bismuth molybdates with special reference to their catalytic activity

    Microsoft Academic Search

    D. J. Buttrey; D. A. Jefferson; J. M. Thomas

    1986-01-01

    Including those reported here for the first time. there are at least seven distinct phases of bismuth molybdate: Bi2O3·nMoO3, with n = 3, n = 2 and n = 1 (three variants); 3Bi2O3·2MoO3; and 19Bi2O3·7MoO3. Hitherto most of these phases have been interpreted to possess quite different, and seemingly unrelated, crystallographic structures. We advance arguments, based largely on high-resolution electron

  2. Stereospecific recognition and quantitative structure-activity relationship between antibodies and enantiomers: ofloxacin as a model hapten.

    PubMed

    Mu, Hongtao; Wang, Baoling; Xu, Zhenlin; Sun, Yuanming; Huang, Xinan; Shen, Yudong; Eremin, Sergei A; Zherdev, Anatoly V; Dzantiev, Boris B; Lei, Hongtao

    2015-02-21

    In this study, ofloxacin stereoisomers were chosen as a simple model to investigate the stereospecific recognition of chiral haptens and antibodies. Three polyclonal antibodies were studied and showed a relatively high enantioselectivity and an excellent sensitivity. Comparative molecular field analysis and comparative molecular similarity indices analysis were employed to investigate the chiral recognition between the antibody and the ofloxacin enantiomer, and all the models yielded high correlation and predictive ability. It was found that the chiral discrimination was probably caused by steric hindrance; the antibody stereospecificity could be ascribed to the variation of the R1 and R3 groups of quinolones; the common structure of the quinolones is also essential in the hapten-antibody recognition. The recognition between the chiral haptens and the antibodies was co-affected by multiple interaction forces, and those forces were defined explicitly at the sub-structural level. An illustrative enhanced model with good simplicity and universality was also developed for a better understanding of the stereospecific recognition of ofloxacin enantiomers and antibodies for the first time. This work provides insights into the stereospecific recognition of chiral haptens and antibodies. PMID:25553733

  3. Synthesis and structure-activity relationship studies of small molecule disruptors of EWS-FLI1 interactions in Ewing's sarcoma.

    PubMed

    Tosso, Perrer N; Kong, Yali; Scher, Lauren; Cummins, Ryan; Schneider, Jeffrey; Rahim, Said; Holman, K Travis; Toretsky, Jeffrey; Wang, Kan; Üren, Aykut; Brown, Milton L

    2014-12-26

    EWS-FLI1 is an oncogenic fusion protein implicated in the development of Ewing's sarcoma family tumors (ESFT). Using our previously reported lead compound 2 (YK-4-279), we designed and synthesized a focused library of analogues. The functional inhibition of the analogues was measured by an EWS-FLI1/NR0B1 reporter luciferase assay and a paired cell screening approach measuring effects on growth inhibition for human cells containing EWS-FLI1 (TC32 and TC71) and control PANC1 cell lines devoid of the oncoprotein. Our data revealed that substitution of electron donating groups at the para-position on the phenyl ring was the most favorable for inhibition of EWS-FLI1 by analogs of 2. Compound 9u (with a dimethylamino substitution) was the most active inhibitor with GI50 = 0.26 ± 0.1 ?M. Further, a correlation of growth inhibition (EWS-FLI1 expressing TC32 cells) and the luciferase reporter activity was established (R(2) = 0.84). Finally, we designed and synthesized a biotinylated analogue and determined the binding affinity for recombinant EWS-FLI1 (Kd = 4.8 ± 2.6 ?M). PMID:25432018

  4. Novel Potent Antagonists of Transient Receptor Potential Channel, Vanilloid Subfamily Member 1: Structure-Activity Relationship of 1,3-Diarylalkyl

    E-print Network

    Suh, Young-Ger

    Recently, 1,3-diarylalkyl thioureas have merged as one of the promising nonvanilloid TRPV1 antagonists-activity relationship for TRPV1 antagonism of a novel series of 1,3-diarylalky thioureas is reported. Exploration-fibers) and small A fibers in the dorsal root, trigeminal, and nodose ganglia. TRPV1 is activated not only

  5. A quantitative structure–activity relationship (QSAR) study on glycan array data to determine the specificities of glycan-binding proteins

    PubMed Central

    Xuan, Pengfei; Zhang, Yuehua; Tzeng, Tzuen-rong Jeremy; Wan, Xiu-Feng; Luo, Feng

    2012-01-01

    Advances in glycan array technology have provided opportunities to automatically and systematically characterize the binding specificities of glycan-binding proteins. However, there is still a lack of robust methods for such analyses. In this study, we developed a novel quantitative structure–activity relationship (QSAR) method to analyze glycan array data. We first decomposed glycan chains into mono-, di-, tri- or tetrasaccharide subtrees. The bond information was incorporated into subtrees to help distinguish glycan chain structures. Then, we performed partial least-squares (PLS) regression on glycan array data using the subtrees as features. The application of QSAR to the glycan array data of different glycan-binding proteins demonstrated that PLS regression using subtree features can obtain higher R2 values and a higher percentage of variance explained in glycan array intensities. Based on the regression coefficients of PLS, we were able to effectively identify subtrees that indicate the binding specificities of a glycan-binding protein. Our approach will facilitate the glycan-binding specificity analysis using the glycan array. A user-friendly web tool of the QSAR method is available at http://bci.clemson.edu/tools/glycan_array. PMID:22156918

  6. Design, synthesis, and structure-activity relationship of a novel series of GluN2C-selective potentiators.

    PubMed

    Zimmerman, Sommer S; Khatri, Alpa; Garnier-Amblard, Ethel C; Mullasseril, Praseeda; Kurtkaya, Natalie L; Gyoneva, Stefka; Hansen, Kasper B; Traynelis, Stephen F; Liotta, Dennis C

    2014-03-27

    NMDA receptors are tetrameric complexes composed of GluN1 and GluN2A-D subunits that mediate a slow Ca(2+)-permeable component of excitatory synaptic transmission. NMDA receptors have been implicated in a wide range of neurological diseases and thus represent an important therapeutic target. We herein describe a novel series of pyrrolidinones that selectively potentiate only NMDA receptors that contain the GluN2C subunit. The most active analogues tested were over 100-fold selective for recombinant GluN2C-containing receptors over GluN2A/B/D-containing NMDA receptors as well as AMPA and kainate receptors. This series represents the first class of allosteric potentiators that are selective for diheteromeric GluN2C-containing NMDA receptors. PMID:24512267

  7. Structure-activity relationships of 4-position diamine quinoline methanols as intermittent preventative treatment (IPT) against Plasmodium falciparum.

    PubMed

    Milner, Erin; Gardner, Sean; Moon, Jay; Grauer, Kristina; Auschwitz, Jennifer; Bathurst, Ian; Caridha, Diana; Gerena, Lucia; Gettayacamin, Montip; Johnson, Jacob; Kozar, Michael; Lee, Patricia; Leed, Susan; Li, Qigui; McCalmont, William; Melendez, Victor; Roncal, Norma; Sciotti, Richard; Smith, Bryan; Sousa, Jason; Tungtaeng, Anchalee; Wipf, Peter; Dow, Geoffrey

    2011-09-22

    A library of diamine quinoline methanols were designed based on the mefloquine scaffold. The systematic variation of the 4-position amino alcohol side chain led to analogues that maintained potency while reducing accumulation in the central nervous system (CNS). Although the mechanism of action remains elusive, these data indicate that the 4-position side chain is critical for activity and that potency (as measured by IC(90)) does not correlate with accumulation in the CNS. A new lead compound, (S)-1-(2,8-bis(trifluoromethyl)quinolin-4-yl)-2-(2-(cyclopropylamino)ethylamino)ethanol (WR621308), was identified with single dose efficacy and substantially lower permeability across MDCK cell monolayers than mefloquine. This compound could be appropriate for intermittent preventative treatment (IPTx) indications or other malaria treatments currently approved for mefloquine. PMID:21854078

  8. Discovery and structure-activity relationship studies of irreversible benzisothiazolinone-based inhibitors against Staphylococcus aureus sortase A transpeptidase.

    PubMed

    Zhulenkovs, Dmitrijs; Rudevica, Zhanna; Jaudzems, Kristaps; Turks, Maris; Leonchiks, Ainars

    2014-11-01

    Gram-positive bacteria, in general, and staphylococci, in particular, are the widespread cause of nosocomial and community-acquired infections. The rapid evolvement of strains resistant to antibiotics currently in use is a serious challenge. Novel antimicrobial compounds have to be developed to fight these resistant bacteria, and sortase A, a bacterial cell wall enzyme, is a promising target for novel therapies. As a transpeptidase that covalently attaches various virulence factors to the cell surface, this enzyme plays a crucial role in the ability of bacteria to invade the host's tissues and to escape the immune response. In this study we have screened a small molecule library against recombinant Staphylococcus aureus sortase A using an in vitro FRET-based assay. The selected hits were validated by NMR methods in order to exclude false positives and to analyze the reversibility of inhibition. Further structural and functional analysis of the best hit allowed the identification of a novel class of benzisothiazolinone-based compounds as potent and promising sortase inhibitors. PMID:25282649

  9. Structure-activity relationships for a series of compounds that inhibit aggregation of the Alzheimer's peptide, A?42.

    PubMed

    McKoy, Angela F; Chen, Jermont; Schupbach, Trudi; Hecht, Michael H

    2014-11-01

    Inhibiting aggregation of the amyloid-beta (A?) peptide may be an effective strategy for combating Alzheimer's disease. As the high-resolution structure of the toxic A? aggregate is unknown, rational design of small molecule inhibitors is not possible, and inhibitors are best isolated by high-throughput screening. We applied high-throughput screening to a collection of 65,000 compounds to identify compound D737 as an inhibitor of A? aggregation. D737 diminished the formation of oligomers and fibrils, and reduced A?42-induced cytotoxicity. Most importantly, D737 increased the life span and locomotive ability of transgenic flies in a Drosophila melanogaster model of Alzheimer's disease (J Biol Chem, 287, 2012, 38992). To explore the chemical features that make D737 an effective inhibitor of A?42 aggregation and toxicity, we tested a small collection of eleven analogues of D737. Overall, the ability of a compound to inhibit A? aggregation was a good predictor of its efficacy in prolonging the life span and locomotive ability of transgenic flies expressing human A?42 in the central nervous system. Two compounds (D744 and D830) with fluorine substitutions on an aromatic ring were effective inhibitors of A?42 aggregation and increased the longevity of transgenic flies beyond that observed for the parent compound, D737. PMID:24751138

  10. Structure-activity relationship of quaternary ion antagonism of levcromakalim-induced relaxation in pig coronary artery.

    PubMed

    Piekarska, A E; McPherson, G A

    1997-03-12

    The aim of this study was to investigate the interaction between the K+ channel opener levcromakalim and several quaternary ions. Cumulative vasorelaxant-response curves to levcromakalim were constructed in the absence and in the presence of the quaternary ions, in the pig coronary artery. The most potent compounds (based on 'apparent pKB' values) were: propyltriphenylphosphonium (7.33), butyltriphenylphosphonium (7.04), tetraphenylarsonium (6.86), tetraphenylphosphonium (6.81), ethyltriphenylphosphonium (6.70), and hexyltriphenylphosphonium (6.63). Tetrabutylphosphonium (6.06), tetrabutylammonium (5.12), methyltriphenylphosphonium (5.25), clofilium (5.66) and guanethidine (5.61) were significantly less potent. Tetrapropylammonium, tetrapentyltin and tetraphenylboron were inactive at the maximum concentrations used (30 microM). Tetraphenylboron (10-100 microM) fully reversed tetraphenylphosphonium, tetraphenylarsonium (both at 3 microM), tetrabutylammonium (30 microM) and clofilium (10 microM) and partially reversed guanethidine (10 microM) antagonism of levcromakalim responses indicating a similarity in the mechanism of action of these chemically distinct compounds. The results show that quaternary ions similar in structure to tetraphenylphosphonium, i.e., containing phosphonium ion centre and phenyl side chains, are the most potent antagonists of levcromakalim, in pig coronary artery. It is also apparent that marked changes can be made in the substitution on the phosphonium ion (ethyl to hexyl) with little or no effect on their potency. PMID:9088868

  11. Redesigning the DNA-targeted chromophore in platinum-acridine anticancer agents: a structure-activity relationship study.

    PubMed

    Pickard, Amanda J; Liu, Fang; Bartenstein, Thomas F; Haines, Laura G; Levine, Keith E; Kucera, Gregory L; Bierbach, Ulrich

    2014-12-01

    Platinum-acridine hybrid agents show low-nanomolar potency in chemoresistant non-small cell lung cancer (NSCLC), but high systemic toxicity in vivo. To reduce the promiscuous genotoxicity of these agents and improve their pharmacological properties, a modular build-click-screen approach was used to evaluate a small library of twenty hybrid agents containing truncated and extended chromophores of varying basicities. Selected derivatives were resynthesized and tested in five NSCLC cell lines representing large cell, squamous cell, and adenocarcinomas. 7-Aminobenz[c]acridine was identified as a promising scaffold in a hybrid agent (P1-B1) that maintained submicromolar activity in several of the DNA-repair proficient and p53-mutant cancer models, while showing improved tolerability in mice by 32-fold compared to the parent platinum-acridine (P1-A1). The distribution and DNA/RNA adduct levels produced by the acridine- and benz[c]acridine-based analogues in NCI-H460 cells (confocal microscopy, ICP-MS), and their ability to bind G-quadruplex forming DNA sequences (CD spectroscopy, HR-ESMS) were studied. P1-B1 emerges as a less genotoxic, more tolerable, and potentially more target-selective hybrid agent than P1-A1. PMID:25302716

  12. Two-electron reduction of quinones by rat liver NAD(P)H:quinone oxidoreductase: quantitative structure-activity relationships.

    PubMed

    Anusevicius, Zilvinas; Sarlauskas, Jonas; Cenas, Narimantas

    2002-08-15

    Mammalian NAD(P)H:quinone oxidoreductase (NQO1, DT-diaphorase, EC 1.6.99.2) catalyzes the two-electron reduction of quinones and plays one of the main roles in the bioactivation of quinoidal drugs. In order to understand the enzyme substrate specificity, we have examined the reactions of rat NQO1 with a number of quinones with available potentials of single-electron (E(1)(7)) reduction and pK(a) of their semiquinones. The hydride transfer potentials (E(7)(H(-))) were calculated from the midpoint potentials of quinones and pK(a) of hydroquinones. Our findings imply that benzo- and naphthoquinones with a van der Waals volume (VdWvol) < or = 200 A(3) are much more reactive than glutathionyl-substituted naphthoquinones, polycyclic quinones, and FMN (VdWvol>200 A(3)) with the same reduction potentials. The entropies of activation (DeltaS(not equal)) in the reduction of "fast" oxidants are equal to -84 to -76 J mol(-1) K(-1), whereas in the reduction of "slow" oxidants Delta S(not equal)=-36 to -11 J mol(-1) K(-1). The large negative Delta S(not equal) in the reduction of fast oxidants may be explained by their better electronic coupling with reduced FAD or the formation of charge-transfer complexes, since fast oxidants bind at the dicumarol binding site, whereas the binding of some slow oxidants outside it has been demonstrated. The reactivity of quinones may be equally well described in terms of the three-step (e(-),H(+),e(-)) hydride transfer, using E(1)(7), pK(a)(QH*), and VdWvol as correlation parameters, or in terms of single-step (H(-)) hydride transfer, using E(7)(H(-)) and VdWvol in the correlation. The analysis of NQO1 reactions with single-electron acceptors and quinones using an "outer-sphere" electron transfer model points to the possibility of a three-step hydride transfer. PMID:12147263

  13. Toxicity of aryl- and benzylhalides to Daphnia magna and classification of their mode of action based on quantitative structure-activity relationship

    SciTech Connect

    Marchini, S.; Passerini, L.; Hoglund, M.D.; Pino, A.; Nendza, M.

    1999-12-01

    The acute toxicity of aryl- and benzylhalides to Daphnia magna was investigated to test the validity of existing classification schemes for chemicals by mode of action, mainly based on fish studies, and the applicability of predictive quantitative structure-activity relationship (QSAR) models. Halobenzenes and halotoluenes are generally agreed to be unambiguous baseline toxicants (class 1) with the major exception of the benzylic structures, which are reactive in fish tests (class 3). Eighty-nine percent of the arylhalides tested in this study match a log P{sub ow}-dependent QSAR, including fluorinated, chlorinated, brominated, and iodinated derivatives, thereby confirming the validity of the baseline models also for variously halogenated compounds (other than only-chloro compounds). The toxicities of the benzylhalides relative to baseline QSARs clearly indicate that these compounds belong to two classes of mode of action, i.e., they either act as narcotic toxicants (class 1) or reveal excess toxicity due to unspecific reactivity (class 3). On some occasions, the assignment to the two classes of F. magna deviates from the structural rules derived from fish, i.e., iodinated compounds as well as {alpha},{alpha}-Cl{sub 2}-toluene's lack reactive excess toxicity but behave as nonpolar nonspecific toxicants. The QSARs derived during this study reveal lower slopes and higher intercepts than typical baseline models and, together with the analysis of mixture toxicity studies, behavioral studies, and critical body burden, advocate the hypothesis that there are several different ways to produce baseline toxicity. Most halobenzenes and halotoluenes are actually baseline chemicals with some extra reactivity and as such form a subgroup, whose limits still have to be defined. Different primary sites of action could explain why the chemicals are discriminated by different classification systems, but still they must have some rate-limiting interaction in common as they fit the same log P{sub ow}-dependent baseline QSAR.

  14. Structure-activity relationships of anthraquinones on the suppression of DNA-binding activity of the aryl hydrocarbon receptor induced by 2,3,7,8-tetrachlorodibenzo-p-dioxin.

    PubMed

    Fukuda, Itsuko; Kaneko, Atsushi; Nishiumi, Shin; Kawase, Masaya; Nishikiori, Rika; Fujitake, Nobuhide; Ashida, Hitoshi

    2009-03-01

    Anthraquinones are widely present in plant kingdom, and clinically used as laxatives. Environmental contaminants, dioxins, develop various adverse effects through transformation of a cytosolic aryl hydrocarbon receptor (AhR). We investigated the effects of 18 anthraquinones and 7 of their structurally related compounds on transformation of the AhR estimated by its DNA-binding activity in the cell-free system. 1,4-Dihydroxyanthraquinone (quinizarin), 1,5-dihydroxyanthraquinone (anthrarufin), 1,8-dihydroxyanthraquinone (danthron), and 5-hydroxy-1,4-naphthoquinone (juglone) strongly suppressed DNA-binding activity of the AhR induced by 0.1 nM 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), with their IC(50) values around 1 muM. On the other hand, anthraquinone, 2,6-dihydroxyanthraquinone (anthraflavic acid), and 2-hydroxy-1,4-naphthalendione (lawsone) showed moderate effects. Quantitative structure-activity relationships analysis demonstrated that hydroxyl groups at C1 or C4 but not C3 position of anthraquinone structure are critical for the suppressive effects. In addition, all compounds except lawsone had no agonistic effect. The suppressive effects of anthraquinones in a cultured cell system were also confirmed. In human hepatoma HepG2 cells, chrysophanol, danthron, and rhein also suppressed the DNA-binding activity in a dose-dependent manner, although aloe-emodin showed a moderate effect. The findings of this study may be useful for the design of the novel antagonists of the AhR. PMID:19269596

  15. Cardiac Contractility Structure-Activity Relationship and Ligand-Receptor Interactions; the Discovery Of Unique and Novel Molecular Switches in Myosuppressin Signaling

    PubMed Central

    Leander, Megan; Bass, Chloe; Marchetti, Kathryn; Maynard, Benjamin F.; Wulff, Juan Pedro; Ons, Sheila; Nichols, Ruthann

    2015-01-01

    Peptidergic signaling regulates cardiac contractility; thus, identifying molecular switches, ligand-receptor contacts, and antagonists aids in exploring the underlying mechanisms to influence health. Myosuppressin (MS), a decapeptide, diminishes cardiac contractility and gut motility. Myosuppressin binds to G protein-coupled receptor (GPCR) proteins. Two Drosophila melanogaster myosuppressin receptors (DrmMS-Rs) exist; however, no mechanism underlying MS-R activation is reported. We predicted DrmMS-Rs contained molecular switches that resembled those of Rhodopsin. Additionally, we believed DrmMS-DrmMS-R1 and DrmMS-DrmMS-R2 interactions would reflect our structure-activity relationship (SAR) data. We hypothesized agonist- and antagonist-receptor contacts would differ from one another depending on activity. Lastly, we expected our study to apply to other species; we tested this hypothesis in Rhodnius prolixus, the Chagas disease vector. Searching DrmMS-Rs for molecular switches led to the discovery of a unique ionic lock and a novel 3–6 lock, as well as transmission and tyrosine toggle switches. The DrmMS-DrmMS-R1 and DrmMS-DrmMS-R2 contacts suggested tissue-specific signaling existed, which was in line with our SAR data. We identified R. prolixus (Rhp)MS-R and discovered it, too, contained the unique myosuppressin ionic lock and novel 3–6 lock found in DrmMS-Rs as well as transmission and tyrosine toggle switches. Further, these motifs were present in red flour beetle, common water flea, honey bee, domestic silkworm, and termite MS-Rs. RhpMS and DrmMS decreased R. prolixus cardiac contractility dose dependently with EC50 values of 140 nM and 50 nM. Based on ligand-receptor contacts, we designed RhpMS analogs believed to be an active core and antagonist; testing on heart confirmed these predictions. The active core docking mimicked RhpMS, however, the antagonist did not. Together, these data were consistent with the unique ionic lock, novel 3–6 lock, transmission switch, and tyrosine toggle switch being involved in mechanisms underlying TM movement and MS-R activation, and the ability of MS agonists and antagonists to influence physiology. PMID:25793503

  16. Associative structure of integrated temporal relationships.

    PubMed

    Polack, Cody W; Molet, Mikael; Miguez, Gonzalo; Miller, Ralph R

    2013-12-01

    According to the temporal-coding hypothesis (TCH; Savastano & Miller, Behavioural Processes 44:147-162, 1998), acquired associations include temporal information concerning the interval between the associated elements. Moreover, the TCH posits that subjects can integrate two independently acquired associations that share a common element (e.g., S2-S1 and S1-US), which results in the creation of a third association with its own temporal relationship (S2-US). Some evidence has suggested that such temporal integration occurs at the time of testing (Molet, Miguez, Cham, & Miller, Journal of Experimental Psychology: Animal Behavior Processes 38:369-380, 2012). Here we report two fear-conditioning experiments with rats conducted to identify the associative structure of the integrated temporal relationship. The goal was to distinguish between two possible associative structures that could exist following an initial test on which temporal integration occurs: (1) Conditioned responding to S2 on subsequent tests could be the result of recurring successive activation of two independently learned temporal maps that remain independently stored in memory (i.e., S2-S1 plus S1-US). (2) Temporal integration at the moment of initial testing could result in the formation of a direct S2-US (or S2-response) temporal map. Integration was found to occur at test and to produce a new association that was independent of associations with the common element (S1). However, the associative status of S1 appeared to modulate whether or not the new association with S2 was US-specific (S2-US) or directly activated a fear response (S2-response). PMID:23949944

  17. Structure/Function Relationships in Electronic Ceramics

    E-print Network

    Ohta, Shigemi

    Structure/Function Relationships in Electronic Ceramics Device applications require concurrent applications range from enhanced electron mobility devices to the realization of ferroelectric memory conjoined with silicon. Strain also alters both the nature and temperature of ferromagnetic, ferroelectric

  18. Physicochemical explanation of peptide binding to HLA-A*0201 major histocompatibility complex: a three-dimensional quantitative structure-activity relationship study.

    PubMed

    Doytchinova, Irini A; Flower, Darren R

    2002-08-15

    A three-dimensional quantitative structure-activity relationship method for the prediction of peptide binding affinities to the MHC class I molecule HLA-A*0201 was developed by applying the CoMSIA technique on a set of 266 peptides. To increase the self consistency of the initial CoMSIA model, the poorly predicted peptides were excluded from the training set in a stepwise manner and then included in the study as a test set. The final model, based on 236 peptides and considering the steric, electrostatic, hydrophobic, hydrogen bond donor, and hydrogen bond acceptor fields, had q2 = 0.683 and r2 = 0.891. The stability of this model was proven by cross-validations in two and five groups and by a bootstrap analysis of the non-cross-validated model. The residuals between the experimental pIC50 (-logIC50) values and those calculated by "leave-one-out" cross-validation were analyzed. According to the best model, 63.2% of the peptides were predicted with /residuals/ < or = 0.5 log unit; 29.3% with 1.0 < or = /residuals/ < 0.5; and 7.5% with /residuals/ > 1.0 log unit. The mean /residual/ value was 0.489. The coefficient contour maps identify the physicochemical property requirements at each position in the peptide molecule and suggest amino acid sequences for high-affinity binding to the HLA-A*0201 molecule. PMID:12112675

  19. Structure-Activity Relationship (SAR) and Preliminary Mode of Action Studies of 3-Substituted Benzylthioquinolinium Iodide as Anti-opportunistic Infection Agents

    PubMed Central

    Bolden, Sidney; Zhu, Xue Y.; Etukala, Jagan R; Boateng, Comfort; Mazu, Tryphon; Flores-Rozas, Hernan; Jacob, Melissa R.; Khan, Shabana I; Walker, Larry A.; Ablordeppey, Seth Y.

    2013-01-01

    Opportunistic infections are devastating to immunocompromised patients. And in especially sub-Saharan Africa where the AIDS epidemic is still raging, the mortality rate was recently as high as 70%. The paucity of anti-opportunistic drugs, the decreasing efficacy and the development of resistance against the azoles and even amphotericin B have stimulated the search for new drugs with new mechanisms of action. In a previous work, we showed that a new chemotype derived from the natural product cryptolepine displayed selective toxicity against opportunistic pathogens with minimal cytotoxicity to normal cells. In this manuscript, we report the design and synthesis of substituted benzylthioquinolinium iodides, evaluated their anti-infective properties and formulated some initial structure-activity relationships around phenyl ring A from the original natural product. The sensitivity of the most potent analog 10l, to selected strains of C. cerevisiae was also evaluated leading to the observation that this scaffold may have a different mode of action from its predecessor, cryptolepine. PMID:24141203

  20. Four-dimensional quantitative structure-activity relationship analysis of a series of interphenylene 7-oxabicycloheptane oxazole thromboxane A2 receptor antagonists.

    PubMed

    Albuquerque, M G; Hopfinger, A J; Barreiro, E J; de Alencastro, R B

    1998-01-01

    A series of 39 (a training set of 29 and a test set of 10) interphenylene 7-oxabicyclo [2.2.1]heptane oxazole thromboxane A2 (TXA2) receptor antagonists were studied using four-dimensional quantitative structure-activity relationship (4D-QSAR) analysis. Two thousand conformations of each analogue were sampled to generate a conformational energy profile (CEP) from a molecular dynamic simulation (MDS) of 100,000 trajectory states. Each conformation was placed in a grid cell lattice for each of six trial alignments. Cubic grid cell sizes of 1 and 2 A were considered. The frequency of occupation of each grid cell was computed for each of seven types of pharmacophoric group classes of atoms of each compound. These grid cell occupancy descriptors (GCODs) were then used as independent variables in constructing three-dimensional (3D)-QSAR models after data reduction. The types of data reduction included doing no reducing, reduction based on individual GCOD correlation with activity, and reduction from minimum variance constraints over the GCOD population. The 3D-QSAR models were generated and evaluated by a scheme that combines a genetic algorithm (GA) optimization with partial least squares (PLS) regression. The 3D-QSAR models were evaluated by cross-validation using the leave-one-out technique. The cross-validated correlation coefficient, Q2, ranged from 0.27 to 0.86. The models are not from chance correlation because a scrambled data set was generated and evaluated (Q2 = 0.25-0.37). A composite 3D-QSAR model was constructed using the best models derived from GCODs of both 1 and 2 A grid cell size lattices. The 3D-QSAR models provide detailed 3D pharmacophore requirements in terms of atom types and corresponding locations needed for high TXA2 inhibition activity. Specific sites in space that should not be occupied by an active inhibitor are also specified. The GCOD measures for the compounds in the training set permit reference points regarding which pharmacophore sites can provide the largest boosts in inhibition activity relative to the existing analogues. PMID:9770304

  1. Social Relationships, Leisure Activity, and Health in Older Adults

    PubMed Central

    Chang, Po-Ju; Wray, Linda; Lin, Yeqiang

    2015-01-01

    Objective Although the link between enhanced social relationships and better health has generally been well established, few studies have examined the role of leisure activity in this link. This study examined how leisure influences the link between social relationships and health in older age. Methods Using data from the 2006 and 2010 waves of the nationally representative U.S. Health and Retirement Study and structural equation modelling analyses, we examined data on 2,965 older participants to determine if leisure activities mediated the link between social relationships and health in 2010, controlling for race, education level, and health in 2006. Results The results demonstrated that leisure activities mediate the link between social relationships and health in these age groups. Perceptions of positive social relationships were associated with greater involvement in leisure activities, and greater involvement in leisure activities was associated with better health in older age. Discussion & Conclusions The contribution of leisure to health in these age groups is receiving increasing attention, and the results of this study add to the literature on this topic, by identifying the mediating effect of leisure activity on the link between social relationships and health. Future studies aimed at increasing leisure activity may contribute to improved health outcomes in older adults. PMID:24884905

  2. Use of Cell Viability Assay Data Improves the Prediction Accuracy of Conventional Quantitative Structure–Activity Relationship Models of Animal Carcinogenicity

    PubMed Central

    Zhu, Hao; Rusyn, Ivan; Richard, Ann; Tropsha, Alexander

    2008-01-01

    Background To develop efficient approaches for rapid evaluation of chemical toxicity and human health risk of environmental compounds, the National Toxicology Program (NTP) in collaboration with the National Center for Chemical Genomics has initiated a project on high-throughput screening (HTS) of environmental chemicals. The first HTS results for a set of 1,408 compounds tested for their effects on cell viability in six different cell lines have recently become available via PubChem. Objectives We have explored these data in terms of their utility for predicting adverse health effects of the environmental agents. Methods and results Initially, the classification k nearest neighbor (kNN) quantitative structure–activity relationship (QSAR) modeling method was applied to the HTS data only, for a curated data set of 384 compounds. The resulting models had prediction accuracies for training, test (containing 275 compounds together), and external validation (109 compounds) sets as high as 89%, 71%, and 74%, respectively. We then asked if HTS results could be of value in predicting rodent carcinogenicity. We identified 383 compounds for which data were available from both the Berkeley Carcinogenic Potency Database and NTP–HTS studies. We found that compounds classified by HTS as “actives” in at least one cell line were likely to be rodent carcinogens (sensitivity 77%); however, HTS “inactives” were far less informative (specificity 46%). Using chemical descriptors only, kNN QSAR modeling resulted in 62.3% prediction accuracy for rodent carcinogenicity applied to this data set. Importantly, the prediction accuracy of the model was significantly improved (72.7%) when chemical descriptors were augmented by HTS data, which were regarded as biological descriptors. Conclusions Our studies suggest that combining NTP–HTS profiles with conventional chemical descriptors could considerably improve the predictive power of computational approaches in toxicology. PMID:18414635

  3. Quantitative structure-activity relationship (QSAR) study of interleukin-1 receptor associated kinase 4 (IRAK-4) inhibitor activity by the genetic algorithm and multiple linear regression (GA-MLR) method.

    PubMed

    Pourbasheer, Eslam; Riahi, Siavash; Ganjali, Mohammad Reza; Norouzi, Parviz

    2010-12-01

    A linear quantitative structure-activity relationship (QSAR) model is presented for the modelling and prediction for the interleukin-1 receptor associated kinase 4 (IRAK-4) inhibition activity of amides and imidazo[1,2-?] pyridines. The model was produced using the multiple linear regression (MLR) technique on a database that consisted of 65 recently discovered amides and imidazo[1,2- ?] pyridines. Among the different constitutional, topological, geometrical, electrostatic and quantum-chemical descriptors that were considered as inputs to the model, seven variables were selected using the genetic algorithm subset selection method (GA). The accuracy of the proposed MLR model was illustrated using the following evaluation techniques: cross-validation, validation through an external test set, and Y-randomisation. The predictive ability of the model was found to be satisfactory and could be used for designing a similar group of compounds. PMID:20429783

  4. Identification of structure-activity relationships for adverse effects of pharmaceuticals in humans: Part B. Use of (Q)SAR systems for early detection of drug-induced hepatobiliary and urinary tract toxicities

    Microsoft Academic Search

    Edwin J. Matthews; Carling J. Ursem; Naomi L. Kruhlak; R. Daniel Benz; David Aragonés Sabaté; Chihae Yang; Gilles Klopman; Joseph F. Contrera

    2009-01-01

    This report describes the development of quantitative structure-activity relationship (QSAR) models for predicting rare drug-induced liver and urinary tract injury in humans based upon a database of post-marketing adverse effects (AEs) linked to ?1600 chemical structures. The models are based upon estimated population exposure using AE proportional reporting ratios. Models were constructed for 5 types of liver injury (liver enzyme

  5. 4Hydroxy2-quinolones 138. Synthesis and study of structure-biological activity relationships in a series of 1-hydroxy-3-oxo-5,6-dihydro-3H-pyrrolo[3,2,1- ij ]quinoline-2-carboxylic acid anilides

    Microsoft Academic Search

    I. V. Ukrainets; E. V. Mospanova; N. L. Bereznyakova; O. I. Naboka

    2007-01-01

    Two methods are discussed and the synthesis of a series of 1-hydroxy-3-oxo-5,6-dihydro-3H-pyrrolo[3,2,1-ij]quinoline-2-carboxylic\\u000a acid anilides has been carried out. The antitubercular activity and the effect on the urinary function of the kidney have\\u000a been studied for the compounds prepared. A structure-biological activity relationship is discussed.

  6. STRUCTURE AND TEXTURE RELATIONSHIPS IN COOKED RICE

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Texture plays a role in cooked rice quality and the structure of cooked rice grain determines the texture. The relationship of texture and structure may be explored by corrlelating compression measurements to observation of the compressed material. Compression ratios of 20 to 70% were measured again...

  7. Synthesis, antitumor activity, and structure-activity relationship study of trihydroxylated 2,4,6-triphenyl pyridines as potent and selective topoisomerase II inhibitors.

    PubMed

    Karki, Radha; Park, Chanmi; Jun, Kyu-Yeon; Jee, Jun-Goo; Lee, Jun-Ho; Thapa, Pritam; Kadayat, Tara Man; Kwon, Youngjoo; Lee, Eung-Seok

    2014-09-12

    A series of eighteen trihydroxylated 2,4,6-triphenyl pyridines were designed and synthesized which contain hydroxyl groups at ortho, meta or para position of each phenyl rings attached to the central pyridine. They were evaluated for topoisomerase I and II inhibitory activity, and cytotoxicity against several human cancer cell lines for the development of novel anticancer agents. Most of the compounds exhibited strong and selective topoisomerase II inhibitory activity compared to the positive control, etoposide, and also displayed significant cytotoxicity in low micromolar range. Trihydroxylated 2,4,6-triphenyl pyridines were more potent than mono- and di-hydroxylated 2,4,6-triphenyl pyridines, which have been previously studied in our research group. Positive correlation between topoisomerase II inhibitory activity and cytotoxicity was observed for the most compounds. Molecular docking study shows qualitatively consistent with the results of biological assays. PMID:25062006

  8. Application of toxicity-based fractionation techniques and structure-activity relationship models for the identification of phototoxic polycyclic aromatic hydrocarbons in sediment pore water

    SciTech Connect

    Kosian, P.A.; Makynen, E.A.; Monson, P.D.; Mount, D.R.; Ankley, G.T. [Environmental Protection Agency, Duluth, MN (United States); Spacie, A. [Purdue Univ., Lafayette, IN (United States); Mekenyan, O.G. [Higher Inst. of Chemical Technology, Bourgas (Bulgaria). Dept. of Physical Chemistry

    1998-06-01

    Recent studies conducted at their laboratory have shown that sediments contaminated with complex mixtures of polycyclic aromatic hydrocarbons (PAHs) can exhibit enhanced toxicity (lethality) to a variety of aquatic species when the samples are tested under ultraviolet (UV) light designed to mimic the wavelengths present in sunlight. However, because these contaminated sediments can contain literally thousands of chemicals, it is difficult to use conventional analytical techniques to identify those compounds responsible for photo-induced toxicity. The purpose of this study was to adapt existing toxicity identification evaluation methods to attempt to identify those compounds contributing to the phototoxicity observed in their sediment samples. Pore water obtained from sediments collected near an oil refinery discharge was toxic to Lumbriculus variegatus following exposure to UV light, while organisms exposed to the same pore water, but without subsequent UV treatment, showed no toxic effect. Solid-phase extraction disks and high-performance liquid chromatography were used, in conjunction with toxicity tests with L. variegatus, to extract and fractionate phototoxic chemicals from the pore water. Phototoxic fractions analyzed by gas chromatography-mass spectrometry revealed the presence of a number of aliphatic hydrocarbons, substituted PAHs, and PAHs containing heteroatoms. Chemicals were screened for their phototoxic potential based on empirical data and predictive models. A refined list of PAHs was then evaluated on the basis of their phototoxic potency as defined by a recently developed quantitative structure-activity relationship model and estimates of their bioaccumulation potential. Based on the model predictions of potency and bioaccumulation, nine likely phototoxic chemicals were identified.

  9. Relationship between chemical and physical surface properties of activated carbon

    Microsoft Academic Search

    F. Julien; M. Baudu; M. Mazet

    1998-01-01

    The relationships between structural (chemical or physical) and more general properties such as the surface electrokinetic potential (zeta potential or isoelectric point) or spreading pressure of water were investigated for three powder activated carbon (PAC) samples (manufactured from woods, coconut shell and coal). The PAC samples were characterized by physical parameter measurements (such as zeta potential, specific surface area, spreading

  10. Antibacterial and antioxidant activity of essential oil terpenes against pathogenic and spoilage-forming bacteria and cell structure-activity relationships evaluated by SEM microscopy.

    PubMed

    Zengin, Hatice; Baysal, Ayse H

    2014-01-01

    The antibacterial activity and antioxidant effect of the compounds ?-terpineol, linalool, eucalyptol and ?-pinene obtained from essential oils (EOs), against pathogenic and spoilage forming bacteria were determined. The antibacterial activities of these compounds were observed in vitro on four Gram-negative and three Gram-positive strains. S. putrefaciens was the most resistant bacteria to all tested components, with MIC values of 2% or higher, whereas E. coli O157:H7 was the most sensitive strain among the tested bacteria. Eucalyptol extended the lag phase of S. Typhimurium, E. coli O157:H7 and S. aureus at the concentrations of 0.7%, 0.6% and 1%, respectively. In vitro cell growth experiments showed the tested compounds had toxic effects on all bacterial species with different level of potency. Synergistic and additive effects were observed at least one dose pair of combination against S. Typhimurium, E. coli O157:H7 and S. aureus, however antagonistic effects were not found in these combinations. The results of this first study are encouraging for further investigations on mechanisms of antimicrobial activity of these EO components. PMID:25372394

  11. COMPUTER-ASSISTED STUDIES OF MOLECULAR STRUCTURE AND GENOTOXIC ACTIVITY BY PATTERN RECOGNITION TECHNIQUES

    EPA Science Inventory

    Often a compound's biological activity is determined by complex relationships between its structural components. Such a relationship often can only be adequately described and exploited by multivariate structure-activity relationship (SAR) studies that can deal with many variable...

  12. Synthesis, topoisomerase I and II inhibitory activity, cytotoxicity, and structure-activity relationship study of 2-phenyl- or hydroxylated 2-phenyl-4-aryl-5H-indeno[1,2-b]pyridines.

    PubMed

    Kadayat, Tara Man; Song, Chanju; Shin, Somin; Magar, Til Bahadur Thapa; Bist, Ganesh; Shrestha, Aarajana; Thapa, Pritam; Na, Younghwa; Kwon, Youngjoo; Lee, Eung-Seok

    2015-07-01

    A series of novel twenty-eight rigid 2-phenyl- or hydroxylated 2-phenyl-4-aryl-5H-indeno[1,2-b]pyridines were synthesized and evaluated for their topoisomerase inhibitory activity as well as their cytotoxicity against several human cancer cell lines. Generally, hydroxylated compounds (16-18, 22-25, and 29-31) containing furyl or thienyl moiety at 4-position of central pyridine exhibited strong topoisomerase I and II inhibitory activity compared to positive control, camptothecin and etoposide, respectively, in low micromolar range. Structure-activity relationship study revealed that indenopyridine compounds with hydroxyl group at 2-phenyl ring in combination with furyl or thienyl moiety at 4-position are important for topoisomerase inhibition. Compounds (22-25) which contain hydroxyl group at meta position of the 2-phenyl ring at 2-position and furanyl or thienyl substitution at 4-position of indenopyridine, showed concrete correlations between topo I and II inhibitory activity, and cytotoxicity against evaluated human cancer cell lines. PMID:26022080

  13. Synthesis and structure-activity relationships of N-{3-[2-(4-alkoxyphenoxy)thiazol-5-yl]-1- methylprop-2-ynyl}carboxy derivatives as selective acetyl-CoA carboxylase 2 inhibitors.

    PubMed

    Gu, Yu Gui; Weitzberg, Moshe; Clark, Richard F; Xu, Xiangdong; Li, Qun; Zhang, Tianyuan; Hansen, T Matthew; Liu, Gang; Xin, Zhili; Wang, Xiaojun; Wang, Rongqi; McNally, Teresa; Zinker, Bradley A; Frevert, Ernst U; Camp, Heidi S; Camp, Heidi; Beutel, Bruce A; Sham, Hing L

    2006-06-29

    A structurally novel acetyl-CoA carboxylase (ACC) inhibitor is identified from high-throughput screening. A preliminary structure-activity relationship study led to the discovery of potent dual ACC1/ACC2 and ACC2 selective inhibitors against human recombinant ACC1 and ACC2. Selective ACC2 inhibitors exhibited IC50<20 nM and >1000-fold selectivity against ACC1. (S)-Enantiomer 9p exhibited high ACC2 activity and lowered muscle malonyl-CoA dose-dependently in acute rodent studies, whereas (R)-enantiomer 9o was weak and had no effect on the malonyl-CoA level. PMID:16789734

  14. Structure-activity relationship studies on acremomannolipin A, the potent calcium signal modulator with a novel glycolipid structure 3: Role of the length of alditol side chain.

    PubMed

    Tsutsui, Nozomi; Tanabe, Genzoh; Morita, Nao; Okayama, Yoshitomo; Kita, Ayako; Sugiura, Reiko; Muraoka, Osamu

    2015-07-01

    Five homologs of a novel glycolipid acremomannolipin A (1a), the potential Ca(2+) signal modulator isolated from Acremonium strictum, bearing alditols of different length (1g-1k) were synthesized by a stereoselective ?-mannosylation of appropriately protected mannosyl sulfoxide (2) with five alditols (1g: C2, 1h: C3, 1i: C4, 1j: C5 and 1k: C7 units), and their potential in modulating Ca(2+) signaling were evaluated. Homologs with alditols of more than 4 carbons (1i, 1j and 1k) were equally or more potent than the parent compound (1a) regardless of the length of the alditol chain. Whereas activities of two homologs with shorter chains (1g and 1h) decreased to a considerable extent. The results indicated that the length of the alditol side chain was a crucial determinant for the potent calcium signal modulating activity. PMID:25910586

  15. A quantitative structure–antifungal activity relationship study of oxygenated aromatic essential oil compounds using data structuring and PLS regression analysis

    Microsoft Academic Search

    Karmen Voda; Bojana Boh; Margareta Vrta?nik

    2004-01-01

    Twenty two oxygenated aromatic essential oil compounds were chosen for the study of the antifungal activity against two wood-decaying fungi, the white-rot Trametes versicolor, which mainly metabolizes lignin, and the brown-rot Coniophoha puteana, which digests cellulose in plant cell walls. Minimal inhibitory concentrations (MICs) were determined by the agar dilution method, using dimethyl sulfoxide (DMSO) as the solvent for the

  16. Synthesis, structure–activity relationship and antiviral activity of 3?- N, N-dimethylamino-2?,3?-dideoxythymidine and its prodrugs

    Microsoft Academic Search

    Ramendra K. Singh; Dipti Yadav; Diwakar Rai; Garima Kumari; C. Pannecouque; Erik De Clercq

    2010-01-01

    A probable NRTI molecule, viz. 3?-N,N-dimethylamino-2?,3?-dideoxythymidine (4) and its 5?-O-carboxyl ester prodrugs – 5?-(N-?-BOC-l-phenylalanyl)-3?-N,N-dimethylamino-2?,3?-dideoxythymidine (5), 5?-l-phenylalanyl-3?-N,N-dimethylamino-2?,3?-dideoxythymidine (6) and 5?-decanoyl-3?-N,N-dimethylamino-2?,3?-dideoxythymidine (7) have been synthesized and screened against HIV, HSV-1 and 2, parainfluenza-3, vesicular stomatitis and several other viruses. The compound 6 showed good antiviral activity with EC50 value 0.03?M (SI=8) against VSV in Hela and HEL cell lines. However, the lead

  17. Development of models for understanding causal relationships among activity and travel variables

    Microsoft Academic Search

    Xin Ye

    2006-01-01

    Understanding joint and causal relationships among multiple endogenous variables has been of much interest to researchers in the field of activity and travel behavior modeling. Structural equation models have been widely developed for modeling and analyzing the causal relationships among travel time, activity duration, car ownership, trip frequency and activity frequency. In the model, travel time and activity duration are

  18. Synthesis, structure-activity relationship and antiviral activity of 3'-N,N-dimethylamino-2',3'-dideoxythymidine and its prodrugs.

    PubMed

    Singh, Ramendra K; Yadav, Dipti; Rai, Diwakar; Kumari, Garima; Pannecouque, C; De Clercq, Erik

    2010-09-01

    A probable NRTI molecule, viz. 3'-N,N-dimethylamino-2',3'-dideoxythymidine (4) and its 5'-O-carboxyl ester prodrugs - 5'-(N-alpha-BOC-L-phenylalanyl)-3'-N,N-dimethylamino-2',3'-dideoxythymidine (5), 5'-L-phenylalanyl-3'-N,N-dimethylamino-2',3'-dideoxythymidine (6) and 5'-decanoyl-3'-N,N-dimethylamino-2',3'-dideoxythymidine (7) have been synthesized and screened against HIV, HSV-1 and 2, parainfluenza-3, vesicular stomatitis and several other viruses. The compound 6 showed good antiviral activity with EC(50) value 0.03 microM (SI=8) against VSV in Hela and HEL cell lines. However, the lead compound 4 and its derivatives 5, 6 and 7 showed no remarkable activity against HIV-1 and other viruses. Molecular docking studies with HIV-1 RT using DS 2.5 and pymol softwares have shown marked differences in the interaction patterns between the lead compound 4 and AZT. PMID:20538384

  19. A structure–activity relationship for pincer palladium(II) complexes — influence of ring-size of metallacycles on the activity in allylic alkylation

    Microsoft Academic Search

    Zhaohui Wang; Michael R Eberhard; Craig M Jensen; Shiro Matsukawa; Yohsuke Yamamoto

    2003-01-01

    A series of new palladium(II) complexes derived from the well-known pincer complex [PdCl{(C6H3)(OPiPr2)2-2,6}] were synthesised: [PdX{(C6H3)(OPiPr2)2-2,6}] (X=Br?, I?, OAc?, OTf?). A novel PCP? pincer ligand 1-(iPr2PO)-3-(iPr2POCH2)(C6H4) was prepared and complexed to palladium(II) to give [PdX{(C6H3)(OPiPr2)-2-(CH2OPiPr2)-6}] (X=Cl?, I?, OAc?, OTf?, BF4?). The X-ray structure of [PdCl{(C6H3)(OPiPr2)-2-(CH2OPiPr2)-6}] was solved and is discussed. These complexes were applied to the catalytic reaction of cinnamyl

  20. Structure-Activity Relationship Studies of a Series of Semisynthetic Lipopeptides Leading to the Discovery of Surotomycin, a Novel Cyclic Lipopeptide Being Developed for the Treatment of Clostridium difficile-Associated Diarrhea.

    PubMed

    Yin, Ning; Li, Jing; He, Yong; Herradura, Prudencio; Pearson, Andre; Mesleh, Michael F; Mascio, Carmela T; Howland, Karen; Steenbergen, Judith; Thorne, Grace M; Citron, Diane; Van Praagh, Andrew D G; Mortin, Lawrence I; Keith, Dennis; Silverman, Jared; Metcalf, Chester

    2015-06-25

    Novel cyclic lipopeptides with different acyl tails were synthesized via a semisynthetic approach. Structure-activity relationship studies revealed that lipophilicity, chain length, and the location of key aromatic functionalities of the tail modulated activity. The lead compound surotomycin exhibited significantly improved in vitro activity compared with daptomycin (MIC90 0.5 vs 2 ?g/mL) against Clostridium difficile including NAP1 epidemic strains. In hamster efficacy studies, surotomycin protected animals at a dose of 0.5 mg/kg, PO. PMID:25993059

  1. Protective activity of (1S,2E,4R,6R,7E,11E)-2,7,11-cembratriene-4,6-diol analogues against diisopropylfluorophosphate neurotoxicity: preliminary structure-activity relationship and pharmacophore modeling.

    PubMed

    Eterovi?, Vesna A; Del Valle-Rodriguez, Angelie; Pérez, Dinely; Carrasco, Marimée; Khanfar, Mohammad A; El Sayed, Khalid A; Ferchmin, Pedro A

    2013-08-01

    Diisopropylfluorophosphate (DFP) is an organophosphorous insecticide used as a surrogate for the more toxic chemical warfare nerve agent sarin. DFP produces neurotoxicity in vivo and irreversibly decreases the area of population spikes recorded from the CA1 region of acute hippocampal slices. (1S,2E,4R,6R,7E,11E)-2,7,11-Cembratriene-4,6-diol (1) is a neuroprotective natural cembranoid that reverses DFP-induced damage both in vivo and in the hippocampal slice. Cembranoid 1 acts by noncompetitive inhibition of the ?7 nicotinic acetylcholine receptor. This study aims at establishing a preliminary structure-activity relationship to define the neuroprotective cembranoid pharmacophores using the hippocampal slice assay and pharmacophore modeling. Fourteen natural, semisynthetic, or biocatalytic cembranoid analogues 2-15 related to 1 were tested for their capacity to protect the population spikes from DFP-induced damage and intrinsic toxicity. Twelve cembranoids caused significant reversal of DFP toxicity; only 3 active analogues displayed minor intrinsic toxicity at 10 ?M. The C-4 epimer of 1 (2) and the 4-O-methyl ether analogue of 1 (3), were totally devoid of neuroprotective activity. The results suggested a model for cembranoid binding where the hydrophobic ring surface binds to a hydrophobic (Hbic) patch on the receptor molecule and an electronegative atom (oxygen or sulfur) in proper spatial relationship to the ring surface interacts with an electropositive group in the receptor binding site. A pharmacophore model consisting of 1 hydrogen bond acceptor (HBA), 2 Hbic, and 10 exclusion spheres was established using HipHop-REFINE and supported the above mentioned pharmacophoric hypothesis. PMID:23769165

  2. Protective activity of (1S,2E,4R,6R,7E,11E)-2,7,11-cembratriene-4,6-diol analogues against diisopropylfluorophosphate neurotoxicity: Preliminary structure-activity relationship and pharmacophore modeling

    PubMed Central

    Eterovi?, Vesna A.; Valle-Rodriguez, Angelie Del; Pérez, Dinely; Carrasco, Marimée; Khanfar, Mohammad A.; El Sayed, Khalid A.; Ferchmin, Pedro A.

    2013-01-01

    Diisopropylfluorophosphate (DFP) is an organophosphorous insecticide used as a surrogate for the more toxic chemical warfare nerve agent sarin. DFP produces neurotoxicity in vivo and irreversibly decreases the area of population spikes recorded from the CA1 region of acute hippocampal slices. (1S,2E,4R,6R,7E,11E)-2,7,11-Cembratriene-4,6-diol (1) is a neuroprotective natural cembranoid that reverses DFP-induced damage both in vivo and in the hippocampal slice. Cembranoid 1 acts by noncompetitive inhibition of the ?7 nicotinic acetylcholine receptor. This study aims at establishing a preliminary structure-activity relationship to define the neuroprotective cembranoid pharmacophores using the hippocampal slice assay and pharmacophore modeling. Fourteen natural, semisyntheti or biocatalytic cembranoid analogues 2-15 related to 1 were tested for their capacity to protect the population spikes from DFP-induced damage and intrinsic toxicity. Twelve cembranoids caused significant reversal of DFP toxicity; only 3 active analogues displayed minor intrinsic toxicity at 10 ?M. The C-4 epimer of 1 (2) and the 4-O-methyl ether analogue of 1 (3), were totally devoid of neuroprotective activity. The results suggested a model for cembranoid binding where the hydrophobic ring surface binds to a hydrophobic (Hbic) patch on the receptor molecule and an electronegative atom (oxygen or sulfur) in proper spatial relationship to the ring surface interacts with an electropositive group in the receptor binding site. A pharmacophore model consisting of 1 hydrogen bond acceptor (HBA), 2 Hbic, and 10 exclusion spheres was established using HipHop-REFINE and supported the above mentioned pharmacophoric hypothesis. PMID:23769165

  3. The refined 1.9-A X-ray crystal structure of D-Phe-Pro-Arg chloromethylketone-inhibited human alpha-thrombin: structure analysis, overall structure, electrostatic properties, detailed active-site geometry, and structure-function relationships.

    PubMed Central

    Bode, W.; Turk, D.; Karshikov, A.

    1992-01-01

    Thrombin is a multifunctional serine proteinase that plays a key role in coagulation while exhibiting several other key cellular bioregulatory functions. The X-ray crystal structure of human alpha-thrombin was determined in its complex with the specific thrombin inhibitor D-Phe-Pro-Arg chloromethylketone (PPACK) using Patterson search methods and a search model derived from trypsinlike proteinases of known spatial structure (Bode, W., Mayr, I., Baumann, U., Huber, R., Stone, S.R., & Hofsteenge, J., 1989, EMBO J. 8, 3467-3475). The crystallographic refinement of the PPACK-thrombin model has now been completed at an R value of 0.156 (8 to 1.92 A); in particular, the amino- and the carboxy-termini of the thrombin A-chain are now defined and all side-chain atoms localized; only proline 37 was found to be in a cis-peptidyl conformation. The thrombin B-chain exhibits the characteristic polypeptide fold of trypsinlike serine proteinases; 195 residues occupy topologically equivalent positions with residues in bovine trypsin and 190 with those in bovine chymotrypsin with a root-mean-square (r.m.s.) deviation of 0.8 A for their alpha-carbon atoms. Most of the inserted residues constitute novel surface loops. A chymotrypsinogen numbering is suggested for thrombin based on the topological equivalences. The thrombin A-chain is arranged in a boomeranglike shape against the B-chain globule opposite to the active site; it resembles somewhat the propeptide of chymotrypsin(ogen) and is similarly not involved in substrate and inhibitor binding. Thrombin possesses an exceptionally large proportion of charged residues. The negatively and positively charged residues are not distributed uniformly over the whole molecule, but are clustered to form a sandwichlike electrostatic potential; in particular, two extended patches of mainly positively charged residues occur close to the carboxy-terminal B-chain helix (forming the presumed heparin-binding site) and on the surface of loop segment 70-80 (the fibrin[ogen] secondary binding exosite), respectively; the negatively charged residues are more clustered in the ringlike region between both poles, particularly around the active site. Several of the charged residues are involved in salt bridges; most are on the surface, but 10 charged protein groups form completely buried salt bridges and clusters. These electrostatic interactions play a particularly important role in the intrachain stabilization of the A-chain, in the coherence between the A- and the B-chain, and in the surface structure of the fibrin(ogen) secondary binding exosite (loop segment 67-80).(ABSTRACT TRUNCATED AT 400 WORDS) PMID:1304349

  4. Self- and cross-reactions of ?-hydroxyperoxy radicals of relevance to tropospheric monoterpene oxidation: structure-activity relationships for rate coefficients

    NASA Astrophysics Data System (ADS)

    Boyd, Andrew A.; Villenave, Eric; Lesclaux, Robert

    The laser flash photolysis technique has been used to measure rate coefficients for the self- and cross-reactions of four peroxy radicals, which have been selected as surrogate of those peroxy radicals resulting from the OH addition to monoterpenes: the 2-hydroxycyclohexylperoxy c-C 6H 10(OH)O 2 (I), 2-hydroxy-1,2-dimethylcyclohexylperoxy c-C 6H 8(CH 3) 2(OH)O 2 (II), 2-hydroxy-2-methylcyclohexylperoxy c-C 6H 9(OH)CH 3O 2 (III) and 2-hydroxy-1-methylcyclohexylperoxy c-C 6H 9CH 3(OH)O 2 (IV) radicals. Those radicals were obtained by addition of OH and O 2 to cyclohexene and 1,2-dimethylcyclohexene for I and II, respectively, and to 1-methylcyclohexene for (III) and (IV). Rate constants for self-reactions of radicals I and II are: k8=(1.60±0.10)×10 -12 and k12=(2.00±0.05)×10 -14 (units of cm 3 molecule -1 s -1, errors 2 ?) at 298°K and in 1 atm air. Assuming that both the secondary radicals I and III and both the tertiary radicals II and IV have similar self-reaction rate constants, the rate constant for cross-reaction (13) between III and IV has been determined: k13=(6.15±0.33)×10 -13 cm 3 molecule -1 s -1. The self-reaction rate constant of the peroxy radical c-C 6H 8(OH)O 2, formed by OH and O 2 addition to 1,4-cyclohexadiene, was also estimated and found to be of same order of magnitude as k8, thus showing that the non-conjugated double bond in the radical has no significant effect on the rate constant. Structure-activity relationships are discussed, particularly for self- and cross-reactions involving secondary and tertiary peroxy radicals, in view of their relevance to tropospheric oxidation modelling of alkenes and monoterpenes. In particular, emphasis is given to the large increase in reactivity resulting from the ?-OH substitution, compared to non-substituted species. As part of this work, a rate constant of (1.5±0.5)×10 -14 cm 3 molecule -1 s -1 was measured for the self-reaction of the ?-OH substituted t-butylperoxy radical (CH 3) 2C(O 2)CH 2OH.

  5. Development of a new Structure-Activity Relationship (SAR) for gas-phase reactions of NO3 radicals with organic compounds

    NASA Astrophysics Data System (ADS)

    Kerdouci, J.; Picquet-Varrault, B.; Doussin, J.

    2010-12-01

    The nitrate radical (NO3) has long been recognized as the dominant night-time oxidant of organic species, in particular of unsaturated compounds. More recently, it has been shown that it can contribute significantly to the oxidation of very reactive VOC (e.g. terpenes) even during the day[1]. Volatile organic compounds are widely emitted into the atmosphere by both anthropogenic and biogenic sources. When released into the troposphere, they can undergo either photolysis or oxidation by OH and NO3 radicals and by ozone. These chemical processes are known to be responsible for the formation of photooxidants and SOA which are involved in photochemical smog events. Hence, to estimate their impact on the tropospheric chemistry, it is necessary to know their reactivity towards the atmospheric oxidants. But because of huge number of VOCs, it is impossible to perform kinetic experiments for all of them. For this reason, estimation methods have been developed to predict rate constants. A number of methods for the estimation of rate constants have been proposed. Many of them utilize the physical or chemical properties of the organic compounds such as the ionization energy[2] or the energy of molecular orbital[3]. However, these methods are restricted in their use because of the limited database concerning molecular properties and the discrepancies between the different molecular models used to calculate these parameters. For this reason, a structure-activity relationship has been developed by Atkinson[4] to predict rate constants of the OH-oxidation of VOCs. This kind of SAR is very easy to use and has been successfully integrated in chemical models[5, 6]. Concerning the reactivity of organic compounds with NO3 radicals, it has long been considered that the number of experimental data was not sufficient to use the approach proposed by Atkinson. But during the last decade, many experimental studies, in particular on the unsaturated oxygenated compounds, have enhanced the kinetic database on NO3-oxidation rate constants. This allowed us to develop a new SAR for the gas-phase reactions of NO3 with organic compounds which is based exclusively on correlations between the molecular structures and the rate constants. This new SAR is based on experimental rate constants of 150 molecules and has been developed for alkanes, alkenes (simple and cyclic alkenes, dienes and terpenes) and saturated and unsaturated oxygenated species (alcohols, carbonyls, ethers and esters). Results and performances of this SAR will be discussed here. References [1] Geyer, A., et al., J. Geophys. Res., 108 (2003), 4368. [2] Grosjean, D. and E.L. Williams, Atmospheric Environment. Part A. General Topics, 26 (1992), 1395-1405. [3] Pfrang, C., et al., Atmospheric Environment, 40 (2006), 1180-1186. [4] Kwok, E.S.C. and R. Atkinson, Atmospheric Environment, 29 (1995), 1685-1695. [5] Jenkin, M.E., S.M. Saunders, and M.J. Pilling, Atmospheric Environment, 31(1997), 81-104. [6] Aumont, B., S. Szopa, and S. Madronich, Atmospheric Chemistry and Physics, 5 (2005), 2497-2517.

  6. Quantitative structure-activity relationship investigation of the role of hydrophobicity in regulating mutagenicity in the Ames test: 2. Mutagenicity of aromatic and heteroaromatic nitro compounds in Salmonella typhimurium TA100

    SciTech Connect

    Debnath, A.K.; Hansch, C. (Pomona Coll., Claremont, CA (United States)); Shusterman, A.J. (Reed Coll., Portland, OR (United States)); Lopez de Compadre, R.L. (Univ. of Arkansas, Little Rock (United States))

    1992-01-01

    A quantitative structure-activity relationship (QSAR) has been derived for the mutagenic activity of 117 aromatic and heteroaromatic nitro compounds acting on Salmonella typhimurium TA100. Relative mutagenic activity is bilinearly dependent on hydrophobicity, with an optimal log P of 5.44, and is linearly dependent on the energy of the lowest unoccupied molecular orbital of the nitro compound. The dependence of mutagenic activity on hydrophobicity and electronic effects is very similar for TA98 and TA100. Mutagenic activity in TA100 does not depend on the size of the aromatic ring system, as it does in TA98. The effect of the choice of assay organism, TA98 versus TA100, on nitroarene QSAR is seen to be similar to the effect previously found for aminoarenes. Lateral verification of QSARs is presented as a tool for establishing the significance of a new QSAR.

  7. Apolipoprotein AI: structure-function relationships

    Microsoft Academic Search

    Philippe G. Frank; Yves L. Marcel

    The inverse relationship between high density lipo- protein (HDL) plasma levels and coronary heart disease has been attributed to the role that HDL and its major constitu- ent, apolipoprotein A-I (apoA-I), play in reverse cholesterol transport (RCT). The efficiency of RCT depends on the spe- cific ability of apoA-I to promote cellular cholesterol efflux, bind lipids, activate lecithin:cholesterol acyltransferase (LCAT),

  8. Structure--properties relationships for manganese perovskites

    SciTech Connect

    Dabrowski, B.; Xiong, X.; Chmaissem, O.; Bukowski, Z.; Jorgensen, J. D.

    1999-10-14

    By combining the results of dc magnetization, ac susceptibility, magnetoresistivity, magnetostriction, and x-ray and neutron powder diffraction data for stoichiometric La{sub 1{minus}x}Sr{sub x}MnO{sub 3} the authors have constructed a phase diagram that describes the magnetic, transport, and structural properties and the relationships among them as a function of composition and temperature. Correlations among physical and structural properties have been observed that are consistent with a competition between ferromagnetism and JT distortion. A metallic state occurs below the Curie temperature when both coherent and incoherent JT distortions are suppressed.

  9. 6-(substituted methylene)penems, potent broad spectrum inhibitors of bacterial beta-lactamase. III. Structure-activity relationships of the 5-membered heterocyclic derivatives.

    PubMed

    Bennett, I; Broom, N J; Bruton, G; Calvert, S; Clarke, B P; Coleman, K; Edmondson, R; Edwards, P; Jones, D; Osborne, N F

    1991-03-01

    Sodium (5RS)-Z-6-(heterocyclylmethylene)penem-3-carboxylates (2) are a series of extremely potent inhibitors of bacterial beta-lactamases. A variety of 5-membered heteroaromatic derivatives have been prepared and structure-activity studies reveal a preferred substituent orientation. One of these derivatives, the 1-methyl-1,2,3-triazolyl compound (5m) is a more potent synergist of amoxycillin than clavulanic acid, sulbactam or tazobactam. PMID:2026558

  10. Quantitative structure-activity relationship analysis as a tool to evaluate the mode of action of chemical hybridizing agents for wheat (Triticum aestivum L.).

    PubMed

    Chakraborty, Kajal; Devakumar, C

    2005-05-01

    Augmentation of wheat production calls for introduction of wheat hybrids in cultivation. In the absence of viable alternative technology of hybrid wheat development, chemical induction of male sterility mediated technology based on chemical hybridizing agents (CHAs) holds a great potential. The QSAR method was applied to two families of CHAs in the N-acylanilines and pyridone class of chemistry. The models for each CHA family gave good correlation between the variations in log percent of male sterility and the steric-electrostatic properties of the sets. QSAR analysis has revealed a direct relationship of the Swain-Lupton constant F(p) and molecular mass but an inverse relationship of MR, ES, and Swain-Lupton resonance constant R in influencing the bioactivity in the N-acylanilines. QSAR analysis of four parent families consisting of two training sets each of pyrid-2-ones and prid-4-ones revealed the positive contributions of field effect exemplified by the Swain-Lupton field constant (F) and the negative contributions of the molar refractivity (MR) of aromatic substituents in all but one training set. The QSAR models also indicated that increased steric bulk at the 4-position on the phenyl ring is associated with enhanced activity. These leads will be useful in explaining the CHA binding fit in the macromolecular receptor site. PMID:15853389

  11. [Quantitative structure activity relationship models based on heuristic method and gene expression programming for the prediction of the pK(a) values of sulfa drugs].

    PubMed

    Li, Yu-qin; Si, Hong-zong; Xiao, Yu-liang; Liu, Cai-hong; Xia, Cheng-cai; Li, Ke; Qi, Yong-xiu

    2009-05-01

    Quantitative structure-property relationships (QSPR) were developed to predict the pK(a) values of sulfa drugs via heuristic method (HM) and gene expression programming (GEP). The descriptors of 31 sulfa drugs were calculated by the software CODESSA, which can calculate constitutional, topological, geometrical, electrostatic, and quantum chemical descriptors. HM was also used for the preselection of 4 appropriate molecular descriptors. Linear and nonlinear QSPR models were developed based on the HM and GEP separately and two prediction models lead to a good correlation coefficient (R) of 0.90 and 0.95. The two QSPR models are tseful in predicting pK(a) during the discovery of new drugs and providing theory information for studying the new drugs. PMID:19618723

  12. Relationship between the structure and the enzymatic activity of crotoxin complex and its phospholipase A2 subunit: an in silico approach.

    PubMed

    Pereañez, Jaime Andrés; Gómez, Iván Dario; Patiño, Arley Camilo

    2012-05-01

    Crotoxin, one of the major toxins of South American rattlesnake Crotalus durissus subspecies, is an heterodimeric complex composed of two distinct subunits: a basic phospholipase A(2) (PLA(2), CB) and an acidic nontoxic catalytically inactive protein, crotapotin (CA). It's well known that CB has a high enzymatic activity; however the molecular aspects that determine this fact remain unknown. In this study, an in silico approach was used to predict the CA structure by homology modeling, and the crotoxin structure by means of molecular docking. CA structure was built using the software Modeller taking Crotalus atrox PLA(2) (1PP2:R) as a template. Different criteria measured by Procheck, Verify 3D and ProSA were indicative of the reliability and the proper fold for the predicted structural model of CA. Then, a combination of this model and CB crystal structure was used to build the structure of crotoxin complex through rigid-body protein-protein docking. The crotoxin-3D model suggested that by means of hydrophobic and ?-? stacking interactions, CA-Y24 and CA-F119 interact with CB-F24 and CB-F119, respectively. Those interactions could prevent the interfacial adsorption of the CB onto the lipid/water interface by blocking part of the interfacial binding surface of the PLA(2). This fact could explain the differences regarding to enzymatic activity between the crotoxin complex and CB. In addition, the crotoxin-3D model showed solvent-exposed regions of CA that could bind the receptor expressed in target cells. PMID:22481077

  13. Structure and Function Relationship of the Autotransport and Proteolytic Activity of EspP from Shiga Toxin-Producing Escherichia coli

    PubMed Central

    Brockmeyer, Jens; Spelten, Sabrina; Kuczius, Thorsten; Bielaszewska, Martina; Karch, Helge

    2009-01-01

    Background The serine protease autotransporter EspP is a proposed virulence factor of Shiga toxin-producing Escherichia coli (STEC). We recently distinguished four EspP subtypes (EspP?, EspP?, EspP?, and EspP?), which display large differences in transport and proteolytic activities and differ widely concerning their distribution within the STEC population. The mechanisms underlying these functional variations in EspP subtypes are, however, unknown. Methodology/Principal Findings The structural basis of proteolytic and autotransport activity was investigated using transposon-based linker scanning mutagenesis, site-directed mutagenesis and structure-function analysis derived from homology modelling of the EspP passenger domain. Transposon mutagenesis of the passenger domain inactivated autotransport when pentapeptide linker insertions occurred in regions essential for overall correct folding or in a loop protruding from the ?-helical core. Loss of proteolytic function was limited to mutations in Domain 1 in the N-terminal third of the EspP passenger. Site-directed mutagenesis demonstrated that His127, Asp156 and Ser263 in Domain 1 form the catalytic triad of EspP. Conclusions/Significance Our data indicate that in EspP i) the correct formation of the tertiary structure of the passenger domain is essential for efficient autotransport, and ii) an elastase-like serine protease domain in the N-terminal Domain 1 is responsible for the proteolytic phenotype. Lack of stabilizing interactions of Domain 1 with the core structure of the passenger domain ablates proteolytic activity in subtypes EspP? and EspP?. PMID:19568421

  14. PCBs: structure-function relationships and mechanism of action

    Microsoft Academic Search

    S. Safe; S. Bandiera; T. Sawyer; L. Robertson; L. Safe; A. Parkinson; P. E. Thomas; D. E. Ryan; L. M. Reik; W. Levin; M. A. Denomme

    1985-01-01

    Quantitative structure-activity relationships within a series of PCBs were determined by comparing their aryl hydrocarbon hydroxylase (AHH) induction potencies (EC50) in rat hepatoma H-4-II-E cells and their binding affinities (ED50) for the 2,3,7,8-TCDD cytosolic receptor protein. The results showed that there was an excellent correlation between AHH induction potencies and receptor binding acidities of these compounds and the order of

  15. An Analysis of Structural Validity of Ternary Relationships in Entity Relationship Modeling

    E-print Network

    Song, Il-Yeol

    1 An Analysis of Structural Validity of Ternary Relationships in Entity Relationship Modeling James cardinality constraints yielding a more complete analysis of the structural validity of ternary relationship ____________________________________________________________________________________________________ This research explores the criteria that contribute to the validity of modeling structures within the entity

  16. Structure-activity relationships of retinoids in developmental toxicology. I. Studies on the nature of the polar terminus of the vitamin A molecule.

    PubMed

    Willhite, C C; Dawson, M I; Williams, K J

    1984-07-01

    The teratogenic activities of all-trans-retinoyl fluoride, all-trans-3-retinylidene-2,4-pentanedione, all-trans-2-retinylidene-1,3-cyclopentanedione, all-trans-2-retinylidene-5,5-dimethyl-1,3-cyclohexanedione, all-trans-2-retinylidene-5-p-methoxyphenyl-1,3-cyclohexanedione, all-trans-2-retinylidene-1,3-cyclooctanedione, all-trans-5-[2,6-dimethyl-8-(2,6,6-trimethylcyclohexen-1-yl)-1,3, 5,7-octatetrae n-1-yl]tetrazole, ethyl all-trans-9-(exo-2-bicyclo[2.2.1.]heptyl)-3,7-dimethyl-2,4,6,8- nonatetraenoate, ethyl all-trans-4-[2-methyl-4-(2,6,6-trimethyl-1-cyclohexen-1-yl)-1,3- butadien-1-yl]benzoate, 13-cis-N-(4-hydroxyphenyl)retinamide, and 13-cis-N-(2-hydroxyethyl)retinamide were determined in the hamster and compared with that of all-trans-retinoic acid. Administration of a single oral dose of the retinoids failed to induce signs of the hypervitaminosis A intoxication syndrome in any of the dams, and the maternal weight gain was not significantly different from the vehicle control value, except following intubation of the retinamides where maternal weight gain was significantly depressed. All of the retinylidene 1,3-diketones studied here were devoid of significant teratogenic activity. The retinamides failed to induce either an elevated mean litter frequency of malformed fetuses or a syndrome of anomalies similar to that induced by administration of an equimolar dose of all-trans-retinoic acid. All of the other retinoids induced a syndrome of malformations similar to that induced by administration of all-trans-retinoic acid and were associated with a significant increase in the number of litters containing one or more malformed fetuses and an elevated mean litter frequency of malformed fetuses. The teratogenic activity in the hamster of this series of retinoids was independent of structural modifications in either the beta-cyclogeranylidene ring or the polyene chain of the molecule. The results of the present study suggest that the changes in teratogenic activity associated with structural modification of vitamin A at C15 were primarily dependent upon the presence of or biotransformation to a free carboxyl or a moiety with an equivalent pKa at C15, not upon the molecular size of the substituent or the stereochemical position about C13. Since major structural modifications of vitamin A were made without the substantial loss of teratogenic activity, the structural requirements of retinoids for induction of terata were not extraordinarily exacting. PMID:6740687

  17. Structure-property relationships in eutectic composites

    NASA Technical Reports Server (NTRS)

    Hertzberg, R. W.

    1976-01-01

    The preparation of a composite material of eutectic composition directly from the molten state is investigated. The manufacture of eutectic composites by unidirectional solidification is reviewed, and it is shown how two-phase composite structures of given relative volume fraction can be produced with a range of particle sizes. Crystallographic relationships and the thermal stability of interfaces in controlled eutectic structures are examined, the mechanical behavior of aligned eutectic microstructures is discussed, and characteristics of eutectic composites having mechanical properties of engineering significance are evaluated. Specific properties of the Ni-Nb eutectic alloy are reviewed to demonstrate the effect of structure control (through directional solidification) on the mechanical response of a eutectic composite. It is noted that unidirectionally solidified eutectic composites possess highly aligned and thermally stable microstructures and also exhibit excellent combinations of strength and ductility to very high temperature levels.

  18. Quantitative structure-pharmacokinetic relationship modelling.

    PubMed

    Fouchécourt, M O; Béliveau, M; Krishnan, K

    2001-07-01

    This article presents the current methods in quantitative structure-pharmacokinetic relationship (QSPkR) modelling along with examples using chemicals of toxicological significance. The common method involves: (i) collecting pharmacokinetic data or determining pharmacokinetic parameters (e.g. elimination half-life, volume of distribution) by fitting to experimental data; and (ii) associating them with the structural features of chemicals using a Free-Wilson model. Such QSPkRs have been developed for a few series of chemicals but their usefulness is limited to the exposure scenario and conditions under which the experimental data were originally collected. The alternative approach involves the development of quantitative structure-property relationship (QSPR) models for parameters, blood:air partition coefficient, tissue:blood partition coefficient, maximal velocity for metabolism and Michaelis affinity constant, of physiologically-based pharmacokinetic (PBPK) models which are useful for conducting species, route, dose and scenario extrapolations of the tissue dose of chemicals. Mechanistic QSPRs are available for predicting tissue:blood and blood:air partition coefficients from molecular structure information of chemicals, whereas such approaches are not currently available for hepatic metabolism parameters. However, at the present time, the pharmacokinetics of inhaled volatile organic chemicals can be simulated adequately by considering the physiological limits of the hepatic extraction ratio (0-1) and molecular structure-based estimates of partition coefficients in the PBPK model. This current state-of-the-art of structure-based modelling of pharmacokinetics will advance with the development of QSPRs for other chemical-specific parameters of PBPK models. Integrated QSPR-PBPK modelling should facilitate the identification of chemicals of a family that possess desired properties of bioaccumulation and blood concentration profile in both test animals and humans. PMID:11453289

  19. Design, synthesis, and quantitative structure-activity relationship study of herbicidal analogues of pyrazolo[5,1-d][1,2,3,5]tetrazin-4(3H)ones.

    PubMed

    Zhu, You-quan; Wu, Chao; Li, Hua-bin; Zou, Xiao-mao; Si, Xue-kai; Hu, Fang-zhong; Yang, Hua-zheng

    2007-02-21

    A series of pyrazolo[5,1-d][1,2,3,5]tetrazin-4(3H)one derivatives were designed, synthesized, and evaluated for their herbicidal activities where some of these compounds provided >80% control of Brassica campestris at 10 microg/mL. Quantitative structure-activity relationship studies were performed on these compounds using physicochemical parameters (electronic, Verloop, or hydrophobic) as independent parameters and herbicidal activity as a dependent parameter, where herbicidal activity correlated best (r > 0.8) with physicochemical parameters in this set of molecules. The herbicidal activity against B. campestris was mainly affected by the molar refractivity (MR) for R1, Taft (Eso) for R2 or R6, Verloop (Lm) for R3 or R5, and electronic parameters (Hammett's constants) for R4. The optimal MR for herbicidal activity is 0.95. The herbicidal activity against Echinochloa crus-galli was mainly related with the substituents' hydrophobic parameter. The optimal pi parameters for R1 and R4 for herbicidal activity are 0.72 and 0.68, respectively. In general, these compounds showed greater herbicidal activity toward B. campestris than E. crus-galli. PMID:17300154

  20. Comparison of benzil and trifluoromethyl ketone (TFK)-mediated carboxylesterase inhibition using classical and 3D-quantitative structure–activity relationship analysis