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Sample records for asv integrase proteins

  1. Localization of ASV Integrase-DNA Contacts by Site-Directed Crosslinking and their Structural Analysis

    PubMed Central

    Merkel, George; Alexandratos, Jerry; Zhou, Dongwen; Bojja, Ravi S.; Satoh, Tadashi; Potapov, Mikhail; Kogon, Alex; Potapov, Viktor; Wlodawer, Alexander; Skalka, Anna Marie

    2011-01-01

    Background We applied crosslinking techniques as a first step in preparation of stable avian sarcoma virus (ASV) integrase (IN)-DNA complexes for crystallographic investigations. These results were then compared with the crystal structures of the prototype foamy virus (PFV) intasome and with published data for other retroviral IN proteins. Methodology/Results Photoaffinity crosslinking and site-directed chemical crosslinking were used to localize the sites of contacts with DNA substrates on the surface of ASV IN. Sulfhydryl groups of cysteines engineered into ASV IN and amino-modified nucleotides in DNA substrates were used for attachment of photocrosslinkers. Analysis of photocrosslinking data revealed several specific DNA-protein contacts. To confirm contact sites, thiol-modified nucleotides were introduced into oligo-DNA substrates at suggested points of contact and chemically crosslinked to the cysteines via formation of disulfide bridges. Cysteines incorporated in positions 124 and 146 in the ASV IN core domain were shown to interact directly with host and viral portions of the Y-mer DNA substrate, respectively. Crosslinking of an R244C ASV IN derivative identified contacts at positions 11 and 12 on both strands of viral DNA. The most efficient disulfide crosslinking was observed for complexes of the ASV IN E157C and D64C derivatives with linear viral DNA substrate carrying a thiol-modified scissile phosphate. Conclusion Analysis of our crosslinking results as well as published results of retroviral IN protein from other laboratories shows good agreement with the structure of PFV IN and derived ASV, HIV, and MuLV models for the core domain, but only partial agreement for the N- and C-terminal domains. These differences might be explained by structural variations and evolutionary selection for residues at alternate positions to perform analogous functions, and by methodological differences: i.e., a static picture of a particular assembly from crystallography vs

  2. Structural Studies of the HIV-1 Integrase Protein: Compound Screening and Characterization of a DNA-Binding Inhibitor

    PubMed Central

    Hassounah, Said; Mesplède, Thibault; Wainberg, Mark A.

    2015-01-01

    Understanding the HIV integrase protein and mechanisms of resistance to HIV integrase inhibitors is complicated by the lack of a full length HIV integrase crystal structure. Moreover, a lentiviral integrase structure with co-crystallised DNA has not been described. For these reasons, we have developed a structural method that utilizes free software to create quaternary HIV integrase homology models, based partially on available full-length prototype foamy virus integrase structures as well as several structures of truncated HIV integrase. We have tested the utility of these models in screening of small anti-integrase compounds using randomly selected molecules from the ZINC database as well as a well characterized IN:DNA binding inhibitor, FZ41, and a putative IN:DNA binding inhibitor, HDS1. Docking studies showed that the ZINC compounds that had the best binding energies bound at the IN:IN dimer interface and that the FZ41 and HDS1 compounds docked at approximately the same location in integrase, i.e. behind the DNA binding domain, although there is some overlap with the IN:IN dimer interface to which the ZINC compounds bind. Thus, we have revealed two possible locations in integrase that could potentially be targeted by allosteric integrase inhibitors, that are distinct from the binding sites of other allosteric molecules such as LEDGF inhibitors. Virological and biochemical studies confirmed that HDS1 and FZ41 share a similar activity profile and that both can inhibit each of integrase and reverse transcriptase activities. The inhibitory mechanism of HDS1 for HIV integrase seems to be at the DNA binding step and not at either of the strand transfer or 3' processing steps of the integrase reaction. Furthermore, HDS1 does not directly interact with DNA. The modeling and docking methodology described here will be useful for future screening of integrase inhibitors as well as for the generation of models for the study of integrase drug resistance. PMID:26046987

  3. Similarities in the HIV-1 and ASV Integrease Active Site Upon Metal Binding

    SciTech Connect

    Lins, Roberto D.; Straatsma, TP; Briggs, J. M.

    2000-04-05

    The HIV-1 integrase, which is essential for viral replication, catalyzes the insertion of viral DNA into the host chromosome thereby recruiting host cell machinery into making viral proteins. It represents the third main HIV enzyme target for inhibitor design, the first two being the reverse transcriptase and the protease. We report here a fully hydrated 2 ns molecular dynamics simulation performed using parallel NWChem3.2.1 with the AMBER95 force field. The HIV-1 integrase catalytic domain previously determined by crystallography (1B9D) and modeling including two Mg2+ ions placed into the active site based on an alignment against an ASV integrase structure containing two divalent metals (1VSH), was used as the starting structure. The simulation reveals a high degree of flexibility in the region of residues 140-149 even in the presence of a second divalent metal ion and a dramatic conformational change of the side chain of E152 when the second metal ion is present. This study shows similarities in the behavior of the catalytic residues in the HIV-1 and ASV integrases upon metal binding. The present simulation also provides support to the hypothesis that the second metal ion is likely to be carried into the HIV-1 integrase active site by the substrate, a strand of DNA.

  4. Host proteins interacting with the Moloney murine leukemia virus integrase: Multiple transcriptional regulators and chromatin binding factors

    PubMed Central

    Studamire, Barbara; Goff, Stephen P

    2008-01-01

    Background A critical step for retroviral replication is the stable integration of the provirus into the genome of its host. The viral integrase protein is key in this essential step of the retroviral life cycle. Although the basic mechanism of integration by mammalian retroviruses has been well characterized, the factors determining how viral integration events are targeted to particular regions of the genome or to regions of a particular DNA structure remain poorly defined. Significant questions remain regarding the influence of host proteins on the selection of target sites, on the repair of integration intermediates, and on the efficiency of integration. Results We describe the results of a yeast two-hybrid screen using Moloney murine leukemia virus integrase as bait to screen murine cDNA libraries for host proteins that interact with the integrase. We identified 27 proteins that interacted with different integrase fusion proteins. The identified proteins include chromatin remodeling, DNA repair and transcription factors (13 proteins); translational regulation factors, helicases, splicing factors and other RNA binding proteins (10 proteins); and transporters or miscellaneous factors (4 proteins). We confirmed the interaction of these proteins with integrase by testing them in the context of other yeast strains with GAL4-DNA binding domain-integrase fusions, and by in vitro binding assays between recombinant proteins. Subsequent analyses revealed that a number of the proteins identified as Mo-MLV integrase interactors also interact with HIV-1 integrase both in yeast and in vitro. Conclusion We identify several proteins interacting directly with both MoMLV and HIV-1 integrases that may be common to the integration reaction pathways of both viruses. Many of the proteins identified in the screen are logical interaction partners for integrase, and the validity of a number of the interactions are supported by other studies. In addition, we observe that some of the

  5. von Hippel–Lindau binding protein 1-mediated degradation of integrase affects HIV-1 gene expression at a postintegration step

    PubMed Central

    Mousnier, Aurélie; Kubat, Nicole; Massias-Simon, Aurélie; Ségéral, Emmanuel; Rain, Jean-Christophe; Benarous, Richard; Emiliani, Stéphane; Dargemont, Catherine

    2007-01-01

    HIV-1 integrase, the viral enzyme responsible for provirus integration into the host genome, can be actively degraded by the ubiquitin–proteasome pathway. Here, we identify von Hippel–Lindau binding protein 1(VBP1), a subunit of the prefoldin chaperone, as an integrase cellular binding protein that bridges interaction between integrase and the cullin2 (Cul2)-based von Hippel–Lindau (VHL) ubiquitin ligase. We demonstrate that VBP1 and Cul2/VHL are required for proper HIV-1 expression at a step between integrase-dependent proviral integration into the host genome and transcription of viral genes. Using both an siRNA approach and Cul2/VHL mutant cells, we show that VBP1 and the Cul2/VHL ligase cooperate in the efficient polyubiquitylation of integrase and its subsequent proteasome-mediated degradation. Results presented here support a role for integrase degradation by the prefoldin–VHL–proteasome pathway in the integration–transcription transition of the viral replication cycle. PMID:17698809

  6. LEDGF dominant interference proteins demonstrate prenuclear exposure of HIV-1 integrase and synergize with LEDGF depletion to destroy viral infectivity.

    PubMed

    Meehan, Anne M; Saenz, Dyana T; Morrison, James; Hu, Chunling; Peretz, Mary; Poeschla, Eric M

    2011-04-01

    Target cell overexpression of the integrase binding domain (IBD) of LEDGF/p75 (LEDGF) inhibits HIV-1 replication. The mechanism and protein structure requirements for this dominant interference are unclear. More generally, how and when HIV-1 uncoating occurs postentry is poorly defined, and it is unknown whether integrase within the evolving viral core becomes accessible to cellular proteins prior to nuclear entry. We used LEDGF dominant interference to address the latter question while characterizing determinants of IBD antiviral activity. Fusions of green fluorescent protein (GFP) with multiple C-terminal segments of LEDGF inhibited HIV-1 replication substantially, but minimal chimeras of either polarity (GFP-IBD or IBD-GFP) were most effective. Combining GFP-IBD expression with LEDGF depletion was profoundly antiviral. CD4(+) T cell lines were rendered virtually uninfectable, with single-cycle HIV-1 infectivity reduced 4 logs and high-input (multiplicity of infection = 5.0) replication completely blocked. We restricted GFP-IBD to specific intracellular locations and found that antiviral activity was preserved when the protein was confined to the cytoplasm or directed to the nuclear envelope. The life cycle block triggered by the cytoplasm-restricted protein manifested after nuclear entry, at the level of integration. We conclude that integrase within the viral core becomes accessible to host cell protein interaction in the cytoplasm. LEDGF dominant interference and depletion impair HIV-1 integration at distinct postentry stages. GFP-IBD may trigger premature or improper integrase oligomerization. PMID:21270171

  7. Sequence-specific binding of DNA by the Moloney murine leukemia virus integrase protein.

    PubMed Central

    Krogstad, P A; Champoux, J J

    1990-01-01

    Genetic studies have indicated that integration of retroviral DNA into the host genome depends on the presence of the inverted repeats at the free termini of the long terminal repeats on the unintegrated DNA and on the product of the 3' end of the pol gene (the integrase [IN] protein). While the precise function of the Moloney murine leukemia virus IN protein is uncertain, others have shown that it is a DNA-binding protein and functions in the processing of the inverted repeats prior to integration. By using site-directed mutagenesis, we cloned and expressed the IN protein in Escherichia coli. Crude extracts of total cellular protein were fractionated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, transferred to nitrocellulose filters, denatured in guanidine, renatured, and incubated with oligonucleotide probes. Single- and double-stranded oligonucleotides corresponding to the termini of unintegrated linear viral DNA were specifically bound by the IN protein in this assay. These data suggest that the role of the Moloney IN protein in the early steps of integration involves sequence-specific recognition of the DNA sequences found at the ends of the long terminal repeats. Images PMID:2186176

  8. Formation of a stable complex between the human immunodeficiency virus integrase protein and viral DNA.

    PubMed Central

    Vink, C; Lutzke, R A; Plasterk, R H

    1994-01-01

    The integrase (IN) protein of the human immunodeficiency virus (HIV) mediates two distinct reactions: (i) specific removal of two nucleotides from the 3' ends of the viral DNA and (ii) integration of the viral DNA into target DNA. Although IN discriminates between specific (viral) DNA and nonspecific DNA in physical in vitro assays, a sequence-specific DNA-binding domain could not be identified in the protein. A nonspecific DNA-binding domain, however, was found at the C terminus of the protein. We examined the DNA-binding characteristics of HIV-1 IN, and found that a stable complex of IN and viral DNA is formed in the presence of Mn2+. The IN-viral DNA complex is resistant to challenge by an excess of competitor DNA. Stable binding of IN to the viral DNA requires that the protein contains an intact N-terminal domain and active site (in the central region of the protein), in addition to the C-terminal DNA-binding domain. Images PMID:7937134

  9. B'-protein phosphatase 2A is a functional binding partner of delta-retroviral integrase.

    PubMed

    Maertens, Goedele N

    2016-01-01

    To establish infection, a retrovirus must insert a DNA copy of its RNA genome into host chromatin. This reaction is catalysed by the virally encoded enzyme integrase (IN) and is facilitated by viral genus-specific host factors. Herein, cellular serine/threonine protein phosphatase 2A (PP2A) is identified as a functional IN binding partner exclusive to δ-retroviruses, including human T cell lymphotropic virus type 1 and 2 (HTLV-1 and HTLV-2) and bovine leukaemia virus (BLV). PP2A is a heterotrimer composed of a scaffold, catalytic and one of any of four families of regulatory subunits, and the interaction is specific to the B' family of the regulatory subunits. B'-PP2A and HTLV-1 IN display nuclear co-localization, and the B' subunit stimulates concerted strand transfer activity of δ-retroviral INs in vitro. The protein-protein interaction interface maps to a patch of highly conserved residues on B', which when mutated render B' incapable of binding to and stimulating HTLV-1 and -2 IN strand transfer activity. PMID:26657642

  10. B′-protein phosphatase 2A is a functional binding partner of delta-retroviral integrase

    PubMed Central

    Maertens, Goedele N.

    2016-01-01

    To establish infection, a retrovirus must insert a DNA copy of its RNA genome into host chromatin. This reaction is catalysed by the virally encoded enzyme integrase (IN) and is facilitated by viral genus-specific host factors. Herein, cellular serine/threonine protein phosphatase 2A (PP2A) is identified as a functional IN binding partner exclusive to δ-retroviruses, including human T cell lymphotropic virus type 1 and 2 (HTLV-1 and HTLV-2) and bovine leukaemia virus (BLV). PP2A is a heterotrimer composed of a scaffold, catalytic and one of any of four families of regulatory subunits, and the interaction is specific to the B′ family of the regulatory subunits. B′-PP2A and HTLV-1 IN display nuclear co-localization, and the B′ subunit stimulates concerted strand transfer activity of δ-retroviral INs in vitro. The protein–protein interaction interface maps to a patch of highly conserved residues on B′, which when mutated render B′ incapable of binding to and stimulating HTLV-1 and -2 IN strand transfer activity. PMID:26657642

  11. Identification of the catalytic and DNA-binding region of the human immunodeficiency virus type I integrase protein.

    PubMed

    Vink, C; Oude Groeneger, A M; Plasterk, R H

    1993-03-25

    The integrase (IN) protein of the human immunodeficiency virus (HIV) is required for specific cleavage of the viral DNA termini, and subsequent integration of the viral DNA into target DNA. To identify the various domains of the IN protein we generated a series of IN deletion mutants as fusions to maltose-binding protein (MBP). The deletion mutants were tested for their ability to bind DNA, to mediate site-specific cleavage of the viral DNA ends, and to carry out integration and disintegration reactions. We found that the DNA-binding region resides between amino acids 200 and 270 of the 288-residues HIV-1 IN protein. The catalytic domain of the protein was mapped between amino acids 50 and 194. For the specific activities of IN, cleavage of the viral DNA and integration, both the DNA-binding domain and the conserved amino-terminal region of IN are required. These regions are dispensable however, for disintegration activity. PMID:8464733

  12. Site-specific hydrolysis and alcoholysis of human immunodeficiency virus DNA termini mediated by the viral integrase protein.

    PubMed Central

    Vink, C; Yeheskiely, E; van der Marel, G A; van Boom, J H; Plasterk, R H

    1991-01-01

    Before integration of the human immunodeficiency virus (HIV) DNA, two nucleotides are removed from the 3' ends of the viral DNA by the integrase (IN) protein. We studied the chemistry of this reaction, and found that IN mediates site-specific hydrolysis of a phosphodiester bond, resulting in release of a dinucleotide. A class of alcohols (including glycerol, 1,2-propanediol, but not 1,3-propanediol) can also act as nucleophile in this reaction, and likewise the alcoholic amino acids L-serine and L-threonine can be covalently linked to the dinucleotide. No evidence was found for a covalent linkage between the IN protein and this dinucleotide, suggesting that IN directs a single nucleophilic attack of water at the specific phosphodiester bond. Images PMID:1662361

  13. Bacteriophage φC31 Integrase Mediated Transgenesis in Xenopus laevis for Protein Expression at Endogenous Levels

    NASA Astrophysics Data System (ADS)

    Allen, Bryan G.; Weeks, Daniel L.

    Bacteriophage φC31 inserts its genome into that of its host bacterium via the integrase enzyme which catalyzes recombination between a phage attachment site (attP) and a bacterial attachment site (attB). Integrase requires no accessory factors, has a high efficiency of recombination, and does not need perfect sequence fidelity for recognition and recombination between these attachment sites. These imperfect attachment sites, or pseudo-attachment sites, are present in many organisms and have been used to insert transgenes in a variety of species. Here we describe the φC31 integrase approach to make transgenic Xenopus laevis embryos.

  14. Exploring the binding of d(GGGT)4 to the HIV-1 integrase: An approach to investigate G-quadruplex aptamer/target protein interactions.

    PubMed

    Esposito, Veronica; Pirone, Luciano; Mayol, Luciano; Pedone, Emilia; Virgilio, Antonella; Galeone, Aldo

    2016-08-01

    The aptamer d(GGGT)4 (T30923 or T30695) forms a 5'-5' dimer of two stacked parallel G-quadruplexes, each characterized by three G-tetrads and three single-thymidine reversed-chain loops. This aptamer has been reported to exhibit anti-HIV activity by targeting the HIV integrase, a viral enzyme responsible for the integration of viral DNA into the host-cell genome. However, information concerning the aptamer/target interaction is still rather limited. In this communication we report microscale thermophoresis investigations on the interaction between the HIV-1 integrase and d(GGGT)4 aptamer analogues containing abasic sites singly replacing thymidines in the original sequence. This approach has allowed the identification of which part of the aptamer G-quadruplex structure is mainly involved in the interaction with the protein. PMID:27109379

  15. Dynamic Modulation of HIV-1 Integrase Structure and Function by Cellular Lens Epithelium-derived Growth Factor (LEDGF) Protein*S⃞

    PubMed Central

    McKee, Christopher J.; Kessl, Jacques J.; Shkriabai, Nikolozi; Dar, Mohd Jamal; Engelman, Alan; Kvaratskhelia, Mamuka

    2008-01-01

    The mandatory integration of the reverse-transcribed HIV-1 genome into host chromatin is catalyzed by the viral protein integrase (IN), and IN activity can be regulated by numerous viral and cellular proteins. Among these, LEDGF has been identified as a cellular cofactor critical for effective HIV-1 integration. The x-ray crystal structure of the catalytic core domain (CCD) of IN in complex with the IN binding domain (IBD) of LEDGF has furthermore revealed essential protein-protein contacts. However, mutagenic studies indicated that interactions between the full-length proteins were more extensive than the contacts observed in the co-crystal structure of the isolated domains. Therefore, we have conducted detailed biochemical characterization of the interactions between full-length IN and LEDGF. Our results reveal a highly dynamic nature of IN subunit-subunit interactions. LEDGF strongly stabilized these interactions and promoted IN tetramerization. Mass spectrometric protein footprinting and molecular modeling experiments uncovered novel intra- and inter-protein-protein contacts in the full-length IN-LEDGF complex that lay outside of the observable IBD-CCD structure. In particular, our studies defined the IN tetramer interface important for enzymatic activities and high affinity LEDGF binding. These findings provide new insight into how LEDGF modulates HIV-1 IN structure and function, and highlight the potential for exploiting the highly dynamic structure of multimeric IN as a novel therapeutic target. PMID:18801737

  16. HIV-1 Integrase-DNA Recognition Mechanisms

    PubMed Central

    Kessl, Jacques J.; McKee, Christopher J.; Eidahl, Jocelyn O.; Shkriabai, Nikolozi; Katz, Ari; Kvaratskhelia, Mamuka

    2009-01-01

    Integration of a reverse transcribed DNA copy of the HIV viral genome into the host chromosome is essential for virus replication. This process is catalyzed by the virally encoded protein integrase. The catalytic activities, which involve DNA cutting and joining steps, have been recapitulated in vitro using recombinant integrase and synthetic DNA substrates. Biochemical and biophysical studies of these model reactions have been pivotal in advancing our understanding of mechanistic details for how IN interacts with viral and target DNAs, and are the focus of the present review. PMID:21994566

  17. Staphylococcus aureus SarA is a Regulatory Protein Responsive to Redox and pH that can Support Bacteriophage Lambda Integrase-Mediated Excision/Recombination

    PubMed Central

    Fujimoto, David F.; Higginbotham, Robin H.; Maleki, Soheila J.; Segall1, Anca M.; Smeltzer, Mark S.; Hurlburt, Barry K.

    2010-01-01

    Summary Staphylococcus aureus produces a wide array of virulence factors and causes a correspondingly diverse array of infections. Production of these virulence factors is under the control of a complex network of global regulatory elements, one of which is sarA. sarA encodes a DNA-binding protein that is considered to function as a transcription factor capable of acting as either a repressor or an activator. Using competitive ELISA assays, we demonstrate that SarA is present at approximately 50,000 copies per cell, which is not characteristic of classical transcription factors. We also demonstrate that SarA is present at all stages of growth in vitro and is capable of binding DNA with high affinity but that its binding affinity and pattern of shifted complexes in electrophoretic mobility shift assays is responsive to the redox state. We also show that SarA binds to the bacteriophage lambda (λ) attachment site, attL, producing SarA-DNA complexes similar to intasomes, which consist of bacteriophage lambda integrase, E. coli integration host factor and attL DNA. In addition, SarA stimulates intramolecular excision recombination in the absence of λ excisionase, a DNA-binding accessory protein. Taken together, these data suggest that SarA may function as an architectural accessory protein. PMID:19919677

  18. Structure of the catalytic domain of avian sarcoma virus integrase with a bound HIV-1 integrase-targeted inhibitor

    PubMed Central

    Lubkowski, Jacek; Yang, Fan; Alexandratos, Jerry; Wlodawer, Alexander; Zhao, He; Burke, Terrence R.; Neamati, Nouri; Pommier, Yves; Merkel, George; Skalka, Anna Marie

    1998-01-01

    The x-ray structures of an inhibitor complex of the catalytic core domain of avian sarcoma virus integrase (ASV IN) were solved at 1.9- to 2.0-Å resolution at two pH values, with and without Mn2+ cations. This inhibitor (Y-3), originally identified in a screen for inhibitors of the catalytic activity of HIV type 1 integrase (HIV-1 IN), was found in the present study to be active against ASV IN as well as HIV-1 IN. The Y-3 molecule is located in close proximity to the enzyme active site, interacts with the flexible loop, alters loop conformation, and affects the conformations of active site residues. As crystallized, a Y-3 molecule stacks against its symmetry-related mate. Preincubation of IN with metal cations does not prevent inhibition, and Y-3 binding does not prevent binding of divalent cations to IN. Three compounds chemically related to Y-3 also were investigated, but no binding was observed in the crystals. Our results identify the structural elements of the inhibitor that likely determine its binding properties. PMID:9560188

  19. New applications for phage integrases.

    PubMed

    Fogg, Paul C M; Colloms, Sean; Rosser, Susan; Stark, Marshall; Smith, Margaret C M

    2014-07-29

    Within the last 25 years, bacteriophage integrases have rapidly risen to prominence as genetic tools for a wide range of applications from basic cloning to genome engineering. Serine integrases such as that from ϕC31 and its relatives have found an especially wide range of applications within diverse micro-organisms right through to multi-cellular eukaryotes. Here, we review the mechanisms of the two major families of integrases, the tyrosine and serine integrases, and the advantages and disadvantages of each type as they are applied in genome engineering and synthetic biology. In particular, we focus on the new areas of metabolic pathway construction and optimization, biocomputing, heterologous expression and multiplexed assembly techniques. Integrases are versatile and efficient tools that can be used in conjunction with the various extant molecular biology tools to streamline the synthetic biology production line. PMID:24857859

  20. New Applications for Phage Integrases

    PubMed Central

    Fogg, Paul C.M.; Colloms, Sean; Rosser, Susan; Stark, Marshall; Smith, Margaret C.M.

    2014-01-01

    Within the last 25 years, bacteriophage integrases have rapidly risen to prominence as genetic tools for a wide range of applications from basic cloning to genome engineering. Serine integrases such as that from ϕC31 and its relatives have found an especially wide range of applications within diverse micro-organisms right through to multi-cellular eukaryotes. Here, we review the mechanisms of the two major families of integrases, the tyrosine and serine integrases, and the advantages and disadvantages of each type as they are applied in genome engineering and synthetic biology. In particular, we focus on the new areas of metabolic pathway construction and optimization, biocomputing, heterologous expression and multiplexed assembly techniques. Integrases are versatile and efficient tools that can be used in conjunction with the various extant molecular biology tools to streamline the synthetic biology production line. PMID:24857859

  1. HIV-1 Group O Integrase Displays Lower Enzymatic Efficiency and Higher Susceptibility to Raltegravir than HIV-1 Group M Subtype B Integrase

    PubMed Central

    Depatureaux, Agnès; Quashie, Peter K.; Mesplède, Thibault; Han, Yingshan; Koubi, Hannah; Plantier, Jean-Christophe; Oliveira, Maureen; Moisi, Daniela; Brenner, Bluma

    2014-01-01

    HIV-1 group O (HIV-O) is a rare HIV-1 variant characterized by a high number of polymorphisms, especially in the integrase coding region. As HIV-O integrase enzymes have not previously been studied, our aim was to assess the impact of HIV-O integrase polymorphisms on enzyme function and susceptibility to integrase inhibitors. Accordingly, we cloned and purified integrase proteins from each of HIV-1 group O clades A and B, an HIV-O divergent strain, and HIV-1 group M (HIV-M, subtype B), used as a reference. To assess enzymatic function of HIV-O integrase, we carried out strand transfer and 3′ processing assays with various concentrations of substrate (DNA target and long terminal repeats [LTR], respectively) and characterized these enzymes for susceptibility to integrase strand transfer inhibitors (INSTIs) in cell-free assays and in tissue culture, in the absence or presence of various concentrations of several INSTIs. The inhibition constant (Ki) and 50% effective concentration (EC50) values were calculated for HIV-O integrases and HIV-O viruses, respectively, and compared with those of HIV-M. The results showed that HIV-O integrase displayed lower activity in strand transfer assays than did HIV-M enzyme, whereas 3′ processing activities were similar to those of HIV-M. HIV-O integrases were more susceptible to raltegravir (RAL) in competitive inhibition assays and in tissue culture than were HIV-M enzymes and viruses, respectively. Molecular modeling suggests that two key polymorphic residues that are close to the integrase catalytic site, 74I and 153A, may play a role in these differences. PMID:25224008

  2. The casposon-encoded Cas1 protein from Aciduliprofundum boonei is a DNA integrase that generates target site duplications.

    PubMed

    Hickman, Alison B; Dyda, Fred

    2015-12-15

    Many archaea and bacteria have an adaptive immune system known as CRISPR which allows them to recognize and destroy foreign nucleic acid that they have previously encountered. Two CRISPR-associated proteins, Cas1 and Cas2, are required for the acquisition step of adaptation, in which fragments of foreign DNA are incorporated into the host CRISPR locus. Cas1 genes have also been found scattered in several archaeal and bacterial genomes, unassociated with CRISPR loci or other cas proteins. Rather, they are flanked by nearly identical inverted repeats and enclosed within direct repeats, suggesting that these genetic regions might be mobile elements ('casposons'). To investigate this possibility, we have characterized the in vitro activities of the putative Cas1 transposase ('casposase') from Aciduliprofundum boonei. The purified Cas1 casposase can integrate both short oligonucleotides with inverted repeat sequences and a 2.8 kb excised mini-casposon into target DNA. Casposon integration occurs without target specificity and generates 14-15 basepair target site duplications, consistent with those found in casposon host genomes. Thus, Cas1 casposases carry out similar biochemical reactions as the CRISPR Cas1-Cas2 complex but with opposite substrate specificities: casposases integrate specific sequences into random target sites, whereas CRISPR Cas1-Cas2 integrates essentially random sequences into a specific site in the CRISPR locus. PMID:26573596

  3. The casposon-encoded Cas1 protein from Aciduliprofundum boonei is a DNA integrase that generates target site duplications

    PubMed Central

    Hickman, Alison B.; Dyda, Fred

    2015-01-01

    Many archaea and bacteria have an adaptive immune system known as CRISPR which allows them to recognize and destroy foreign nucleic acid that they have previously encountered. Two CRISPR-associated proteins, Cas1 and Cas2, are required for the acquisition step of adaptation, in which fragments of foreign DNA are incorporated into the host CRISPR locus. Cas1 genes have also been found scattered in several archaeal and bacterial genomes, unassociated with CRISPR loci or other cas proteins. Rather, they are flanked by nearly identical inverted repeats and enclosed within direct repeats, suggesting that these genetic regions might be mobile elements (‘casposons’). To investigate this possibility, we have characterized the in vitro activities of the putative Cas1 transposase (‘casposase’) from Aciduliprofundum boonei. The purified Cas1 casposase can integrate both short oligonucleotides with inverted repeat sequences and a 2.8 kb excised mini-casposon into target DNA. Casposon integration occurs without target specificity and generates 14–15 basepair target site duplications, consistent with those found in casposon host genomes. Thus, Cas1 casposases carry out similar biochemical reactions as the CRISPR Cas1-Cas2 complex but with opposite substrate specificities: casposases integrate specific sequences into random target sites, whereas CRISPR Cas1-Cas2 integrates essentially random sequences into a specific site in the CRISPR locus. PMID:26573596

  4. Multifunctional facets of retrovirus integrase

    PubMed Central

    Grandgenett, Duane P; Pandey, Krishan K; Bera, Sibes; Aihara, Hideki

    2015-01-01

    The retrovirus integrase (IN) is responsible for integration of the reverse transcribed linear cDNA into the host DNA genome. First, IN cleaves a dinucleotide from the 3’ OH blunt ends of the viral DNA exposing the highly conserved CA sequence in the recessed ends. IN utilizes the 3’ OH ends to catalyze the concerted integration of the two ends into opposite strands of the cellular DNA producing 4 to 6 bp staggered insertions, depending on the retrovirus species. The staggered ends are repaired by host cell machinery that results in a permanent copy of the viral DNA in the cellular genome. Besides integration, IN performs other functions in the replication cycle of several studied retroviruses. The proper organization of IN within the viral internal core is essential for the correct maturation of the virus. IN plays a major role in reverse transcription by interacting directly with the reverse transcriptase and by binding to the viral capsid protein and a cellular protein. Recruitment of several other host proteins into the viral particle are also promoted by IN. IN assists with the nuclear transport of the preintegration complex across the nuclear membrane. With several retroviruses, IN specifically interacts with different host protein factors that guide the preintegration complex to preferentially integrate the viral genome into specific regions of the host chromosomal target. Human gene therapy using retrovirus vectors is directly affected by the interactions of IN with these host factors. Inhibitors directed against the human immunodeficiency virus (HIV) IN bind within the active site of IN containing viral DNA ends thus preventing integration and subsequent HIV/AIDS. PMID:26322168

  5. Multifunctional facets of retrovirus integrase.

    PubMed

    Grandgenett, Duane P; Pandey, Krishan K; Bera, Sibes; Aihara, Hideki

    2015-08-26

    The retrovirus integrase (IN) is responsible for integration of the reverse transcribed linear cDNA into the host DNA genome. First, IN cleaves a dinucleotide from the 3' OH blunt ends of the viral DNA exposing the highly conserved CA sequence in the recessed ends. IN utilizes the 3' OH ends to catalyze the concerted integration of the two ends into opposite strands of the cellular DNA producing 4 to 6 bp staggered insertions, depending on the retrovirus species. The staggered ends are repaired by host cell machinery that results in a permanent copy of the viral DNA in the cellular genome. Besides integration, IN performs other functions in the replication cycle of several studied retroviruses. The proper organization of IN within the viral internal core is essential for the correct maturation of the virus. IN plays a major role in reverse transcription by interacting directly with the reverse transcriptase and by binding to the viral capsid protein and a cellular protein. Recruitment of several other host proteins into the viral particle are also promoted by IN. IN assists with the nuclear transport of the preintegration complex across the nuclear membrane. With several retroviruses, IN specifically interacts with different host protein factors that guide the preintegration complex to preferentially integrate the viral genome into specific regions of the host chromosomal target. Human gene therapy using retrovirus vectors is directly affected by the interactions of IN with these host factors. Inhibitors directed against the human immunodeficiency virus (HIV) IN bind within the active site of IN containing viral DNA ends thus preventing integration and subsequent HIV/AIDS. PMID:26322168

  6. RETROVIRAL INTEGRASE: THEN AND NOW

    PubMed Central

    Andrake, Mark D.; Skalka, Anna Marie

    2016-01-01

    The retroviral integrases are virally encoded, specialized recombinases that catalyze the insertion of viral DNA into the host cell’s DNA, a process that is essential for virus propagation. We have learned a great deal since the existence of an integrated form of retroviral DNA (the provirus) was first proposed by Howard Temin in 1964. Initial studies focused on the genetics and biochemistry of avian and murine virus DNA integration, but the pace of discovery increased substantially with advances in technology, and an influx of investigators focused on the human immunodeficiency virus (HIV). We begin with a brief account of the scientific landscape in which some of the earliest discoveries were made, and summarize research that led to our current understanding of the biochemistry of integration. A more detailed account of recent analyses of integrase structure follows, as they have provided valuable insights into enzyme function and raised important new questions. PMID:26958915

  7. Expression of an active form of recombinant Ty1 reverse transcriptase in Escherichia coli: a fusion protein containing the C-terminal region of the Ty1 integrase linked to the reverse transcriptase-RNase H domain exhibits polymerase and RNase H activities.

    PubMed Central

    Wilhelm, M; Boutabout, M; Wilhelm, F X

    2000-01-01

    Replication of the Saccharomyces cerevisiae Ty1 retrotransposon requires a reverse transcriptase capable of synthesizing Ty1 DNA. The first description of an active form of a recombinant Ty1 enzyme with polymerase and RNase H activities is reported here. The Ty1 enzyme was expressed as a hexahistidine-tagged fusion protein in Escherichia coli to facilitate purification of the recombinant protein by metal-chelate chromatography. Catalytic activity of the recombinant protein was detected only when amino acid residues encoded by the integrase gene were added to the N-terminus of the reverse transcriptase-RNase H domain. This suggests that the integrase domain could play a role in proper folding of reverse transcriptase. Several biochemical properties of the Ty1 enzyme were analysed, including the effect of MgCl(2), NaCl, temperature and of the chain terminator dideoxy GTP on its polymerase activity. RNase H activity was examined by monitoring the cleavage of a RNA-DNA template-primer. Our results suggest that the distance between the RNase H and polymerase active sites corresponds to the length of a 14-nucleotide RNA-DNA heteroduplex. The recombinant protein produced in E. coli should be useful for further biochemical and structural analyses and for a better understanding of the role of integrase in the activation of reverse transcriptase. PMID:10816427

  8. Developing a Dynamic Pharmacophore Model for HIV-1 Integrase

    SciTech Connect

    Carlson, Heather A.; Masukawa, Keven M.; Rubins, Kathleen; Bushman, Frederic; Jorgensen, William L.; Lins, Roberto; Briggs, James; Mccammon, Andy

    2000-05-11

    We present the first receptor-based pharmacophore model for HIV-1 integrase. The development of ''dynamic'' pharmacophore models is a new method that accounts for the inherent flexibility of the active site and aims to reduce the entropic penalties associated with binding a ligand. Furthermore, this new drug discovery method overcomes the limitation of an incomplete crystal structure of the target protein. A molecular dynamics (MD) simulation describes the flexibility of the uncomplexed protein. Many conformational models of the protein are saved from the MD simulations and used in a series of multi-unit search for interacting conformers (MUSIC) simulations. MUSIC is a multiple-copy minimization method, available in the BOSS program; it is used to determine binding regions for probe molecules containing functional groups that complement the active site. All protein conformations from the MD are overlaid, and conserved binding regions for the probe molecules are identified. Those conserved binding regions define the dynamic pharmacophore model. Here, the dynamic model is compared to known inhibitors of the integrase as well as a three-point, ligand-based pharmacophore model from the literature. Also, a ''static'' pharmacophore model was determined in the standard fashion, using a single crystal structure. Inhibitors thought to bind in the active site of HIV-1 integrase fit the dynamic model but not the static model. Finally, we have identified a set of compounds from the Available Chemicals Directory that fit the dynamic pharmacophore model, and experimental testing of the compounds has confirmed several new inhibitors.

  9. Developing a dynamic pharmacophore model for HIV-1 integrase.

    PubMed

    Carlson, H A; Masukawa, K M; Rubins, K; Bushman, F D; Jorgensen, W L; Lins, R D; Briggs, J M; McCammon, J A

    2000-06-01

    We present the first receptor-based pharmacophore model for HIV-1 integrase. The development of "dynamic" pharmacophore models is a new method that accounts for the inherent flexibility of the active site and aims to reduce the entropic penalties associated with binding a ligand. Furthermore, this new drug discovery method overcomes the limitation of an incomplete crystal structure of the target protein. A molecular dynamics (MD) simulation describes the flexibility of the uncomplexed protein. Many conformational models of the protein are saved from the MD simulations and used in a series of multi-unit search for interacting conformers (MUSIC) simulations. MUSIC is a multiple-copy minimization method, available in the BOSS program; it is used to determine binding regions for probe molecules containing functional groups that complement the active site. All protein conformations from the MD are overlaid, and conserved binding regions for the probe molecules are identified. Those conserved binding regions define the dynamic pharmacophore model. Here, the dynamic model is compared to known inhibitors of the integrase as well as a three-point, ligand-based pharmacophore model from the literature. Also, a "static" pharmacophore model was determined in the standard fashion, using a single crystal structure. Inhibitors thought to bind in the active site of HIV-1 integrase fit the dynamic model but not the static model. Finally, we have identified a set of compounds from the Available Chemicals Directory that fit the dynamic pharmacophore model, and experimental testing of the compounds has confirmed several new inhibitors. PMID:10841789

  10. Biochemical and virological analysis of the 18-residue C-terminal tail of HIV-1 integrase

    PubMed Central

    Dar, Mohd J; Monel, Blandine; Krishnan, Lavanya; Shun, Ming-Chieh; Di Nunzio, Francesca; Helland, Dag E; Engelman, Alan

    2009-01-01

    Background The 18 residue tail abutting the SH3 fold that comprises the heart of the C-terminal domain is the only part of HIV-1 integrase yet to be visualized by structural biology. To ascertain the role of the tail region in integrase function and HIV-1 replication, a set of deletion mutants that successively lacked three amino acids was constructed and analyzed in a variety of biochemical and virus infection assays. HIV-1/2 chimers, which harbored the analogous 23-mer HIV-2 tail in place of the HIV-1 sequence, were also studied. Because integrase mutations can affect steps in the replication cycle other than integration, defective mutant viruses were tested for integrase protein content and reverse transcription in addition to integration. The F185K core domain mutation, which increases integrase protein solubility, was furthermore analyzed in a subset of mutants. Results Purified proteins were assessed for in vitro levels of 3' processing and DNA strand transfer activities whereas HIV-1 infectivity was measured using luciferase reporter viruses. Deletions lacking up to 9 amino acids (1-285, 1-282, and 1-279) displayed near wild-type activities in vitro and during infection. Further deletion yielded two viruses, HIV-11-276 and HIV-11-273, that displayed approximately two and 5-fold infectivity defects, respectively, due to reduced integrase function. Deletion mutant HIV-11-270 and the HIV-1/2 chimera were non-infectious and displayed approximately 3 to 4-fold reverse transcription in addition to severe integration defects. Removal of four additional residues, which encompassed the C-terminal β strand of the SH3 fold, further compromised integrase incorporation into virions and reverse transcription. Conclusion HIV-11-270, HIV-11-266, and the HIV-1/2 chimera were typed as class II mutant viruses due to their pleiotropic replication defects. We speculate that residues 271-273 might play a role in mediating the known integrase-reverse transcriptase interaction, as

  11. Molecular Dynamics Studies on the HIV-1 Integrase Catalytic Domain

    SciTech Connect

    Lins, Roberto D.; Briggs, J. M.; Straatsma, TP; Carlson, Heather A.; Greenwald, Jason; Choe, Senyon; Mccammon, Andy

    1999-06-30

    The HIV-1 integrase, which is essential for viral replication, catalyzes the insertion of viral DNA into the host chromosome, thereby recruiting host cell machinery into making viral proteins. It represents the third main HIV enzyme target for inhibitor design, the first two being the reverse transcriptase and the protease. Two 1-ns molecular dynamics simulations have been carried out on completely hydrated models of the HIV-1 integrase catalytic domain, one with no metal ions and another with one magnesium ion in the catalytic site. The simulations predict that the region of the active site that is missing in the published crystal structures has (at the time of this work) more secondary structure than previously thought. The flexibility of this region has been discussed with respect to the mechanistic function of the enzyme. The results of these simulations will be used as part of inhibitor design projects directed against the catalytic domain of the enzyme.

  12. Identification of Residues in the C-terminal Domain of HIV-1 Integrase That Mediate Binding to the Transportin-SR2 Protein*

    PubMed Central

    De Houwer, Stephanie; Demeulemeester, Jonas; Thys, Wannes; Taltynov, Oliver; Zmajkovicova, Katarina; Christ, Frauke; Debyser, Zeger

    2012-01-01

    Transportin-SR2 (TRN-SR2 and TNPO3) is a cellular cofactor of HIV replication that has been implicated in the nuclear import of HIV. TRN-SR2 was originally identified in a yeast two-hybrid screen as an interaction partner of HIV integrase (IN) and in two independent siRNA screens as a cofactor of viral replication. We have now studied the interaction of TRN-SR2 and HIV IN in molecular detail and identified the TRN-SR2 interacting regions of IN. A weak interaction with the catalytic core domain (CCD) and a strong interaction with the C-terminal domain (CTD) of IN were detected. By dissecting the catalytic core domain (CCD) of IN into short structural fragments, we identified a peptide (INIP1, amino acids 170EHLKTAVQMAVFIHNFKRKGGI191) retaining the ability to interact with TRN-SR2. By dissecting the C-terminal domain (CTD) of IN, we could identify two interacting peptides (amino acids 214QKQITKIQNFRVYYR228 and 262RRKVKIIRDYGK273) that come together in the CTD tertiary structure to form an exposed antiparallel β-sheet. Through site-specific mutagenesis, we defined the following sets of amino acids in IN as important for the interaction with TRN-SR2: Phe-185/Lys-186/Arg-187/Lys-188 in the CCD and Arg-262/Arg-263/Lys-264 and Lys-266/Arg-269 in the CTD. An HIV-1 strain carrying K266A/R269A in IN was replication-defective due to a block in reverse transcription, confounding the study of nuclear import. Insight into the IN/TRN-SR2 interaction interface is necessary to guide drug discovery efforts targeting the nuclear entry step of replication. PMID:22872638

  13. Correlation of Recombinant Integrase Activity and Functional Preintegration Complex Formation during Acute Infection by Replication-Defective Integrase Mutant Human Immunodeficiency Virus

    PubMed Central

    Li, Xiang; Koh, Yasuhiro

    2012-01-01

    Previous studies characterized two types of replication-defective human immunodeficiency virus type 1 (HIV-1) integrase mutants: class I, which are specifically blocked at the integration step, and class II, which harbor additional virion production and/or reverse transcription defects. Class I mutant enzymes supported little if any metal ion-dependent 3′-processing and DNA strand transfer activities in vitro, whereas class II enzymes displayed partial or full catalytic function in studies with simplified assay designs, suggesting that defective interaction(s) with heterologous integrase binding proteins might underlie the class II mutant viral phenotype. To address this hypothesis, class I and II mutant enzymes were interrogated under expanded sets of in vitro conditions. The majority failed to catalyze the concerted integration of two viral DNA ends into target DNA, highlighting defective integrase function as the root cause of most class II in addition to all class I mutant virus infection defects. One mutant protein, K264E, in contrast, could support the wild-type level of concerted integration activity. After accounting for its inherent reverse transcription defect, HIV-1K264E moreover formed preintegration complexes that supported the efficient integration of endogenous viral DNA in vitro and normal levels and sequences of 2-long terminal repeat-containing circle junctions during acute infection. K264E integrase furthermore efficiently interacted in vitro with two heterologous binding partners, LEDGF/p75 and reverse transcriptase. Our results underscore the physiological relevance of concerted integration assays for tests of integrase mutant function and suggest that the K264E mutation disrupts an interaction with an intranuclear integrase binding partner that is important for HIV-1 integration. PMID:22278243

  14. Uneven Genetic Robustness of HIV-1 Integrase

    PubMed Central

    Rihn, Suzannah J.; Hughes, Joseph; Wilson, Sam J.

    2014-01-01

    ABSTRACT Genetic robustness (tolerance of mutation) may be a naturally selected property in some viruses, because it should enhance adaptability. Robustness should be especially beneficial to viruses like HIV-1 that exhibit high mutation rates and exist in immunologically hostile environments. Surprisingly, however, the HIV-1 capsid protein (CA) exhibits extreme fragility. To determine whether fragility is a general property of HIV-1 proteins, we created a large library of random, single-amino-acid mutants in HIV-1 integrase (IN), covering >40% of amino acid positions. Despite similar degrees of sequence variation in naturally occurring IN and CA sequences, we found that HIV-1 IN was significantly more robust than CA, with random nonsilent IN mutations only half as likely to cause lethal defects. Interestingly, IN and CA were similar in that a subset of mutations with high in vitro fitness were rare in natural populations. IN mutations of this type were more likely to occur in the buried interior of the modeled HIV-1 intasome, suggesting that even very subtle fitness effects suppress variation in natural HIV-1 populations. Lethal mutations, in particular those that perturbed particle production, proteolytic processing, and particle-associated IN levels, were strikingly localized at specific IN subunit interfaces. This observation strongly suggests that binding interactions between particular IN subunits regulate proteolysis during HIV-1 virion morphogenesis. Overall, use of the IN mutant library in conjunction with structural models demonstrates the overall robustness of IN and highlights particular regions of vulnerability that may be targeted in therapeutic interventions. IMPORTANCE The HIV-1 integrase (IN) protein is responsible for the integration of the viral genome into the host cell chromosome. To measure the capacity of IN to maintain function in the face of mutation, and to probe structure/function relationships, we created a library of random single

  15. Reversion of a human immunodeficiency virus type 1 integrase mutant at a second site restores enzyme function and virus infectivity.

    PubMed Central

    Taddeo, B; Carlini, F; Verani, P; Engelman, A

    1996-01-01

    The integration of a DNA copy of the retroviral RNA genome into the host cell genome is essential for viral replication. The virion-associated integrase protein, encoded by the 3' end of the viral pol gene, is required for integration. Stable virus-producing T-cell lines were established for replication-defective human immunodeficiency virus type 1 carrying single amino acid substitutions at conserved residues in the catalytic domain of integrase. Phenotypically reverted virus was detected 12 weeks after transfection with the integrase mutant carrying the P-109-->S mutation (P109S). Unlike the defective P109S virus, the revertant virus (designated P109SR) grew in CD4+ SupT1 cells. In addition to the Ser substitution at Pro-109, P109SR had a second substitution of Ala for Thr at position 125 in integrase. Site-directed mutagenesis was used to show that the P109S T125A genotype was responsible for the P109SR replication phenotype. The T125A substitution also rescued the in vitro enzyme activities of recombinant P109S integrase protein. P109S integrase did not display detectable 3' processing or DNA strand transfer activity, although 5 to 10% of wild-type disintegration activity was detected. P109S T125A integrase displayed nearly wild-type levels of 3' processing, DNA strand transfer, and disintegration activities, confirming that T125A is a second-site intragenic suppressor of P109S. P109S integrase ran as a large aggregate on a size exclusion column, whereas wild-type integrase ran as a monomer and P109S T125A integrase ran as a mixed population. Pro-109 and Thr-125 are not immediately adjacent in the crystal structure of the integrase catalytic domain. We suggest that the T125A substitution restores integrase function by stabilizing a structural alteration(s) induced by the P109S mutation. PMID:8970947

  16. Prevalence of SOS-mediated control of integron integrase expression as an adaptive trait of chromosomal and mobile integrons

    PubMed Central

    2011-01-01

    Background Integrons are found in hundreds of environmental bacterial species, but are mainly known as the agents responsible for the capture and spread of antibiotic-resistance determinants between Gram-negative pathogens. The SOS response is a regulatory network under control of the repressor protein LexA targeted at addressing DNA damage, thus promoting genetic variation in times of stress. We recently reported a direct link between the SOS response and the expression of integron integrases in Vibrio cholerae and a plasmid-borne class 1 mobile integron. SOS regulation enhances cassette swapping and capture in stressful conditions, while freezing the integron in steady environments. We conducted a systematic study of available integron integrase promoter sequences to analyze the extent of this relationship across the Bacteria domain. Results Our results showed that LexA controls the expression of a large fraction of integron integrases by binding to Escherichia coli-like LexA binding sites. In addition, the results provide experimental validation of LexA control of the integrase gene for another Vibrio chromosomal integron and for a multiresistance plasmid harboring two integrons. There was a significant correlation between lack of LexA control and predicted inactivation of integrase genes, even though experimental evidence also indicates that LexA regulation may be lost to enhance expression of integron cassettes. Conclusions Ancestral-state reconstruction on an integron integrase phylogeny led us to conclude that the ancestral integron was already regulated by LexA. The data also indicated that SOS regulation has been actively preserved in mobile integrons and large chromosomal integrons, suggesting that unregulated integrase activity is selected against. Nonetheless, additional adaptations have probably arisen to cope with unregulated integrase activity. Identifying them may be fundamental in deciphering the uneven distribution of integrons in the Bacteria

  17. Characterization of the bacteriophage lambda excisionase (Xis) protein: the C-terminus is required for Xis-integrase cooperativity but not for DNA binding.

    PubMed Central

    Numrych, T E; Gumport, R I; Gardner, J F

    1992-01-01

    We have performed a mutational analysis of the xis gene of bacteriophage lambda. The Xis protein is 72 amino acids in length and required for excisive recombination. Twenty-six mutants of Xis were isolated that were impaired or deficient in lambda excision. Mutant proteins that contained amino acid substitutions in the N-terminal 49 amino acids of Xis were defective in excisive recombination and were unable to bind DNA. In contrast, one mutant protein containing a leucine to proline substitution at position 60 and two truncated proteins containing either the N-terminal 53 or 64 amino acids continued to bind lambda DNA, interact cooperatively with FIS and promote excision. However, these three mutants were unable to bind DNA cooperatively with Int. Cooperativity between wild-type Xis and Int required the presence of FIS, but not the Int core-type binding sites. This study shows that Xis has at least two functional domains and also demonstrates the importance of the cooperativity in DNA binding of FIS, Xis and Int in lambda excision. Images PMID:1396573

  18. Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein-ligand binding challenge.

    PubMed

    Perryman, Alexander L; Santiago, Daniel N; Forli, Stefano; Santos-Martins, Diogo; Olson, Arthur J

    2014-04-01

    To rigorously assess the tools and protocols that can be used to understand and predict macromolecular recognition, and to gain more structural insight into three newly discovered allosteric binding sites on a critical drug target involved in the treatment of HIV infections, the Olson and Levy labs collaborated on the SAMPL4 challenge. This computational blind challenge involved predicting protein-ligand binding against the three allosteric sites of HIV integrase (IN), a viral enzyme for which two drugs (that target the active site) have been approved by the FDA. Positive control cross-docking experiments were utilized to select 13 receptor models out of an initial ensemble of 41 different crystal structures of HIV IN. These 13 models of the targets were selected using our new "Rank Difference Ratio" metric. The first stage of SAMPL4 involved using virtual screens to identify 62 active, allosteric IN inhibitors out of a set of 321 compounds. The second stage involved predicting the binding site(s) and crystallographic binding mode(s) for 57 of these inhibitors. Our team submitted four entries for the first stage that utilized: (1) AutoDock Vina (AD Vina) plus visual inspection; (2) a new common pharmacophore engine; (3) BEDAM replica exchange free energy simulations, and a Consensus approach that combined the predictions of all three strategies. Even with the SAMPL4's very challenging compound library that displayed a significantly lower amount of structural diversity than most libraries that are conventionally employed in prospective virtual screens, these approaches produced hit rates of 24, 25, 34, and 27 %, respectively, on a set with 19 % declared binders. Our only entry for the second stage challenge was based on the results of AD Vina plus visual inspection, and it ranked third place overall according to several different metrics provided by the SAMPL4 organizers. The successful results displayed by these approaches highlight the utility of the computational

  19. The mechanism of ϕC31 integrase directionality: experimental analysis and computational modelling

    PubMed Central

    Pokhilko, Alexandra; Zhao, Jia; Ebenhöh, Oliver; Smith, Margaret C. M.; Stark, W. Marshall; Colloms, Sean D.

    2016-01-01

    Serine integrases, DNA site-specific recombinases used by bacteriophages for integration and excision of their DNA to and from their host genomes, are increasingly being used as tools for programmed rearrangements of DNA molecules for biotechnology and synthetic biology. A useful feature of serine integrases is the simple regulation and unidirectionality of their reactions. Recombination between the phage attP and host attB sites is promoted by the serine integrase alone, giving recombinant attL and attR sites, whereas the ‘reverse’ reaction (between attL and attR) requires an additional protein, the recombination directionality factor (RDF). Here, we present new experimental data on the kinetics and regulation of recombination reactions mediated by ϕC31 integrase and its RDF, and use these data as the basis for a mathematical model of the reactions. The model accounts for the unidirectionality of the attP × attB and attL × attR reactions by hypothesizing the formation of structurally distinct, kinetically stable integrase–DNA product complexes, dependent on the presence or absence of RDF. The model accounts for all the available experimental data, and predicts how mutations of the proteins or alterations of reaction conditions might increase the conversion efficiency of recombination. PMID:27387286

  20. Minimal size of prototype foamy virus integrase for nuclear localization.

    PubMed

    Hyun, U; Lee, D H; Shin, C G

    2011-01-01

    We have reported previously that the prototype foamy virus (PFV) integrase (IN) has a strong nuclear localization signal (NLS) in its C-terminal domain, in particular in a region of aa 306-334 including highly karyophilic arginines or lysines at positions 308, 313, 318, 324, and 329. In this study, we used various mutants of the C-terminal domain to further analyze its karyophilic determinants. Plasmids expressing these mutants fused to maltose binding protein (MBP) and enhanced green fluorescent protein (EGFP) were transfected to COS-1 cells and subcellular localization of these fluorescent fusion proteins was determined by fluorescent microscopy. The results revealed that a maximum karyophilicity was exhibited by a region longer than the previously described one of 29 aa (aa 306-334), in particular by a 64 aa region (aa 289-352) with Arg341 and Lys349 as critical determinants. PMID:21692567

  1. Consensus HIV-1 subtype A integrase and its raltegravir-resistant variants: design and characterization of the enzymatic properties.

    PubMed

    Shadrina, Olga; Krotova, Olga; Agapkina, Julia; Knyazhanskaya, Ekaterina; Korolev, Sergey; Starodubova, Elizaveta; Viklund, Alecia; Lukashov, Vladimir; Magnani, Mauro; Medstrand, Patrik; Karpov, Vadim; Gottikh, Marina; Isaguliants, Maria

    2014-07-01

    Model studies of the subtype B and non-subtype B integrases are still required to compare their susceptibility to antiretroviral drugs, evaluate the significance of resistance mutations and identify the impact of natural polymorphisms on the level of enzymatic reactivity. We have therefore designed the consensus integrase of the HIV-1 subtype A strain circulating in the former Soviet Union territory (FSU-A) and two of its variants with mutations of resistance to the strand transfer inhibitor raltegravir. Their genes were synthesized, and expressed in E coli; corresponding His-tagged proteins were purified using the affinity chromatography. The enzymatic properties of the consensus integrases and their sensitivity to raltegravir were examined in a series of standard in vitro reactions and compared to the properties of the integrase of HIV-1 subtype B strain HXB2. The consensus enzyme demonstrated similar DNA-binding properties, but was significantly more active than HXB-2 integrase in the reactions of DNA cleavage and integration. All integrases were equally susceptible to inhibition by raltegravir and elvitegravir, indicating that the sporadic polymorphisms inherent to the HXB-2 enzyme have little effect on its susceptibility to drugs. Insensitivity of the mutated enzymes to the inhibitors of strand transfer occurred at a cost of a 30-90% loss of the efficacies of both 3'-processing and strand transfer. This is the first study to describe the enzymatic properties of the consensus integrase of HIV-1 clade A and the effects of the resistance mutations when the complex actions of sporadic sequence polymorphisms are excluded. PMID:24594066

  2. HIV pharmacotherapy: A review of integrase inhibitors.

    PubMed

    Wong, Elaine; Trustman, Nathan; Yalong, April

    2016-02-01

    Integrase strand transfer inhibitors (INSTIs) are a class of antiretroviral agents used to treat HIV. These drugs--raltegravir, elvitegravir, and dolutegravir--are preferred options for treatment-naïve patients when used in combination with two nucleoside reverse transcriptase inhibitors. Based on clinical trials, INSTIs have been proven to be effective with minimal safety concerns. This article reviews the pharmacologic profile, role in therapy, and safety and efficacy of each agent. PMID:26818644

  3. Enhancement of As(V) adsorption onto activated sludge by methylation treatment.

    PubMed

    Kang, So-Young; Kim, Dong-Wook; Kim, Kyoung-Woong

    2007-08-01

    Biosorption properties of arsenate [As(V)] onto activated sludge were investigated in batch systems. The adsorption of As(V) onto sludge increased from 23 to 266 microg/g dry weight through the methylation of the activated sludge. This increase resulted from neutralization of carboxylic groups via the methylation process. The pH effect of As(V) uptake was also investigated and As(V) adsorption by methylated sludge decreased significantly at high pH (pH > 11) due to competition between As(V) and OH(-) ions for binding sites distributed on sludge surfaces. In contrast, low pH favored As(V) adsorption by methylated sludge because of the elevated quantities of positively charged functional groups. The results suggest that methylated activated sludge may provide promising applications for the simultaneous removal and separation of As(V) from aqueous effluents. PMID:17505894

  4. Catalytically-active complex of HIV-1 integrase with a viral DNA substrate binds anti-integrase drugs.

    PubMed

    Alian, Akram; Griner, Sarah L; Chiang, Vicki; Tsiang, Manuel; Jones, Gregg; Birkus, Gabriel; Geleziunas, Romas; Leavitt, Andrew D; Stroud, Robert M

    2009-05-19

    HIV-1 integration into the host cell genome is a multistep process catalyzed by the virally-encoded integrase (IN) protein. In view of the difficulty of obtaining a stable DNA-bound IN at high concentration as required for structure determination, we selected IN-DNA complexes that form disulfide linkages between 5'-thiolated DNA and several single mutations to cysteine around the catalytic site of IN. Mild reducing conditions allowed for selection of the most thermodynamically-stable disulfide-linked species. The most stable complexes induce tetramer formation of IN, as happens during the physiological integration reaction, and are able to catalyze the strand transfer step of retroviral integration. One of these complexes also binds strand-transfer inhibitors of HIV antiviral drugs, making it uniquely valuable among the mutants of this set for understanding portions of the integration reaction. This novel complex may help define substrate interactions and delineate the mechanism of action of known integration inhibitors. PMID:19416821

  5. IntI2 Integron Integrase in Tn7

    PubMed Central

    Hansson, Karin; Sundström, Lars; Pelletier, Alex; Roy, Paul H.

    2002-01-01

    Integrons can insert and excise antibiotic resistance genes on plasmids in bacteria by site-specific recombination. Class 1 integrons code for an integrase, IntI1 (337 amino acids in length), and are generally borne on elements derived from Tn5090, such as that found in the central part of Tn21. A second class of integron is found on transposon Tn7 and its relatives. We have completed the sequence of the Tn7 integrase gene, intI2, which contains an internal stop codon. This codon was found to be conserved among intI2 genes on three other Tn7-like transposons harboring different cassettes. The predicted peptide sequence (IntI2*) is 325 amino acids long and is 46% identical to IntI1. In order to detect recombination activity, the internal stop codon at position 179 in the parental allele was changed to a triplet coding for glutamic acid. The sequences flanking the cassette arrays in the class 1 and 2 integrons are not closely related, but a common pool of mobile cassettes is used by the different integron classes; two of the three antibiotic resistance cassettes on Tn7 and its close relatives are also found in various class 1 integrons. We also observed a fourth excisable cassette downstream of those described previously in Tn7. The fourth cassette encodes a 165-amino-acid protein of unknown function with 6.5 contiguous repeats of a sequence coding for 7 amino acids. IntI2*179E promoted site-specific excision of each of the cassettes in Tn7 at different frequencies. The integrases from Tn21 and Tn7 showed limited cross-specificity in that IntI1 could excise all cassettes from both Tn21 and Tn7. However, we did not observe a corresponding excision of the aadA1 cassette from Tn21 by IntI2*179E. PMID:11872723

  6. Brujita Integrase: A Simple, Arm-Less, Directionless, and Promiscuous Tyrosine Integrase System.

    PubMed

    Lunt, Bryce L; Hatfull, Graham F

    2016-06-01

    Mycobacteriophage Brujita is an unusual temperate phage in which establishment of superinfection immunity is dependent on chromosomal integration. Integration is mediated by a non-canonical tyrosine integrase (Int) lacking an N-terminal domain typically associated with binding to arm-type sites within the phage attachment site (attP). This raises the question as to how these Ints bind their DNA substrates, if they form higher-order protein DNA complexes, and how site selection and recombinational directionality are determined. Here we show that Brujita Int is a simple recombinase, whose properties more closely resemble those of FLP and Cre than it does the canonical phage Ints. Brujita Int uses relatively small DNA substrates, fails to discriminate between attP and attB, cleaves attachment site DNA to form a 6-base overlap region, and lacks directional control. Brujita Int also has an unusual pattern of binding to its DNA substrates. It binds to two half sites (B and B') at attB, although binding to the B half site is strongly dependent on occupancy of B'. In contrast, binding to the P half site is not observed, even when Int is bound at P'. However, an additional Int binding site (P1) is displaced to the left of the crossover site at attP, is required for recombination and is predicted to facilitate binding of Int to the P half site during synapsis. These simple phage Int systems may reflect ancestral states of phage evolution with the complexities of higher-order complex formation and directional control representing subsequent adaptations. PMID:27113630

  7. Tight Regulation of the intS Gene of the KplE1 Prophage: A New Paradigm for Integrase Gene Regulation

    PubMed Central

    Panis, Gaël; Duverger, Yohann; Courvoisier-Dezord, Elise; Champ, Stéphanie; Talla, Emmanuel; Ansaldi, Mireille

    2010-01-01

    Temperate phages have the ability to maintain their genome in their host, a process called lysogeny. For most, passive replication of the phage genome relies on integration into the host's chromosome and becoming a prophage. Prophages remain silent in the absence of stress and replicate passively within their host genome. However, when stressful conditions occur, a prophage excises itself and resumes the viral cycle. Integration and excision of phage genomes are mediated by regulated site-specific recombination catalyzed by tyrosine and serine recombinases. In the KplE1 prophage, site-specific recombination is mediated by the IntS integrase and the TorI recombination directionality factor (RDF). We previously described a sub-family of temperate phages that is characterized by an unusual organization of the recombination module. Consequently, the attL recombination region overlaps with the integrase promoter, and the integrase and RDF genes do not share a common activated promoter upon lytic induction as in the lambda prophage. In this study, we show that the intS gene is tightly regulated by its own product as well as by the TorI RDF protein. In silico analysis revealed that overlap of the attL region with the integrase promoter is widely encountered in prophages present in prokaryotic genomes, suggesting a general occurrence of negatively autoregulated integrase genes. The prediction that these integrase genes are negatively autoregulated was biologically assessed by studying the regulation of several integrase genes from two different Escherichia coli strains. Our results suggest that the majority of tRNA-associated integrase genes in prokaryotic genomes could be autoregulated and that this might be correlated with the recombination efficiency as in KplE1. The consequences of this unprecedented regulation for excisive recombination are discussed. PMID:20949106

  8. Tight regulation of the intS gene of the KplE1 prophage: a new paradigm for integrase gene regulation.

    PubMed

    Panis, Gaël; Duverger, Yohann; Courvoisier-Dezord, Elise; Champ, Stéphanie; Talla, Emmanuel; Ansaldi, Mireille

    2010-10-01

    Temperate phages have the ability to maintain their genome in their host, a process called lysogeny. For most, passive replication of the phage genome relies on integration into the host's chromosome and becoming a prophage. Prophages remain silent in the absence of stress and replicate passively within their host genome. However, when stressful conditions occur, a prophage excises itself and resumes the viral cycle. Integration and excision of phage genomes are mediated by regulated site-specific recombination catalyzed by tyrosine and serine recombinases. In the KplE1 prophage, site-specific recombination is mediated by the IntS integrase and the TorI recombination directionality factor (RDF). We previously described a sub-family of temperate phages that is characterized by an unusual organization of the recombination module. Consequently, the attL recombination region overlaps with the integrase promoter, and the integrase and RDF genes do not share a common activated promoter upon lytic induction as in the lambda prophage. In this study, we show that the intS gene is tightly regulated by its own product as well as by the TorI RDF protein. In silico analysis revealed that overlap of the attL region with the integrase promoter is widely encountered in prophages present in prokaryotic genomes, suggesting a general occurrence of negatively autoregulated integrase genes. The prediction that these integrase genes are negatively autoregulated was biologically assessed by studying the regulation of several integrase genes from two different Escherichia coli strains. Our results suggest that the majority of tRNA-associated integrase genes in prokaryotic genomes could be autoregulated and that this might be correlated with the recombination efficiency as in KplE1. The consequences of this unprecedented regulation for excessive recombination are discussed. PMID:20949106

  9. The Competitive Interplay between Allosteric HIV-1 Integrase Inhibitor BI/D and LEDGF/p75 during the Early Stage of HIV-1 Replication Adversely Affects Inhibitor Potency.

    PubMed

    Feng, Lei; Dharmarajan, Venkatasubramanian; Serrao, Erik; Hoyte, Ashley; Larue, Ross C; Slaughter, Alison; Sharma, Amit; Plumb, Matthew R; Kessl, Jacques J; Fuchs, James R; Bushman, Frederic D; Engelman, Alan N; Griffin, Patrick R; Kvaratskhelia, Mamuka

    2016-05-20

    Allosteric HIV-1 integrase inhibitors (ALLINIs) have recently emerged as a promising class of antiretroviral agents and are currently in clinical trials. In infected cells, ALLINIs potently inhibit viral replication by impairing virus particle maturation but surprisingly exhibit a reduced EC50 for inhibiting HIV-1 integration in target cells. To better understand the reduced antiviral activity of ALLINIs during the early stage of HIV-1 replication, we investigated the competitive interplay between a potent representative ALLINI, BI/D, and LEDGF/p75 with HIV-1 integrase. While the principal binding sites of BI/D and LEDGF/p75 overlap at the integrase catalytic core domain dimer interface, we show that the inhibitor and the cellular cofactor induce markedly different multimerization patterns of full-length integrase. LEDGF/p75 stabilizes an integrase tetramer through the additional interactions with the integrase N-terminal domain, whereas BI/D induces protein-protein interactions in C-terminal segments that lead to aberrant, higher-order integrase multimerization. We demonstrate that LEDGF/p75 binds HIV-1 integrase with significantly higher affinity than BI/D and that the cellular protein is able to reverse the inhibitor induced aberrant, higher-order integrase multimerization in a dose-dependent manner in vitro. Consistent with these observations, alterations of the cellular levels of LEDGF/p75 markedly affected BI/D EC50 values during the early steps of HIV-1 replication. Furthermore, genome-wide sequencing of HIV-1 integration sites in infected cells demonstrate that LEDGF/p75-dependent integration site selection is adversely affected by BI/D treatment. Taken together, our studies elucidate structural and mechanistic details of the interplay between LEDGF/p75 and BI/D during the early stage of HIV-1 replication. PMID:26910179

  10. Comparison of Newly Assembled Full Length HIV-1 Integrase With Prototype Foamy Virus Integrase: Structure-Function Prospective

    PubMed Central

    Dayer, Mohammad Reza

    2016-01-01

    Background Drug design against human immunodeficiency virus type 1 (HIV-1) integrase through its mechanistic study is of great interest in the area in biological research. The main obstacle in this area is the absence of the full-length crystal structure for HIV-1 integrase to be used as a model. A complete structure, similar to HIV-1 of a prototype foamy virus integrase in complex with DNA, including all conservative residues, is available and has been extensively used in recent investigations. Objectives The aim of this study was to determine whether the above model is precisely representative of HIV-1 integrase. This would critically determine the success of any designed drug using the model in deactivation of integrase and AIDS treatment. Materials and Methods Primarily, a new structure for HIV-1 was constructed, using a crystal structure of prototype foamy virus as the starting structure. The constructed structure of HIV-1 integrase was simultaneously simulated with a prototype foamy virus integrase on a separate occasion. Results Our results indicate that the HIV-1 system behaves differently from the prototype foamy virus in terms of folding, hydration, hydrophobicity of binding site and stability. Conclusions Based on our findings, we can conclude that HIV-1 integrase is vastly different from the prototype foamy virus integrase and does not resemble it, and the modeling output of the prototype foamy virus simulations could not be simply generalized to HIV-1 integrase. Therefore, our HIV-1 model seems to be more representative and more useful for future research. PMID:27540450

  11. The hunt for HIV-1 integrase inhibitors.

    PubMed

    Lataillade, Max; Kozal, Michael J

    2006-07-01

    Currently, there are three distinct mechanistic classes of antiretrovirals: inhibitors of the HIV- 1 reverse transcriptase and protease enzymes and inhibitors of HIV entry, including receptor and coreceptor binding and cell fusion. A new drug class that inhibits the HIV-1 integrase enzyme (IN) is in development and may soon be available in the clinic. IN is an attractive drug target because it is essential for a stable and productive HIV-1 infection and there is no mammalian homologue of IN. Inhibitors of integrase enzyme (INI) block the integration of viral double-stranded DNA into the host cell's chromosomal DNA. HIV-1 integration has many potential steps that can be inhibited and several new compounds that target specific integration steps have been identified by drug developers. Recently, two INIs, GS-9137 and MK-0518, demonstrated promising early clinical trial results and have been advanced into later stage trials. In this review, we describe how IN facilitates HIV-1 integration, the needed enzyme cofactors, and the resultant byproducts created during integration. Furthermore, we review the different INIs under development, their mechanism of actions, site of IN inhibition, potency, resistance patterns, and discuss the early clinical trial results. PMID:16839248

  12. Outer domains of integrase within retroviral intasomes are dispensible for catalysis of DNA integration.

    PubMed

    Li, Min; Lin, Shiqiang; Craigie, Robert

    2016-02-01

    Retroviral DNA integration is mediated by nucleoprotein complexes (intasomes) comprising a pair of viral DNA ends synapsed by a tetramer of integrase. Current integrase inhibitors act on intasomes rather than free integrase protein. Structural and functional studies of intasomes are essential to understand their mechanism of action and how the virus can escape by mutation. To date, prototype foamy virus (PFV) is the only retrovirus for which high-resolution structures of intasomes have been determined. In the PFV intasome structure, only the core domains of the outer subunits are ordered; the N-terminal domain, C-terminal domain, and N-terminal extension domain are disordered. Are these "missing domains" required for function or are they dispensable? We have devised a strategy to assemble "hetero-intasomes" in which the outer domains are not present as a tool to assess the functional role of the missing domains for catalysis of integration. We find that the disordered domains of outer subunits are not required for intasome assembly or catalytic activity as catalytic core domains can substitute for the outer subunits in the case of both PFV and HIV-1 intasomes. PMID:26537415

  13. HIV type 1 integrase inhibitors: from basic research to clinical implications.

    PubMed

    Jegede, Oyebisi; Babu, John; Di Santo, Roberto; McColl, Damian J; Weber, Jan; Quiñones-Mateu, Miguel

    2008-01-01

    Similar to other retroviruses, productive infection with HIV-1 requires three key steps in the viral replication: (i) reverse transcription of viral genomic RNA into viral cDNA by the viral reverse transcriptase; (ii) integration of viral cDNA into host cell genome using the viral integrase; and (iii) cleavage of newly synthesized viral polypeptide by the viral protease into individual viral proteins during new virion assembly. Following their discovery, all three viral enzymes were considered as targets for antiretroviral drugs. However, while multiple reverse transcriptase and protease inhibitors have been used for more than 12 years to treat HIV-infected individuals, only recently has the viral integrase enzyme emerged as an alternative, clinically validated target to block HIV-1 replication. Here we review the biology of HIV-1 integration, the mechanisms of action and development of resistance to integrase inhibitors, and the latest data on the most recent clinical trials involving this promising, novel class of antiretroviral drugs. PMID:18820719

  14. Novel Bifunctional Quinolonyl Diketo Acid Derivatives as HIV-1 Integrase Inhibitors: Design, Synthesis, Biological Activities and Mechanism of Action

    PubMed Central

    Di Santo, Roberto; Costi, Roberta; Roux, Alessandra; Artico, Marino; Lavecchia, Antonio; Marinelli, Luciana; Novellino, Ettore; Palmisano, Lucia; Andreotti, Mauro; Amici, Roberta; Galluzzo, Clementina Maria; Nencioni, Lucia; Palamara, Anna Teresa; Pommier, Yves; Marchand, Christophe

    2008-01-01

    The virally encoded integrase protein is an essential enzyme in the life cycle of the HIV-1 virus and represents an attractive and validated target in the development of therapeutics against HIV infection. Drugs that selectively inhibit this enzyme, when used in combination with inhibitors of reverse transcriptase and protease, are believed to be highly effective in suppressing the viral replication. Among the HIV-1 integrase inhibitors, the β-diketo acids (DKAs) represent a major lead for anti-HIV-1drug development. In this study, novel bifunctional quinolonyl diketo acid derivatives were designed, synthesized and tested for their inhibitory ability against HIV-1 integrase. The compounds are potent inhibitors of integrase activity. Particularly, derivative 8 is a potent IN inhibitor for both steps of the reaction (3′-processing and strand transfer) and exhibits both high antiviral activity against HIV-1 infected cells and low cytotoxicity. Molecular modeling studies provide a plausible mechanism of action, which is consistent with ligand SARs and enzyme photo-crosslinking experiments. PMID:16539381

  15. Pyridoxine hydroxamic acids as novel HIV-integrase inhibitors.

    PubMed

    Stranix, Brent R; Wu, Jinzi J; Milot, Guy; Beaulieu, Françis; Bouchard, Jean-Emanuel; Gouveia, Kristine; Forte, André; Garde, Seema; Wang, Zhigang; Mouscadet, Jean-François; Delelis, Olivier; Xiao, Yong

    2016-02-15

    A series of pyridoxine hydroxamic acid analog bearing a 5-aryl-spacers were synthesized. Evaluation of these novel HIV integrase complex inhibitors revealed compounds with high potency against wild-type HIV virus. PMID:26826732

  16. Identification of cellular factors binding to acetylated HIV-1 integrase.

    PubMed

    Allouch, Awatef; Cereseto, Anna

    2011-11-01

    The viral protein integrase (IN) catalyzes the integration of the HIV-1 cDNA into the host cellular genome. We have recently demonstrated that IN is acetylated by a cellular histone acetyltransferase, p300, which modifies three lysines located in the C-terminus of the viral factor (Cereseto et al. in EMBO J 24:3070-3081, 2005). This modification enhances IN catalytic activity, as demonstrated by in vitro assays. Consistently, mutations introduced in the targeted lysines greatly decrease the efficiency of HIV-1 integration. Acetylation was proven to regulate protein functions by modulating protein-protein interactions. HIV-1 to efficiently complete its replication steps, including the integration reaction, requires interacting with numerous cellular factors. Therefore, we sought to investigate whether acetylation might modulate the interaction between IN and the cellular factors. To this aim we performed a yeast two-hybrid screening that differs from the screenings so far performed (Rain et al. in Methods 47:291-297, 2009; Studamire and Goff in Retrovirology 5:48, 2008) for using as bait IN constitutively acetylated. From this analysis we have identified thirteen cellular factors involved in transcription, chromatin remodeling, nuclear transport, RNA binding, protein synthesis regulation and microtubule organization. To validate these interactions, binding assays were performed showing that acetylation increases the affinity of IN with specific factors. Nevertheless, few two-hybrid hits bind with the same affinity the acetylated and the unmodified IN. These results further underlie the relevance of IN post-translational modification by acetylation in HIV-1 replication cycle. PMID:20016921

  17. Cryo-EM reveals a novel octameric integrase structure for betaretroviral intasome function.

    PubMed

    Ballandras-Colas, Allison; Brown, Monica; Cook, Nicola J; Dewdney, Tamaria G; Demeler, Borries; Cherepanov, Peter; Lyumkis, Dmitry; Engelman, Alan N

    2016-02-18

    Retroviral integrase catalyses the integration of viral DNA into host target DNA, which is an essential step in the life cycle of all retroviruses. Previous structural characterization of integrase-viral DNA complexes, or intasomes, from the spumavirus prototype foamy virus revealed a functional integrase tetramer, and it is generally believed that intasomes derived from other retroviral genera use tetrameric integrase. However, the intasomes of orthoretroviruses, which include all known pathogenic species, have not been characterized structurally. Here, using single-particle cryo-electron microscopy and X-ray crystallography, we determine an unexpected octameric integrase architecture for the intasome of the betaretrovirus mouse mammary tumour virus. The structure is composed of two core integrase dimers, which interact with the viral DNA ends and structurally mimic the integrase tetramer of prototype foamy virus, and two flanking integrase dimers that engage the core structure via their integrase carboxy-terminal domains. Contrary to the belief that tetrameric integrase components are sufficient to catalyse integration, the flanking integrase dimers were necessary for mouse mammary tumour virus integrase activity. The integrase octamer solves a conundrum for betaretroviruses as well as alpharetroviruses by providing critical carboxy-terminal domains to the intasome core that cannot be provided in cis because of evolutionarily restrictive catalytic core domain-carboxy-terminal domain linker regions. The octameric architecture of the intasome of mouse mammary tumour virus provides new insight into the structural basis of retroviral DNA integration. PMID:26887496

  18. Crystal structure of the HIV-1 integrase core domain in complex with sucrose reveals details of an allosteric inhibitory binding site

    SciTech Connect

    Wielens, Jerome; Headey, Stephen J.; Jeevarajah, Dharshini; Rhodes, David I.; Deadman, John; Chalmers, David K.; Scanlon, Martin J.; Parker, Michael W.

    2010-04-19

    HIV integrase (IN) is an essential enzyme in HIV replication and an important target for drug design. IN has been shown to interact with a number of cellular and viral proteins during the integration process. Disruption of these important interactions could provide a mechanism for allosteric inhibition of IN. We present the highest resolution crystal structure of the IN core domain to date. We also present a crystal structure of the IN core domain in complex with sucrose which is bound at the dimer interface in a region that has previously been reported to bind integrase inhibitors.

  19. Investigation on the sucrose binding pocket of HIV-1 Integrase by molecular dynamics and synergy experiments.

    PubMed

    Tintori, Cristina; Esposito, Francesca; Morreale, Francesca; Martini, Riccardo; Tramontano, Enzo; Botta, Maurizio

    2015-08-01

    Enzymes whose catalytic activity depends on multimeric assembly are targets for inhibitors that perturb the interactions between the protein subunits such as the HIV-1 Integrase (IN). Sucrose has been recently crystallized in complex with IN revealing an allosteric binding pocket at the monomer-monomer interface. Herein, molecular dynamics were applied to theoretically test the effect of this small ligand on IN. As a result, such a compound increases the mutual free energy of binding between the two interacting monomers. Biological experiments confirmed the computational forecast. PMID:26048795

  20. Catalytically-active complex of HIV-1 integrase with a viral DNA substrate binds anti-integrase drugs

    PubMed Central

    Alian, Akram; Griner, Sarah L.; Chiang, Vicki; Tsiang, Manuel; Jones, Gregg; Birkus, Gabriel; Geleziunas, Romas; Leavitt, Andrew D.; Stroud, Robert M.

    2009-01-01

    HIV-1 integration into the host cell genome is a multistep process catalyzed by the virally-encoded integrase (IN) protein. In view of the difficulty of obtaining a stable DNA-bound IN at high concentration as required for structure determination, we selected IN–DNA complexes that form disulfide linkages between 5′-thiolated DNA and several single mutations to cysteine around the catalytic site of IN. Mild reducing conditions allowed for selection of the most thermodynamically-stable disulfide-linked species. The most stable complexes induce tetramer formation of IN, as happens during the physiological integration reaction, and are able to catalyze the strand transfer step of retroviral integration. One of these complexes also binds strand-transfer inhibitors of HIV antiviral drugs, making it uniquely valuable among the mutants of this set for understanding portions of the integration reaction. This novel complex may help define substrate interactions and delineate the mechanism of action of known integration inhibitors. PMID:19416821

  1. Allosteric Inhibition of Human Immunodeficiency Virus Integrase

    PubMed Central

    Gupta, Kushol; Brady, Troy; Dyer, Benjamin M.; Malani, Nirav; Hwang, Young; Male, Frances; Nolte, Robert T.; Wang, Liping; Velthuisen, Emile; Jeffrey, Jerry; Van Duyne, Gregory D.; Bushman, Frederic D.

    2014-01-01

    HIV-1 replication in the presence of antiviral agents results in evolution of drug-resistant variants, motivating the search for additional drug classes. Here we report studies of GSK1264, which was identified as a compound that disrupts the interaction between HIV-1 integrase (IN) and the cellular factor lens epithelium-derived growth factor (LEDGF)/p75. GSK1264 displayed potent antiviral activity and was found to bind at the site occupied by LEDGF/p75 on IN by x-ray crystallography. Assays of HIV replication in the presence of GSK1264 showed only modest inhibition of the early infection steps and little effect on integration targeting, which is guided by the LEDGF/p75·IN interaction. In contrast, inhibition of late replication steps was more potent. Particle production was normal, but particles showed reduced infectivity. GSK1264 promoted aggregation of IN and preformed LEDGF/p75·IN complexes, suggesting a mechanism of inhibition. LEDGF/p75 was not displaced from IN during aggregation, indicating trapping of LEDGF/p75 in aggregates. Aggregation assays with truncated IN variants revealed that a construct with catalytic and C-terminal domains of IN only formed an open polymer associated with efficient drug-induced aggregation. These data suggest that the allosteric inhibitors of IN are promising antiviral agents and provide new information on their mechanism of action. PMID:24904063

  2. Rapid Optimization of Engineered Metabolic Pathways with Serine Integrase Recombinational Assembly (SIRA).

    PubMed

    Merrick, C A; Wardrope, C; Paget, J E; Colloms, S D; Rosser, S J

    2016-01-01

    Metabolic pathway engineering in microbial hosts for heterologous biosynthesis of commodity compounds and fine chemicals offers a cheaper, greener, and more reliable method of production than does chemical synthesis. However, engineering metabolic pathways within a microbe is a complicated process: levels of gene expression, protein stability, enzyme activity, and metabolic flux must be balanced for high productivity without compromising host cell viability. A major rate-limiting step in engineering microbes for optimum biosynthesis of a target compound is DNA assembly, as current methods can be cumbersome and costly. Serine integrase recombinational assembly (SIRA) is a rapid DNA assembly method that utilizes serine integrases, and is particularly applicable to rapid optimization of engineered metabolic pathways. Using six pairs of orthogonal attP and attB sites with different central dinucleotide sequences that follow SIRA design principles, we have demonstrated that ΦC31 integrase can be used to (1) insert a single piece of DNA into a substrate plasmid; (2) assemble three, four, and five DNA parts encoding the enzymes for functional metabolic pathways in a one-pot reaction; (3) generate combinatorial libraries of metabolic pathway constructs with varied ribosome binding site strengths or gene orders in a one-pot reaction; and (4) replace and add DNA parts within a construct through targeted postassembly modification. We explain the mechanism of SIRA and the principles behind designing a SIRA reaction. We also provide protocols for making SIRA reaction components and practical methods for applying SIRA to rapid optimization of metabolic pathways. PMID:27417934

  3. Human immunodeficiency virus type 1 integrase: effect on viral replication of mutations at highly conserved residues.

    PubMed

    Cannon, P M; Wilson, W; Byles, E; Kingsman, S M; Kingsman, A J

    1994-08-01

    Sequence comparisons of the integrase (IN) proteins from different retroviruses have identified several highly conserved residues. We have introduced mutations at 16 of these sites into the integrase gene of human immunodeficiency virus type 1 and analyzed the phenotypes of the resulting viruses. The viruses were all normal for p24 content and reverse transcriptase activity. In addition, all of the mutants could infect T-cell lines and undergo reverse transcription, as assessed by PCR analysis. Most of the mutant viruses also had normal Western blot (immunoblot) profiles, although three of the mutations resulted in reduced signals for IN relative to the wild type on the immunoblots and mutation of residue W235 completely abolished recognition of the protein by pooled sera from human immunodeficiency virus type 1-positive patients. Mutations that have previously been shown to abolish activity in in vitro studies produced noninfectious viruses. The substitution of W235 was notable in producing a noninfectious virus, despite previous reports of this residue being nonessential for IN activity in vitro (A.D. Leavitt, L. Shiue, and H.E. Varmus, J. Biol. Chem. 268:2113-2119, 1993). In addition, we have identified four highly conserved residues that can be mutated without any affect on viral replication in T-cell lines. PMID:8035478

  4. HIV-1 Integrase Strand Transfer Inhibitors with Reduced Susceptibility to Drug Resistant Mutant Integrases.

    PubMed

    Zhao, Xue Zhi; Smith, Steven J; Maskell, Daniel P; Metifiot, Mathieu; Pye, Valerie E; Fesen, Katherine; Marchand, Christophe; Pommier, Yves; Cherepanov, Peter; Hughes, Stephen H; Burke, Terrence R

    2016-04-15

    HIV integrase (IN) strand transfer inhibitors (INSTIs) are among the newest anti-AIDS drugs; however, mutant forms of IN can confer resistance. We developed noncytotoxic naphthyridine-containing INSTIs that retain low nanomolar IC50 values against HIV-1 variants harboring all of the major INSTI-resistant mutations. We found by analyzing crystal structures of inhibitors bound to the IN from the prototype foamy virus (PFV) that the most successful inhibitors show striking mimicry of the bound viral DNA prior to 3'-processing and the bound host DNA prior to strand transfer. Using this concept of "bi-substrate mimicry," we developed a new broadly effective inhibitor that not only mimics aspects of both the bound target and viral DNA but also more completely fills the space they would normally occupy. Maximizing shape complementarity and recapitulating structural components encompassing both of the IN DNA substrates could serve as a guiding principle for the development of new INSTIs. PMID:26808478

  5. The role of lysine 186 in HIV-1 integrase multimerization

    SciTech Connect

    Berthoux, Lionel; Sebastian, Sarah; Muesing, Mark A.; Luban, Jeremy . E-mail: luban@irb.unisi.ch

    2007-07-20

    HIV-1 integrase (IN) catalyzes biochemical reactions required for viral cDNA insertion into host cell chromosomal DNA, an essential step in the HIV-1 replication cycle. In one of these reactions, the two ends of the linear viral cDNA are believed to be simultaneously ligated to chromosomal DNA by a tetrameric form of IN. The structure of the full-length IN tetramer is not known but a model consisting of the N-terminal domain and the catalytic core revealed basic residues 186 to 188 at the interface between the two IN dimers. We found that alteration of these residues, in particular changing IN lysine residue 186 to glutamate (K186Q), impairs IN oligomerization in the yeast two-hybrid system and decreases oligomeric forms of IN within virions. When expressed independently of other viral proteins in human cells, IN-K186Q did not concentrate in the nucleus as did wild-type IN. Co-expression of wild-type IN restored the multimerization defects of IN-K186Q, in both the two-hybrid system and in virions, and also rescued the nuclear targeting defects. Virions bearing IN-K186Q were not infectious in a single cycle of replication but when mixed virions containing two different IN mutants were produced, IN-K186Q was capable of complementing the catalytically inactive mutant IN-D116A. Our biochemical and functional data support the crystallographic model in which IN residue K186 lies at the interface between IN dimers and suggest that tetramerization is important, not only for concerted integration, but also for IN nuclear targeting.

  6. Characterization of the relationship between integrase, excisionase and antirepressor activities associated with a superinfecting Shiga toxin encoding bacteriophage

    PubMed Central

    Fogg, P. C. M.; Rigden, D. J.; Saunders, J. R.; McCarthy, A. J.; Allison, H. E.

    2011-01-01

    Shigatoxigenic Escherichia coli emerged as new food borne pathogens in the early 1980s, primarily driven by the dispersal of Shiga toxin-encoding lambdoid bacteriophages. At least some of these Stx phages display superinfection phenotypes, which differ significantly from lambda phage itself, driving through in situ recombination further phage evolution, increasing host range and potentially increasing the host's pathogenic profile. Here, increasing levels of Stx phage Φ24B integrase expression in multiple lysogen cultures are demonstrated along with apparently negligible repression of integrase expression by the cognate CI repressor. The Φ24B int transcription start site and promoter region were identified and found to differ from in silico predictions. The unidirectional activity of this integrase was determined in an in situ, inducible tri-partite reaction. This indicated that Φ24B must encode a novel directionality factor that is controlling excision events during prophage induction. This excisionase was subsequently identified and characterized through complementation experiments. In addition, the previous proposal that a putative antirepressor was responsible for the lack of immunity to superinfection through inactivation of CI has been revisited and a new hypothesis involving the role of this protein in promoting efficient induction of the Φ24B prophage is proposed. PMID:21062824

  7. The effects of oil on As(V) adsorption on illite, kaolinite, montmorillonite and chlorite

    NASA Astrophysics Data System (ADS)

    Wainipee, Wimolporn; Cuadros, Javier; Sephton, Mark A.; Unsworth, Catherine; Gill, Martin G.; Strekopytov, Stanislav; Weiss, Dominik J.

    2013-11-01

    The effect of oil on As(V) adsorption on clay minerals has been investigated using batch experiments at low and high pH, NaCl concentration and oil contents. Four clay minerals were chosen because of their abundance in sediments and their different crystal chemistry: illite, kaolinite, montmorillonite, and chlorite. The values for pH were 4 and 8 and salt concentrations were 0.001 and 0.7 M NaCl to appreciate the effects of changing salinity, e.g. from fresh water to seawater conditions. For the coating experiments, a well-characterised oil was used to survey the main effects of complex organic mixtures on adsorption and oil to clay mineral (w/w) ratios were 0.0325 and 0.3250. As(V) adsorption increased with increasing NaCl concentration, suggesting that the mechanisms of As(V) adsorption are related to the formation of surface complexes in which Na+ ions act as bridges between the clay surface and the As(V) anions. Cation bridging is also indicated by zeta potential measurements which show that higher NaCl concentrations along with the presence of As(V) can cause the clay particles and adsorbed ions to have a more negative overall charge. Adsorption is lower at higher pH due to the reduced number of positively charged sites on the edge of clay mineral layers. Oil coating reduces As(V) adsorption by decreasing the available surface area of clay minerals, except in the case of oil-coated montmorillonite, where surface area following dispersion in water is increased. The main variables controlling As(V) adsorption are surface area and surface charge density, as confirmed by a simplified quantitative model. These findings advance our ability to predict the effects of complex pollution events in various freshwater and marine settings.

  8. Adsorption, desorption and fractionation of As(V) on untreated and mussel shell-treated granitic material

    NASA Astrophysics Data System (ADS)

    Seco-Reigosa, N.; Cutillas-Barreiro, L.; Nóvoa-Muñoz, J. C.; Arias-Estévez, M.; Álvarez-Rodríguez, E.; Fernández-Sanjurjo, M. J.; Núñez-Delgado, A.

    2015-03-01

    As(V) adsorption and desorption were studied on granitic material, coarse and fine mussel shell and granitic material amended with 12 and 24 t ha-1 fine shell, investigating the effect of different As(V) concentrations and different pH as well as the fractions where the adsorbed As(V) was retained. As(V) adsorption was higher on fine than on coarse shell. Mussel shell amendment increased As(V) adsorption on granitic material. Adsorption data corresponding to the unamended and shell-amended granitic material were satisfactory fitted to the Langmuir and Freundlich models. Desorption was always <19% when the highest As(V) concentration (100 mg L-1) was added. Regarding the effect of pH, the granitic material showed its highest adsorption (66%) at pH <6, and it was lower as pH increased. Fine shell presented notable adsorption in the whole pH range between 6 and 12, with a maximum of 83%. The shell-amended granitic material showed high As(V) adsorption, with a maximum (99%) at pH near 8, but decreased as pH increased. Desorption varying pH was always <26%. In the granitic material, desorption increased progressively when pH increased from 4 to 6, contrary to what happened to mussel shell. Regarding the fractionation of the adsorbed As(V), most of it was in the soluble fraction (weakly bound). The granitic material did not show high As(V) retention capacity, which could facilitate As(V) transfer to water courses and to the food chain in case of As(V) compounds being applied on this material; however, the mussel shell amendment increased As(V) retention, making this practice recommendable.

  9. A novel family of integrases associated with prophages and genomic islands integrated within the tRNA-dihydrouridine synthase A (dusA) gene.

    PubMed

    Farrugia, Daniel N; Elbourne, Liam D H; Mabbutt, Bridget C; Paulsen, Ian T

    2015-05-19

    Genomic islands play a key role in prokaryotic genome plasticity. Genomic islands integrate into chromosomal loci such as transfer RNA genes and protein coding genes, whilst retaining various cargo genes that potentially bestow novel functions on the host organism. A gene encoding a putative integrase was identified at a single site within the 5' end of the dusA gene in the genomes of over 200 bacteria. This integrase was discovered to be a component of numerous genomic islands, which appear to share a target site within the dusA gene. dusA encodes the tRNA-dihydrouridine synthase A enzyme, which catalyses the post-transcriptional reduction of uridine to dihydrouridine in tRNA. Genomic islands encoding homologous dusA-associated integrases were found at a much lower frequency within the related dusB and dusC genes, and non-dus genes. Excision of these dusA-associated islands from the chromosome as circularized intermediates was confirmed by polymerase chain reaction. Analysis of the dusA-associated islands indicated that they were highly diverse, with the integrase gene representing the only universal common feature. PMID:25883135

  10. As(V) adsorption onto nanoporous titania adsorbents (NTAs): effects of solution composition.

    PubMed

    Han, Dong Suk; Batchelor, Bill; Park, Sung Hyuk; Abdel-Wahab, Ahmed

    2012-08-30

    This study has focused on developing two nanoporous titania adsorbents (NTA) to enhance removal efficiency of adsorption process for As(V) by characterizing the effects of pH and phosphate concentration on their sorption capacities and behaviors. One type of adsorbent is a mesoporous titania (MT) solid phase and the other is group of a highly ordered mesoporous silica solids (SBA-15) that can incorporate different levels of reactive titania sorption sites. Microscopic analysis showed that Ti((25))-SBA-15 (Ti/SBA=0.25 g/g) had titania nanostructured mesopores that do not rupture the highly ordered hexagonal silica framework. However, MT has disordered, wormhole-like mesopores that are caused by interparticle porosity. Adsorption experiments showed that Ti((25))-SBA-15 had a greater sorption capacity for As(V) than did Ti((15))-SBA-15 or Ti((35))-SBA-15 and the amount of As(V) adsorbed generally decreased as pH increased. Higher removal of As(V) was observed with Ti((25))-SBA-15 than with MT at pH 4, but MT had higher removals at higher pH (7, 9.5), even though MT has a lower specific surface area. However, in the presence of phosphate, MT showed higher removal of As(V) at low pH rather than did Ti((25))-SBA-15. As expected, the NTAs showed very fast sorption kinetics, but they followed a bi-phasic sorption pattern. PMID:22727482

  11. Theoretical study on the HIV-1 integrase-5CITEP complex based on polarized force fields

    NASA Astrophysics Data System (ADS)

    Wei, Caiyi; Mei, Ye; Zhang, Dawei

    2010-07-01

    Molecular dynamics studies of 5CITEP binding with HIV-1 integrase (IN) are presented using both polarized and nonpolarized force fields. When nonpolarized force field is used, the ligand drifts away from the original binding site. However, this depressing behavior can be curbed by introducing electronic polarization effect into the force field that stabilizes the protein structure and keeps the ligand in the binding pocket. Moreover, simulation under polarized force field gives a binding energy of -4.85 kcal/mol which is in excellent agreement with the experimental Δ G of -4.38 kcal/mol. The results demonstrate the importance of intra-protein electronic polarization in stabilizing the binding complex of IN-5CITEP and accurately predicting the binding energy.

  12. Biological responses of duckweed (Lemna minor L.) exposed to the inorganic arsenic species As(III) and As(V): effects of concentration and duration of exposure.

    PubMed

    Duman, Fatih; Ozturk, Fatma; Aydin, Zeki

    2010-06-01

    The accumulation of arsenic (As) and physiological responses of Lemna minor L. under different concentration (0, 1, 4, 16 and 64 microM) and duration (1, 2, 4 and 6 days) of two species As, NaAsO(2) and Na(2)HAsO(4).7H(2)O, were studied in hydroponics. The accumulation of both As species depended on As concentration and exposure duration. The highest accumulation of As was found as 17408 and 8674 microg g(-1), for plants exposed to 64 microM of As(III) and As(V), respectively, after 6 days. Two-way ANOVA analyses indicated that, for plants exposed to arsenite (As(III)), exposure duration had a greater effect than concentration on As accumulation. Conversely, exposure concentration had a greater effect on As accumulation in plants exposed to arsenate (As(V)). Arsenic exposure levels, approaching 16 microM for As(III) and 64 microM for As(V), did not significantly affect EC values. Beyond these exposure concentrations, EC values increased in a manner that depended on duration. Significant effect of As(III) on lipid peroxidation was observed at 1 microM application whereas, this effect started to be significant after an exposure to 16 microM As(V). For both As(III) and As(V), photosynthetic pigment levels slightly increased for the first day with respect to the control, followed by a gradual decline at higher concentrations and durations. An increase in protein content and enzyme activity was observed at moderate exposure conditions, followed by a decrease. Significant positive correlations were determined between accumulated As and ion leakage and lipid peroxidation. Negative correlations were found between accumulated As and total chlorophyll and protein content. Our results suggested that exposure duration and concentration had a strong synergetic effect on antioxidant enzyme activity. The findings of the present study may be useful when this plant is used as a phytoremediator in arsenic-polluted water. PMID:20221688

  13. Dolutegravir (S/GSK1349572) exhibits significantly slower dissociation than raltegravir and elvitegravir from wild-type and integrase inhibitor-resistant HIV-1 integrase-DNA complexes.

    PubMed

    Hightower, Kendra E; Wang, Ruolan; Deanda, Felix; Johns, Brian A; Weaver, Kurt; Shen, Yingnian; Tomberlin, Ginger H; Carter, H Luke; Broderick, Timothy; Sigethy, Scott; Seki, Takahiro; Kobayashi, Masanori; Underwood, Mark R

    2011-10-01

    The integrase inhibitor (INI) dolutegravir (DTG; S/GSK1349572) has significant activity against HIV-1 isolates with raltegravir (RAL)- and elvitegravir (ELV)-associated resistance mutations. As an initial step in characterizing the different resistance profiles of DTG, RAL, and ELV, we determined the dissociation rates of these INIs with integrase (IN)-DNA complexes containing a broad panel of IN proteins, including IN substitutions corresponding to signature RAL and ELV resistance mutations. DTG dissociates slowly from a wild-type IN-DNA complex at 37°C with an off-rate of 2.7 × 10(-6) s(-1) and a dissociative half-life (t(1/2)) of 71 h, significantly longer than the half-lives for RAL (8.8 h) and ELV (2.7 h). Prolonged binding (t(1/2), at least 5 h) was observed for DTG with IN-DNA complexes containing E92, Y143, Q148, and N155 substitutions. The addition of a second substitution to either Q148 or N155 typically resulted in an increase in the off-rate compared to that with the single substitution. For all of the IN substitutions tested, the off-rate of DTG from IN-DNA complexes was significantly slower (from 5 to 40 times slower) than the off-rate of RAL or ELV. These data are consistent with the potential for DTG to have a higher genetic barrier to resistance, provide evidence that the INI off-rate may be an important component of the mechanism of INI resistance, and suggest that the slow dissociation of DTG may contribute to its distinctive resistance profile. PMID:21807982

  14. Magnetite nanoparticles coated glass wool for As(V) removal from drinking water

    NASA Astrophysics Data System (ADS)

    Kango, Sarita; Kumar, Rajesh

    2015-08-01

    Arsenic (As) removal from contaminated groundwater is a key environmental concern worldwide. In this study, glass wool was coated with magnetite nanoparticles under argon gas flow and magnetite coated glass wool have been investigated for application as an adsorbent for As(V) removal from water. The adsorbent was characterized by using Scanning Electron Microscopy (SEM) and arsenic contaminated water treated with adsorbent was analyzed by Inductively Coupled Plasma Mass Spectroscopy (ICP-MS). The ICP-MS results showed that 10 g/L of adsorbent removed 99.4% of As(V) within 5 hours at pH-7 and initial arsenic concentration of 360µg/L. Adsorption kinetics data fitted well in pseudo-first-order kinetics model with high correlation coefficient (R2 = 0.995). As magnetite nanoparticles coated glass wool showed favorable adsorption behavior for As(V), it can be a promising tool for water purification.

  15. As(V) and P Competitive Sorption on Soils, By-Products and Waste Materials.

    PubMed

    Rivas-Pérez, Ivana María; Paradelo-Núñez, Remigio; Nóvoa-Muñoz, Juan Carlos; Arias-Estévez, Manuel; Fernández-Sanjurjo, María José; Álvarez-Rodríguez, Esperanza; Núñez-Delgado, Avelino

    2015-12-01

    Batch-type experiments were used to study competitive As(V) and P sorption on various soils and sorbent materials. The materials assayed were a forest soil, a vineyard soil, pyritic material, granitic material, coarsely and finely ground mussel shell, calcinated mussel shell ash, pine sawdust and slate processing fines. Competition between As(V) and P was pronounced in the case of both soils, granitic material, slate fines, both shells and pine sawdust, showing more affinity for P. Contrary, the pyritic material and mussel shell ash showed high and similar affinity for As(V) and P. These results could be useful to make a correct use of the soils and materials assayed when focusing on As and P removal in solid or liquid media, in circumstances where both pollutants may compete for sorption sites. PMID:26690456

  16. Magnetite nanoparticles coated glass wool for As(V) removal from drinking water

    SciTech Connect

    Kango, Sarita; Kumar, Rajesh

    2015-08-28

    Arsenic (As) removal from contaminated groundwater is a key environmental concern worldwide. In this study, glass wool was coated with magnetite nanoparticles under argon gas flow and magnetite coated glass wool have been investigated for application as an adsorbent for As(V) removal from water. The adsorbent was characterized by using Scanning Electron Microscopy (SEM) and arsenic contaminated water treated with adsorbent was analyzed by Inductively Coupled Plasma Mass Spectroscopy (ICP-MS). The ICP-MS results showed that 10 g/L of adsorbent removed 99.4% of As(V) within 5 hours at pH-7 and initial arsenic concentration of 360µg/L. Adsorption kinetics data fitted well in pseudo-first-order kinetics model with high correlation coefficient (R{sup 2} = 0.995). As magnetite nanoparticles coated glass wool showed favorable adsorption behavior for As(V), it can be a promising tool for water purification.

  17. Adsorption of As(V) inside the pores of porous hematite in water.

    PubMed

    Dai, Min; Xia, Ling; Song, Shaoxian; Peng, Changsheng; Lopez-Valdivieso, Alejandro

    2016-04-15

    As(V) adsorption inside the pores of porous hematite in water has been studied in this work. This study was performed on nonporous hematite and porous hematite prepared from the thermal decomposition of goethite and siderite through the measurements of adsorption isotherm, SEM-EDX, XRD and BET. The results demonstrated that the As(V) adsorption was difficult to be realized inside pores if they were too small. This observation might be due to that the pore entrances were blocked by the adsorbed ions and thus the inside surfaces became invalid for the adsorption. Only if the pore size is large enough, the effective surface area inside pores would be close to that on non-porous hematite for As(V) adsorption. In addition, it was found that siderite is better than goethite for preparing porous hematite with thermal decomposition as adsorbent for arsenic removal. PMID:26799222

  18. As(V) and P Competitive Sorption on Soils, By-Products and Waste Materials

    PubMed Central

    Rivas-Pérez, Ivana María; Paradelo-Núñez, Remigio; Nóvoa-Muñoz, Juan Carlos; Arias-Estévez, Manuel; Fernández-Sanjurjo, María José; Álvarez-Rodríguez, Esperanza; Núñez-Delgado, Avelino

    2015-01-01

    Batch-type experiments were used to study competitive As(V) and P sorption on various soils and sorbent materials. The materials assayed were a forest soil, a vineyard soil, pyritic material, granitic material, coarsely and finely ground mussel shell, calcinated mussel shell ash, pine sawdust and slate processing fines. Competition between As(V) and P was pronounced in the case of both soils, granitic material, slate fines, both shells and pine sawdust, showing more affinity for P. Contrary, the pyritic material and mussel shell ash showed high and similar affinity for As(V) and P. These results could be useful to make a correct use of the soils and materials assayed when focusing on As and P removal in solid or liquid media, in circumstances where both pollutants may compete for sorption sites. PMID:26690456

  19. Application of Liquid Emulsion Membrane Technique for the Removal of As(V) from Aqueous Solutions

    NASA Astrophysics Data System (ADS)

    Binnal, Prakash; Hiremath, Poornima G.

    2012-08-01

    Liquid emulsion membrane technique was used to remove As(V) from synthetic aqueous solutions. The emulsion was composed of Aliquat 336 as an extractant, commercial kerosene as a diluent and Span 80 (Sorbiton monooleate) as an emulsifying agent. Different types of internal phases were used, namely, sodium hydroxide, sodium carbonate, ammonium bicarbonate, sodium sulphate and sodium chloride. The effect of process parameters affecting extraction efficiency, such as, initial concentration of As(V) in feed solution, pH of feed solution, concentrations of Aliquat 336 and Span 80 in membrane phase, volume ratio of stripping phase to membrane phase, concentration of internal phase, type of internal phase, volume ratio of emulsion to feed, agitation speed during extraction and time of extraction was investigated. The optimum conditions for the extraction were determined. A maximum As(V) removal rate of 97.8 was observed under optimum conditions.

  20. Next-Generation Site-Directed Transgenesis in the Malaria Vector Mosquito Anopheles gambiae: Self-Docking Strains Expressing Germline-Specific phiC31 Integrase

    PubMed Central

    Meredith, Janet M.; Underhill, Ann; McArthur, Clare C.; Eggleston, Paul

    2013-01-01

    Diseases transmitted by mosquitoes have a devastating impact on global health and the situation is complicated due to difficulties with both existing control measures and the impact of climate change. Genetically modified mosquitoes that are refractory to disease transmission are seen as having great potential in the delivery of novel control strategies. The Streptomyces phage phiC31 integrase system has been successfully adapted for site-directed transgene integration in a range of insects, thus overcoming many limitations due to size constraints and random integration associated with transposon-mediated transformation. Using this technology, we previously published the first site-directed transformation of Anopheles gambiae, the principal vector of human malaria. Mosquitoes were initially engineered to incorporate the phiC31 docking site at a defined genomic location. A second phase of genetic modification then achieved site-directed integration of an anti-malarial effector gene. In the current publication we report improved efficiency and utility of the phiC31 integrase system following the generation of Anopheles gambiae self-docking strains. Four independent strains, with docking sites at known locations on three different chromosome arms, were engineered to express integrase under control of the regulatory regions of the nanos gene from Anopheles gambiae. The resulting protein accumulates in the posterior oocyte to provide integrase activity at the site of germline development. Two self-docking strains, exhibiting significantly different levels of integrase expression, were assessed for site-directed transgene integration and found to demonstrate greatly improved survival and efficiency of transformation. In the fight against malaria, it is imperative to establish a broad repertoire of both anti-malarial effector genes and tissue-specific promoters to regulate their expression, enabling those offering maximum effect with minimum fitness cost to be identified

  1. As(V) and As(III) reactions on pristine pyrite and on surface-oxidized pyrite.

    PubMed

    Sun, Fenglong; Dempsey, Brian A; Osseo-Asare, Kwadwo A

    2012-12-15

    Reactions of As(III) and As(V) with pyrite were investigated using pristine pyrite (produced and reacted in a rigorously anoxic environment with P(O2)<10(-8)atm) and using surface-oxidized pyrite (produced under anoxic conditions, exposed to air, then stored and reacted under rigorously anoxic conditions). Results with surface-oxidized pyrite were similar to previously reported arsenic-pyrite results. However As(III) adsorbed over a broader pH range on pristine pyrite than on surface-oxidized pyrite, As(V) adsorbed over a narrower pH range on pristine pyrite than on surface-oxidized pyrite, and adsorbed As(V) on pristine pyrite was reduced to As(III) but adsorbed As(V) was not reduced with surface-oxidized pyrite. Reduction of As(V) with pristine pyrite was first-order in total As(V), Fe(II) was released, and sulfur was oxidized. The proposed mechanism for pyrite oxidation by As(V) was similar to the published mechanism for oxidation by O(2) and rates were compared. The results can be used to predict the removals of As(V) and As(III) on pyrite in continuously anoxic environments or on pyrite in intermittently oxic/anoxic environments. Rigorous cleanup and continuous maintenance of strictly anoxic conditions are required if commercial or produced pyrites are to be used as surrogates for pristine pyrite. PMID:23000211

  2. Solution structure of the DNA binding domain of HIV-1 integrase.

    PubMed

    Lodi, P J; Ernst, J A; Kuszewski, J; Hickman, A B; Engelman, A; Craigie, R; Clore, G M; Gronenborn, A M

    1995-08-01

    The solution structure of the DNA binding domain of HIV-1 integrase (residues 220-270) has been determined by multidimensional NMR spectroscopy. The protein is a dimer in solution, and each subunit is composed of a five-stranded beta-barrel with a topology very similar to that of the SH3 domain. The dimer is formed by a stacked beta-interface comprising strands 2, 3, and 4, with the two triple-stranded antiparallel beta-sheets, one from each subunit, oriented antiparallel to each other. One surface of the dimer, bounded by the loop between strands beta 1 and beta 2, forms a saddle-shaped groove with dimensions of approximately 24 x 23 x 12 A in cross section. Lys264, which has been shown from mutational data to be involved in DNA binding, protrudes from this surface, implicating the saddle-shaped groove as the potential DNA binding site. PMID:7632683

  3. The same site on the integrase-binding domain of lens epithelium–derived growth factor is a therapeutic target for MLL leukemia and HIV

    PubMed Central

    Murai, Marcelo J.; Pollock, Jonathan; He, Shihan; Miao, Hongzhi; Purohit, Trupta; Yokom, Adam; Hess, Jay L.; Muntean, Andrew G.; Grembecka, Jolanta

    2014-01-01

    Lens epithelium-derived growth factor (LEDGF) is a chromatin-associated protein implicated in leukemia and HIV type 1 infection. LEDGF associates with mixed-lineage leukemia (MLL) fusion proteins and menin and is required for leukemic transformation. To better understand the molecular mechanism underlying the LEDGF integrase-binding domain (IBD) interaction with MLL fusion proteins in leukemia, we determined the solution structure of the MLL-IBD complex. We found a novel MLL motif, integrase domain binding motif 2 (IBM2), which binds to a well-defined site on IBD. Point mutations within IBM2 abolished leukemogenic transformation by MLL-AF9, validating that this newly identified motif is essential for the oncogenic activity of MLL fusion proteins. Interestingly, the IBM2 binding site on IBD overlaps with the binding site for the HIV integrase (IN), and IN was capable of efficiently sequestering IBD from the menin-MLL complex. A short IBM2 peptide binds to IBD directly and inhibits both the IBD-MLL/menin and IBD-IN interactions. Our findings show that the same site on IBD is involved in binding to MLL and HIV-IN, revealing an attractive approach to simultaneously target LEDGF in leukemia and HIV. PMID:25305204

  4. HIV-1 Integrase Strand Transfer Inhibitors Stabilize an Integrase-Single Blunt-Ended DNA Complex

    PubMed Central

    Bera, Sibes; Pandey, Krishan K.; Vora, Ajaykumar C.; Grandgenett, Duane P.

    2011-01-01

    Summary Integration of HIV (human immunodeficiency virus) cDNA ends by integrase (IN) into host chromosomes involves a concerted integration mechanism. IN juxtaposes two DNA blunt-ends to form the synaptic complex (SC) which is the intermediate in the concerted integration pathway. SC is inactivated by strand transfer inhibitors (STI) with IC50 values of ~20 nM for inhibition of concerted integration. We detected a new nucleoprotein complex on native agarose that was produced in the presence of STI >200 nM, termed IN-single DNA (ISD) complex. Two IN dimers appear to bind in a parallel fashion at the DNA terminus producing a ~32 bp DNaseI protective footprint. In the presence of Raltegravir, MK-2048 and L-841,411, IN incorporated ~20 to 25% of the input blunt-ended DNA substrate into the stabilized ISD complex. Seven other STI also produced the ISD complex (≤ 5% of input DNA). The formation of the ISD complex was not dependent upon 3’ OH processing and the DNA was predominately blunt-ended in the complex. Raltegravir-resistant IN mutant N155H weakly form the ISD complex in the presence of Raltegravir at ~25% level of wild type IN. In contrast, MK-2048 and L-841,411 produced ~3 to 5-fold more ISD than Raltegravir with N155H IN, which is susceptible to these two inhibitors. The results suggest STI are slow binding inhibitors and the potency to form and stabilize the ISD complex is not always related to inhibition of concerted integration. Rather, the apparent binding and dissociation properties of each STI influenced the production of the ISD complex. PMID:21295584

  5. ON-SITE MERCURY ANALYSIS OF SOIL AT HAZARDOUS WASTE SITES BY IMMUNOASSAY AND ASV

    EPA Science Inventory

    Two field methods for Hg, immunoassay and anodic stripping voltammetry (ASV), that can provide onsite results for quick decisions at hazardous waste sites were evaluated. Each method was applied to samples from two Superfund sites that contain high levels of Hg; Sulphur Bank Me...

  6. Biosorption of As(V) onto dried alligator weed root: role of metal (hydro) oxides.

    PubMed

    Chen, Jian; Tao, Weihua; Sun, Cheng

    2016-01-01

    The present work investigates the adsorption of As(V) onto the dried powder of alligator weed root as bio-sorbent, using acid pre-treated alligator weed root powder as the reference. The isotherm study suggested there is a favorable As(V) adsorption happened on the AWR surface. The batch adsorption experimental results indicated that the ionic strength has little impact on the adsorption, while the solution pH has a significant effect on the adsorption with apparent inhibition appearing in both extreme acidic and alkaline pH region. In addition, the properties of the biosorbent were characterized by various techniques including SEM-EDS, FT-IR, and ICP detection. The analysis results suggested that the metals including Mn, Fe, and Al enrich over the alligator weed root surface in the morphology of metal (hydro) oxide. Based on the nature of the biosorbent and As(V) besides the adsorption performance, the metal (hydro) oxides over biosorbent surface is suggested as the essential role to drive the adsorption. With the metal (hydro) oxides denuded in the pre-treatment, the biosorbent loses its adsorption capability for As(V) totally. PMID:26458188

  7. Adsorption, desorption and fractionation of As(V) on untreated and mussel shell-treated granitic material

    NASA Astrophysics Data System (ADS)

    Seco-Reigosa, N.; Cutillas-Barreiro, L.; Nóvoa-Muñoz, J. C.; Arias-Estévez, M.; Álvarez-Rodríguez, E.; Fernández-Sanjurjo, M. J.; Núñez-Delgado, A.

    2014-12-01

    As(V) adsorption and desorption were studied on granitic material, coarse and fine mussel shell, and granitic material amended with 12 and 24 t ha-1 fine shell, investigating the effect of different As(V) concentrations and different pH, as well as the fractions where the adsorbed As(V) was retained. As(V) adsorption was higher on fine than on coarse shell. Mussel shell amendment increased As(V) adsorption on granitic material. Adsorption data corresponding to the un-amended and shell-amended granitic material were satisfactory fitted to the Langmuir and Freundlich models. Desorption was always < 19% when the highest As(V) concentration (100 mg L-1) was added. Regarding the effect of pH, the granitic material showed its highest adsorption (66%) at pH < 6, and it was lower as pH increased. Fine shell presented notable adsorption in the whole pH range between 6 and 12, with a maximum of 83%. The shell-amended granitic material showed high As(V) adsorption, with a maximum (99%) at pH near 8, but decreasing as pH increased. Desorption varying pH was always < 26%. In the granitic material, desorption increased progressively when pH increased from 4 to 6, contrary to what happened to mussel shell. Regarding the fractionation of the adsorbed As(V), most of it was in the soluble fraction (weakly bound). Globally, the granitic material did not show high As(V) retention capacity, which implies risks of water pollution and transfer to the food chain; however, the mussel shell amendment increased As(V) retention, making this practice recommendable.

  8. Removal of As(V) using iron oxide impregnated carbon prepared from Tamarind hull.

    PubMed

    Maiti, Abhijit; Agarwal, Vaibhav; De, Sirshendu; Basu, Jayanta K

    2010-08-01

    Iron oxide impregnated tamarind hull carbon (IOITHC) was developed for use as an adsorbent for the removal of As(V) from water. Tamarind hull was used as the source of carbonaceous material, which was first treated with ferric chloride and ammonium hydroxide solutions with successive calcination at 873-974 K in a muffle furnace for 1 h to prepare an arsenic adsorbent. The B.E.T surface area of IOITHC was found to be 304.6 m(2) g(-1) and the average iron content in the adsorbent was found to be 7 wt%. The point of zero charge (pH(zpc)) of IOITHC was found to be 6.9. As(V) and arsenic (as total) adsorption on IOITHC were investigated in batch mode using As(V) spiked distilled water and real contaminated groundwater (CGW). The effects of speed of agitation, adsorbent particle size, temperature, pH of the solution, and concentration of the adsorbate on the adsorption process were investigated. The maximum adsorption capacity of about 1.2 mg g(-1) As(V) was achieved. The removal of As(V) on IOITHC was compared with the untreated tamarind hull carbon as well as with the activated commercial carbon and IOITHC was found to be better adsorbent. Arsenic adsorption from arsenic contaminated groundwater (CGW) on IOITHC in batch mode indicates that 98% removal was achieved for adsorbent loading of 3.0 g L(-1) with initial arsenic concentration of 264 microg L(-1). Desorption study of arsenic from As(V)-loaded IOITHC was performed using aqueous solution in the pH range of 3 to 12. PMID:20563914

  9. Natural Stilbenoids Isolated from Grapevine Exhibiting Inhibitory Effects against HIV-1 Integrase and Eukaryote MOS1 Transposase In Vitro Activities

    PubMed Central

    Chaignepain, Stéphane; Subra, Frederic; Munir, Soundasse; Delelis, Olivier; Lesbats, Paul; Calmels, Christina; Andreola, Marie-Line; Merillon, Jean-Michel; Auge-Gouillou, Corinne; Parissi, Vincent

    2013-01-01

    Polynucleotidyl transferases are enzymes involved in several DNA mobility mechanisms in prokaryotes and eukaryotes. Some of them such as retroviral integrases are crucial for pathogenous processes and are therefore good candidates for therapeutic approaches. To identify new therapeutic compounds and new tools for investigating the common functional features of these proteins, we addressed the inhibition properties of natural stilbenoids deriving from resveratrol on two models: the HIV-1 integrase and the eukaryote MOS-1 transposase. Two resveratrol dimers, leachianol F and G, were isolated for the first time in Vitis along with fourteen known stilbenoids: E-resveratrol, E-piceid, E-pterostilbene, E-piceatannol, (+)-E-ε-viniferin, E-ε-viniferinglucoside, E-scirpusin A, quadragularin A, ampelopsin A, pallidol, E-miyabenol C, E-vitisin B, hopeaphenol, and isohopeaphenol and were purified from stalks of Vitis vinifera (Vitaceae), and moracin M from stem bark of Milliciaexelsa (Moraceae). These compounds were tested in in vitro and in vivo assays reproducing the activity of both enzymes. Several molecules presented significant inhibition on both systems. Some of the molecules were found to be active against both proteins while others were specific for one of the two models. Comparison of the differential effects of the molecules suggested that the compounds could target specific intermediate nucleocomplexes of the reactions. Additionally E-pterostilbene was found active on the early lentiviral replication steps in lentiviruses transduced cells. Consequently, in addition to representing new original lead compounds for further modelling of new active agents against HIV-1 integrase, these molecules could be good tools for identifying such reaction intermediates in DNA mobility processes. PMID:24312275

  10. HIV-1 Protease, Reverse Transcriptase, and Integrase Variation

    PubMed Central

    Sankaran, Kris; Varghese, Vici; Winters, Mark A.; Hurt, Christopher B.; Eron, Joseph J.; Parkin, Neil; Holmes, Susan P.; Holodniy, Mark; Shafer, Robert W.

    2016-01-01

    ABSTRACT HIV-1 protease (PR), reverse transcriptase (RT), and integrase (IN) variability presents a challenge to laboratories performing genotypic resistance testing. This challenge will grow with increased sequencing of samples enriched for proviral DNA such as dried blood spots and increased use of next-generation sequencing (NGS) to detect low-abundance HIV-1 variants. We analyzed PR and RT sequences from >100,000 individuals and IN sequences from >10,000 individuals to characterize variation at each amino acid position, identify mutations indicating APOBEC-mediated G-to-A editing, and identify mutations resulting from selective drug pressure. Forty-seven percent of PR, 37% of RT, and 34% of IN positions had one or more amino acid variants with a prevalence of ≥1%. Seventy percent of PR, 60% of RT, and 60% of IN positions had one or more variants with a prevalence of ≥0.1%. Overall 201 PR, 636 RT, and 346 IN variants had a prevalence of ≥0.1%. The median intersubtype prevalence ratios were 2.9-, 2.1-, and 1.9-fold for these PR, RT, and IN variants, respectively. Only 5.0% of PR, 3.7% of RT, and 2.0% of IN variants had a median intersubtype prevalence ratio of ≥10-fold. Variants at lower prevalences were more likely to differ biochemically and to be part of an electrophoretic mixture compared to high-prevalence variants. There were 209 mutations indicative of APOBEC-mediated G-to-A editing and 326 mutations nonpolymorphic treatment selected. Identification of viruses with a high number of APOBEC-associated mutations will facilitate the quality control of dried blood spot sequencing. Identifying sequences with a high proportion of rare mutations will facilitate the quality control of NGS. IMPORTANCE Most antiretroviral drugs target three HIV-1 proteins: PR, RT, and IN. These proteins are highly variable: many different amino acids can be present at the same position in viruses from different individuals. Some of the amino acid variants cause drug

  11. Alternative nucleophilic substrates for the endonuclease activities of human immunodeficiency virus type 1 integrase

    SciTech Connect

    Ealy, Julie B.; Sudol, Malgorzata; Krzeminski, Jacek; Amin, Shantu; Katzman, Michael

    2012-11-10

    Retroviral integrase can use water or some small alcohols as the attacking nucleophile to nick DNA. To characterize the range of compounds that human immunodeficiency virus type 1 integrase can accommodate for its endonuclease activities, we tested 45 potential electron donors (having varied size and number or spacing of nucleophilic groups) as substrates during site-specific nicking at viral DNA ends and during nonspecific nicking reactions. We found that integrase used 22 of the 45 compounds to nick DNA, but not all active compounds were used for both activities. In particular, 13 compounds were used for site-specific and nonspecific nicking, 5 only for site-specific nicking, and 4 only for nonspecific nicking; 23 other compounds were not used for either activity. Thus, integrase can accommodate a large number of nucleophilic substrates but has selective requirements for its different activities, underscoring its dynamic properties and providing new information for modeling and understanding integrase.

  12. Fragment Based Strategies for Discovery of Novel HIV-1 Reverse Transcriptase and Integrase Inhibitors.

    PubMed

    Latham, Catherine F; La, Jennifer; Tinetti, Ricky N; Chalmers, David K; Tachedjian, Gilda

    2016-01-01

    Human immunodeficiency virus (HIV) remains a global health problem. While combined antiretroviral therapy has been successful in controlling the virus in patients, HIV can develop resistance to drugs used for treatment, rendering available drugs less effective and limiting treatment options. Initiatives to find novel drugs for HIV treatment are ongoing, although traditional drug design approaches often focus on known binding sites for inhibition of established drug targets like reverse transcriptase and integrase. These approaches tend towards generating more inhibitors in the same drug classes already used in the clinic. Lack of diversity in antiretroviral drug classes can result in limited treatment options, as cross-resistance can emerge to a whole drug class in patients treated with only one drug from that class. A fresh approach in the search for new HIV-1 drugs is fragment-based drug discovery (FBDD), a validated strategy for drug discovery based on using smaller libraries of low molecular weight molecules (<300 Da) screened using primarily biophysical assays. FBDD is aimed at not only finding novel drug scaffolds, but also probing the target protein to find new, often allosteric, inhibitory binding sites. Several fragment-based strategies have been successful in identifying novel inhibitory sites or scaffolds for two proven drug targets for HIV-1, reverse transcriptase and integrase. While any FBDD-generated HIV-1 drugs have yet to enter the clinic, recent FBDD initiatives against these two well-characterised HIV-1 targets have reinvigorated antiretroviral drug discovery and the search for novel classes of HIV-1 drugs. PMID:26324045

  13. Kinetics and Longevity of ϕC31 Integrase in Mouse Liver and Cultured Cells

    PubMed Central

    Chavez, Christopher L.; Keravala, Annahita; Woodard, Lauren E.; Hillman, Robert T.; Stowe, Timothy R.; Chu, Jacqueline N.

    2010-01-01

    Abstract The ϕC31 integrase system provides genomic integration of plasmid DNA that may be useful in gene therapy. For example, the ϕC31 system has been used in combination with hydrodynamic injection to achieve long-term expression of factor IX in mouse liver. However, a concern is that prolonged expression of ϕC31 integrase within cells could potentially stimulate chromosome rearrangements or an immune response. Western blot and immunofluorescence analyses were performed to investigate the duration of ϕC31 integrase expression in mouse liver. Integrase was expressed within 2 to 3 hr after hydrodynamic injection of a plasmid expressing ϕC31 integrase. Expression peaked between 8 and 16 hr and fell to background levels by 24–48 hr postinjection. Analysis of the amount of integrase plasmid DNA present in the liver over time suggested that the brief period of integrase expression could largely be accounted for by rapid loss of the bulk of the plasmid DNA, as well as by silencing of plasmid expression. PCR analysis of integration indicated that ϕC31 integrase carried out genomic integration of a codelivered attB-containing plasmid by 3 hr after plasmid injection. Integrase was expressed for longer times and at higher levels in transfected cultured cells compared with liver. Inhibitor studies suggested that the enzyme had a short half-life and was degraded by the 26S proteasome. The short duration of integrase expression in liver and rapid integration reaction appear to be features favorable for use in gene therapy. PMID:20497035

  14. Use of a Novel Integrase-Deficient Lentivirus for Targeted Anti-Cancer Therapy With Survivin Promoter-Driven Diphtheria Toxin A.

    PubMed

    Lin, Baoshun; Gao, Anding; Zhang, Rui; Ma, Hongyu; Shen, Haifeng; Hu, Qiong; Zhang, Hua; Zhao, Meng; Lan, Xiaopeng; Liu, Kuancan

    2015-08-01

    As an immunotoxin, diphtheria toxin has been widely used in gene therapy and gene function assays for its roles in protein synthesis inhibition, and the aim of our study is to set up a nonintegrating lentiviral system for specific expression of diphtheria toxin A (DTA) used in cancer gene therapy.Here, we established a lentiviral system that could coordinately express fluorescent protein and DTA driven by the cytomegalovirus (CMV) promoter, which is convenient for us to precisely trace the expression of DTA and monitor the process of lentivirus packaging. To achieve safer cancer therapy, we replaced the CMV promoter with the Survivin promoter, a specific promoter that is dramatically activated in cancer tissues and cells, but not in normal tissues and cells, and that will impose greater therapeutic potential because a significant expression difference occurred between these 2 groups. Meanwhile, we obtained integrase-deficient lentivirus (IDLV) after packaging with the integrase mutant, which expresses defective integrase RRK262263264AAH, to minimize the side effects that derived from the insertional mutagenesis of the host genome.Our results suggest that the IDLV system that we generated possesses therapeutic potential in cancers in vitro and in vivo. PMID:26252309

  15. Use of a Novel Integrase-Deficient Lentivirus for Targeted Anti-Cancer Therapy With Survivin Promoter-Driven Diphtheria Toxin A

    PubMed Central

    Lin, Baoshun; Gao, Anding; Zhang, Rui; Ma, Hongyu; Shen, Haifeng; Hu, Qiong; Zhang, Hua; Zhao, Meng; Lan, Xiaopeng; Liu, Kuancan

    2015-01-01

    Abstract As an immunotoxin, diphtheria toxin has been widely used in gene therapy and gene function assays for its roles in protein synthesis inhibition, and the aim of our study is to set up a nonintegrating lentiviral system for specific expression of diphtheria toxin A (DTA) used in cancer gene therapy. Here, we established a lentiviral system that could coordinately express fluorescent protein and DTA driven by the cytomegalovirus (CMV) promoter, which is convenient for us to precisely trace the expression of DTA and monitor the process of lentivirus packaging. To achieve safer cancer therapy, we replaced the CMV promoter with the Survivin promoter, a specific promoter that is dramatically activated in cancer tissues and cells, but not in normal tissues and cells, and that will impose greater therapeutic potential because a significant expression difference occurred between these 2 groups. Meanwhile, we obtained integrase-deficient lentivirus (IDLV) after packaging with the integrase mutant, which expresses defective integrase RRK262263264AAH, to minimize the side effects that derived from the insertional mutagenesis of the host genome. Our results suggest that the IDLV system that we generated possesses therapeutic potential in cancers in vitro and in vivo. PMID:26252309

  16. Influence of Drug Resistance Mutations on the Activity of HIV-1 Subtypes A and B Integrases: a Comparative Study

    PubMed Central

    Shadrina, O. A.; Zatsepin, T. S.; Agapkina, Yu. Yu.; Isaguliants, M. G.; Gottikh, M. B.

    2015-01-01

    Integration of human immunodeficiency virus (HIV-1) DNA into the genome of an infected cell is one of the key steps in the viral replication cycle. The viral enzyme integrase (IN), which catalyzes the integration, is an attractive target for the development of new antiviral drugs. However, the HIV-1 therapy often results in the IN gene mutations inducing viral resistance to integration inhibitors. To assess the impact of drug resistance mutations on the activity of IN of HIV-1 subtype A strain FSU-A, which is dominant in Russia, variants of the consensus IN of this subtype containing the primary resistance mutations G118R and Q148K and secondary compensatory substitutions E138K and G140S were prepared and characterized. Comparative study of these enzymes with the corresponding mutants of IN of HIV-1 subtype B strains HXB-2 was performed. The mutation Q148K almost equally reduced the activity of integrases of both subtypes. Its negative effect was partially compensated by the secondary mutations E138K and G140S. Primary substitution G118R had different influence on the activity of proteins of the subtypes A and B, and the compensatory effect of the secondary substitution E138K also depended on the viral subtype. Comparison of the mutants resistance to the known strand transfer inhibitors raltegravir and elvitegravir, and a new inhibitor XZ-259 (a dihydro-1H-isoindol derivative), showed that integrases of both subtypes with the Q148K mutation were insensitive to raltegravir and elvitegravir but were effectively inhibited by XZ-259. The substitution G118R slightly reduced the efficiency of IN inhibition by raltegravir and elvitegravir and caused no resistance to XZ_259. PMID:25927004

  17. Architecture of a Full-length Retroviral Integrase Monomer and Dimer, Revealed by Small Angle X-ray Scattering and Chemical Cross-linking

    SciTech Connect

    Bojja, Ravi S.; Andrake, Mark D.; Weigand, Steven; Merkel, George; Yarychkivska, Olya; Henderson, Adam; Kummerling, Marissa; Skalka, Anna Marie

    2012-02-07

    We determined the size and shape of full-length avian sarcoma virus (ASV) integrase (IN) monomers and dimers in solution using small angle x-ray scattering. The low resolution data obtained establish constraints for the relative arrangements of the three component domains in both forms. Domain organization within the small angle x-ray envelopes was determined by combining available atomic resolution data for individual domains with results from cross-linking coupled with mass spectrometry. The full-length dimer architecture so revealed is unequivocally different from that proposed from x-ray crystallographic analyses of two-domain fragments, in which interactions between the catalytic core domains play a prominent role. Core-core interactions are detected only in cross-linked IN tetramers and are required for concerted integration. The solution dimer is stabilized by C-terminal domain (CTD-CTD) interactions and by interactions of the N-terminal domain in one subunit with the core and CTD in the second subunit. These results suggest a pathway for formation of functional IN-DNA complexes that has not previously been considered and possible strategies for preventing such assembly.

  18. Bimodal high-affinity association of Brd4 with murine leukemia virus integrase and mononucleosomes.

    PubMed

    Larue, Ross C; Plumb, Matthew R; Crowe, Brandon L; Shkriabai, Nikoloz; Sharma, Amit; DiFiore, Julia; Malani, Nirav; Aiyer, Sriram S; Roth, Monica J; Bushman, Frederic D; Foster, Mark P; Kvaratskhelia, Mamuka

    2014-04-01

    The importance of understanding the molecular mechanisms of murine leukemia virus (MLV) integration into host chromatin is highlighted by the development of MLV-based vectors for human gene-therapy. We have recently identified BET proteins (Brd2, 3 and 4) as the main cellular binding partners of MLV integrase (IN) and demonstrated their significance for effective MLV integration at transcription start sites. Here we show that recombinant Brd4, a representative of the three BET proteins, establishes complementary high-affinity interactions with MLV IN and mononucleosomes (MNs). Brd4(1-720) but not its N- or C-terminal fragments effectively stimulate MLV IN strand transfer activities in vitro. Mass spectrometry- and NMR-based approaches have enabled us to map key interacting interfaces between the C-terminal domain of BRD4 and the C-terminal tail of MLV IN. Additionally, the N-terminal fragment of Brd4 binds to both DNA and acetylated histone peptides, allowing it to bind tightly to MNs. Comparative analyses of the distributions of various histone marks along chromatin revealed significant positive correlations between H3- and H4-acetylated histones, BET protein-binding sites and MLV-integration sites. Our findings reveal a bimodal mechanism for BET protein-mediated MLV integration into select chromatin locations. PMID:24520112

  19. Bovine Lactoferrampin, Human Lactoferricin, and Lactoferrin 1-11 Inhibit Nuclear Translocation of HIV Integrase.

    PubMed

    Wang, Winston Yan; Wong, Jack Ho; Ip, Denis Tsz Ming; Wan, David Chi Cheong; Cheung, Randy Chifai; Ng, Tzi Bun

    2016-08-01

    This study aimed to investigate fragments derived from human and bovine lactoferrins for ability to inhibit nuclear translocation of HIV-1 integrase. It was shown that human lactoferricin, human lactoferrin 1-11, and bovine lactoferrampin reduced nuclear distribution of HIV-1 integrase. Bovine lactoferrampin could inhibit both the activity and nuclear translocation of HIV-1 integrase. Human lactoferrampin, bovine lactoferricin, and bovine lactoferrin 1-11 had no effect on HIV-1 integrase nuclear translocation. Human lactoferrampin which inhibited the activity of integrase did not prevent its nuclear translocation. Human lactoferricin and lactoferrin 1-11 did not inhibit HIV-1 integrase nuclear translocation despite their ability to attenuate the enzyme activity. The discrepancy between the findings on reduction of HIV-1 activity and inhibition of nuclear translocation of HIV-1 integrase was due to the different mechanisms involved. A similar reasoning can also be applied to the different inhibitory potencies of the milk peptides on different HIV enzymes, i.e., nuclear translocation. PMID:27022750

  20. Oxidation of As(III) to As(V) using ozone microbubbles.

    PubMed

    Khuntia, Snigdha; Majumder, Subrata Kumar; Ghosh, Pallab

    2014-02-01

    The use of ozone in the treatment of water and wastewater is rapidly increasing due to its high oxidizing power. Arsenic is one the most toxic elements found in water. As(III) and As(V) are the major sources of arsenic poisoning. It is known that As(V) can be more easily removed from water by adsorptive methods than As(III). In this work, oxidation of more toxic As(III) to less toxic As(V) was studied in a pilot-plant by using ozone microbubbles. The microbubbles were effective in dissolving ozone in water. The oxidation was fast over a wide range of pH (e.g., 4-9). The role of hydroxyl radical in the oxidation of As(III) under acidic conditions was investigated by using 2-propanol as the hydroxyl radical scavenger. Under acidic conditions, the addition of 2-propanol slowed down the oxidation, which proves that hydroxyl radicals were involved in the oxidation process. The effect of carbonate ions on the rate of oxidation was investigated. It was found that the generation of carbonate ion radical from the carbonate ion accelerated the oxidation of As(III). The kinetics of oxidation of As(III) by ozone was studied. PMID:24268174

  1. Modeling and fixed bed column adsorption of As(V) on laterite soil.

    PubMed

    Maji, Sanjoy K; Pal, Anjali; Pal, Tarasankar; Adak, Asok

    2007-09-01

    Laterite soil, an abundant locally available natural adsorbent, has been evaluated for As(V) removal from aqueous solutions in column mode operation. The column studies were conducted using columns of 10, 20, 30 cm bed depth with 2 cm internal diameter. Initial As(V) concentration was 0.5 mg/L and flow rate was 7.75 mL/min. Bohart and Adams sorption model was employed for the determination of different parameters like height of exchange zone, adsorption rate, time required for exchange zone to move, and the adsorption capacity. Effect of flow rate and initial concentration was studied. The adsorption capacity of the laterite soil for 0.5 mg/L of As(V) was found to be 62.32 mg/L, and the adsorption rate constant was 1.0911 L/mg h for the minimum bed depth of 8.47 cm. The column was designed by the BDST model. Freundlich isotherm model was used to compare the theoretical and experimental breakthrough profile in the dynamic process. The bed saturation obtained was 36-80%. Regeneration of the exhausted column was possible with 1M NaOH. PMID:17849300

  2. Electromembrane extraction and spectrophotometric determination of As(V) in water samples.

    PubMed

    Kamyabi, Mohammad Ali; Aghaei, Ali

    2016-12-01

    In this study, for the first time electromembrane extraction (EME) was used as a highly efficient sample pre-treatment method for the UV-VIS spectrophotometric determination of As(V) in water samples. The influences of experimental parameters during EME were investigated and optimized using one-variable-at-a-time methodology as follows: organic solvent: 1-octanol+2.5% (V/V) di-(2-ethylhexyl) phosphate, applied voltage: 70V, extraction time: 15min, pH of acceptor: 13, stirring rate: 750rpm. The method allowed the determination of As(V) in the range of 5-300ngmL(-1). The relative standard deviation was found to be within the range of 3.4-7.6%. The limit of detection, corresponding to a signal to noise ratio of three, was 1.5ngmL(-1). The proposed method was finally applied to the determination of As(V) in water samples and relative recoveries ranging from 95 to 102% were obtained. PMID:27374507

  3. The sorption property of As(III) and As(V) from aqueous solution using waste cast iron

    NASA Astrophysics Data System (ADS)

    Kim, Wooram; Lee, Yunsub; Kim, Yangsu; Choi, Jinyoung; Han*, Ohhyung

    2015-04-01

    The sorption property of As(III) and As(V) from aqueous solution was investigated using waste cast iron(WCI), which is a byproduct of the iron casting process in foundries. Two types of WCI were used in the experiment: grind precipitate dust (GPD) and cast iron shot (CIS). Non-equilibrium batch experiments were performed under different concentrations of As(III) and As(V). Results showed that waste cast iron was effective in the removal of As(III) and As(V). The phase changes of sorbed As species on the GPD using XPS (X-ray Photoelectron Spectroscopy) were investigated. The results showed the binding energy of 45.19eV for As(V) were obtained, whereas two of 45.3eV and 43.91eV for As(III) were shown in GPD. It can be strongly suggested that GPD mediated As(V) had no evidence for the reduction of ionized As(V) species into As(III), whereas GPD mediated As(III) showed a partial oxidation of As(III) into As(V). The qualitative and quantitative analysis of As distribution and metal containing phase in WCI surface through the XRF, XRD, EPMA, EDS patterns, BSE and SEM image were investigated. The GPD and CIS are a spherical shape with Fe0 composition in correspondence with XRF and XRD analysis results. Quantitative analysis for molar ratio of Fe and As indicated a 1.1% and 1.5% of As(V) and As(III) molar fractions were observed in GPD, while 5.1% and 0.9% fractions in CIS.

  4. Clinical Use of HIV Integrase Inhibitors: A Systematic Review and Meta-Analysis

    PubMed Central

    Messiaen, Peter; Wensing, Annemarie M. J.; Fun, Axel; Nijhuis, Monique; Brusselaers, Nele; Vandekerckhove, Linos

    2013-01-01

    Background Optimal regimen choice of antiretroviral therapy is essential to achieve long-term clinical success. Integrase inhibitors have swiftly been adopted as part of current antiretroviral regimens. The purpose of this study was to review the evidence for integrase inhibitor use in clinical settings. Methods MEDLINE and Web-of-Science were screened from April 2006 until November 2012, as were hand-searched scientific meeting proceedings. Multiple reviewers independently screened 1323 citations in duplicate to identify randomized controlled trials, nonrandomized controlled trials and cohort studies on integrase inhibitor use in clinical practice. Independent, duplicate data extraction and quality assessment were conducted. Results 48 unique studies were included on the use of integrase inhibitors in antiretroviral therapy-naive patients and treatment-experienced patients with either virological failure or switching to integrase inhibitors while virologically suppressed. On the selected studies with comparable outcome measures and indication (n = 16), a meta-analysis was performed based on modified intention-to-treat (mITT), on-treatment (OT) and as-treated (AT) virological outcome data. In therapy-naive patients, favorable odds ratios (OR) for integrase inhibitor-based regimens were observed, (mITT OR 0.71, 95% CI 0.59–0.86). However, integrase inhibitors combined with protease inhibitors only did not result in a significant better virological outcome. Evidence further supported integrase inhibitor use following virological failure (mITT OR 0.27; 95% CI 0.11–0.66), but switching to integrase inhibitors from a high genetic barrier drug during successful treatment was not supported (mITT OR 1.43; 95% CI 0.89–2.31). Integrase inhibitor-based regimens result in similar immunological responses compared to other regimens. A low genetic barrier to drug-resistance development was observed for raltegravir and elvitegravir, but not for dolutegravir. Conclusion

  5. D77, one benzoic acid derivative, functions as a novel anti-HIV-1 inhibitor targeting the interaction between integrase and cellular LEDGF/p75

    SciTech Connect

    Du Li; Zhao Yaxue; Chen, Jing; Yang Liumeng; Zheng Yongtang; Tang Yun Shen Xu Jiang Hualiang

    2008-10-10

    Integration of viral-DNA into host chromosome mediated by the viral protein HIV-1 integrase (IN) is an essential step in the HIV-1 life cycle. In this process, Lens epithelium-derived growth factor (LEDGF/p75) is discovered to function as a cellular co-factor for integration. Since LEDGF/p75 plays an important role in HIV integration, disruption of the LEDGF/p75 interaction with IN has provided a special interest for anti-HIV agent discovery. In this work, we reported that a benzoic acid derivative, 4-[(5-bromo-4-{l_brace}[2,4-dioxo-3-(2-oxo-2-phenylethyl) -1,3-thiazolidin-5-ylidene]methyl{r_brace}-2-ethoxyphenoxy)methyl]benzoic acid (D77) could potently inhibit the IN-LEDGF/p75 interaction and affect the HIV-1 IN nuclear distribution thus exhibiting antiretroviral activity. Molecular docking with site-directed mutagenesis analysis and surface plasmon resonance (SPR) binding assays has clarified possible binding mode of D77 against HIV-1 integrase. As the firstly discovered small molecular compound targeting HIV-1 integrase interaction with LEDGF/p75, D77 might supply useful structural information for further anti-HIV agent discovery.

  6. Cellular Cofactors of Lentiviral Integrase: From Target Validation to Drug Discovery

    PubMed Central

    Taltynov, Oliver; Desimmie, Belete A.; Demeulemeester, Jonas; Christ, Frauke; Debyser, Zeger

    2012-01-01

    To accomplish their life cycle, lentiviruses make use of host proteins, the so-called cellular cofactors. Interactions between host cell and viral proteins during early stages of lentiviral infection provide attractive new antiviral targets. The insertion of lentiviral cDNA in a host cell chromosome is a step of no return in the replication cycle, after which the host cell becomes a permanent carrier of the viral genome and a producer of lentiviral progeny. Integration is carried out by integrase (IN), an enzyme playing also an important role during nuclear import. Plenty of cellular cofactors of HIV-1 IN have been proposed. To date, the lens epithelium-derived growth factor (LEDGF/p75) is the best studied cofactor of HIV-1 IN. Moreover, small molecules that block the LEDGF/p75-IN interaction have recently been developed for the treatment of HIV infection. The nuclear import factor transportin-SR2 (TRN-SR2) has been proposed as another interactor of HIV IN-mediating nuclear import of the virus. Using both proteins as examples, we will describe approaches to be taken to identify and validate novel cofactors as new antiviral targets. Finally, we will highlight recent advances in the design and the development of small-molecule inhibitors binding to the LEDGF/p75-binding pocket in IN (LEDGINs). PMID:22928108

  7. Structural Basis for the Recognition Between HIV-1 Integrase and Transcriptional Coactivator p75

    SciTech Connect

    Cherepanov,P.; Ambrosio, A.; Rahman, S.; Ellenberger, T.; Engelman, A.

    2005-01-01

    Integrase (IN) is an essential retroviral enzyme, and human transcriptional coactivator p75, which is also referred to as lens epithelium-derived growth factor (LEDGF), is the dominant cellular binding partner of HIV-1 IN. Here, we report the crystal structure of the dimeric catalytic core domain of HIV-1 IN complexed to the IN-binding domain of LEDGF. Previously identified LEDGF hotspot residues anchor the protein to both monomers at the IN dimer interface. The principal structural features of IN that are recognized by the host factor are the backbone conformation of residues 168-171 from one monomer and a hydrophobic patch that is primarily comprised of {alpha}-helices 1 and 3 of the second IN monomer. Inspection of diverse retroviral primary and secondary sequence elements helps to explain the apparent lentiviral tropism of the LEDGF-IN interaction. Because the lethal phenotypes of HIV-1 mutant viruses unable to interact with LEDGF indicate that IN function is highly sensitive to perturbations of the structure around the LEDGF-binding site, we propose that small molecule inhibitors of the protein-protein interaction might similarly disrupt HIV-1 replication.

  8. Plasmid integration in a wide range of bacteria mediated by the integrase of Lactobacillus delbrueckii bacteriophage mv4.

    PubMed Central

    Auvray, F; Coddeville, M; Ritzenthaler, P; Dupont, L

    1997-01-01

    Bacteriophage mv4 is a temperate phage infecting Lactobacillus delbrueckii subsp. bulgaricus. During lysogenization, the phage integrates its genome into the host chromosome at the 3' end of a tRNA(Ser) gene through a site-specific recombination process (L. Dupont et al., J. Bacteriol., 177:586-595, 1995). A nonreplicative vector (pMC1) based on the mv4 integrative elements (attP site and integrase-coding int gene) is able to integrate into the chromosome of a wide range of bacterial hosts, including Lactobacillus plantarum, Lactobacillus casei (two strains), Lactococcus lactis subsp. cremoris, Enterococcus faecalis, and Streptococcus pneumoniae. Integrative recombination of pMC1 into the chromosomes of all of these species is dependent on the int gene product and occurs specifically at the pMC1 attP site. The isolation and sequencing of pMC1 integration sites from these bacteria showed that in lactobacilli, pMC1 integrated into the conserved tRNA(Ser) gene. In the other bacterial species where this tRNA gene is less or not conserved; secondary integration sites either in potential protein-coding regions or in intergenic DNA were used. A consensus sequence was deduced from the analysis of the different integration sites. The comparison of these sequences demonstrated the flexibility of the integrase for the bacterial integration site and suggested the importance of the trinucleotide CCT at the 5' end of the core in the strand exchange reaction. PMID:9068626

  9. Integrase-Deficient Lentiviral Vectors Mediate Efficient Gene Transfer to Human Vascular Smooth Muscle Cells with Minimal Genotoxic Risk

    PubMed Central

    Chick, Helen E.; Nowrouzi, Ali; Fronza, Raffaele; McDonald, Robert A.; Kane, Nicole M.; Alba, Raul; Delles, Christian; Sessa, William C.; Schmidt, Manfred; Thrasher, Adrian J.

    2012-01-01

    Abstract We have previously shown that injury-induced neointima formation was rescued by adenoviral-Nogo-B gene delivery. Integrase-competent lentiviral vectors (ICLV) are efficient at gene delivery to vascular cells but present a risk of insertional mutagenesis. Conversely, integrase-deficient lentiviral vectors (IDLV) offer additional benefits through reduced mutagenesis risk, but this has not been evaluated in the context of vascular gene transfer. Here, we have investigated the performance and genetic safety of both counterparts in primary human vascular smooth muscle cells (VSMC) and compared gene transfer efficiency and assessed the genotoxic potential of ICLVs and IDLVs based on their integration frequency and insertional profile in the human genome. Expression of enhanced green fluorescent protein (eGFP) mediated by IDLVs (IDLV-eGFP) demonstrated efficient transgene expression in VSMCs. IDLV gene transfer of Nogo-B mediated efficient overexpression of Nogo-B in VSMCs, leading to phenotypic effects on VSMC migration and proliferation, similar to its ICLV version and unlike its eGFP control and uninfected VSMCs. Large-scale integration site analyses in VSMCs indicated that IDLV-mediated gene transfer gave rise to a very low frequency of genomic integration compared to ICLVs, revealing a close-to-random genomic distribution in VSMCs. This study demonstrates for the first time the potential of IDLVs for safe and efficient vascular gene transfer. PMID:22931362

  10. Small-Molecule Inhibitors of the LEDGF/p75 Binding Site of Integrase Block HIV Replication and Modulate Integrase Multimerization

    PubMed Central

    Christ, Frauke; Shaw, Stephen; Demeulemeester, Jonas; Desimmie, Belete A.; Marchand, Arnaud; Butler, Scott; Smets, Wim; Chaltin, Patrick; Westby, Mike

    2012-01-01

    Targeting the HIV integrase (HIV IN) is a clinically validated approach for designing novel anti-HIV therapies. We have previously described the discovery of a novel class of integration inhibitors, 2-(quinolin-3-yl)acetic acid derivatives, blocking HIV replication at a low micromolar concentration through binding in the LEDGF/p75 binding pocket of HIV integrase, hence referred to as LEDGINs. Here we report the detailed characterization of their mode of action. The design of novel and more potent analogues with nanomolar activity enabled full virological evaluation and a profound mechanistic study. As allosteric inhibitors, LEDGINs bind to the LEDGF/p75 binding pocket in integrase, thereby blocking the interaction with LEDGF/p75 and interfering indirectly with the catalytic activity of integrase. Detailed mechanism-of-action studies reveal that the allosteric mode of inhibition is likely caused by an effect on HIV-1 integrase oligomerization. The multimodal inhibition by LEDGINs results in a block in HIV integration and in a replication deficiency of progeny virus. The allosteric nature of LEDGINs leads to synergy in combination with the clinically approved active site HIV IN strand transfer inhibitor (INSTI) raltegravir, and cross-resistance profiling proves the distinct mode of action of LEDGINs and INSTIs. The allosteric nature of inhibition and compatibility with INSTIs underline an interest in further (clinical) development of LEDGINs. PMID:22664975

  11. Computer tools in the discovery of HIV-I integrase inhibitors

    PubMed Central

    Liao, Chenzhong; Nicklaus, Marc C

    2010-01-01

    Computer-aided drug design (CADD) methodologies have made great advances and contributed significantly to the discovery and/or optimization of many clinically used drugs in recent years. CADD tools have likewise been applied to the discovery of inhibitors of HIV-I integrase, a difficult and worthwhile target for the development of efficient anti-HIV drugs. This article reviews the application of CADD tools, including pharmacophore search, quantitative structure–activity relationships, model building of integrase complexed with viral DNA and quantum-chemical studies in the discovery of HIV-I integrase inhibitors. Different structurally diverse integrase inhibitors have been identified by, or with significant help from, various CADD tools. PMID:21426160

  12. Unmasking the ancestral activity of integron integrases reveals a smooth evolutionary transition during functional innovation

    PubMed Central

    Escudero, Jose Antonio; Loot, Celine; Parissi, Vincent; Nivina, Aleksandra; Bouchier, Christiane; Mazel, Didier

    2016-01-01

    Tyrosine (Y)-recombinases have evolved to deliver mechanistically different reactions on a variety of substrates, but these evolutionary transitions are poorly understood. Among them, integron integrases are hybrid systems recombining single- and double-stranded DNA partners. These reactions are asymmetric and need a replicative resolution pathway, an exception to the canonical second strand exchange model of Y-recombinases. Integron integrases possess a specific domain for this specialized pathway. Here we show that despite this, integrases are still capable of efficiently operating the ancestral second strand exchange in symmetrical reactions between double-stranded substrates. During these reactions, both strands are reactive and Holliday junction resolution can follow either pathway. A novel deep-sequencing approach allows mapping of the crossover point for the second strand exchange. The persistence of the ancestral activity in integrases illustrates their robustness and shows that innovation towards new recombination substrates and resolution pathways was a smooth evolutionary process. PMID:26961432

  13. Development of a receptor model for efficient in silico screening of HIV-1 integrase inhibitors.

    PubMed

    Quevedo, Mario A; Ribone, Sergio R; Briñón, Margarita C; Dehaen, Wim

    2014-07-01

    Integrase (IN) is a key viral enzyme for the replication of the type-1 human immunodeficiency virus (HIV-1), and as such constitutes a relevant therapeutic target for the development of anti-HIV agents. However, the lack of crystallographic data of HIV IN complexed with the corresponding viral DNA has historically hindered the application of modern structure-based drug design techniques to the discovery of new potent IN inhibitors (INIs). Consequently, the development and validation of reliable HIV IN structural models that may be useful for the screening of large databases of chemical compounds is of particular interest. In this study, four HIV-1 IN homology models were evaluated respect to their capability to predict the inhibition potency of a training set comprising 36 previously reported INIs with IC50 values in the low nanomolar to the high micromolar range. Also, 9 inactive structurally related compounds were included in this training set. In addition, a crystallographic structure of the IN-DNA complex corresponding to the prototype foamy virus (PFV) was also evaluated as structural model for the screening of inhibitors. The applicability of high throughput screening techniques, such as blind and ligand-guided exhaustive rigid docking was assessed. The receptor models were also refined by molecular dynamics and clustering techniques to assess protein sidechain flexibility and solvent effect on inhibitor binding. Among the studied models, we conclude that the one derived from the X-ray structure of the PFV integrase exhibited the best performance to rank the potencies of the compounds in the training set, with the predictive power being further improved by explicitly modeling five water molecules within the catalytic side of IN. Also, accounting for protein sidechain flexibility enhanced the prediction of inhibition potencies among the studied compounds. Finally, an interaction fingerprint pattern was established for the fast identification of potent IN

  14. HIV-1 integrase inhibitor resistance and its clinical implications.

    PubMed

    Blanco, Jose-Luis; Varghese, Vici; Rhee, Soo-Yon; Gatell, Jose M; Shafer, Robert W

    2011-05-01

    With the approval in 2007 of the first integrase inhibitor (INI), raltegravir, clinicians became better able to suppress virus replication in patients infected with human immunodeficiency virus type 1 (HIV-1) who were harboring many of the most highly drug-resistant viruses. Raltegravir also provided clinicians with additional options for first-line therapy and for the simplification of regimens in patients with stable virological suppression. Two additional INIs in advanced clinical development-elvitegravir and S/GSK1349572-may prove equally versatile. However, the INIs have a relatively low genetic barrier to resistance in that 1 or 2 mutations are capable of causing marked reductions in susceptibility to raltegravir and elvitegravir, the most well-studied INIs. This perspective reviews the genetic mechanisms of INI resistance and their implications for initial INI therapy, the treatment of antiretroviral-experienced patients, and regimen simplification. PMID:21459813

  15. QSAR study of curcumine derivatives as HIV-1 integrase inhibitors.

    PubMed

    Gupta, Pawan; Sharma, Anju; Garg, Prabha; Roy, Nilanjan

    2013-03-01

    A QSAR study was performed on curcumine derivatives as HIV-1 integrase inhibitors using multiple linear regression. The statistically significant model was developed with squared correlation coefficients (r(2)) 0.891 and cross validated r(2) (r(2) cv) 0.825. The developed model revealed that electronic, shape, size, geometry, substitution's information and hydrophilicity were important atomic properties for determining the inhibitory activity of these molecules. The model was also tested successfully for external validation (r(2) pred = 0.849) as well as Tropsha's test for model predictability. Furthermore, the domain analysis was carried out to evaluate the prediction reliability of external set molecules. The model was statistically robust and had good predictive power which can be successfully utilized for screening of new molecules. PMID:23286784

  16. As(V), Cr(III) and Cr(VI) sorption on biochars and soil

    NASA Astrophysics Data System (ADS)

    Diamadopoulos, Evan; Agrafioti, Evita; Kalderis, Dimitrios

    2014-05-01

    The use of biochar, as a cost effective sorbent for heavy metal removal from contaminated water and soils is becoming a very promising practice. In this study, rice husk, the organic fraction of solid wastes, as well as sewage sludge were used as precursors for biochar production. The first was chosen as one of the most abundant types of biomass worldwide and the other two in order to find alternative innovative uses of these wastes. A series of batch kinetic and equilibrium (sorption and desorption) experiments was conducted using As(V), Cr(III) and Cr(VI) as adsorbates. The specific heavy metals were chosen in order to assess biochars removal capacity towards both anionic and cationic metals. Apart from biochars, a sandy loam soil was also used as adsorbent for metal removal. Knowing the separate behavior of biochars and soil towards metal sorption, it could be the first step in explaining the fate of heavy metals in a biochar amended soil. The kinetic study showed that, for all adsorbents and metals examined, sorption can be well described by the pseudo-second order kinetic model. What is more, simulation of sorption isotherms gave a better fit for the Freundlich model, possibly due to the heterogeneous surface of the initial biomasses and the fine aggregates that soil consists of. Based on the equilibrium study, the materials examined removed more than 95% of the initial Cr(III). This is possibly related to the electrostatic interactions between adsorbents negative surface charge and Cr(III) cations. However, removal rates for As(V) and Cr(VI) anions were significantly lower. Biochar derived from sewage sludge was efficient in removing 89% of Cr(VI) and 53% of As(V). Its ash high Fe2O3 content may have enhanced metal adsorption via precipitation. Soil was the most effective material for the removal of As(V), yet it could not strongly retain metal anions compared to biochars, as a significant amount of the adsorbed metal was released during desorption

  17. Surface speciation of As(III) and As(V) in relation to charge distribution.

    PubMed

    Stachowicz, Monika; Hiemstra, Tjisse; van Riemsdijk, Willem H

    2006-10-01

    The adsorption of As(III) and As(V) on goethite has been studied as a function of pH and loading. The data can be successfully described with the charge distribution (CD) model (extended Stern layer option) using realistic species observed by EXAFS. The CD values have been derived theoretically. Therefore, the Brown bond valence approach has been applied to MO/DFT optimized geometries of a series of hydrated complexes of As(III) and As(V) with Fe(III) (hydr)oxide. The calculated ionic CD values have been corrected for the effect of dipole orientation of interfacial water, resulting in overall interfacial CD coefficients that can be used to describe the surface speciation as a function of pH and loading. For As(III), the main surface species is a bidentate complex and a minor contribution of a monodentate species is found, which is in agreement with EXAFS. The CD values have also been fitted. Such an analysis of the adsorption data resulted in the same surface species. The fitted CD values for the bidentate complex points to the presence of strong AsO bonds with the surface and a weaker AsOH bond with the free OH ligand. This agrees quantitatively with the MO/DFT optimized geometry. Interpretation of free fitted CD values for As(V) binding suggests that the main surface species is a non-protonated bidentate complex (B) with a contribution of a singly protonated surface complex (MH) at sub-neutral pH and high loading. In addition, a protonated bidentate surface complex (BH) may be present. The same species are found if the theoretical CD values are used in the data analysis. The pH dependency of surface speciation is strongly influenced by the charge attribution of adsorbed species to the electrostatic surface plane while the effect of loading is primarily controlled by the amount of charge attributed to the 1-plane, illustrating the different action of the CD value. The MO/DFT geometry optimizations furthermore suggest that for As(V) the B, MH and BH surface

  18. Removal of As(III) and As(V) from water by copper oxide incorporated mesoporous alumina.

    PubMed

    Pillewan, Pradnya; Mukherjee, Shrabanti; Roychowdhury, Tarit; Das, Sera; Bansiwal, Amit; Rayalu, Sadhana

    2011-02-15

    In the present manuscript a new adsorbent namely copper oxide incorporated mesoporous alumina (COIMA) for removal of arsenic from water is reported. The COIMA was prepared by treating mesoporous alumina with copper sulphate solution followed by calcination at 450°C in the presence of air. Various adsorption isotherm and kinetic parameters were computed using batch adsorption studies to determine the adsorption capacity for As(III) and As(V) and to understand the mechanism of adsorption. It was observed that incorporation of copper oxide improves the adsorption capacity of unmodified alumina from 0.92 to 2.16 mg g(-1) for As(III) and from 0.84 to 2.02 mg g(-1) for As(V). The results revealed that the adsorption follows Langmuir isotherm and pseudo-second-order kinetic models for both As(III) and As(V). The material is capable of simultaneously removing As(III) and As(V) with removal efficiencies of more than 95% for both As(III) and As(V). Assessment of the water quality before and after treatment with COIMA also confirmed that the there is no leaching of copper and other parameters were also within permissible limits of Indian drinking water standard indicating that the COIMA can be used for treatment of arsenic contaminated drinking water. PMID:21186080

  19. Blind prediction of HIV integrase binding from the SAMPL4 challenge

    PubMed Central

    Mobley, David L.; Liu, Shuai; Lim, Nathan M.; Wymer, Karisa L.; Perryman, Alexander L.; Forli, Stefano; Deng, Nanjie; Su, Justin; Branson, Kim; Olson, Arthur J.

    2015-01-01

    Here, we give an overview of the protein-ligand binding portion of the SAMPL4 challenge, which focused on predicting binding of HIV integrase inhibitors in the catalytic core domain. The challenge encompassed three components – a small “virtual screening” challenge, a binding mode prediction component, and a small affinity prediction component. Here, we give summary results and statistics concerning the performance of all submissions at each of these challenges. Virtual screening was particularly challenging here in part because, in contrast to more typical virtual screening test sets, the inactive compounds were tested because they were thought to be likely binders, so only the very top predictions performed significantly better than random. Pose prediction was also quite challenging, in part because inhibitors in the set bind to three different sites, so even identifying the correct binding site was challenging. Still, the best methods managed low RMSD predictions in many cases. Here, we give an overview of results, highlight some features of methods which worked particularly well, and refer the interested reader to papers in this issue which describe specific submissions for additional details. PMID:24595873

  20. The long-acting integrase inhibitor GSK744 protects macaques from repeated intravaginal SHIV challenge.

    PubMed

    Radzio, Jessica; Spreen, William; Yueh, Yun Lan; Mitchell, James; Jenkins, Leecresia; García-Lerma, J Gerardo; Heneine, Walid

    2015-01-14

    Daily preexposure prophylaxis (PrEP) with Truvada is a proven HIV prevention strategy; however, its effectiveness is limited by low adherence. Antiretroviral drug formulations that require infrequent dosing may increase adherence and thus PrEP effectiveness. We investigated whether monthly injections of a long-acting formulation of the HIV integrase inhibitor GSK1265744 (GSK744 LA) prevented simian/human immunodeficiency virus (SHIV) infection by vaginal challenge in macaques. Female pigtail macaques (n = 12) were exposed to intravaginal inoculations of SHIV twice a week for up to 11 weeks. Half of the animals received a GSK744 LA injection every 4 weeks, and half received placebo. GSK744 LA, at plasma concentrations achievable with quarterly injections in humans, protected all six macaques from infection. Placebo controls were all infected after a median of 4 (range, 2 to 20) vaginal challenges with SHIV. Efficacy was related to high and sustained vaginal and plasma drug concentrations that remained above the protein-adjusted 90% inhibitory concentration during the dosing cycles. These data support advancement of GSK744 LA as a potential PrEP candidate for women. PMID:25589631

  1. Kuwanon-L as a New Allosteric HIV-1 Integrase Inhibitor: Molecular Modeling and Biological Evaluation.

    PubMed

    Esposito, Francesca; Tintori, Cristina; Martini, Riccardo; Christ, Frauke; Debyser, Zeger; Ferrarese, Roberto; Cabiddu, Gianluigi; Corona, Angela; Ceresola, Elisa Rita; Calcaterra, Andrea; Iovine, Valentina; Botta, Bruno; Clementi, Massimo; Canducci, Filippo; Botta, Maurizio; Tramontano, Enzo

    2015-11-01

    HIV-1 integrase (IN) active site inhibitors are the latest class of drugs approved for HIV treatment. The selection of IN strand-transfer drug-resistant HIV strains in patients supports the development of new agents that are active as allosteric IN inhibitors. Here, a docking-based virtual screening has been applied to a small library of natural ligands to identify new allosteric IN inhibitors that target the sucrose binding pocket. From theoretical studies, kuwanon-L emerged as the most promising binder and was thus selected for biological studies. Biochemical studies showed that kuwanon-L is able to inhibit the HIV-1 IN catalytic activity in the absence and in the presence of LEDGF/p75 protein, the IN dimerization, and the IN/LEDGF binding. Kuwanon-L also inhibited HIV-1 replication in cell cultures. Overall, docking and biochemical results suggest that kuwanon-L binds to an allosteric binding pocket and can be considered an attractive lead for the development of new allosteric IN antiviral agents. PMID:26360521

  2. [Mechanism of groundwater As(V) removal with ferric flocculation and direct filtration].

    PubMed

    Kang, Ying; Duan, Jin-Ming; Jing, Chuan-Yong

    2015-02-01

    The As removal process and mechanism from groundwater using ferric flocculation-direct filtration system was investigated using batch, field pilot tests, extended X-ray absorption fine structure ( EXAFS) spectroscopy, and charge-distribution multisite complexation (CD-MUSIC) model. The results showed that arsenate [As(V)] was the dominant As species in the groundwater with a concentration of 40 μg x L(-1). The treatment system could supply 64 984 L As-safe drinking water (< 10 μg L(-1)) using Fe 1.5 mg x L(-1). Toxicity characteristic leaching procedure (TCLP) demonstrated that the leachate As was 3.4 μg x L(-1), much lower than the EPA regulatory concentration (5 mg x L(-1)). EXAFS and CD-MUSIC model indicated that As(V) was adsorbed onto ferric hydroxide via bidentate binuclear complexes in the pH range of 3 to 9.5, while formation of precipitate with Ca or Mg dominated the As removal at pH > 9.5. PMID:26031078

  3. The mechanisms of detoxification of As(III), dimethylarsinic acid (DMA) and As(V) in the microalga Chlorella vulgaris.

    PubMed

    Pantoja Munoz, L; Purchase, D; Jones, H; Raab, A; Urgast, D; Feldmann, J; Garelick, H

    2016-06-01

    The response of Chlorella vulgaris when challenged by As(III), As(V) and dimethylarsinic acid (DMA) was assessed through experiments on adsorption, efflux and speciation of arsenic (reduction, oxidation, methylation and chelation with glutathione/phytochelatin [GSH/PC]). Our study indicates that at high concentrations of phosphate (1.62mM of HPO4(2-)), upon exposure to As(V), cells are able to shift towards methylation of As(V) rather than PC formation. Treatment with As(V) caused a moderate decrease in intracellular pH and a strong increase in the concentration of free thiols (GSH). Passive surface adsorption was found to be negligible for living cells exposed to DMA and As(V). However, adsorption of As(III) was observed to be an active process in C. vulgaris, because it did not show saturation at any of the exposure periods. Chelation of As(III) with GS/PC and to a lesser extent hGS/hPC is a major detoxification mechanism employed by C. vulgaris cells when exposed to As(III). The increase of bound As-GS/PC complexes was found to be strongly related to an increase in concentration of As(III) in media. C. vulgaris cells did not produce any As-GS/PC complex when exposed to As(V). This may indicate that a reduction step is needed for As(V) complexation with GSH/PC. C. vulgaris cells formed DMAS(V)-GS upon exposure to DMA independent of the exposure period. As(III) triggers the formation of arsenic complexes with PC and homophytochelatins (hPC) and their compartmentalisation to vacuoles. A conceptual model was devised to explain the mechanisms involving ABCC1/2 transport. The potential of C. vulgaris to bio-remediate arsenic from water appeared to be highly selective and effective without the potential hazard of reducing As(V) to As(III), which is more toxic to humans. PMID:26994369

  4. Application of personal computers in the analytical laboratory-III ASV analysis.

    PubMed

    Kaplan, D; Raphaeli, D; Ben-Yaakov, S

    1987-08-01

    Automatic operation and data-processing of ASV analysis is achieved by interfacing a general-purpose polarograph to a personal computer. The software package, written in SUPER BASIC, includes graphic routines that are used to display the voltamperograms and calibration curve, and as an interface with the operator. Data-processing can be done manually, interactively or automatically. In the last of these modes, peak position and height are evaluated by first correcting for baseline drift and then fitting the peaks to a Gaussian function. It is found that this procedure is relatively insensitive to noise. The system is used routinely in the analysis of treated domestic wastewater and soils irrigated by effluents. The flexibility of the programming and the feature of interactive work are important in this connection, which calls for careful examination of peaks distorted by matrix interferences. PMID:18964391

  5. Using ΦC31 integrase to mediate insertion of DNA in Xenopus embryos.

    PubMed

    Li, You E; Allen, Bryan G; Weeks, Daniel L

    2012-01-01

    The two most common methods used to generate transgenic Xenopus embryos, restriction enzyme-mediated insertion, and I-SceI meganuclease take advantage of relatively common but spatially unpredictable double-stranded breaks in sperm, egg, or early embryo genomes. These methods also tend to insert multimeric copies of the transgene. An alternative is to use bacteriophage- or transposon-derived integrase or recombinase to mediate more site-specific insertion of the transgene. The use of phiC31 integrase requires a defined sequence for insertion and is compatible with insertion of a single copy of the transgene. We describe the protocol we use to facilitate phiC31 integrase transgene insertion including the use of insulator sequences to reduce position effect disruption of transgene activity. PMID:22956091

  6. Use of Integrase Inhibitors in HIV-Infected Children and Adolescents.

    PubMed

    Dehority, Walter; Abadi, Jacobo; Wiznia, Andrew; Viani, Rolando M

    2015-09-01

    Resistance to antiretroviral drugs is an increasingly prevalent challenge affecting both the adult and pediatric HIV-infected populations. Though data on the safety, pharmacokinetics, and efficacy of newer antiretroviral agents in children typically lags behind adult data, newer agents are becoming available for use in HIV-infected children who are failing to respond to or are experiencing toxicities with traditional antiretroviral regimens. Integrase strand transfer inhibitors are one such new class of antiretrovirals. Raltegravir has been US Food and Drug Administration (FDA) approved for use in patients over the age of 4 weeks. Elvitegravir is a second member of this class, and has the potential for use in children but does not yet have a Pediatric FDA indication. Dolutegravir, a second-generation integrase inhibitor, is approved for those older than 12 years. This review summarizes the use of integrase inhibitors in children and adolescents, and highlights the results of recent clinical trials. PMID:26242765

  7. HIV Virions as Nanoscopic Test Tubes for Probing Oligomerization of the Integrase Enzyme

    PubMed Central

    2015-01-01

    Employing viruses as nanoscopic lipid-enveloped test tubes allows the miniaturization of protein–protein interaction (PPI) assays while preserving the physiological environment necessary for particular biological processes. Applied to the study of the human immunodeficiency virus type 1 (HIV-1), viral biology and pathology can also be investigated in novel ways, both in vitro as well as in infected cells. In this work we report on an experimental strategy that makes use of engineered HIV-1 viral particles, to allow for probing PPIs of the HIV-1 integrase (IN) inside viruses with single-molecule Förster resonance energy transfer (FRET) using fluorescent proteins (FP). We show that infectious fluorescently labeled viruses can be obtained and that the quantity of labels can be accurately measured and controlled inside individual viral particles. We demonstrate, with proper control experiments, the formation of IN oligomers in single viral particles and inside viral complexes in infected cells. Finally, we show a clear effect on IN oligomerization of small molecule inhibitors of interactions of IN with its natural human cofactor LEDGF/p75, corroborating that IN oligomer enhancing drugs are active already at the level of the virus and strongly suggesting the presence of a dynamic, enhanceable equilibrium between the IN dimer and tetramer in viral particles. Although applied to the HIV-1 IN enzyme, our methodology for utilizing HIV virions as nanoscopic test tubes for probing PPIs is generic, i.e., other PPIs targeted into the HIV-1, or PPIs targeted into other viruses, can potentially be studied with a similar strategy. PMID:24654558

  8. Hybrid Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of HIV-1 Integrase/Inhibitor Complexes

    PubMed Central

    Nunthaboot, Nadtanet; Pianwanit, Somsak; Parasuk, Vudhichai; Ebalunode, Jerry O.; Briggs, James M.; Kokpol, Sirirat

    2007-01-01

    Human immunodeficiency virus (HIV)-1 integrase (IN) is an attractive target for development of acquired immunodeficiency syndrome chemotherapy. In this study, conventional and coupled quantum mechanical and molecular mechanical (QM/MM) molecular dynamics (MD) simulations of HIV-1 IN complexed with 5CITEP (IN-5CITEP) were carried out. In addition to differences in the bound position of 5CITEP, significant differences at the two levels of theory were observed in the metal coordination geometry and the areas involving residues 116–119 and 140–166. In the conventional MD simulation, the coordination of Mg2+ was found to be a near-perfect octahedral geometry whereas a distorted octahedral complex was observed in QM/MM. All of the above reasons lead to a different pattern of protein-ligand salt link formation that was not observed in the classical MD simulation. Furthermore to provide a theoretical understanding of inhibition mechanisms of 5CITEP and its derivative (DKA), hybrid QM/MM MD simulations of the two complexes (IN-5CITEP and IN-DKA) have been performed. The results reveal that areas involving residues 60–68, 116–119, and 140–149 were substantially different among the two systems. The two systems show similar pattern of metal coordination geometry, i.e., a distorted octahedron. In IN-DKA, both OD1 and OD2 of Asp-64 coordinate the Mg2+ in a monodentate fashion whereas only OD1 is chelated to the metal as observed in IN-5CITEP. The high potency of DKA as compared to 5CITEP is supported by a strong salt link formed between its carboxylate moiety and the ammonium group of Lys-159. Detailed comparisons between HIV-1 IN complexed with DKA and with 5CITEP provide information about ligand structure effects on protein-ligand interactions in particular with the Lys-159. This is useful for the design of new selective HIV-1 IN inhibitors. PMID:17693479

  9. A rat brain mRNA encoding a transcriptional activator homologous to the DNA binding domain of retroviral integrases.

    PubMed Central

    Duilio, A; Zambrano, N; Mogavero, A R; Ammendola, R; Cimino, F; Russo, T

    1991-01-01

    We have isolated a rat cDNA, named FE65, hybridizing to an mRNA of about 2,300 nucleotides present in rat brain, undetectable in rat liver and very poorly represented in other tissues. An mRNA of the same size is present in human neuroblastoma cells and is absent from other human cell lines. The FE65 cDNA contains an open reading frame (ORF) coding for a polypeptide of 499 amino acids in which 143 residues can be aligned with the DNA binding domain of the integrases encoded by mammalian immunodeficiency viruses. The remaining part of the FE65 ORF is not homologous with the correspondent regions of the integrases; the first 206 residues of the FE65 ORF show numerous negative charges and a short sequence not dispensable for the function of the transactivating acidic domain of the jun family transcriptional factors. A plasmid which expresses FE65 amino acids 1-232 fused to the yeast GAL4 DNA binding domain was co-transfected with a plasmid containing five GAL4 binding sites upstream of a minimal Adenovirus promoter controlling the expression of the CAT gene. This experiment showed that the fused protein GAL4-FE65 is able to obtain a 30-40 fold increase of the CAT gene expression compared to the expression observed in the presence of the GAL4 DNA binding domain alone. Two types of FE65 mRNA are present in rat brain, differing only for six nucleotides. We demonstrate that this is the consequence of a neuron-specific alternative splicing of a six-nucleotide miniexon, which is also present in the human genome, in an intron/exon context very similar to that of the rat FE65 gene. Images PMID:1923810

  10. Pharmacovirological impact of an integrase inhibitor on human immunodeficiency virus type 1 cDNA species in vivo.

    PubMed

    Goffinet, Christine; Allespach, Ina; Oberbremer, Lena; Golden, Pamela L; Foster, Scott A; Johns, Brian A; Weatherhead, Jason G; Novick, Steven J; Chiswell, Karen E; Garvey, Edward P; Keppler, Oliver T

    2009-08-01

    Clinical trials of the first approved integrase inhibitor (INI), raltegravir, have demonstrated a drop in the human immunodeficiency virus type 1 (HIV-1) RNA loads of infected patients that was unexpectedly more rapid than that with a potent reverse transcriptase inhibitor, and apparently dose independent. These clinical outcomes are not understood. In tissue culture, although their inhibition of integration is well documented, the effects of INIs on levels of unintegrated HIV-1 cDNAs have been variable. Furthermore, there has been no report to date on an INI's effect on these episomal species in vivo. Here, we show that prophylactic treatment of transgenic rats with the strand transfer INI GSK501015 reduced levels of viral integrants in the spleen by up to 99.7%. Episomal two-long-terminal-repeat (LTR) circles accumulated up to sevenfold in this secondary lymphoid organ, and this inversely correlated with the impact on the proviral burden. Contrasting raltegravir's dose-ranging study with HIV patients, titration of GSK501015 in HIV-infected animals demonstrated dependence of the INI's antiviral effect on its serum concentration. Furthermore, the in vivo 50% effective concentration calculated from these data best matched GSK501015's in vitro potency when serum protein binding was accounted for. Collectively, this study demonstrates a titratable, antipodal impact of an INI on integrated and episomal HIV-1 cDNAs in vivo. Based on these findings and known biological characteristics of viral episomes, we discuss how integrase inhibition may result in additional indirect antiviral effects that contribute to more rapid HIV-1 decay in HIV/AIDS patients. PMID:19458008

  11. Antiviral characteristics of GSK1265744, an HIV integrase inhibitor dosed orally or by long-acting injection.

    PubMed

    Yoshinaga, Tomokazu; Kobayashi, Masanori; Seki, Takahiro; Miki, Shigeru; Wakasa-Morimoto, Chiaki; Suyama-Kagitani, Akemi; Kawauchi-Miki, Shinobu; Taishi, Teruhiko; Kawasuji, Takashi; Johns, Brian A; Underwood, Mark R; Garvey, Edward P; Sato, Akihiko; Fujiwara, Tamio

    2015-01-01

    GSK1265744 is a new HIV integrase strand transfer inhibitor (INSTI) engineered to deliver efficient antiviral activity with a once-daily, low-milligram dose that does not require a pharmacokinetic booster. The in vitro antiviral profile and mechanism of action of GSK1265744 were established through integrase enzyme assays, resistance passage experiments, and cellular assays with site-directed molecular (SDM) HIV clones resistant to other classes of anti-HIV-1 agents and earlier INSTIs. GSK1265744 inhibited HIV replication with low or subnanomolar efficacy and with a selectivity index of at least 22,000 under the same culture conditions. The protein-adjusted half-maximal inhibitory concentration (PA-EC50) extrapolated to 100% human serum was 102 nM. When the virus was passaged in the presence of GSK1265744, highly resistant mutants with more than a 10-fold change (FC) in EC50 relative to that of the wild-type were not observed for up to 112 days of culture. GSK1265744 demonstrated activity against SDM clones containing the raltegravir (RAL)-resistant Y143R, Q148K, N155H, and G140S/Q148H signature variants (FC less than 6.1), while these mutants had a high FC in the EC50 for RAL (11 to >130). Either additive or synergistic effects were observed when GSK1265744 was tested in combination with representative anti-HIV agents, and no antagonistic effects were seen. These findings demonstrate that, similar to dolutegravir, GSK1265744 is differentiated as a new INSTI, having a markedly distinct resistance profile compared with earlier INSTIs, RAL, and elvitegravir (EVG). The collective data set supports further clinical development of GSK1265744. PMID:25367908

  12. A method for producing transgenic cells using a multi-integrase system on a human artificial chromosome vector.

    PubMed

    Yamaguchi, Shigeyuki; Kazuki, Yasuhiro; Nakayama, Yuji; Nanba, Eiji; Oshimura, Mitsuo; Ohbayashi, Tetsuya

    2011-01-01

    The production of cells capable of expressing gene(s) of interest is important for a variety of applications in biomedicine and biotechnology, including gene therapy and animal transgenesis. The ability to insert transgenes at a precise location in the genome, using site-specific recombinases such as Cre, FLP, and ΦC31, has major benefits for the efficiency of transgenesis. Recent work on integrases from ΦC31, R4, TP901-1 and Bxb1 phages demonstrated that these recombinases catalyze site-specific recombination in mammalian cells. In the present study, we examined the activities of integrases on site-specific recombination and gene expression in mammalian cells. We designed a human artificial chromosome (HAC) vector containing five recombination sites (ΦC31 attP, R4 attP, TP901-1 attP, Bxb1 attP and FRT; multi-integrase HAC vector) and de novo mammalian codon-optimized integrases. The multi-integrase HAC vector has several functions, including gene integration in a precise locus and avoiding genomic position effects; therefore, it was used as a platform to investigate integrase activities. Integrases carried out site-specific recombination at frequencies ranging from 39.3-96.8%. Additionally, we observed homogenous gene expression in 77.3-87.5% of colonies obtained using the multi-integrase HAC vector. This vector is also transferable to another cell line, and is capable of accepting genes of interest in this environment. These data suggest that integrases have high DNA recombination efficiencies in mammalian cells. The multi-integrase HAC vector enables us to produce transgene-expressing cells efficiently and create platform cell lines for gene expression. PMID:21390305

  13. Discovery of small-molecule HIV-1 fusion and integrase inhibitors oleuropein and hydroxytyrosol: Part I. Integrase inhibition

    SciTech Connect

    Lee-Huang, Sylvia . E-mail: sylvia.lee-huang@med.nyu.edu; Huang, Philip Lin; Zhang Dawei; Lee, Jae Wook; Bao Ju; Sun Yongtao; Chang, Young-Tae; Zhang, John; Huang, Paul Lee

    2007-03-23

    We have identified oleuropein (Ole) and hydroxytyrosol (HT) as a unique class of HIV-1 inhibitors from olive leaf extracts effective against viral fusion and integration. We used molecular docking simulation to study the interactions of Ole and HT with viral targets. We find that Ole and HT bind to the conserved hydrophobic pocket on the surface of the HIV-gp41 fusion domain by hydrogen bonds with Q577 and hydrophobic interactions with I573, G572, and L568 on the gp41 N-terminal heptad repeat peptide N36, interfering with formation of the gp41 fusion-active core. To test and confirm modeling predications, we examined the effect of Ole and HT on HIV-1 fusion complex formation using native polyacrylamide gel electrophoresis and circular dichroism spectroscopy. Ole and HT exhibit dose-dependent inhibition on HIV-1 fusion core formation with EC{sub 50}s of 66-58 nM, with no detectable toxicity. Our findings on effects of HIV-1 integrase are reported in the subsequent article.

  14. TISSUE DISTRIBUTION OF INORGANIC ARSENIC (AS) AND ITS METHYLATED METABOLITES IN MICE FOLLOWING ORAL ADMINISTRATION OF ARSENATE (ASV)

    EPA Science Inventory

    TISSUE DISTRIBUTION OF INORGANIC ARSENIC (iAs) AND ITS METHYLATED METABOLITES IN MICE FOLLOWING ORAL ADMINISTRATION OF ARSENATE (AsV). E M Kenyon1, L M Del Razo2, and M F Hughes1. 1NHEERL, ORD, US EPA, RTP, NC, USA; 2CINVESTAV-IPN, Mexico City, Mexico.

    The relationship o...

  15. Removal of Cr(VI) and As(V) ions from aqueous solutions by polyacrylate and polystyrene anion exchange resins

    NASA Astrophysics Data System (ADS)

    Jachuła, Justyna; Hubicki, Zbigniew

    2013-09-01

    The sorption of Cr(VI) and As(V) from the aqueous solutions with the polyacrylate anion exchangers of the strong base functional groups Amberlite IRA 458 and Amberlite IRA 958 was studied. The studies were carried out by the static-batch method. The concentration of Cr(VI) and As(V) ions in the aqueous solution was determined by the UV-VIS spectrophotometer. The influence of several parameters was studied with respect to sorption equilibrium. The phase contact time and the concentration affect the sorption process. The equilibrium state was established already after 15 min of phase contact time. Maximum uptake of Cr(VI) and As(V) occurred at pH 5 and 10, respectively. The determined kinetic parameters imply that the sorption process proceeds according to the equation type of pseudo second-order. Sorption equilibrium data were correlated with the Langmuir and Freundlich isotherms. Removal of As(V) ions on macroporous Amberlite IRA 900 decreased about 12 % in presence of other anions (Cl-, NO3 -, SO4 2-) in the solution. The sorption was temperature dependent.

  16. Subtype diversity associated with the development of HIV-1 resistance to integrase inhibitors.

    PubMed

    Brenner, Bluma G; Lowe, Matthew; Moisi, Daniela; Hardy, Isabelle; Gagnon, Simon; Charest, Hugues; Baril, Jean Guy; Wainberg, Mark A; Roger, Michel

    2011-05-01

    We used genotypic and phylogenetic analysis to determine integrase diversity among subtypes, and studied natural polymorphisms and mutations implicated in resistance to integrase inhibitors (INI) in treatment-naïve persons (n = 220) and -experienced individuals (n = 24). Phylogenetics revealed 7 and 10% inter-subtype diversity in the integrase and reverse transcriptase (RT)/protease regions, respectively. Integrase sequencing identified a novel A/B recombinant in which all viruses in a male-sex-male (MSM) transmission cluster (n = 12) appeared to possess subtype B in integrase and subtype A in the remainder of the pol region. Natural variations and signature polymorphisms were observed at codon positions 140, 148, 151, 157, and 160 among HIV subtypes. These variations predicted higher genetic barriers to G140S and G140C in subtypes C, CRF02_AG, and A/CRF01_AE, as well as higher genetic barriers toward acquisition of V151I in subtypes CRF02_AG and A/CRF01_AE. The E157Q and E160Q mutational motif was observed in 35% of INI-naïve patients harboring subtype C infections, indicating intra-subtype variations. Thirteen patients failed raltegravir (RAL)-containing regimens within 8 ± 1 months, in association with the major Q148K/R/H and G140A/S (n = 8/24) or N155H (n = 5/24) mutational pathways. Of note, the remaining patients on RAL regimens for 14 ± 3 months harbored no or only minor integrase mutations/polymorphisms (T66I, T97A, H114P, S119P, A124S, G163R, I203M, R263K). These results demonstrate the importance of understanding subtype variability in the development of resistance to INIs. PMID:21360548

  17. Preliminary study on the DNA-binding properties of phage ΦC31 integrase.

    PubMed

    Li, Zhihui; Fang, Yuxiang; Wang, Rencheng; Xue, Jinglun; Chen, Jinzhong

    2011-09-15

    ΦC31 integrase is a member of the large serine subfamily and is required for the recombination of the phage genome into the host chromosome, either to establish or exit from the lysogenic state. This enzyme can also mediate site-specific integration in mammalian cells in a cofactor-independent manner and has been considered as a potentially powerful tool for gene therapy. It has previously been reported that DAXX interacts with ΦC31 integrase and markedly inhibits its integration efficiency, and the 451RFGK454 tetramer of ΦC31 integrase has been identified as the interacting motif. Here, we report that both the deletion of the tetramer or the replacement of Arg with His greatly reduced the recombination activity of the ΦC31 integrase. Electrophoretic mobility shift assays further demonstrated that the DNA-binding ability and binding specificity of the two mutants were dramatically reduced. Bioinformatic analysis indicated a probable helix-turn-helix-like DNA-binding motif between residues 415-525, a region that contains the tetramer motif. However, neither truncated Int(415-525) nor Int(△415-525) alone could bind to the attB target sequence. Results of a circular dichroism spectroscopy assay indicated that Int(415-525) did not fold correctly into a helix-turn-helix-like structure, which may be one of the reasons for its lack of DNA-binding ability. Thus, the identification and confirmation of four key amino acids in the DNA-binding specificity and recombination activity of ΦC31 integrase provide information about the domain structure and function of the large C-terminal region and suggest important implications for the more efficient use of integrase in gene transfer and gene therapy. PMID:21679753

  18. Development of tricyclic hydroxy-1H-pyrrolopyridine-trione containing HIV-1 integrase inhibitors.

    PubMed

    Zhao, Xue Zhi; Maddali, Kasthuraiah; Metifiot, Mathieu; Smith, Steven J; Vu, B Christie; Marchand, Christophe; Hughes, Stephen H; Pommier, Yves; Burke, Terrence R

    2011-05-15

    New tricyclic HIV-1 integrase (IN) inhibitors were prepared that combined structural features of bicyclic pyrimidinones with recently disclosed 4,5-dihydroxy-1H-isoindole-1,3(2H)-diones. This combination resulted in the introduction of a nitrogen into the aryl ring and the addition of a fused third ring to our previously described inhibitors. The resulting analogues showed low micromolar inhibitory potency in in vitro HIV-1 integrase assays, with good selectivity for strand transfer relative to 3'-processing. PMID:21493066

  19. Role of human immunodeficiency virus type 1 integrase in uncoating of the viral core.

    PubMed

    Briones, Marisa S; Dobard, Charles W; Chow, Samson A

    2010-05-01

    After membrane fusion with a target cell, the core of human immunodeficiency virus type 1 (HIV-1) enters into the cytoplasm, where uncoating occurs. The cone-shaped core is composed of the viral capsid protein (CA), which disassembles during uncoating. The underlying factors and mechanisms governing uncoating are poorly understood. Several CA mutations can cause changes in core stability and a block at reverse transcription, demonstrating the requirement for optimal core stability during viral replication. HIV-1 integrase (IN) catalyzes the insertion of the viral cDNA into the host genome, and certain IN mutations are pleiotropic. Similar to some CA mutants, two IN mutants, one with a complete deletion of IN (NL-DeltaIN) and the other with a Cys-to-Ser substitution (NL-C130S), were noninfectious, with a replication block at reverse transcription. Compared to the wild type (WT), the cytoplasmic CA levels of the IN mutants in infected cells were reduced, suggesting accelerated uncoating. The role of IN during uncoating was examined by isolating and characterizing cores from NL-DeltaIN and NL-C130S. Both IN mutants could form functional cores, but the core yield and stability were decreased. Also, virion incorporation of cyclophilin A (CypA), a cellular peptidyl-prolyl isomerase that binds specifically to CA, was decreased in the IN mutants. Cores isolated from WT virus depleted of CypA had an unstable-core phenotype, confirming a role of CypA in promoting optimal core stability. Taken together, our results indicate that IN is required during uncoating for maintaining CypA-CA interaction, which promotes optimal stability of the viral core. PMID:20219923

  20. DNA Physical Properties and Nucleosome Positions Are Major Determinants of HIV-1 Integrase Selectivity

    PubMed Central

    Naughtin, Monica; Haftek-Terreau, Zofia; Xavier, Johan; Meyer, Sam; Silvain, Maud; Jaszczyszyn, Yan; Levy, Nicolas; Miele, Vincent; Benleulmi, Mohamed Salah; Ruff, Marc; Parissi, Vincent; Vaillant, Cédric; Lavigne, Marc

    2015-01-01

    Retroviral integrases (INs) catalyse the integration of the reverse transcribed viral DNA into the host cell genome. This process is selective, and chromatin has been proposed to be a major factor regulating this step in the viral life cycle. However, the precise underlying mechanisms are still under investigation. We have developed a new in vitro integration assay using physiologically-relevant, reconstituted genomic acceptor chromatin and high-throughput determination of nucleosome positions and integration sites, in parallel. A quantitative analysis of the resulting data reveals a chromatin-dependent redistribution of the integration sites and establishes a link between integration sites and nucleosome positions. The co-activator LEDGF/p75 enhanced integration but did not modify the integration sites under these conditions. We also conducted an in cellulo genome-wide comparative study of nucleosome positions and human immunodeficiency virus type-1 (HIV-1) integration sites identified experimentally in vivo. These studies confirm a preferential integration in nucleosome-covered regions. Using a DNA mechanical energy model, we show that the physical properties of DNA probed by IN binding are important in determining IN selectivity. These novel in vitro and in vivo approaches confirm that IN has a preference for integration into a nucleosome, and suggest the existence of two levels of IN selectivity. The first depends on the physical properties of the target DNA and notably, the energy required to fit DNA into the IN catalytic pocket. The second depends on the DNA deformation associated with DNA wrapping around a nucleosome. Taken together, these results indicate that HIV-1 IN is a shape-readout DNA binding protein. PMID:26075397

  1. Tracer test with As(V) under variable redox conditions controlling arsenic transport in the presence of elevated ferrous iron concentrations.

    PubMed

    Höhn, R; Isenbeck-Schröter, M; Kent, D B; Davis, J A; Jakobsen, R; Jann, S; Niedan, V; Scholz, C; Stadler, S; Tretner, A

    2006-11-20

    To study transport and reactions of arsenic under field conditions, a small-scale tracer test was performed in an anoxic, iron-reducing zone of a sandy aquifer at the USGS research site on Cape Cod, Massachusetts, USA. For four weeks, a stream of groundwater with added As(V) (6.7 muM) and bromide (1.6 mM), was injected in order to observe the reduction of As(V) to As(III). Breakthrough of bromide (Br(-)), As(V), and As(III) as well as additional parameters characterizing the geochemical conditions was observed at various locations downstream of the injection well over a period of 104 days. After a short lag period, nitrate and dissolved oxygen from the injectate oxidized ferrous iron and As(V) became bound to the freshly formed hydrous iron oxides. Approximately one week after terminating the injection, anoxic conditions had been reestablished and increases in As(III) concentrations were observed within 1 m of the injection. During the observation period, As(III) and As(V) were transported to a distance of 4.5 m downgradient indicating significant retardation by sorption processes for both species. Sediment assays as well as elevated concentrations of hydrogen reflected the presence of As(V) reducing microorganisms. Thus, microbial As(V) reduction was thought to be one major process driving the release of As(III) during the tracer test in the Cape Cod aquifer. PMID:16945450

  2. Dithiothreitol causes HIV-1 integrase dimer dissociation while agents interacting with the integrase dimer interface promote dimer formation.

    PubMed

    Tsiang, Manuel; Jones, Gregg S; Hung, Magdeleine; Samuel, Dharmaraj; Novikov, Nikolai; Mukund, Susmith; Brendza, Katherine M; Niedziela-Majka, Anita; Jin, Debi; Liu, Xiaohong; Mitchell, Michael; Sakowicz, Roman; Geleziunas, Romas

    2011-03-15

    We have developed a homogeneous time-resolved fluorescence resonance energy transfer (FRET)-based assay that detects the formation of HIV-1 integrase (IN) dimers. The assay utilizes IN monomers that express two different epitope tags that are recognized by their respective antibodies, coupled to distinct fluorophores. Surprisingly, we found that dithiothreitol (DTT), a reducing agent essential for in vitro enzymatic activity of IN, weakened the interaction between IN monomers. This effect of DTT on IN is dependent on its thiol groups, since the related chemical threitol, which contains hydroxyls in place of thiols, had no effect on IN dimer formation. By studying mutants of IN, we determined that cysteines in IN appear to be dispensable for the dimer dissociation effect of DTT. Peptides derived from the IN binding domain (IBD) of lens epithelium derived growth factor/transcriptional coactivator p75 (LEDGF), a cellular cofactor that interacts with the IN dimer interface, were tested in this IN dimerization assay. These peptides, which compete with LEDGF for binding to IN, displayed an intriguing equilibrium binding dose-response curve characterized by a plateau rising to a peak, then descending to a second plateau. Mathematical modeling of this binding system revealed that these LEDGF-derived peptides promote IN dimerization and block subunit exchange between IN dimers. This dose-response behavior was also observed with a small molecule that interacts with the IN dimer interface and inhibits LEDGF binding to IN. In conclusion, this novel IN dimerization assay revealed that peptide and small molecule inhibitors of the IN-LEDGF interaction also stabilize IN dimers and promote their formation. PMID:21222490

  3. Evaluation of Serum Creatinine Changes With Integrase Inhibitor Use in Human Immunodeficiency Virus-1 Infected Adults

    PubMed Central

    Lindeman, Tara A.; Duggan, Joan M.; Sahloff, Eric G.

    2016-01-01

    This retrospective chart review evaluated changes in serum creatinine and creatinine clearance (CrCl) after initiation of an integrase inhibitor (INSTI)-based regimen as initial treatment in human immunodeficiency virus-infected adults. Serum creatinine and CrCl changes were similar to those seen in clinical trials for INSTIs. No renal-related serious adverse events or discontinuations occurred. PMID:27092314

  4. Integrase Inhibitor Prodrugs: Approaches to Enhancing the Anti-HIV Activity of β-Diketo Acids.

    PubMed

    Nair, Vasu; Okello, Maurice

    2015-01-01

    HIV integrase, encoded at the 3'-end of the HIV pol gene, is essential for HIV replication. This enzyme catalyzes the incorporation of HIV DNA into human DNA, which represents the point of "no-return" in HIV infection. Integrase is a significant target in anti-HIV drug discovery. This review article focuses largely on the design of integrase inhibitors that are β-diketo acids constructed on pyridinone scaffolds. Methodologies for synthesis of these compounds are discussed. Integrase inhibition data for the strand transfer (ST) step are compared with in vitro anti-HIV data. The review also examines the issue of the lack of correlation between the ST enzymology data and anti-HIV assay results. Because this disconnect appeared to be a problem associated with permeability, prodrugs of these inhibitors were designed and synthesized. Prodrugs dramatically improved the anti-HIV activity data. For example, for compound, 96, the anti-HIV activity (EC50) improved from 500 nM for this diketo acid to 9 nM for its prodrug 116. In addition, there was excellent correlation between the IC50 and IC90 ST enzymology data for 96 (6 nM and 97 nM, respectively) and the EC50 and EC90 anti-HIV data for its prodrug 116 (9 nM and 94 nM, respectively). Finally, it was confirmed that the prodrug 116 was rapidly hydrolyzed in cells to the active compound 96. PMID:26184144

  5. Discovery of HIV-1 integrase inhibitors: pharmacophore mapping, virtual screening, molecular docking, synthesis, and biological evaluation.

    PubMed

    Bhatt, Hardik; Patel, Paresh; Pannecouque, Christophe

    2014-02-01

    HIV-1 integrase enzyme plays an important role in the life cycle of HIV and responsible for integration of virus into human genome. Here, both computational and synthetic approaches were used to design and synthesize newer HIV-1 integrase inhibitors. Pharmacophore mapping was performed on 20 chemically diverse molecules using DISCOtech, and refinement was carried out using GASP. Ten pharmacophore models were generated, and model 2, containing four features including two donor sites, one acceptor atom, and one hydrophobic region, was considered the best model as it has the highest fitness score. It was used as a query in NCI and Maybridge databases. Molecules having more than 99% Q(fit) value were used to design 30 molecules bearing pteridine ring and were docked on co-crystal structure of HIV-1 integrase enzyme. Among these, six molecules, showing good docking score compared with the reference standards, were synthesized by conventional as well as microwave-assisted methods. All compounds were characterized by physical and spectral data and evaluated for in vitro anti-HIV activity against the replication of HIV-1 (IIIB) in MT-4 cells. The used approach of molecular docking and anti-HIV activity data of designed molecules will provide significant insights to discover novel HIV-1 Integrase Inhibitors. PMID:23957390

  6. Resistance against Integrase Strand Transfer Inhibitors and Relevance to HIV Persistence.

    PubMed

    Mesplède, Thibault; Wainberg, Mark A

    2015-07-01

    Drug resistance prevents the successful treatment of HIV-positive individuals by decreasing viral sensitivity to a drug or a class of drugs. In addition to transmitted resistant viruses, treatment-naïve individuals can be confronted with the problem of drug resistance through de novo emergence of such variants. Resistant viruses have been reported for every antiretroviral drug tested so far, including the integrase strand transfer inhibitors raltegravir, elvitegravir and dolutegravir. However, de novo resistant variants against dolutegravir have been found in treatment-experienced but not in treatment-naïve individuals, a characteristic that is unique amongst antiretroviral drugs. We review here the issue of drug resistance against integrase strand transfer inhibitors as well as both pre-clinical and clinical studies that have led to the identification of the R263K mutation in integrase as a signature resistance substitution for dolutegravir. We also discuss how the topic of drug resistance against integrase strand transfer inhibitors may have relevance in regard to the nature of the HIV reservoir and possible HIV curative strategies. PMID:26198244

  7. The Stringent Response Promotes Antibiotic Resistance Dissemination by Regulating Integron Integrase Expression in Biofilms

    PubMed Central

    Strugeon, Emilie; Tilloy, Valentin; Ploy, Marie-Cécile

    2016-01-01

    ABSTRACT Class 1 integrons are genetic systems that enable bacteria to capture and express gene cassettes. These integrons, when isolated in clinical contexts, most often carry antibiotic resistance gene cassettes. They play a major role in the dissemination of antibiotic resistance among Gram-negative bacteria. The key element of integrons is the integrase, which allows gene cassettes to be acquired and shuffled. Planktonic culture experiments have shown that integrase expression is regulated by the bacterial SOS response. In natural settings, however, bacteria generally live in biofilms, which are characterized by strong antibiotic resilience and by increased expression of stress-related genes. Here, we report that under biofilm conditions, the stringent response, which is induced upon starvation, (i) increases basal integrase and SOS regulon gene expression via induction of the SOS response and (ii) exerts biofilm-specific regulation of the integrase via the Lon protease. This indicates that biofilm environments favor integron-mediated acquisition of antibiotic resistance and other adaptive functions encoded by gene cassettes. PMID:27531906

  8. Biosorption of Cr(VI) and As(V) at high concentrations by organic and inorganic wastes

    NASA Astrophysics Data System (ADS)

    María Rivas Pérez, Ivana; Paradelo Núñez, Remigio; Nóvoa Muñoz, Juan Carlos; Arias Estévez, Manuel; José Fernández Sanjurjo, María; Álvarez Rodríguez, Esperanza; Núñez Delgado, Avelino

    2016-04-01

    The potential reutilization of several wastes as biosorbents for As(V) and Cr(VI) has been assessed in batch-type experiments. The materials studied were one inorganic: mussel shell, and three organic: pine bark, oak ash and hemp waste. Batch experiments were performed in order to determine the removal capacity of the wastes under conditions of high As(V) and Cr(VI) loads. For this, 3 g of each waste material were added with 30 mL NaNO3 0.01 M dissolutions containing 0, 0.5, 1.5, 3 and 6 mmol As(V) L‑1 or Cr(VI) L‑1, prepared from analytical grade Na2HAsO4 or K2Cr2O7. The resulting suspensions were shaken for 24 h, centrifuged and filtered. Once each batch experiment corresponding to the sorption trials ended, each individual sample was added with 30 mL of NaNO3 0.01 M to desorb As(V) or Cr(VI), shaken for 24 h, centrifuged and filtered as in the sorption trials. Oak ash showed high sorption (>76%) and low desorption (<7%) for As(V), which was lower on mussel shell (<31%), hemp waste (<16%) and pine bark (<9.9%). In turn, pine bark showed the highest Cr(VI) sorption (>98%) with very low desorption (<0.5%), followed by oak ash (27% sorption), and hemp waste and mussel shell, that presented very low Cr(VI) sorption (<10%). Sorption data for both elements were better described by the Freundlich than by the Langmuir model. The variable results obtained for the removal of the two anionic contaminants for a given sorbent suggest that different mechanisms govern removal from the solution in each case. In summary, oak ash would be an efficient sorbent material for As(V), but not for Cr(VI), while pine bark would be the best sorbent for Cr(VI) removal.

  9. Pharmacokinetics and dose-range finding toxicity of a novel anti-HIV active integrase inhibitor.

    PubMed

    Nair, Vasu; Okello, Maurice; Mishra, Sanjay; Mirsalis, Jon; O'Loughlin, Kathleen; Zhong, Yu

    2014-08-01

    Integration of viral DNA into human chromosomal DNA catalyzed by HIV integrase represents the "point of no return" in HIV infection. For this reason, HIV integrase is considered a crucial target in the development of new anti-HIV therapeutic agents. We have discovered a novel HIV integrase inhibitor 1, that exhibits potent antiviral activity and a favorable metabolism profile. This paper reports on the pharmacokinetics and toxicokinetics of compound 1 and the relevance of these findings with respect to further development of this integrase-targeted antiviral agent. Oral administration of compound 1 in Sprague Dawley rats revealed rapid absorption. Drug exposure increased with increasing drug concentration, indicative of appropriate dose-dependence correlation. Compound 1 exhibited suitable plasma half-life, extensive extravascular distribution and acceptable bioavailability. Toxicity studies revealed no compound-related clinical pathology findings. There were no changes in erythropoietic, white blood cell or platelet parameters in male and female rats. There was no test-article related change in other clinical chemistry parameters. In addition, there were no detectable levels of bilirubin in the urine and there were no treatment-related effects on urobilinogen or other urinalysis parameters. The preclinical studies also revealed that the no observed adverse effect level and the maximum tolerated dose were both high (>500mg/kg/day). The broad and significant antiviral activity and favorable metabolism profile of this integrase inhibitor, when combined with the in vivo pharmacokinetic and toxicokinetic data and their pharmacological relevance, provide compelling and critical support for its further development as an anti-HIV therapeutic agent. PMID:24821255

  10. Simulink-Based Simulation Architecture for Evaluating Controls for Aerospace Vehicles (SAREC-ASV)

    NASA Technical Reports Server (NTRS)

    Christhilf, David m.; Bacon, Barton J.

    2006-01-01

    The Simulation Architecture for Evaluating Controls for Aerospace Vehicles (SAREC-ASV) is a Simulink-based approach to providing an engineering quality desktop simulation capability for finding trim solutions, extracting linear models for vehicle analysis and control law development, and generating open-loop and closed-loop time history responses for control system evaluation. It represents a useful level of maturity rather than a finished product. The layout is hierarchical and supports concurrent component development and validation, with support from the Concurrent Versions System (CVS) software management tool. Real Time Workshop (RTW) is used to generate pre-compiled code for substantial component modules, and templates permit switching seamlessly between original Simulink and code compiled for various platforms. Two previous limitations are addressed. Turn around time for incorporating tabular model components was improved through auto-generation of required Simulink diagrams based on data received in XML format. The layout was modified to exploit a Simulink "compile once, evaluate multiple times" capability for zero elapsed time for use in trimming and linearizing. Trim is achieved through a Graphical User Interface (GUI) with a narrow, script definable interface to the vehicle model which facilitates incorporating new models.

  11. Behaviour of Silica and Florisil as Solid Supports in the Removal Process of As(V) from Aqueous Solutions

    PubMed Central

    Gabor, Andreea; Davidescu, Corneliu Mircea; Negrea, Adina; Ciopec, Mihaela; Lupa, Lavinia

    2015-01-01

    In this study two solid supports, silica and florisil, were impregnated with crown ether (dibenzo-18-crown-6) and Fe(III) ions and their efficiency was compared in the adsorption process of As(V) from aqueous solutions. The solid supports were impregnated with crown ether due to their ability to build complexes with positives ions. Fe(III) was used because of As(V) affinity for it. The impregnated solid supports were characterized by energy dispersive X-ray analysis, scanning electron microscopy, Fourier transform infrared spectroscopy, and the specific surface area. The influence of the solid : liquid ratio on the adsorption process, kinetic studies for the pseudo-first-order and pseudo-second-order, and activation energy were studied. Thermodynamic studies as well as equilibrium studies were carried out. The obtained results showed that, from the two considered materials, impregnated silica presents a higher efficiency with a good selectivity, able to remove As(V) from aqueous solutions containing trace concentrations. PMID:25821633

  12. Discovery of a novel HIV-1 integrase inhibitor from natural compounds through structure based virtual screening and cell imaging.

    PubMed

    Gu, Wan-Gang; Zhang, Xuan; Ip, Denis Tsz-Ming; Yang, Liu-Meng; Zheng, Yong-Tang; Wan, David Chi-Cheong

    2014-09-17

    The interaction between HIV-1 integrase and LEDGF/P75 has been validated as a target for anti-HIV drug development. Based on the crystal structure of integrase in complex with LEDGF/P75, a library containing 80 thousand natural compounds was filtered with virtual screening. 11 hits were selected for cell based assays. One compound, 3-(1,3-benzothiazol-2-yl)-8-{[bis(2-hydroxyethyl)amino]methyl}-7-hydroxy-2H-chromen-2-one (D719) inhibited integrase nuclear translocation in cell imaging. The binding mode of D719 was analyzed with molecular simulation. The anti-HIV activity of D719 was assayed by measuring the p24 antigen production in acute infection. The structure characteristics of D719 may provide valuable information for integrase inhibitor design. PMID:25128456

  13. Activities, crystal structures and molecular dynamics of dihydro-1H-isoindole derivatives, inhibitors of HIV-1 integrase

    PubMed Central

    Métifiot, Mathieu; Maddali, Kasthuraiah; Johnson, Barry C.; Hare, Stephen; Smith, Steven J.; Zhao, XueZhi; Marchand, Christophe; Burke, Terrence R.; Hughes, Stephen H.; Cherepanov, Peter; Pommier, Yves

    2013-01-01

    Based on a series of lactam and phthalimide derivatives that inhibit HIV-1 integrase, we developed a new derivative, XZ-259, with biochemical and antiviral activities comparable to raltegravir. We determined the crystal structures of XZ-259 and four other derivatives in complex with the prototype foamy virus intasome. The compounds bind at the integrase-Mg2+-DNA interface of the integrase active site. In biochemical and antiviral assays, XZ-259 inhibits raltegravir-resistant HIV-1 integrases harboring the Y143R mutation. Molecular modeling is also presented suggesting that XZ-259 can bind in the HIV-1 intasome with its dimethyl sulfonamide group adopting two opposite orientations. Molecular dynamics analyses of the HIV-1 intasome highlight the importance of the viral DNA in drug potency. PMID:23075516

  14. Actinophage R4 integrase-based site-specific chromosomal integration of non-replicative closed circular DNA.

    PubMed

    Miura, Takamasa; Nishizawa, Akito; Nishizawa, Tomoyasu; Asayama, Munehiko; Shirai, Makoto

    2016-06-01

    The actinophage R4 integrase (Sre)-based molecular genetic engineering system was developed for the chromosomal integration of multiple genes in Escherichia coli. A cloned DNA fragment containing two attP sites, green fluorescent protein (gfp) as a first transgene, and an antibiotic resistance gene as a selection marker was self-ligated to generate non-replicative closed circular DNA (nrccDNA) for integration. nrccDNA was introduced into attB-inserted E. coli cells harboring the plasmid expressing Sre by electroporation. The expressed Sre catalyzed site-specific integration between one of the two attP sites on nrccDNA and the attB site on the E. coli chromosome. The integration frequency was affected by the chromosomal location of the target site. A second nrccDNA containing two attB sites, lacZα encoding the alpha fragment of β-galactosidase as a transgene, and another antibiotic resistance gene was integrated into the residual attP site on the gfp-integrated E. coli chromosome via one of the two attB sites according to reiterating site-specific recombination. The integrants clearly exhibited β-galactosidase activity and green fluorescence, suggesting the simultaneous expression of multiple recombinant proteins in E. coli. The results of the present study showed that a step-by-step integration procedure using nrccDNA achieved the chromosomal integration of multiple genes. PMID:26870903

  15. Clinical Pharmacokinetic, Pharmacodynamic and Drug-Interaction Profile of the Integrase Inhibitor Dolutegravir

    PubMed Central

    Cottrell, Mackenzie L.; Hadzic, Tanja

    2013-01-01

    Dolutegravir is a second generation integrase strand transfer inhibitor (INSTI) currently under review by the US FDA for marketing approval. Dolutegravir’s in vitro, protein adjusted 90% inhibitory concentration (IC90) for wild-type virus is 0.064 μg/ml, and it retains in vitro anti-HIV 1 activity across a broad range of viral phenotypes known to confer resistance to the currently marketed INSTIs, raltegravir and elvitegravir. Dolutegravir has a half-life (t½) of 13 to 14 hours and maintains concentrations over the in vitro, protein adjusted IC90 for more than 30 hours following a single dose. Additionally, dolutegravir has comparatively low intersubject variability compared to raltegravir and elvitegravir. A plasma exposure-response relationship has been well described, with antiviral activity strongly correlating to trough concentration (Ctrough) values. Phase III trials have assessed the antiviral activity of dolutegravir compared with efavirenz and raltegravir in antiretroviral (ARV)-naïve patients and found dolutegravir to achieve more rapid and sustained virologic suppression in both instances. Additionally, studies of dolutegravir activity in patients with known INSTI-resistant mutations have been favorable, indicating that dolutegravir retains activity in a variety of INSTI resistant phenotypes. Much like currently marketed INSTIs, dolutegravir is very well tolerated. Because dolutegravir inhibits the renal transporter, organic cation transporter (OCT) 2, reduced tubular secretion of creatinine leads to non-progressive increases in serum creatinine. These serum creatinine increases have not been associated with decreased glomerular filtration rate or progressive renal impairment. Dolutegravir’s major and minor metabolic pathways are UDP glucuronosyltransferase (UGT)1A1 and cytochrome (CYP)3A4, respectively, and it neither induces nor inhibits CYP isozymes. Thus dolutegravir has a modest drug interaction profile. However, antacids significantly

  16. Comparison of Fe-Al-modified natural materials by an electrochemical method and chemical precipitation for the adsorption of F- and As(V).

    PubMed

    Vázquez Mejía, G; Martínez-Miranda, V; Fall, C; Linares-Hernández, I; Solache-Ríos, M

    2016-01-01

    The adsorption of fluoride and arsenic ions by modified natural materials may have an impact on the removal of F- and As(V) from waters. In this work, a zeolitic material and pozzolan (commonly known as pumicite) were modified with aluminium an iron by an electrochemical method and chemical precipitation, respectively. The adsorbents were characterized by X-ray diffraction, scanning electron microscopy with energy X-ray disperse spectroscopy analysis and the point of zero charge (pHzpc). F- and As(V) adsorption properties of both materials were investigated. Adsorption kinetic data were best fitted to pseudo-second-order model and equilibrium data to the Langmuir isotherm model. The highest F- and As(V) sorption capacities were obtained for modified zeolitic (0.866 mg/g) and pozzolan (3.35 mg/g) materials, respectively, with initial F- or As(V) concentrations of 10 mg/L. It was found that the unmodified materials did not show either adsorption of F- ions or As(V), which indicated that Al and Fe in the adsorbents are responsible for the adsorption of these ions. In general, both modified materials show similar capacities for the adsorption of F- and As(V). PMID:26362939

  17. Organo-modified sericite in the remediation of an aquatic environment contaminated with As(III) or As(V).

    PubMed

    Lee, Seung Mok; Tiwari, Diwakar

    2014-01-01

    The aim of this investigation was to obtain the hybrid material precursor to the naturally and abundantly available sericite, a mica-based clay; the materials were further employed in the remediation of arsenic from aqueous solutions. The study was intended to provide a cost-effective and environmentally benign treatment technology. The hybrid organo-modified sericite was obtained using hexadecyltrimethylammonium bromide (HDTMA) and alkyldimethylbenzylammonium chloride (AMBA) organic surfactants by introducing regulated doses of HDTMA or AMBA. The materials were characterized using infrared and X-ray diffraction analytical data, whereas the surface morphology was discussed by taking its SEM images. These materials were employed to assess the pre-concentration and speciation of As(III) and As(V) from aqueous solutions. The batch reactor data showed that increasing the sorptive concentration (from 1.0 to 15.0 mg/L) and pH (i.e., pH 2.0 to 10.0) caused the percent uptake of As(III) and As(V) to decrease significantly. The kinetic data showed that a sharp initial uptake of arsenic reached its equilibrium state within about 50 min of contact time, and the sorption kinetics followed a pseudo-second-order rate law both for As(III) and As(V) sorption. A 1,000 times increase in the background electrolyte concentration, i.e., NaNO3, caused a significant decrease in As(III) removal, whereas As(V) was almost unaffected, which inferred that As(III) was adsorbed, mainly by the van der Waals or even by the electrostatic attraction, whereas As(V) was adsorbed chemically and formed "inner-sphere" complexes at the solid/solution interface. The equilibrium state modeling studies indicated that the sorption data fitted well the Freundlich and Langmuir adsorption isotherms. Henceforth, the removal capacity was calculated under these equilibrium conditions. It was noted that organo-modified sericite possessed a significantly higher removal capacity compared to its virgin sericite

  18. Advances in Shallow-Water, High-Resolution Seafloor Mapping: Integrating an Autonomous Surface Vessel (ASV) Into Nearshore Geophysical Studies

    NASA Astrophysics Data System (ADS)

    Denny, J. F.; O'Brien, T. F.; Bergeron, E.; Twichell, D.; Worley, C. R.; Danforth, W. W.; Andrews, B. A.; Irwin, B.

    2006-12-01

    The U.S. Geological Survey (USGS) has been heavily involved in geological mapping of the seafloor since the 1970s. Early mapping efforts such as GLORIA provided broad-scale imagery of deep waters (depths > 400 meters) within the Exclusive Economic Zone (EEZ). In the early 1990's, the USGS research emphasis shifted from deep- to shallow-water environments (inner continental shelf, nearshore, estuaries) to address pertinent coastal issues such as erosion, sediment availability, sediment transport, vulnerability of coastal areas to natural and anthropogenic hazards, and resource management. Geologic framework mapping in these shallow- water environments has provided valuable data used to 1) define modern sediment distribution and thickness, 2) determine underlying stratigraphic and structural controls on shoreline behavior, and 3) enable onshore-to- offshore geologic mapping within the coastal zone when coupled with subaerial techniques such as GPR and topographic LIDAR. Research in nearshore areas presents technological challenges due to the dynamics of the environment, high volume of data collected, and the geophysical limitations of operating in very shallow water. In 2004, the USGS, in collaboration with NOAA's Coastal Services Center, began a multi-year seafloor mapping effort to better define oyster habitats within Apalachicola Bay, Florida, a shallow water estuary along the northern Gulf of Mexico. The bay poses a technological challenge due to its shallow depths (< 4-m) and high turbidity that prohibits the use of bathymetric LIDAR. To address this extreme shallow water setting, the USGS incorporated an Autonomous Surface Vessel (ASV) into seafloor mapping operations, in June 2006. The ASV is configured with a chirp sub-bottom profiler (4 24 kHz), dual-frequency chirp sidescan-sonar (100/500 kHz), single-beam echosounder (235 kHz), and forward-looking digital camera, and will be used to delineate the distribution and thickness of surficial sediment, presence

  19. Quantitative prediction of integrase inhibitor resistance from genotype through consensus linear regression modeling

    PubMed Central

    2013-01-01

    Background Integrase inhibitors (INI) form a new drug class in the treatment of HIV-1 patients. We developed a linear regression modeling approach to make a quantitative raltegravir (RAL) resistance phenotype prediction, as Fold Change in IC50 against a wild type virus, from mutations in the integrase genotype. Methods We developed a clonal genotype-phenotype database with 991 clones from 153 clinical isolates of INI naïve and RAL treated patients, and 28 site-directed mutants. We did the development of the RAL linear regression model in two stages, employing a genetic algorithm (GA) to select integrase mutations by consensus. First, we ran multiple GAs to generate first order linear regression models (GA models) that were stochastically optimized to reach a goal R2 accuracy, and consisted of a fixed-length subset of integrase mutations to estimate INI resistance. Secondly, we derived a consensus linear regression model in a forward stepwise regression procedure, considering integrase mutations or mutation pairs by descending prevalence in the GA models. Results The most frequently occurring mutations in the GA models were 92Q, 97A, 143R and 155H (all 100%), 143G (90%), 148H/R (89%), 148K (88%), 151I (81%), 121Y (75%), 143C (72%), and 74M (69%). The RAL second order model contained 30 single mutations and five mutation pairs (p < 0.01): 143C/R&97A, 155H&97A/151I and 74M&151I. The R2 performance of this model on the clonal training data was 0.97, and 0.78 on an unseen population genotype-phenotype dataset of 171 clinical isolates from RAL treated and INI naïve patients. Conclusions We describe a systematic approach to derive a model for predicting INI resistance from a limited amount of clonal samples. Our RAL second order model is made available as an Additional file for calculating a resistance phenotype as the sum of integrase mutations and mutation pairs. PMID:23282253

  20. Targeted transgene insertion into the CHO cell genome using Cre recombinase-incorporating integrase-defective retroviral vectors.

    PubMed

    Kawabe, Yoshinori; Shimomura, Takuya; Huang, Shuohao; Imanishi, Suguru; Ito, Akira; Kamihira, Masamichi

    2016-07-01

    Retroviral vectors have served as efficient gene delivery tools in various biotechnology fields. However, viral DNA is randomly inserted into the genome, which can cause problems, such as insertional mutagenesis and gene silencing. Previously, we reported a site-specific gene integration system, in which a transgene is integrated into a predetermined chromosomal locus of Chinese hamster ovary (CHO) cells using integrase-defective retroviral vectors (IDRVs) and Cre recombinase. In this system, a Cre expression plasmid is transfected into founder cells before retroviral transduction. In practical applications of site-specific gene modification such as for hard-to-transfect cells or for in vivo gene delivery, both the transgene and the Cre protein into retroviral virions should be encapsulate. Here, we generated novel hybrid IDRVs in which viral genome and enzymatically active Cre can be delivered (Cre-IDRVs). Cre-IDRVs encoding marker genes, neomycin resistance and enhanced green fluorescent protein (EGFP), flanked by wild-type and mutated loxP sites were produced using an expression plasmid for a chimeric protein of Cre and retroviral gag-pol. After analyzing the incorporation of the Cre protein into retroviral virions by Western blotting, the Cre-IDRV was infected into founder CHO cells, in which marker genes (hygromycin resistance and red fluorescent protein) flanked with corresponding loxP sites are introduced into the genome. G418-resistant colonies expressing GFP appeared and the site-specific integration of the transgene into the expected chromosomal site was confirmed by PCR and sequencing of amplicons. Moreover, when Cre-IDRV carried a gene expression unit for a recombinant antibody, the recombinant cells in which the antibody expression cassette was integrated in a site-specific manner were generated and the cells produced the recombinant antibody. This method may provide a promising tool to perform site-specific gene modification according to Cre

  1. Prevalent Polymorphisms in Wild-Type HIV-1 Integrase Are Unlikely To Engender Drug Resistance to Dolutegravir (S/GSK1349572)

    PubMed Central

    Hasan, Samiul; Madsen, Heather; Horton, Joseph; DeAnda, Felix; Martin-Carpenter, Louise; Sato, Akihiko; Cuffe, Robert; Chen, Shuguang; Underwood, Mark; Nichols, Garrett

    2013-01-01

    The majority of HIV-1 integrase amino acid sites are highly conserved, suggesting that most are necessary to carry out the critical structural and functional roles of integrase. We analyzed the 34 most variable sites in integrase (>10% variability) and showed that prevalent polymorphic amino acids at these positions did not affect susceptibility to the integrase inhibitor dolutegravir (S/GSK1349572), as demonstrated both in vitro (in site-directed mutagenesis studies) and in vivo (in a phase IIa study of dolutegravir monotherapy in HIV-infected individuals). Ongoing clinical trials will provide additional data on the virologic activity of dolutegravir across subject viruses with and without prevalent polymorphic substitutions. PMID:23295935

  2. Cancer-specific binary expression system activated in mice by bacteriophage HK022 Integrase.

    PubMed

    Elias, Amer; Spector, Itay; Sogolovsky-Bard, Ilana; Gritsenko, Natalia; Rask, Lene; Mainbakh, Yuli; Zilberstein, Yael; Yagil, Ezra; Kolot, Mikhail

    2016-01-01

    Binary systems based on site-specific recombination have been used for tumor specific transcription targeting of suicide genes in animal models. In these binary systems a site specific recombinase or integrase that is expressed from a tumor specific promoter drives tumor specific expression of a cytotoxic gene. In the present study we developed a new cancer specific binary expression system activated by the Integrase (Int) of the lambdoid phage HK022. We demonstrate the validity of this system by the specific expression of a luciferase (luc) reporter in human embryonic kidney 293T (HEK293T) cells and in a lung cancer mouse model. Due to the absence viral vectors and of cytotoxicity the Int based binary system offers advantages over previously described counterparts and may therefore be developed into a safer cancer cell killing system. PMID:27117628

  3. Isolation, structure, and HIV-1-integrase inhibitory activity of structurally diverse fungal metabolites.

    PubMed

    Singh, Sheo B; Jayasuriya, Hiranthi; Dewey, Raymond; Polishook, Jon D; Dombrowski, Anne W; Zink, Deborah L; Guan, Ziqiang; Collado, Javier; Platas, Gonzalo; Pelaez, Fernando; Felock, Peter J; Hazuda, Daria J

    2003-12-01

    HIV-1 integrase is a critical enzyme for replication of HIV, and its inhibition is one of the most promising new drug strategies for anti-retroviral therapy, with potentially significant advantages over existing therapies. In this report, a series of HIV-1 inhibitors isolated from the organic extract of fermentations from terrestrial fungi is described. These fungal species, belonging to a variety of genera, were collected from throughout the world following the strict guidelines of Rio Convention on Biodiversity. The polyketide- and terpenoid-derived inhibitors are represented by two naphthoquinones, a biphenyl and two triphenyls, a benzophenone, four aromatics with or without catechol units, a linear aliphatic terpenoid, a diterpenoid, and a sesterterpenoid. These compounds inhibited the coupled and strand-transfer reaction of HIV-1 integrase with an IC(50) value of 0.5-120 micro M. The bioassay-directed isolation, structure elucidation, and HIV-1 inhibitory activity of these compounds are described. PMID:14714192

  4. Cancer-specific binary expression system activated in mice by bacteriophage HK022 Integrase

    PubMed Central

    Elias, Amer; Spector, Itay; Sogolovsky-Bard, Ilana; Gritsenko, Natalia; Rask, Lene; Mainbakh, Yuli; Zilberstein, Yael; Yagil, Ezra; Kolot, Mikhail

    2016-01-01

    Binary systems based on site-specific recombination have been used for tumor specific transcription targeting of suicide genes in animal models. In these binary systems a site specific recombinase or integrase that is expressed from a tumor specific promoter drives tumor specific expression of a cytotoxic gene. In the present study we developed a new cancer specific binary expression system activated by the Integrase (Int) of the lambdoid phage HK022. We demonstrate the validity of this system by the specific expression of a luciferase (luc) reporter in human embryonic kidney 293T (HEK293T) cells and in a lung cancer mouse model. Due to the absence viral vectors and of cytotoxicity the Int based binary system offers advantages over previously described counterparts and may therefore be developed into a safer cancer cell killing system. PMID:27117628

  5. Identification of an evolutionarily conserved domain in human lens epithelium-derived growth factor/transcriptional co-activator p75 (LEDGF/p75) that binds HIV-1 integrase.

    PubMed

    Cherepanov, Peter; Devroe, Eric; Silver, Pamela A; Engelman, Alan

    2004-11-19

    Human lens epithelium-derived growth factor/transcriptional co-activator p75 (LEDGF/p75) protein was recently identified as a binding partner for HIV-1 integrase (IN) in human cells. In this work, we used biochemical and bioinformatic approaches to define the domain organization of LEDGF/p75. Using limited proteolysis and deletion mutagenesis we show that the protein contains a pair of evolutionarily conserved domains, assuming about 35% of its sequence. Whereas the N-terminal PWWP domain had been recognized previously, the second domain is novel. It is comprised of approximately 80 amino acid residues and is both necessary and sufficient for binding to HIV-1 IN. Strikingly, the integrase binding domain (IBD) is not unique to LEDGF/p75, as a second human protein, hepatoma-derived growth factor-related protein 2 (HRP2), contains a homologous sequence. LEDGF/p75 and HRP2 IBDs avidly bound HIV-1 IN in an in vitro GST pull-down assay and each full-length protein potently stimulated HIV-1 IN activity in vitro. LEDGF/p75 and HRP2 are predicted to share a similar domain organization and have an evident evolutionary and likely functional relationship. PMID:15371438

  6. The design of 8-hydroxyquinoline tetracyclic lactams as HIV-1 integrase strand transfer inhibitors.

    PubMed

    Velthuisen, Emile J; Johns, Brian A; Temelkoff, David P; Brown, Kevin W; Danehower, Susan C

    2016-07-19

    A novel series of HIV-1 integrase strand transfer inhibitors were designed using the venerable two-metal binding pharmacophore model and incorporating structural elements from two different literature scaffolds. This manuscript describes a number of 8-hydroxyquinoline tetracyclic lactams with exceptional antiviral activity against HIV-1 and little loss of potency against the IN signature resistance mutations Q148K and G140S/Q148H. PMID:27092410

  7. Preclinical Profile of BI 224436, a Novel HIV-1 Non-Catalytic-Site Integrase Inhibitor

    PubMed Central

    Amad, Ma'an; Bailey, Murray D.; Bethell, Richard; Bös, Michael; Bonneau, Pierre; Cordingley, Michael; Coulombe, René; Duan, Jianmin; Edwards, Paul; Faucher, Anne-Marie; Garneau, Michel; Jakalian, Araz; Kawai, Stephen; Lamorte, Louie; LaPlante, Steven; Luo, Laibin; Mason, Steve; Poupart, Marc-André; Rioux, Nathalie; Schroeder, Patricia; Simoneau, Bruno; Tremblay, Sonia; Tsantrizos, Youla; Witvrouw, Myriam; Yoakim, Christiane

    2014-01-01

    BI 224436 is an HIV-1 integrase inhibitor with effective antiviral activity that acts through a mechanism that is distinct from that of integrase strand transfer inhibitors (INSTIs). This 3-quinolineacetic acid derivative series was identified using an enzymatic integrase long terminal repeat (LTR) DNA 3′-processing assay. A combination of medicinal chemistry, parallel synthesis, and structure-guided drug design led to the identification of BI 224436 as a candidate for preclinical profiling. It has antiviral 50% effective concentrations (EC50s) of <15 nM against different HIV-1 laboratory strains and cellular cytotoxicity of >90 μM. BI 224436 also has a low, ∼2.1-fold decrease in antiviral potency in the presence of 50% human serum and, by virtue of a steep dose-response curve slope, exhibits serum-shifted EC95 values ranging between 22 and 75 nM. Passage of virus in the presence of inhibitor selected for either A128T, A128N, or L102F primary resistance substitutions, all mapping to a conserved allosteric pocket on the catalytic core of integrase. BI 224436 also retains full antiviral activity against recombinant viruses encoding INSTI resistance substitutions N155S, Q148H, and E92Q. In drug combination studies performed in cellular antiviral assays, BI 224436 displays an additive effect in combination with most approved antiretrovirals, including INSTIs. BI 224436 has drug-like in vitro absorption, distribution, metabolism, and excretion (ADME) properties, including Caco-2 cell permeability, solubility, and low cytochrome P450 inhibition. It exhibited excellent pharmacokinetic profiles in rat (clearance as a percentage of hepatic flow [CL], 0.7%; bioavailability [F], 54%), monkey (CL, 23%; F, 82%), and dog (CL, 8%; F, 81%). Based on the excellent biological and pharmacokinetic profile, BI 224436 was advanced into phase 1 clinical trials. PMID:24663024

  8. Efficacy and Tolerability of Integrase Inhibitors in Antiretroviral-Naive Patients.

    PubMed

    D'Abbraccio, Maurizio; Busto, Annunziata; De Marco, Mario; Figoni, Mario; Maddaloni, Adelaide; Abrescia, Nicola

    2015-01-01

    Integrase strand transfer inhibitors are a new class of antiretroviral agents recently licensed for the treatment of both naive and experienced HIV-infected patients. They inhibit the catalytic activity of the HIV-encoded enzyme integrase and prevent the integration of the HIV genome into the host cell genome, so slowing the propagation of the infection. Integrase strand transfer inhibitors cause a rapid drop in viral load, exhibit very low drug interactions (except elvitegravir/cobicistat), and have low pill burden and convenient dosing frequency. Drugs in this class have been compared to others in antiretroviral-naive patients with efavirenz and with protease inhibitors. Final results of the STARTMRK trial highlighted the better virologic and immunologic performance of raltegravir over efavirenz/emtricitabine/tenofovir disoproxil co-formulation. Raltegravir was also superior to atazanavir/ritonavir and darunavir/ritonavir in the ACTG 5257 study for the combined virologic/tolerability endpoint. Elvitegravir/cobicistat/emtricitabine/tenofovir was non-inferior to efavirenz/emtricitabine/tenofovir and to atazanavir/ritonavir plus emtricitabine/tenofovir in terms of confirmed virologic response in the GS-US-236-0102 and GS-US-236-0103 studies, respectively. Finally, dolutegravir showed non-inferiority compared to raltegravir in the SPRING-2 study and was superior to efavirenz and darunavir/ritonavir in the SINGLE and FLAMINGO trials, respectively. The aim of this review is to analyze the data on efficacy and safety of integrase strand transfer inhibitors in antiretroviral-naive HIV patients and discuss the strengths and weaknesses of drugs within this class. PMID:26450805

  9. The systemic effects of sclerostin overexpression using ΦC31 integrase in mice.

    PubMed

    Zhang, Dongdong; Park, Bo Mi; Kang, Myengmo; Nam, HeeJin; Kim, Eun Jin; Bae, ChuHyun; Lim, Sung Kil

    2016-04-01

    Sclerostin, encoded by the Sost gene, is mainly produced by osteocytes in bone and antagonizes the Wnt/β-catenin signaling pathway, which is a requisite for bone formation. Currently, human anti-sclerostin antibodies are being tested in phase III clinical trials. In addition, serum sclerostin levels are reported to be associated with bone mineral density and fracture risk in normal individuals; however, the correlation between serum sclerostin and bone mass remains controversial. To study the effects of the continuous exposure of exogenous sclerostin on bone, a ΦC31 integrase system, which has the characteristics of site-specificity and efficiency, was applied for the delivery of the Sost gene in this study. We injected Sost-attB plasmid with or without ΦC31 integrase plasmid into the mouse tail vein using a hydrodynamic-based method. The site-specific integration of the Sost gene into the mouse genome was confirmed by examining a pseudo-attP site on the hepatic genomic DNA. Sclerostin was expressed in the hepatocytes, secreted into the blood flow, and maintained at high concentrations in the mice with both Sost-attB plasmid and ΦC31 integrase plasmid injections, which was observed by serial measurement. Moreover, the mice with long-term high levels of serum sclerostin showed trabecular bone loss on micro-CT analysis. Peripheral B cell populations were not affected. Our results suggested that sclerostin could be expressed in the liver and sustained successfully at high levels in the blood by using the ΦC31 integrase system, leading to trabecular bone loss. These findings may help to further ascertain the effects of sclerostin introduced exogenously on the skeleton. PMID:26845353

  10. Sketching the historical development of pyrimidones as the inhibitors of the HIV integrase.

    PubMed

    Patel, Rahul V; Keum, Young-Soo; Park, Se Won

    2015-06-01

    Heterocyclic substances perform a very unique role in drug design and discovery. This article provides the primary objectives of the analysis within pyrimidine centered new heterocyclic elements chronologically from their finding focusing on one of the essential enzyme of HIV virus particle that is integrase upon suppressing its strand transfer function. The class of compounds reviewed here includes bicyclic pyrimidines, dihydroxypyrimidines, pyrimidine-2,4-dinones, N-methylpyrimidones, pyranopyrimidine, pyridine-quinoline conjugates, pyrimidine-2-carboxamides, N-3 hydroxylated pyrimidine-2,4-diones as well as their various substituted analogues. Such initiatives released an effective drug Raltegravir as a first FDA approved anti-HIV integrase inhibitor as well as several of its derivatives along with other pyrimidones is under clinical or preclinical growth. Some of the provided scaffolds indicated dual anti-HIV efficacies against HIV reverse transcriptase and integrase enzymes at both cites as 3'-processing and strand transfer, while several scaffolds exhibited potency against Raltegravir resistant HIV mutant strains determining themselves a potent class of compounds having appealing upcoming implementations. Connections of the new compounds' molecular structure and HIV viral target has been overviewed to be able to accomplish further growth of promising anti-HIV agents in future drug discovery process. PMID:25084622

  11. Structural Properties of HIV Integrase. Lens Epithelium-derived Growth Factor Oligomers

    SciTech Connect

    Gupta, K.; Diamond, T; Hwang, Y; Bushman, F; Van Duyne, G

    2010-01-01

    Integrase (IN) is the catalytic component of the preintegration complex, a large nucleoprotein assembly critical for the integration of the retroviral genome into a host chromosome. Although partial crystal structures of human immunodeficiency virus IN alone and its complex with the integrase binding domain of the host factor PSIP1/lens epithelium-derived growth factor (LEDGF)/p75 are available, many questions remain regarding the properties and structures of LEDGF-bound IN oligomers. Using analytical ultracentrifugation, multiangle light scattering, and small angle x-ray scattering, we have established the oligomeric state, stoichiometry, and molecular shapes of IN {center_dot} LEDGF complexes in solution. Analyses of intact IN tetramers bound to two different LEDGF truncations allow for placement of the integrase binding domain by difference analysis. Modeling of the small angle x-ray scattering envelopes using existing structural data suggests domain arrangements in the IN oligomers that support and extend existing biochemical data for IN {center_dot} LEDGF complexes and lend new insights into the quaternary structure of LEDGF-bound IN tetramers. These IN oligomers may be involved in stages of the viral life cycle other than integration, including assembly, budding, and early replication.

  12. Molecular Features Related to HIV Integrase Inhibition Obtained from Structure- and Ligand-Based Approaches

    PubMed Central

    de Carvalho, Luciana L.; Maltarollo, Vinícius G.; de Lima, Emmanuela Ferreira; Weber, Karen C.; Honorio, Kathia M.; da Silva, Albérico B. F.

    2014-01-01

    Among several biological targets to treat AIDS, HIV integrase is a promising enzyme that can be employed to develop new anti-HIV agents. The aim of this work is to propose a mechanistic interpretation of HIV-1 integrase inhibition and to rationalize the molecular features related to the binding affinity of studied ligands. A set of 79 HIV-1 integrase inhibitors and its relationship with biological activity are investigated employing 2D and 3D QSAR models, docking analysis and DFT studies. Analyses of docking poses and frontier molecular orbitals revealed important features on the main ligand-receptor interactions. 2D and 3D models presenting good internal consistency, predictive power and stability were obtained in all cases. Significant correlation coefficients (r2 = 0.908 and q2 = 0.643 for 2D model; r2 = 0.904 and q2 = 0.719 for 3D model) were obtained, indicating the potential of these models for untested compounds. The generated holograms and contribution maps revealed important molecular requirements to HIV-1 IN inhibition and several evidences for molecular modifications. The final models along with information resulting from molecular orbitals, 2D contribution and 3D contour maps should be useful in the design of new inhibitors with increased potency and selectivity within the chemical diversity of the data. PMID:24416129

  13. The Promise of Dolutegravir: A Novel Second Generation Integrase Strand Transfer Inhibitor.

    PubMed

    Singh, Harmanjit; Kaur, Mandeep; Kakkar, Ashish K; Kumar, Harish

    2016-01-01

    Dolutegravir (DTG), a novel integrase strand transfer inhibitor (INSTI), is one of the newest addition to the arsenal of anti-human immunodeficiency virus (HIV) therapeutics. Dolutegravir is the first member of the class of second generation integrase strand transfer inhibitors aimed primarily to address the current unmet need for novel unboosted integrase inhibitors with convenient once-daily dosing and a superior resistance profile. During its clinical development, DTG has demonstrated noninferior or superior efficacy in both treatment-naive as well as treatmentexperienced individuals including those who have previously failed first generation INSTIs. Other potential advantages include a favorable safety profile, low propensity for drug-drug interactions, and prolonged serum half-life permitting once-daily administration in treatment-naive or treatment-experienced INSTI naive HIV patients. Twice-daily administration is recommended in individuals with established or suspected resistance to first-generation INSTIs. This review outlines the need for new HIV therapeutics and summarizes the efficacy, safety, and pharmacokinetic profile of dolutegravir. PMID:27157040

  14. Adeno-associated virus Rep-mediated targeting of integrase-defective retroviral vector DNA circles into human chromosome 19

    SciTech Connect

    Huang, Shuohao; Kawabe, Yoshinori; Ito, Akira; Kamihira, Masamichi

    2012-01-06

    Highlights: Black-Right-Pointing-Pointer Adeno-associated virus (AAV) is capable of targeted integration in human cells. Black-Right-Pointing-Pointer Integrase-defective retroviral vector (IDRV) enables a circular DNA delivery. Black-Right-Pointing-Pointer A targeted integration system of IDRV DNA using the AAV integration mechanism. Black-Right-Pointing-Pointer Targeted IDRV integration ameliorates the safety concerns for retroviral vectors. -- Abstract: Retroviral vectors have been employed in clinical trials for gene therapy owing to their relative large packaging capacity, alterable cell tropism, and chromosomal integration for stable transgene expression. However, uncontrollable integrations of transgenes are likely to cause safety issues, such as insertional mutagenesis. A targeted transgene integration system for retroviral vectors, therefore, is a straightforward way to address the insertional mutagenesis issue. Adeno-associated virus (AAV) is the only known virus capable of targeted integration in human cells. In the presence of AAV Rep proteins, plasmids possessing the p5 integration efficiency element (p5IEE) can be integrated into the AAV integration site (AAVS1) in the human genome. In this report, we describe a system that can target the circular DNA derived from non-integrating retroviral vectors to the AAVS1 site by utilizing the Rep/p5IEE integration mechanism. Our results showed that after G418 selection 30% of collected clones had retroviral DNA targeted at the AAVS1 site.

  15. Integrase-independent HIV-1 infection is augmented under conditions of DNA damage and produces a viral reservoir

    SciTech Connect

    Ebina, Hirotaka Kanemura, Yuka; Suzuki, Yasutsugu; Urata, Kozue; Misawa, Naoko; Koyanagi, Yoshio

    2012-05-25

    HIV-1 possesses a viral protein, integrase (IN), which is necessary for its efficient integration in target cells. However, it has been reported that an IN-defective HIV strain is still capable of integration. Here, we assessed the ability of wild type (WT) HIV-1 to establish infection in the presence of IN inhibitors. We observed a low, yet clear infection of inhibitor-incubated cells infected with WT HIV which was identical to cells infected with IN-deficient HIV, D64A. Furthermore, the IN-independent integration could be enhanced by the pretreatment of cells with DNA-damaging agents suggesting that integration is mediated by a DNA repair system. Moreover, significantly faster viral replication kinetics with augmented viral DNA integration was observed after infection in irradiated cells treated with IN inhibitor compared to nonirradiated cells. Altogether, our results suggest that HIV DNA has integration potential in the presence of an IN inhibitor and may serve as a virus reservoir.

  16. Four-tiered {pi} interaction at the dimeric interface of HIV-1 integrase critical for DNA integration and viral infectivity

    SciTech Connect

    Al-Mawsawi, Laith Q.; Hombrouck, Anneleen; Dayam, Raveendra; Debyser, Zeger; Neamati, Nouri

    2008-08-01

    HIV-1 integrase (IN) is an essential enzyme for viral infection. Here, we report an extensive {pi} electron orbital interaction between four amino acids, W132, M178, F181 and F185, located at the dimeric interface of IN that is critical for the strand transfer activity alone. Catalysis of nine different mutant IN proteins at these positions were evaluated. Whereas the 3'-processing activity is predominantly strong, the strand transfer activity of each enzyme was completely dependent on an intact {pi} electron orbital interaction at the dimeric interface. Four representative IN mutants were constructed in the context of the infectious NL4.3 HIV-1 viral clone. Whereas viruses with an intact {pi} electron orbital interaction at the IN dimeric interface replicated comparable to wild type, viruses containing an abolished {pi} interaction were non-infectious. Q-PCR analysis of viral DNA forms during viral replication revealed pleiotropic effects of most mutations. We hypothesize that the {pi} interaction is a critical contact point for the assembly of functional IN multimeric complexes, and that IN multimerization is required for a functional pre-integration complex. The rational design of small molecule inhibitors targeting the disruption of this {pi}-{pi} interaction should lead to powerful anti-retroviral drugs.

  17. Huwe1, a novel cellular interactor of Gag-Pol through integrase binding, negatively influences HIV-1 infectivity.

    PubMed

    Yamamoto, Seiji P; Okawa, Katsuya; Nakano, Takashi; Sano, Kouichi; Ogawa, Kanako; Masuda, Takao; Morikawa, Yuko; Koyanagi, Yoshio; Suzuki, Youichi

    2011-04-01

    Integration, an indispensable step for retrovirus replication, is executed by integrase (IN), which is expressed as a part of a Gag-Pol precursor. Although mechanistic detail of the IN-catalyzed integration reaction is well defined, numerous evidence have demonstrated that IN is involved in multiple steps of retrovirus replication other than integration. In this study, Huwe1, a HECT-type E3 ubiquitin ligase, was identified as a new cellular interactor of human immunodeficiency virus type 1 (HIV-1) IN. The interaction was mediated through the catalytic core domain of IN and a wide-range region of Huwe1. Interestingly, although depletion of Huwe1 in target cells did not affect the early phase of HIV-1 infection in a human T cell line, we found that infectivity of HIV-1 released from the Huwe1 knockdown cells was significantly augmented more than that of virus produced from control cells. The increase in infectivity occurred in proviral DNA synthesis. Further analysis revealed that Huwe1 interacted with HIV-1 Gag-Pol precursor protein through an IN domain. Our results suggest that Huwe1 in HIV-1 producer cells has a negative impact on early post-entry events during the next round of virus infection via association with an IN region of Gag-Pol. PMID:21167302

  18. Purification, solution properties and crystallization of SIV integrase containing a continuous core and C-terminal domain.

    PubMed

    Li, Y; Yan, Y; Zugay-Murphy, J; Xu, B; Cole, J L; Witmer, M; Felock, P; Wolfe, A; Hazuda, D; Sardana, M K; Chen, Z; Kuo, L C; Sardana, V V

    1999-11-01

    The C-terminal two-thirds segment of integrase derived from the simian immunodeficiency virus has been cloned, expressed in Escherichia coli, and purified to greater than 95% homogeneity. The protein encompasses amino-acid residues 50-293 and contains a F185H substitution to enhance solubility. In dilute solutions at concentrations below 1 mg ml(-1), the enzyme is predominantly dimeric. At the higher concentrations (>10 mg ml(-1)) required to enable crystallization, the enzyme self-associates to form species with molecular weights greater than 200 kDa. Despite the apparent high aggregation in solution, the enzyme crystallizes from a 8%(v/v) polyethylene glycol (molecular weight 6000) solution in a form suitable for X-ray diffraction studies. The resulting single crystals belong to the space group P2(1)2(1)2(1), with unit-cell parameters a = 79.76, b = 99.98, c = 150.2 A, alpha = beta = gamma = 90 degrees and Z = 4. Under X-ray irradiation generated with a rotating-anode generator, the crystals diffract to 2.8 A resolution and allow collection of a native 3 A resolution diffraction data set. PMID:10531491

  19. Structural requirements for potential HIV-integrase inhibitors identified using pharmacophore-based virtual screening and molecular dynamics studies.

    PubMed

    Islam, Md Ataul; Pillay, Tahir S

    2016-02-23

    Acquired immunodeficiency syndrome (AIDS) is a life-threatening disease which is a collection of symptoms and infections caused by a retrovirus, human immunodeficiency virus (HIV). There is currently no curative treatment and therapy is reliant on the use of existing anti-retroviral drugs. Pharmacoinformatics approaches have already proven their pivotal role in the pharmaceutical industry for lead identification and optimization. In the current study, we analysed the binding preferences and inhibitory activity of HIV-integrase inhibitors using pharmacoinformatics. A set of 30 compounds were selected as the training set of a total 540 molecules for pharmacophore model generation. The final model was validated by statistical parameters and further used for virtual screening. The best mapped model (R = 0.940, RMSD = 2.847, Q(2) = 0.912, se = 0.498, Rpred(2) = 0.847 and rm(test)(2) = 0.636) explained that two hydrogen bond acceptor and one aromatic ring features were crucial for the inhibition of HIV-integrase. From virtual screening, initial hits were sorted using a number of parameters and finally two compounds were proposed as promising HIV-integrase inhibitors. Drug-likeness properties of the final screened compounds were compared to FDA approved HIV-integrase inhibitors. HIV-integrase structure in complex with the most active and final screened compounds were subjected to 50 ns molecular dynamics (MD) simulation studies to check comparative stability of the complexes. The study suggested that the screened compounds might be promising HIV-integrase inhibitors. The new chemical entities obtained from the NCI database will be subjected to experimental studies to confirm potential inhibition of HIV integrase. PMID:26809073

  20. Biochemical analysis of the role of G118R-linked dolutegravir drug resistance substitutions in HIV-1 integrase.

    PubMed

    Quashie, Peter K; Mesplède, Thibault; Han, Ying-Shan; Veres, Tamar; Osman, Nathan; Hassounah, Said; Sloan, Richard D; Xu, Hong-Tao; Wainberg, Mark A

    2013-12-01

    Drug resistance mutations (DRMs) have been reported for all currently approved anti-HIV drugs, including the latest integrase strand transfer inhibitors (INSTIs). We previously used the new INSTI dolutegravir (DTG) to select a G118R integrase resistance substitution in tissue culture and also showed that secondary substitutions emerged at positions H51Y and E138K. Now, we have characterized the impact of the G118R substitution, alone or in combination with either H51Y or E138K, on 3' processing and integrase strand transfer activity. The results show that G118R primarily impacted the strand transfer step of integration by diminishing the ability of integrase-long terminal repeat (LTR) complexes to bind target DNA. The addition of H51Y and E138K to G118R partially restored strand transfer activity by modulating the formation of integrase-LTR complexes through increasing LTR DNA affinity and total DNA binding, respectively. This unique mechanism, in which one function of HIV integrase partially compensates for the defect in another function, has not been previously reported. The G118R substitution resulted in low-level resistance to DTG, raltegravir (RAL), and elvitegravir (EVG). The addition of either of H51Y or E138K to G118R did not enhance resistance to DTG, RAL, or EVG. Homology modeling provided insight into the mechanism of resistance conferred by G118R as well as the effects of H51Y or E138K on enzyme activity. The G118R substitution therefore represents a potential avenue for resistance to DTG, similar to that previously described for the R263K substitution. For both pathways, secondary substitutions can lead to either diminished integrase activity and/or increased INSTI susceptibility. PMID:24080645

  1. Removal of As(III) and As(V) from water using a natural Fe and Mn enriched sample.

    PubMed

    Deschamps, Eleonora; Ciminelli, Virginia S T; Höll, Wolfgang H

    2005-12-01

    The arsenic removal capacity of a natural oxide sample consisting basically of Mn-minerals (birnessite, cryptomelane, todorokite), and Fe-oxides (goethite, hematite), collected in the Iron Quadrangle mineral province in Minas Gerais, Brazil, has been investigated. As-spiked tap water and an As-rich mining effluent with As-concentrations from 100 microg L(-1) to 100 mg L(-1) were used for the experiments. Sorbent fractions of different particle sizes (<38 microm to 0.5 mm), including spherical material (diameter 2 mm), have been used. Batch and column experiments (pH values of 3.0, 5.5, and 8.5 for batch, and about pH 7.0 for column) demonstrated the high adsorption capacity of the material, with the sorption of As(III) being higher than that of As(V). At pH 3.0, the maximum uptake for As(V) and for As(III)-treated materials were 8.5 and 14.7 mg g(-1), respectively. The Mn-minerals promoted the oxidation of As(III) to As(V), for both sorbed and dissolved As-species. Column experiments with the cFeMn-c sample for an initial As-concentration of 100 microg L(-1) demonstrated a very efficient elimination of As(III), since the drinking water limit of 10 microg L(-1) was exceeded only after 7400 BV total throughput. The As-release from the loaded samples was below the limit established by the toxicity characteristic leaching procedure, thus making the spent material suitable for discharge in landfill deposits. PMID:16290184

  2. The Allosteric HIV-1 Integrase Inhibitor BI-D Affects Virion Maturation but Does Not Influence Packaging of a Functional RNA Genome

    PubMed Central

    van Bel, Nikki; van der Velden, Yme; Bonnard, Damien; Le Rouzic, Erwann; Das, Atze T.; Benarous, Richard; Berkhout, Ben

    2014-01-01

    The viral integrase (IN) is an essential protein for HIV-1 replication. IN inserts the viral dsDNA into the host chromosome, thereby aided by the cellular co-factor LEDGF/p75. Recently a new class of integrase inhibitors was described: allosteric IN inhibitors (ALLINIs). Although designed to interfere with the IN-LEDGF/p75 interaction to block HIV DNA integration during the early phase of HIV-1 replication, the major impact was surprisingly found on the process of virus maturation during the late phase, causing a reverse transcription defect upon infection of target cells. Virus particles produced in the presence of an ALLINI are misformed with the ribonucleoprotein located outside the virus core. Virus assembly and maturation are highly orchestrated and regulated processes in which several viral proteins and RNA molecules closely interact. It is therefore of interest to study whether ALLINIs have unpredicted pleiotropic effects on these RNA-related processes. We confirm that the ALLINI BI-D inhibits virus replication and that the produced virus is non-infectious. Furthermore, we show that the wild-type level of HIV-1 genomic RNA is packaged in virions and these genomes are in a dimeric state. The tRNAlys3 primer for reverse transcription was properly placed on this genomic RNA and could be extended ex vivo. In addition, the packaged reverse transcriptase enzyme was fully active when extracted from virions. As the RNA and enzyme components for reverse transcription are properly present in virions produced in the presence of BI-D, the inhibition of reverse transcription is likely to reflect the mislocalization of the components in the aberrant virus particle. PMID:25072705

  3. Comparative evaluation of magnetite-graphene oxide and magnetite-reduced graphene oxide composite for As(III) and As(V) removal.

    PubMed

    Yoon, Yeojoon; Park, Won Kyu; Hwang, Tae-Mun; Yoon, Dae Ho; Yang, Woo Seok; Kang, Joon-Wun

    2016-03-01

    Arsenic removal using Fe3O4-graphene oxide composite (M-GO) and Fe3O4-reduced graphene oxide composite (M-rGO) was investigated. The M-GO was more effective to adsorb both As(III) and As(V) than M-rGO, because the more functional groups existing on the M-GO could lead to synthesize more Fe3O4 with M-GO. As(III) was more favorable to be adsorbed than As(V) onto both M-GO and M-rGO. According to the effect of pH on arsenic removal, the electrostatic interaction between the positively charged surface of Fe3O4-graphene based adsorbents and anionic As(V) species was a major factor to adsorb As(V). The adsorption mechanism of As(III), on the other hand, was strongly affected by a surface complexation, rather than electrostatic interactions. Consequently, in terms of the process energy consumption, energy saving could be achieved via omitting the reduction process to fabricate M-rGO from M-GO and the pre-oxidation process to convert As(III) to As(V). PMID:26551223

  4. As(III) and As(V) removal from the aqueous phase via adsorption onto acid mine drainage sludge (AMDS) alginate beads and goethite alginate beads.

    PubMed

    Lee, Hongkyun; Kim, Dohyeong; Kim, Jongsik; Ji, Min-Kyu; Han, Young-Soo; Park, Young-Tae; Yun, Hyun-Shik; Choi, Jaeyoung

    2015-07-15

    Acid mine drainage sludge (AMDS) is a solid waste generated following the neutralization of acid mine drainage (AMD). This material entrapped in calcium alginate was investigated for the sorption of As(III) and As(V). Three different adsorbent materials were prepared: AMDS alginate beads (AABs), goethite alginate beads (GABs), and pure alginate beads. The effects of pH and the adsorption kinetics were investigated, and the adsorption isotherms were also evaluated. The optimum pH range using the AABs was determined to be within 2-10 for As(III) and 2-9 for As(V). Adsorption equilibrium data were evaluated using the Langmuir isotherm model, and the maximum adsorption capacity qmax was 18.25 and 4.97 mg g(-1) for As(III) on AAB and GAB, respectively, and 21.79 and 10.92 mg g(-1) for As(V) on AAB and GAB, respectively. The adsorption of As(III) and As(V) was observed to follow pseudo-second order kinetics. The As K-edge X-ray absorption near-edge structure (XANES) revealed that the adsorbed As(III) on the AABs was oxidized to As(V) via manganese oxide in the AMDS. PMID:25804789

  5. A new large-DNA-fragment delivery system based on integrase activity from an integrative and conjugative element.

    PubMed

    Miyazaki, Ryo; van der Meer, Jan Roelof

    2013-07-01

    During the past few decades, numerous plasmid vectors have been developed for cloning, gene expression analysis, and genetic engineering. Cloning procedures typically rely on PCR amplification, DNA fragment restriction digestion, recovery, and ligation, but increasingly, procedures are being developed to assemble large synthetic DNAs. In this study, we developed a new gene delivery system using the integrase activity of an integrative and conjugative element (ICE). The advantage of the integrase-based delivery is that it can stably introduce a large DNA fragment (at least 75 kb) into one or more specific sites (the gene for glycine-accepting tRNA) on a target chromosome. Integrase recombination activity in Escherichia coli is kept low by using a synthetic hybrid promoter, which, however, is unleashed in the final target host, forcing the integration of the construct. Upon integration, the system is again silenced. Two variants with different genetic features were produced, one in the form of a cloning vector in E. coli and the other as a mini-transposable element by which large DNA constructs assembled in E. coli can be tagged with the integrase gene. We confirmed that the system could successfully introduce cosmid and bacterial artificial chromosome (BAC) DNAs from E. coli into the chromosome of Pseudomonas putida in a site-specific manner. The integrase delivery system works in concert with existing vector systems and could thus be a powerful tool for synthetic constructions of new metabolic pathways in a variety of host bacteria. PMID:23686268

  6. Structure of the Brd4 ET domain bound to a C-terminal motif from γ-retroviral integrases reveals a conserved mechanism of interaction

    PubMed Central

    Crowe, Brandon L.; Larue, Ross C.; Yuan, Chunhua; Hess, Sonja; Kvaratskhelia, Mamuka; Foster, Mark P.

    2016-01-01

    The bromodomain and extraterminal domain (BET) protein family are promising therapeutic targets for a range of diseases linked to transcriptional activation, cancer, viral latency, and viral integration. Tandem bromodomains selectively tether BET proteins to chromatin by engaging cognate acetylated histone marks, and the extraterminal (ET) domain is the focal point for recruiting a range of cellular and viral proteins. BET proteins guide γ-retroviral integration to transcription start sites and enhancers through bimodal interaction with chromatin and the γ-retroviral integrase (IN). We report the NMR-derived solution structure of the Brd4 ET domain bound to a conserved peptide sequence from the C terminus of murine leukemia virus (MLV) IN. The complex reveals a protein–protein interaction governed by the binding-coupled folding of disordered regions in both interacting partners to form a well-structured intermolecular three-stranded β sheet. In addition, we show that a peptide comprising the ET binding motif (EBM) of MLV IN can disrupt the cognate interaction of Brd4 with NSD3, and that substitutions of Brd4 ET residues essential for binding MLV IN also impair interaction of Brd4 with a number of cellular partners involved in transcriptional regulation and chromatin remodeling. This suggests that γ-retroviruses have evolved the EBM to mimic a cognate interaction motif to achieve effective integration in host chromatin. Collectively, our findings identify key structural features of the ET domain of Brd4 that allow for interactions with both cellular and viral proteins. PMID:26858406

  7. The optimization of As(V) removal over mesoporous alumina by using response surface methodology and adsorption mechanism.

    PubMed

    Han, Caiyun; Pu, Hongping; Li, Hongying; Deng, Lian; Huang, Si; He, Sufang; Luo, Yongming

    2013-06-15

    The Box-Behnken Design of the response surface methodology was employed to optimize four most important adsorption parameters (initial arsenic concentration, pH, adsorption temperature and time) and to investigate the interactive effects of these variables on arsenic(V) adsorption capacity of mesoporous alumina (MA). According to analysis of variance (ANOVA) and response surface analyses, the experiment data were excellent fitted to the quadratic model, and the interactive influence of initial concentration and pH on As(V) adsorption capacity was highly significant. The predicted maximum adsorption capacity was about 39.06 mg/g, and the corresponding optimal parameters of adsorption process were listed as below: time 720 min, temperature 52.8 °C, initial pH 3.9 and initial concentration 130 mg/L. Based on the results of arsenate species definition, FT-IR and pH change, As(V) adsorption mechanisms were proposed as follows: (1) at pH 2.0, H₃AsO₄ and H₂AsO₄(-) were adsorbed via hydrogen bond and electrostatic interaction, respectively; (2) at pH 6.6, arsenic species (H₂AsO₄(-) and HAsO₄(2-)) were removed via adsorption and ion exchange, (3) at pH 10.0, HAsO₄(2-) was adsorbed by MA via ion exchange together with adsorption, while AsO₄(3-) was removed by ion exchange. PMID:23643954

  8. The λ Integrase Site-specific Recombination Pathway.

    PubMed

    Landy, Arthur

    2015-04-01

    The site-specific recombinase encoded by bacteriophage λ (Int) is responsible for integrating and excising the viral chromosome into and out of the chromosome of its Escherichia coli host. Int carries out a reaction that is highly directional, tightly regulated, and depends upon an ensemble of accessory DNA bending proteins acting on 240 bp of DNA encoding 16 protein binding sites. This additional complexity enables two pathways, integrative and excisive recombination, whose opposite, and effectively irreversible, directions are dictated by different physiological and environmental signals. Int recombinase is a heterobivalent DNA binding protein and each of the four Int protomers, within a multiprotein 400 kDa recombinogenic complex, is thought to bind and, with the aid of DNA bending proteins, bridge one arm- and one core-type DNA site. In the 12 years since the publication of the last review focused solely on the λ site-specific recombination pathway in Mobile DNA II, there has been a great deal of progress in elucidating the molecular details of this pathway. The most dramatic advances in our understanding of the reaction have been in the area of X-ray crystallography where protein-DNA structures have now been determined for of all of the DNA-protein interfaces driving the Int pathway. Building on this foundation of structures, it has been possible to derive models for the assembly of components that determine the regulatory apparatus in the P-arm, and for the overall architectures that define excisive and integrative recombinogenic complexes. The most fundamental additional mechanistic insights derive from the application of hexapeptide inhibitors and single molecule kinetics. PMID:26104711

  9. Bacterial ability in AsIII oxidation and AsV reduction: Relation to arsenic tolerance, P uptake, and siderophore production.

    PubMed

    Ghosh, Piyasa; Rathinasabapathi, Bala; Teplitski, Max; Ma, Lena Q

    2015-11-01

    The relationship between bacterial ability in arsenic transformation, siderophore production, and P uptake was investigated using six arsenic-resistant bacteria isolated from the rhizosphere of arsenic-hyperaccumulator Pteris vittata. Bacterial strains of PG5 and 12 were better arsenite (AsIII) oxidizers (31-46 vs. 6.2-21% of 1 mM AsIII) whereas PG 6, 9, 10 and 16 were better arsenate (AsV) reducers (58-95 vs. 7.5-46% of 1 mM AsV). Increase in AsV concentration from 0 to 1 mM induced 3.0-8.4 times more P uptake by bacteria but increase in P concentration from 0.1 to 1 mM reduced AsV uptake by 17-71%, indicating that P and AsV were taken up by P transporters. Bacteria producing more siderophores (PG5 and 12; >73 μM equiv) showed greater AsIII oxidation and AsIII resistance than those producing less siderophore (PG 6, 9, 10 and 16; <23 μM equiv). This observation was further supported by results obtained from mutants of Pseudomonas fluorescens impaired in siderophore production, as they were 23-25% less tolerant to AsIII than the wild-type. Arsenic-resistant bacteria increased their arsenic tolerance by retaining less arsenic in cells via efficient AsIII oxidation and AsV reduction, which were impacted by P uptake and siderophore production. PMID:25576133

  10. The use of artificial neural network for modelling of phycoremediation of toxic elements As(III) and As(V) from wastewater using Botryococcus braunii

    NASA Astrophysics Data System (ADS)

    Podder, M. S.; Majumder, C. B.

    2016-02-01

    In the present study, a thorough investigation has been done on the removal efficiency of both As(III) and As (V) from synthetic wastewater by phycoremediation of Botryococcus braunii algal biomass. Artificial neural networks (ANNs) are practised for predicting % phycoremediation efficiency of both As(III) and As(V) ions. The influence of several parameters for example initial pH, inoculum size, contact time and initial arsenic concentration (either As(III) or As(V)) was examined systematically. The maximum phycoremediation of As(III) and As(V) was found to be 85.22% and 88.15% at pH 9.0, equilibrium time of 144 h by using algal inoculum size of 10% (v/v) and initial arsenic concentration of 50 mg/L. The data acquired from laboratory scale experimental set up was utilized for training a three-layer feed-forward back propagation (BP) with Levenberg-Marquardt (LM) training algorithm having 4:5:1 architecture. A comparison between the experimental data and model outputs provided a high correlation coefficient (R2all_ANN equal to 0.9998) and exhibited that the model was capable for predicting the phycoremediation of both As(III) and As(V) from wastewater. The network topology was optimized by changing number of neurons in hidden layers. ANNs are efficient to model and simulate highly non-liner multivariable relationships. Absolute error and Standard deviation (SD) with respect to experimental output were calculated for ANN model outputs. The comparison of phycoremediation efficiencies of both As(III) and As(V) between experimental results and ANN model outputs exhibited that ANN model can determine the behaviour of As(III) and As(V) elimination process under various circumstances.

  11. Genetic diversity on the integrase region of the pol gene among HIV type 1-infected patients naive for integrase inhibitors in São Paulo City, Brazil.

    PubMed

    Arruda, Liã Bárbara; Fonseca, Luiz Augusto M; Duarte, Alberto J S; Casseb, Jorge

    2010-01-01

    The presence of mutations associated with integrase inhibitor (INI) resistance among INI-naive patients may play an important clinical role in the use of those drugs Samples from 76 HIV-1-infected subjects naive to INIs were submitted to direct sequencing. No differences were found between naive (25%) subjects and subjects on HAART (75%). No primary mutation associated with raltegravir or elvitegravir resistance was found. However, 78% of sequences showed at least one accessory mutation associated with resistance. The analysis of the 76 IN sequences showed a high polymorphic level on this region among Brazilian HIV-1-infected subjects, including a high prevalence of aa substitutions related to INI resistance. The impact of these findings remains unclear and further studies are necessary to address these questions. PMID:20055590

  12. Detection of heavy metals released at the sediment/water interface by combining Anodic Stripping Voltammetry (ASV) and Scanning Electrochemical Microscopy (SECM) measurements

    NASA Astrophysics Data System (ADS)

    Daniele, S.; Ciani, I.; Bragato, C.; Baldo, M. A.

    2003-05-01

    Hemisphere mercury microelectrodes are investigated in combine anodic stripping voltammetry (ASV) and scanning electrochemical microscopy (SECM) experiments for the detection of heavy metal ions at the solid/solution interface of a sediment sample. Relatively large anodic stripping peaks due to lead are monitored at μm distances from the solid particles, while, under the same experimental conditions, no or lower ASV peaks are found in the bulk solution. This suggests that diffusion gradients at sediment/water interface is monitored. This method, therefore, offers a new possibility for investigating on spatial differences of immobilization and remobilization processes of heavy metals at sediment/water interfaces.

  13. Development of magnetic graphene oxide adsorbent for the removal and preconcentration of As(III) and As(V) species from environmental water samples.

    PubMed

    Rashidi Nodeh, Hamid; Wan Ibrahim, Wan Aini; Ali, Imran; Sanagi, Mohd Marsin

    2016-05-01

    New-generation adsorbent, Fe3O4@SiO2/GO, was developed by modification of graphene oxide (GO) with silica-coated (SiO2) magnetic nanoparticles (Fe3O4). The synthesized adsorbent was characterized using Fourier transform infrared spectroscopy, X-ray diffractometry, energy-dispersive X-ray spectroscopy, and field emission scanning electron microscopy. The developed adsorbent was used for the removal and simultaneous preconcentration of As(III) and As(V) from environmental waters prior to ICP-MS analysis. Fe3O4@SiO2/GO provided high adsorption capacities, i.e., 7.51 and 11.46 mg g(-1) for As(III) and As(V), respectively, at pH 4.0. Adsorption isotherm, kinetic, and thermodynamic were investigated for As(III) and As(V) adsorption. Preconcentration of As(III) and As(V) were studied using magnetic solid-phase extraction (MSPE) method at pH 9.0 as the adsorbent showed selective adsorption for As(III) only in pH range 7-10. MSPE using Fe3O4@SiO2/GO was developed with good linearities (0.05-2.0 ng mL(-1)) and high coefficient of determination (R (2) = 0.9992 and 0.9985) for As(III) and As(V), respectively. The limits of detection (LODs) (3× SD/m, n = 3) obtained were 7.9 pg mL(-1) for As(III) and 28.0 pg mL(-1) for As(V). The LOD obtained is 357-1265× lower than the WHO maximum permissible limit of 10.0 ng mL(-1). The developed MSPE method showed good relative recoveries (72.55-109.71 %) and good RSDs (0.1-4.3 %, n = 3) for spring water, lake, river, and tap water samples. The new-generation adsorbent can be used for the removal and simultaneous preconcentration of As(III) and As(V) from water samples successfully. The adsorbent removal for As(III) is better than As(V). PMID:26850098

  14. Screening of potential pseudo att sites of Streptomyces phage ΦC31 integrase in the human genome

    PubMed Central

    Hu, Zhi-peng; Chen, Lu-sheng; Jia, Cai-yan; Zhu, Huan-zhang; Wang, Wei; Zhong, Jiang

    2013-01-01

    Aim: ΦC31 integrase mediates site-specific recombination between two short sequences, attP and attB, in phage and bacterial genomes, which is a promising tool in gene regulation-based therapy since the zinc finger structure is probably the DNA recognizing domain that can further be engineered. The aim of this study was to screen potential pseudo att sites of ΦC31 integrase in the human genome, and evaluate the risks of its application in human gene therapy. Methods: TFBS (transcription factor binding sites) were found on the basis of reported pseudo att sites using multiple motif-finding tools, including AlignACE, BioProspector, Consensus, MEME, and Weeder. The human genome with the proposed motif was scanned to find the potential pseudo att sites of ΦC31 integrase. Results: The possible recognition motif of ΦC31 integrase was identified, which was composed of two co-occurrence conserved elements that were reverse complement to each other flanking the core sequence TTG. In the human genome, a total of 27924 potential pseudo att sites of ΦC31 integrase were found, which were distributed in each human chromosome with high-risk specificity values in the chromosomes 16, 17, and 19. When the risks of the sites were evaluate more rigorously, 53 hits were discovered, and some of them were just the vital functional genes or regulatory regions, such as ACYP2, AKR1B1, DUSP4, etc. Conclusion: The results provide clues for more comprehensive evaluation of the risks of using ΦC31 integrase in human gene therapy and for drug discovery. PMID:23416928

  15. Effects of etravirine on the pharmacokinetics of the integrase inhibitor S/GSK1265744.

    PubMed

    Ford, Susan L; Gould, Elizabeth; Chen, Shuguang; Lou, Yu; Dumont, Etienne; Spreen, William; Piscitelli, Stephen

    2013-01-01

    HIV integrase inhibitors such as raltegravir and elvitegravir halt HIV progression, but treatment-emergent resistance and cross-resistance have been observed. The nonnucleoside reverse transcriptase inhibitor etravirine (ETR) may be used in combination with integrase inhibitors in patients with drug resistance. This single-center, open-label, two-period, single-sequence crossover study evaluated the effects of ETR coadministration on the pharmacokinetic profile of S/GSK1265744, an investigational integrase inhibitor in phase 2 studies. Healthy subjects received 30 mg of S/GSK1265744 alone once daily for 10 days (period 1) and in combination with 200 mg of ETR twice daily for 14 days (period 2). Serial plasma samples for pharmacokinetic analyses were collected on day 10 during period 1 and on day 14 during period 2. All treatments were well tolerated. Etravirine had no effects on S/GSK1265744 geometric mean ratios of the area under the curve from time zero until the end of the dosing interval (1.01; 90% confidence interval [CI], 0.956 to 1.06), of the maximum observed plasma concentration (1.04; 90% CI, 0.987 to 1.09), or of the plasma concentration at the end of the dosing interval (0.999; 90% CI, 0.942 to 1.06). Etravirine pharmacokinetics (PK) parameters observed following coadministration with S/GSK1265744 were in the range of historical values reported for ETR alone in healthy subjects. These results indicate that 30 mg of S/GSK1265744 for 10 days as monotherapy followed by an additional 14 days in combination with ETR was well tolerated in healthy subjects and that no dose adjustment of S/GSK1265744 is required when it is coadministered with ETR. PMID:23114768

  16. Effects of Etravirine on the Pharmacokinetics of the Integrase Inhibitor S/GSK1265744

    PubMed Central

    Ford, Susan L.; Gould, Elizabeth; Chen, Shuguang; Lou, Yu; Dumont, Etienne; Spreen, William

    2013-01-01

    HIV integrase inhibitors such as raltegravir and elvitegravir halt HIV progression, but treatment-emergent resistance and cross-resistance have been observed. The nonnucleoside reverse transcriptase inhibitor etravirine (ETR) may be used in combination with integrase inhibitors in patients with drug resistance. This single-center, open-label, two-period, single-sequence crossover study evaluated the effects of ETR coadministration on the pharmacokinetic profile of S/GSK1265744, an investigational integrase inhibitor in phase 2 studies. Healthy subjects received 30 mg of S/GSK1265744 alone once daily for 10 days (period 1) and in combination with 200 mg of ETR twice daily for 14 days (period 2). Serial plasma samples for pharmacokinetic analyses were collected on day 10 during period 1 and on day 14 during period 2. All treatments were well tolerated. Etravirine had no effects on S/GSK1265744 geometric mean ratios of the area under the curve from time zero until the end of the dosing interval (1.01; 90% confidence interval [CI], 0.956 to 1.06), of the maximum observed plasma concentration (1.04; 90% CI, 0.987 to 1.09), or of the plasma concentration at the end of the dosing interval (0.999; 90% CI, 0.942 to 1.06). Etravirine pharmacokinetics (PK) parameters observed following coadministration with S/GSK1265744 were in the range of historical values reported for ETR alone in healthy subjects. These results indicate that 30 mg of S/GSK1265744 for 10 days as monotherapy followed by an additional 14 days in combination with ETR was well tolerated in healthy subjects and that no dose adjustment of S/GSK1265744 is required when it is coadministered with ETR. PMID:23114768

  17. Characterization of the Drug Resistance Profiles of Integrase Strand Transfer Inhibitors in Simian Immunodeficiency Virus SIVmac239

    PubMed Central

    Hassounah, Said A.; Liu, Yannan; Quashie, Peter K.; Oliveira, Maureen; Moisi, Daniela; Brenner, Bluma G.; Sandstrom, Paul A.; Mesplède, Thibault

    2015-01-01

    ABSTRACT We previously showed that the simian immunodeficiency virus SIVmac239 is susceptible to human immunodeficiency virus (HIV) integrase (IN) strand transfer inhibitors (INSTIs) and that the same IN drug resistance mutations result in similar phenotypes in both viruses. Now we wished to determine whether tissue culture drug selection studies with SIV would yield the same resistance mutations as in HIV. Tissue culture selection experiments were performed using rhesus macaque peripheral blood mononuclear cells (PBMCs) infected with SIVmac239 viruses in the presence of increasing concentrations of dolutegravir (DTG), elvitegravir (EVG), and raltegravir (RAL). We now show that 22 weeks of selection pressure with DTG yielded a mutation at position R263K in SIV, similar to what has been observed in HIV, and that selections with EVG led to emergence of the E92Q substitution, which is a primary INSTI resistance mutation in HIV associated with EVG treatment failure. To study this at a biochemical level, purified recombinant SIVmac239 wild-type (WT) and E92Q, T97A, G118R, Y143R, Q148R, N155H, R263K, E92Q T97A, E92Q Y143R, R263K H51Y, and G140S Q148R recombinant substitution-containing IN enzymes were produced, and each of the characteristics strand transfer, 3′-processing activity, and INSTI inhibitory constants was assessed in cell-free assays. The results show that the G118R and G140S Q148R substitutions decreased Km′ and Vmax′/Km′ for strand transfer compared to those of the WT. RAL and EVG showed reduced activity against both viruses and against enzymes containing Q148R, E92Q Y143R, and G140S Q148R. Both viruses and enzymes containing Q148R and G140S Q148R showed moderate levels of resistance against DTG. This study further confirms that the same mutations associated with drug resistance in HIV display similar profiles in SIV. IMPORTANCE Our goal was to definitively establish whether HIV and simian immunodeficiency virus (SIV) share similar resistance

  18. 3-Hydroxypyrimidine-2,4-diones as an Inhibitor Scaffold of HIV Integrase

    PubMed Central

    Tang, Jing; Maddali, Kasthuraiah; Sham, Yuk Y.; Vince, Robert; Pommier, Yves; Wang, Zhengqiang

    2011-01-01

    Integrase (IN) represents a clinically validated target for the development of antivirals against human immunodeficiency virus (HIV). Inhibitors with a novel structure core are essential for combating resistance associated with known IN inhibitors (INIs). We have previously disclosed a novel dual inhibitor scaffold of HIV IN and reverse transcriptase (RT). Here we report the complete structure-activity relationship (SAR), molecular modeling and resistance profile of this inhibitor type on IN inhibition. These studies support an antiviral mechanism of dual inhibition against both IN and RT and validate 3-hydroxypyrimidine-2,4-diones as an IN inhibitor scaffold. PMID:21381765

  19. 3-Hydroxypyrimidine-2,4-diones as an inhibitor scaffold of HIV integrase.

    PubMed

    Tang, Jing; Maddali, Kasthuraiah; Metifiot, Mathieu; Sham, Yuk Y; Vince, Robert; Pommier, Yves; Wang, Zhengqiang

    2011-04-14

    Integrase (IN) represents a clinically validated target for the development of antivirals against human immunodeficiency virus (HIV). Inhibitors with a novel structure core are essential for combating resistance associated with known IN inhibitors (INIs). We have previously disclosed a novel dual inhibitor scaffold of HIV IN and reverse transcriptase (RT). Here we report the complete structure-activity relationship (SAR), molecular modeling, and resistance profile of this inhibitor type on IN inhibition. These studies support an antiviral mechanism of dual inhibition against both IN and RT and validate 3-hydroxypyrimidine-2,4-diones as an IN inhibitor scaffold. PMID:21381765

  20. Review of integrase strand transfer inhibitors for the treatment of human immunodeficiency virus infection.

    PubMed

    Park, Tae Eun; Mohamed, Abdilahi; Kalabalik, Julie; Sharma, Roopali

    2015-10-01

    Integrase strand transfer inhibitors (INSTIs) are oral antiretroviral agents used against HIV infection. There are three agents available, including raltegravir, elvitegravir and dolutegravir, some of which are available as combination medications with other antiretroviral drugs. The efficacy and safety of INSTIs in treatment-naïve and experienced HIV-infected patients have been established by multiple studies. Based on the current practice guidelines, INSTI-based regimens are considered as one of the first-line therapies for treatment-naïve HIV-infected patients. There are new INSTIs in development to improve the resistance profile and to decrease the frequency of drug administration. PMID:26293294

  1. Feline leukemia virus integrase and capsid packaging functions do not change the insertion profile of standard Moloney retroviral vectors.

    PubMed

    Métais, J-Y; Topp, S; Doty, R T; Borate, B; Nguyen, A-D; Wolfsberg, T G; Abkowitz, J L; Dunbar, C E

    2010-06-01

    Adverse events linked to perturbations of cellular genes by vector insertion reported in gene therapy trials and animal models have prompted attempts to better understand the mechanisms directing viral vector integration. The integration profiles of vectors based on MLV, ASLV, SIV and HIV have all been shown to be non-random, and novel vectors with a safer integration pattern have been sought. Recently, we developed a producer cell line called CatPac that packages standard MoMLV vectors with feline leukemia virus (FeLV) gag, pol and env gene products. We now report the integration profile of this vector, asking if the FeLV integrase and capsid proteins could modify the MoMLV integration profile, potentially resulting in a less genotoxic pattern. We transduced rhesus macaque CD34+ hematopoietic progenitor cells with CatPac or standard MoMLV vectors, and determined their integration profile by LAM-PCR. We obtained 184 and 175 unique integration sites (ISs) respectively for CatPac and standard MoMLV vectors, and these were compared with 10 000 in silico-generated random IS. The integration profile for CatPac vector was similar to MoMLV and equally non-random, with a propensity for integration near transcription start sites and in highly dense gene regions. We found an IS for CatPac vector localized 715 nucleotides upstream of LMO-2, the gene involved in the acute lymphoblastic leukemia developed by X-SCID patients treated by gene therapy using MoMLV vectors. In conclusion, we found that replacement of MoMLV env, gag and pol gene products with FeLV did not alter the basic integration profile. Thus, there appears to be no safety advantage for this packaging system. However, considering the stability and efficacy of CatPac vectors, further development is warranted, using potentially safer vector backbones, for instance those with a SIN configuration. PMID:20237508

  2. COMPARATIVE TISSUE DISTRIBUTION AND URINARY EXCRETION OF INORGANIC ARSENIC (IAS) AND ITS METHYLATED METABOLITES IN MICE FOLLOWING ORAL ADMINISTRATION OF ARSENATE (ASV) AND ARSENITE (ASIII)

    EPA Science Inventory

    COMPARATIVE TISSUE DISTRIBUTION AND URINARY EXCRETION OF INORGANIC ARSENIC (iAs) AND ITS METHYLATED METABOLITES IN MICE FOLLOWING ORAL ADMINISTRATION OF ARSENATE (AsV) AND ARSENITE (AsIII). E M Kenyon, L M Del Razo and M F Hughes. U.S. EPA, ORD, NHEERL, ETD, PKB, RTP, NC, USA; ...

  3. TISSUE DISTRIBUTION AND URINARY EXCRETION OF INORGANIC ARSENIC AND ITS METHYLATED METABOLITES IN C57BL/6 MICE FOLLOWING SUBCHRONIC EXPOSURE TO ARSENATE (ASV) IN DRINKING WATER

    EPA Science Inventory

    The relationship of exposure and tissue concentration of parent chemical and metabolites over prolonged exposure is a critical issue for chronic toxicities mediated by metabolite(s) rather than parent chemical alone. This is an issue for AsV because its trivalent metabolites hav...

  4. Removal of As(V), Cr(III) and Cr(VI) from aqueous environments by poly(acrylonitril-co-acrylamidopropyl-trimethyl ammonium chloride)-based hydrogels.

    PubMed

    Dudu, Tuba Ersen; Sahiner, Mehtap; Alpaslan, Duygu; Demirci, Sahin; Aktas, Nahit

    2015-09-15

    Cationic poly(Acrylonitril-co-Acrylamidopropyl-trimethyl Ammonium Chloride) (p(AN-co-APTMACl)) hydrogels in bulk were synthesized by using acrylonitrile (AN) and 3-acrylamidopropyl-trimethyl ammonium chloride (APTMACl) as monomers. The prepared hydrogels were exposed to amidoximation reaction to replace hydrophobic nitrile groups with hydrophilic amidoxime groups that have metal ion binding ability. Those replacements were increased the hydrogels absorption capacity for As(V) and Cr(VI). Langmuir and Freundlich isotherms equations were utilized to obtain the best-fitted isotherm model for the absorption of the ions at different metal ion concentrations. The absorption data of As(V) ion were fitted well to Freundlich isotherm while those of Cr(VI) and Cr(III) ions were fitted well to Langmuir isotherm. The maximum absorption of poly(3-acrylamidopropyl-trimethyl ammonium chloride (p(APTMACl)) and amid-p(AN-co-APTMACl) macro gels were 22.39 mg and 21.83 mg for As(V), and 30.65 mg and 18.16 mg for Cr(VI) ion per unit gram dried gel, respectively. Kinetically, the absorption behaviors of Cr(III) and Cr(VI) ions were fitted well to a pseudo 2nd-order kinetic model and those of As(V) ions were fitted well to a pseudo 1st order kinetic model. PMID:26188989

  5. Speciation of AsIII and AsV in fruit juices by dispersive liquid–liquid microextraction and hydride generation-atomic fluorescence spectrometry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A new procedure was developed to speciate and quantify As(III) and As(V) in fruit juices. At pH 3.0, As(III) and ammonium pyrrolidine dithiocarbamate (APDC) formed a complex, which was extracted into carbon tetrachloride by dispersive liquid–liquid microextraction (DLLME) and subsequently quantified...

  6. Impact of carbon nanotubes on the toxicity of inorganic arsenic [AS(III) and AS(V)] to Daphnia magna: The role of certain arsenic species.

    PubMed

    Wang, Xinghao; Qu, Ruijuan; Allam, Ahmed A; Ajarem, Jamaan; Wei, Zhongbo; Wang, Zuoyao

    2016-07-01

    As a type of emerging nanomaterial, hydroxylated multiwalled carbon nanotubes (OH-MWCNTs) may interact with other pollutants in the aquatic environments and further influence their toxicity, transport, and fate. Thus, evaluation of toxicity to arsenic in the presence of CNTs needs to receive much more attention. The present study was conducted to explore the underlying mechanisms of OH-MWCNT-induced arsenic (As[III] and As[V]) toxicity changes in the aquatic organism Daphnia magna at different pH levels. The most toxic species for As(III) and As(V) to D. magna were found to be H2 AsO3 (-) and H2 AsO4 (-) . It appeared that the pH values were of greatest importance when the biological toxicity of As(III) and As(V) was compared. Furthermore, the effects of OH-MWCNTs on arsenic toxicity to D. magna indicated that the presence of OH-MWCNTs could enhance the toxicity of arsenic. The interactions of arsenic with OH-MWCNTs were further investigated by conducting adsorption experiments. The adsorption capacity of As(V) by OH-MWCNTs was found to be higher than that of As(III). To conclude, adsorption of certain arsenic species onto OH-MWCNTs is crucial for a reliable interpretation of enhanced toxicity. Environ Toxicol Chem 2016;35:1852-1859. © 2016 SETAC. PMID:26681408

  7. Nature and reactivity of layered double hydroxides formed by coprecipitating Mg, Al and As(V): Effect of arsenic concentration, pH, and aging.

    PubMed

    Sommella, Alessia; Caporale, Antonio G; Denecke, Melissa A; Mangold, Stefan; Pigna, Massimo; Santoro, Anna; Terzano, Roberto; Violante, Antonio

    2015-12-30

    Arsenic (As) co-precipitation is one of the major processes controlling As solubility in soils and waters. When As is co-precipitated with Al and Mg, the possible formation of layered double hydroxides (LDHs) and other nanocomposites can stabilize As in their structures thus making this toxic element less available. We investigated the nature and reactivity of Mg-Al-arsenate [As(V)] co-precipitated LDHs formed in solution affected by As concentration, pH, and aging. At the beginning of the co-precipitation process, poorly crystalline LDH and non-crystalline Al(Mg)-oxides form. Prolonged aging of the samples promotes crystallization of LDHs, evidenced by an increase in As K XANES intensities and XRD peak intensities. During aging Al- and/or Mg-oxides are likely transformed by dissolution/re-precipitation processes into more crystalline but still defective LDHs. Surface area, chemical composition, reactivity of the precipitates, and anion exchange properties of As(V) in the co-precipitates are influenced by pH, aging, and As concentration. This study demonstrates that (i) As(V) retards or inhibits the formation and transformation of LDHs and (ii) more As(V) is removed from solution if co-precipitated with Mg and Al than by sorption onto well crystallized LDHs. PMID:26241870

  8. Site-specific transformation of Drosophila via phiC31 integrase-mediated cassette exchange.

    PubMed

    Bateman, Jack R; Lee, Anne M; Wu, C-ting

    2006-06-01

    Position effects can complicate transgene analyses. This is especially true when comparing transgenes that have inserted randomly into different genomic positions and are therefore subject to varying position effects. Here, we introduce a method for the precise targeting of transgenic constructs to predetermined genomic sites in Drosophila using the C31 integrase system in conjunction with recombinase-mediated cassette exchange (RMCE). We demonstrate the feasibility of this system using two donor cassettes, one carrying the yellow gene and the other carrying GFP. At all four genomic sites tested, we observed exchange of donor cassettes with an integrated target cassette carrying the mini-white gene. Furthermore, because RMCE-mediated integration of the donor cassette is necessarily accompanied by loss of the target cassette, we were able to identify integrants simply by the loss of mini-white eye color. Importantly, this feature of the technology will permit integration of unmarked constructs into Drosophila, even those lacking functional genes. Thus, C31 integrase-mediated RMCE should greatly facilitate transgene analysis as well as permit new experimental designs. PMID:16547094

  9. Design and synthesis of bicyclic pyrimidinones as potent and orally bioavailable HIV-1 integrase inhibitors.

    PubMed

    Muraglia, Ester; Kinzel, Olaf; Gardelli, Cristina; Crescenzi, Benedetta; Donghi, Monica; Ferrara, Marco; Nizi, Emanuela; Orvieto, Federica; Pescatore, Giovanna; Laufer, Ralph; Gonzalez-Paz, Odalys; Di Marco, Annalise; Fiore, Fabrizio; Monteagudo, Edith; Fonsi, Massimiliano; Felock, Peter J; Rowley, Michael; Summa, Vincenzo

    2008-02-28

    HIV integrase is one of the three enzymes encoded by HIV genome and is essential for viral replication, but integrase inhibitors as marketed drugs have just very recently started to emerge. In this study, we show the evolution from the N-methylpyrimidinone structure to bicyclic pyrimidinones. Introduction of a suitably substituted amino moiety modulated the physical-chemical properties of the molecules and conferred nanomolar activity in the inhibition of spread of HIV-1 infection in cell culture. An extensive SAR study led to sulfamide (R)- 22b, which inhibited the strand transfer with an IC50 of 7 nM and HIV infection in MT4 cells with a CIC95 of 44 nM, and ketoamide (S)- 28c that inhibited strand transfer with an IC50 of 12 nM and the HIV infection in MT4 cells with a CIC95 of 13 nM and exhibited a good pharmacokinetic profile when dosed orally to preclinical species. PMID:18217703

  10. HIV-1 integrase strand-transfer inhibitors: design, synthesis and molecular modeling investigation.

    PubMed

    De Luca, Laura; De Grazia, Sara; Ferro, Stefania; Gitto, Rosaria; Christ, Frauke; Debyser, Zeger; Chimirri, Alba

    2011-02-01

    This study is focused on a new series of benzylindole derivatives with various substituents at the benzene-fused ring, suggested by our 3D pharmacophore model developed for HIV-1 integrase inhibitors (INIs). All synthesized compounds proved to be active in the nanomolar range (6-35 nM) on the strand-transfer step (ST). In particular, derivative 4-[1-(4-fluorobenzyl)-5,7-dimethoxy-1H-indol-3-yl]-2-hydroxy-4-oxobut-2-enoic acid (8e), presenting the highest best-fit value on pharmacophore model, showed a potency comparable to that of clinical INSTIs GS 9137 (1) and MK-0518 (2). The binding mode of our molecules has been investigated using the recently published crystal structure of the complex of full-length integrase from the prototype foamy virus in complex with its cognate DNA (PFV-IN/DNA). The results highlighted the ability of derivative 8e to assume the same binding mode of MK-0518 and GS 9137. PMID:21227550

  11. Simian-tropic HIV as a model to study drug resistance against integrase inhibitors.

    PubMed

    Wares, Melissa; Hassounah, Said; Mesplède, Thibault; Sandstrom, Paul A; Wainberg, Mark A

    2015-04-01

    Drug resistance represents a key aspect of human immunodeficiency virus (HIV) treatment failure. It is important to develop nonhuman primate models for studying issues of drug resistance and the persistence and transmission of drug-resistant viruses. However, relatively little work has been conducted using either simian immunodeficiency virus (SIV) or SIV/HIV recombinant viruses for studying resistance against integrase strand transfer inhibitors (INSTIs). Here, we used a T-cell-tropic SIV/HIV recombinant virus in which the capsid and vif regions of HIV-1 were replaced with their SIV counterparts (simian-tropic HIV-1 [stHIV-1](SCA,SVIF)) to study the impact of a number of drug resistance substitutions in the integrase coding region at positions E92Q, G118R, E138K, Y143R, S153Y, N155H, and R263K on drug resistance, viral infectivity, and viral replication capacity. Our results show that each of these substitutions exerted effects that were similar to their effects in HIV-1. Substitutions associated with primary resistance against dolutegravir were more detrimental to stHIV-1(SCA,SVIF) infectiousness than were resistance substitutions associated with raltegravir and elvitegravir, consistent with data that have been reported for HIV-1. These findings support the role of stHIV-1(SCA,SVIF) as a useful model with which to evaluate the role of INSTI resistance substitutions on viral persistence, transmissibility, and pathogenesis in a nonhuman primate model. PMID:25583721

  12. Pyrroloaryls and pyrroloheteroaryls: Inhibitors of the HIV fusion/attachment, reverse transcriptase and integrase.

    PubMed

    Patel, Rahul V; Park, Se Won

    2015-09-01

    Heterocyclic compounds execute a very important role in drug design and discovery. This article provides the basic milestones of the research for pyrroloaryl and pyrroloheteroaryl based components targeting HIV viral replication cycle. Anti-HIV activity is elaborated for several classes of pyrrolo-compounds as pyrrolopyridines, pyrrolopyrimidines, pyrrolopyridazines, pyrrolobenzodiazepinones, pyrrolobenzothiazepines, pyrrolobenzoxazepinones, pyrrolophenanthridines, pyrroloquinoxalines, pyrrolotriazines, pyrroloquinolines, pyrrolopyrazinones, pyrrolothiatriazines, arylthiopyrroles and pyrrolopyrazolones targeting two essential HIV enzymes, reverse transcriptase and integrase as well as attachment/fusion of HIV virons to the host CD-4 cell. Such attempts were resulted in a discovery of highly potent anti-HIV agents suitable for clinical trials, for example, BMS-378806, BMS-585248, BMS-626529, BMS-663068, BMS-488043 and BMS-663749, etc. as anti-HIV attachment agents, triciribine, QX432, BI-1 and BI-2 as HIV RT inhibitors which are in preclinical or clinical development. Mechanism of action of compounds presented in this article towards the suppression of HIV attachment/fusion as well as against the activities of HIV enzymes reverse transcriptase and integrase has been discussed. Relationships of new compounds' molecular framework and HIV viral target has been overviewed in order to facilitate further construction of promising anti-HIV agents in future drug discovery process. PMID:26116177

  13. [Research progress of dual inhibitors targeting HIV-1 reverse transcriptase and integrase].

    PubMed

    Liu, Hong; Zhan, Peng; Liu, Xin-Yong

    2013-04-01

    Both reverse transcriptase (RT) and integrase (IN) play crucial roles in the life cycle of HIV-1, which are also key targets in the area of anti-HIV drug research. Reverse transcriptase inhibitors are involved in the most employed drugs used to treat AIDS patients and HIV-infected people, while one of the integrase inhibitors has already been approved by US FDA to appear on the market. Great achievement has been made in the research on both, separately. Recently, much more attention of medicinal chemistry researchers has been attracted to the strategies of multi-target drugs. Compounds with excellent potency against both HIV RT and IN, evidently defined as dual inhibitors targeting both enzymes, have been obtained through considerable significant exploration, which can be classified into two categories according to different strategies. Combinatorial chemistry approach together with high throughput screening methods and multi-target-based virtual screening strategy have been useful tools for identifying selective anti-HIV compounds for long times; Rational drug design based on pharmacophore combination has also led to remarkable results. In this paper, latest progress of both categories in the discovery and structural modification will be covered, with a view to contribute to the career of anti-HIV research. PMID:23833931

  14. Nanobody-based chimeric receptor gene integration in Jurkat cells mediated by PhiC31 integrase

    SciTech Connect

    Iri-Sofla, Farnoush Jafari; Rahbarizadeh, Fatemeh; Ahmadvand, Davoud; Rasaee, Mohammad J.

    2011-11-01

    The crucial role of T lymphocytes in anti-tumor immunity has led to the development of novel strategies that can target and activate T cells against tumor cells. Recombinant DNA technology has been used to generate non-MHC-restricted chimeric antigen receptors (CARs). Here, we constructed a panel of recombinant CAR that harbors the anti-MUC1 nanobody and the signaling and co-signaling moieties (CD3{zeta}/CD28) with different spacer regions derived from human IgG3 with one or two repeats of the hinge sequence or the hinge region of Fc{gamma}RII. The PhiC31 integrase system was employed to investigate if the recombination efficiency could be recruited for high and stable expression of T cell chimeric receptor genes. The effect of nuclear localization signal (NLS) and two different promoters (CMV and CAG) on efficacy of PhiC31 integrase in human T cell lines was evaluated. The presence of integrase in combination with NLS, mediated up to 7.6 and 8.5 fold increases in CAR expression in ZCHN-attB and ZCHHN-attB cassette integrated T cells, respectively. Our results showed that highly efficient and stable transduction of the Jurkat cell line by PhiC31 integrase is a feasible modality for generating anti-cancer chimeric T cells for use in cancer immunotherapy.

  15. The Naphthyridinone GSK364735 Is a Novel, Potent Human Immunodeficiency Virus Type 1 Integrase Inhibitor and Antiretroviral▿

    PubMed Central

    Garvey, Edward P.; Johns, Brian A.; Gartland, Margaret J.; Foster, Scott A.; Miller, Wayne H.; Ferris, Robert G.; Hazen, Richard J.; Underwood, Mark R.; Boros, Eric E.; Thompson, James B.; Weatherhead, Jason G.; Koble, Cecilia S.; Allen, Scott H.; Schaller, Lee T.; Sherrill, Ronald G.; Yoshinaga, Tomokazu; Kobayashi, Masanori; Wakasa-Morimoto, Chiaki; Miki, Shigeru; Nakahara, Koichiro; Noshi, Takeshi; Sato, Akihiko; Fujiwara, Tamio

    2008-01-01

    The naphthyridinone GSK364735 potently inhibited recombinant human immunodeficiency virus type 1 (HIV-1) integrase in a strand transfer assay (mean 50% inhibitory concentration ± standard deviation, 8 ± 2 nM). As expected based on the structure of the drug, it bound competitively with another two-metal binding inhibitor (Kd [binding constant], 6 ± 4 nM). In a number of different cellular assays, GSK364735 inhibited HIV replication with potency at nanomolar concentrations (e.g., in peripheral blood mononuclear cells and MT-4 cells, 50% effective concentrations were 1.2 ± 0.4 and 5 ± 1 nM, respectively), with selectivity indexes of antiviral activity versus in-assay cytotoxicity of at least 2,200. When human serum was added, the antiviral potency decreased (e.g., a 35-fold decrease in the presence of 100% human serum was calculated by extrapolation from the results of the MT-4 cell assay). In cellular assays, GSK364735 blocked viral DNA integration, with a concomitant increase in two-long-terminal-repeat circles. As expected, this integrase inhibitor was equally active against wild-type viruses and mutant viruses resistant to approved drugs targeting either reverse transcriptase or protease. In contrast, some but not all viruses resistant to other integrase inhibitors were resistant to GSK364735. When virus was passaged in the presence of the inhibitor, we identified resistance mutations within the integrase active site that were the same as or similar to mutations arising in response to other two-metal binding inhibitors. Finally, either additive or synergistic effects were observed when GSK364735 was tested in combination with approved antiretrovirals (i.e., no antagonistic effects were seen). Thus, based on all the data, GSK364735 exerted potent antiviral activity through the inhibition of viral DNA integration by interacting at the two-metal binding site within the catalytic center of HIV integrase. PMID:18160521

  16. Removal and co-transport of Zn, As(V), and Cd during leachate seepage through downgradient mine soils: A batch sorption and column study.

    PubMed

    Kim, Juhee; Nam, Seung Mo; Hyun, Seunghun

    2016-05-01

    The removal of Zn, As(V), and Cd during the leachate seepage process was measured in single, binary, and ternary solute systems by batch sorption and 1-D column flow experiments, followed by a sequential extraction procedure (SEP). In single-solute systems, sorption (Kd(⁎)) occurred in the order of As(V)>Zn≫Cd, and this sequence did not change in the presence of other solutes. In multi-solute systems, the sorption of Zn (~20%) and Cd (~27%) was enhanced by As(V), while Zn and Cd suppressed the sorption of each other. In all cases, As(V) sorption was not affected by the cations, indicating that As(V) is prioritized by sorption sites to a much greater degree than Zn and Cd. Element retention by column soils was strongly correlated (r(2)=0.77) with Kd(⁎). Across column segments, mass retention was in the order of inlet (36-54%)>middle (26-35%)>outlet (20-31%), except for Cd in the Zn-Cd binary system. The result of SEP revealed that most of the retained Cd (98-99%) and Zn (56-71%) was in the labile fraction (e.g., the sum of F1 and F2) while only 9-12% of As(V) was labile and most (>55%) was specifically adsorbed to Fe/Al oxides. Plots of the labile fraction (f(labile)) and the fast sorption fraction (f(fast)) suggested that the kinetics of specific As(V) sorption occur rapidly (f(fast)>f(labile)), whereas labile Zn and Cd sorption occurs slowly (f(labile)>f(fast)), indicating the occurrence of kinetically limited labile sorption sites, probably due to Zn-Cd competition. In conclusion, the element leaching potential of mine leachate can be greatly attenuated during downgradient soil seepage. However, when assessing the soil attenuation process, the impact of sorption competitors and the lability of adsorbed elements should first be considered. PMID:26896586

  17. The HIV-1 Integrase Mutant R263A/K264A Is 2-fold Defective for TRN-SR2 Binding and Viral Nuclear Import*

    PubMed Central

    De Houwer, Stéphanie; Demeulemeester, Jonas; Thys, Wannes; Rocha, Susana; Dirix, Lieve; Gijsbers, Rik; Christ, Frauke; Debyser, Zeger

    2014-01-01

    Transportin-SR2 (Tnpo3, TRN-SR2), a human karyopherin encoded by the TNPO3 gene, has been identified as a cellular cofactor of HIV-1 replication, specifically interacting with HIV-1 integrase (IN). Whether this interaction mediates the nuclear import of HIV remains controversial. We previously characterized the TRN-SR2 binding interface in IN and introduced mutations at these positions to corroborate the biological relevance of the interaction. The pleiotropic nature of IN mutations complicated the interpretation. Indeed, all previously tested IN interaction mutants also affected RT. Here we report on a virus with a pair of IN mutations, INR263A/K264A, that significantly reduce interaction with TRN-SR2. The virus retains wild-type reverse transcription activity but displays a block in nuclear import and integration, as measured by quantitative PCR. The defect in integration of this mutant resulted in a smaller increase in the number of two-long terminal repeat circles than for virus specifically blocked at integration by raltegravir or catalytic site mutations (IND64N/D116N/E152Q). Finally, using an eGFP-IN-labeled HIV fluorescence-based import assay, the defect in nuclear import was corroborated. These data altogether underscore the importance of the HIV-IN TRN-SR2 protein-protein interaction for HIV nuclear import and validate the IN/TRN-SR2 interaction interface as a promising target for future antiviral therapy. PMID:25063804

  18. Development and Identification of a Novel Anti-HIV-1 Peptide Derived by Modification of the N-Terminal Domain of HIV-1 Integrase

    PubMed Central

    Sala, Marina; Spensiero, Antonia; Esposito, Francesca; Scala, Maria C.; Vernieri, Ermelinda; Bertamino, Alessia; Manfra, Michele; Carotenuto, Alfonso; Grieco, Paolo; Novellino, Ettore; Cadeddu, Marta; Tramontano, Enzo; Schols, Dominique; Campiglia, Pietro; Gomez-Monterrey, Isabel M.

    2016-01-01

    The viral enzyme integrase (IN) is essential for the replication of human immunodeficiency virus type 1 (HIV-1) and represents an important target for the development of new antiretroviral drugs. In this study, we focused on the N-terminal domain (NTD), which is mainly involved into protein oligomerization process, for the development and synthesis of a library of overlapping peptide sequences, with specific length and specific offset covering the entire native protein sequence NTD IN 1–50. The most potent fragment, VVAKEIVAH (peptide 18), which includes a His residue instead of the natural Ser at position 39, inhibits the HIV-1 IN activity with an IC50 value of 4.5 μM. Amino acid substitution analysis on this peptide revealed essential residues for activity and allowed us to identify two nonapeptides (peptides 24 and 25), that show a potency of inhibition similar to the one of peptide 18. Interestingly, peptide 18 does not interfere with the dynamic interplay between IN subunits, while peptides 24 and 25 modulated these interactions in different manners. In fact, peptide 24 inhibited the IN-IN dimerization, while peptide 25 promoted IN multimerization, with IC50 values of 32 and 4.8 μM, respectively. In addition, peptide 25 has shown to have selective anti-infective cell activity for HIV-1. These results confirmed peptide 25 as a hit for further development of new chemotherapeutic agents against HIV-1. PMID:27375570

  19. Development and Identification of a Novel Anti-HIV-1 Peptide Derived by Modification of the N-Terminal Domain of HIV-1 Integrase.

    PubMed

    Sala, Marina; Spensiero, Antonia; Esposito, Francesca; Scala, Maria C; Vernieri, Ermelinda; Bertamino, Alessia; Manfra, Michele; Carotenuto, Alfonso; Grieco, Paolo; Novellino, Ettore; Cadeddu, Marta; Tramontano, Enzo; Schols, Dominique; Campiglia, Pietro; Gomez-Monterrey, Isabel M

    2016-01-01

    The viral enzyme integrase (IN) is essential for the replication of human immunodeficiency virus type 1 (HIV-1) and represents an important target for the development of new antiretroviral drugs. In this study, we focused on the N-terminal domain (NTD), which is mainly involved into protein oligomerization process, for the development and synthesis of a library of overlapping peptide sequences, with specific length and specific offset covering the entire native protein sequence NTD IN 1-50. The most potent fragment, VVAKEIVAH (peptide 18), which includes a His residue instead of the natural Ser at position 39, inhibits the HIV-1 IN activity with an IC50 value of 4.5 μM. Amino acid substitution analysis on this peptide revealed essential residues for activity and allowed us to identify two nonapeptides (peptides 24 and 25), that show a potency of inhibition similar to the one of peptide 18. Interestingly, peptide 18 does not interfere with the dynamic interplay between IN subunits, while peptides 24 and 25 modulated these interactions in different manners. In fact, peptide 24 inhibited the IN-IN dimerization, while peptide 25 promoted IN multimerization, with IC50 values of 32 and 4.8 μM, respectively. In addition, peptide 25 has shown to have selective anti-infective cell activity for HIV-1. These results confirmed peptide 25 as a hit for further development of new chemotherapeutic agents against HIV-1. PMID:27375570

  20. Long-Acting Integrase Inhibitor Protects Macaques from Intrarectal Simian/Human Immunodeficiency Virus

    PubMed Central

    Andrews, Chasity D.; Spreen, William R.; Mohri, Hiroshi; Moss, Lee; Ford, Susan; Gettie, Agegnehu; Russell-Lodrigue, Kasi; Bohm, Rudolf P.; Cheng-Mayer, Cecilia; Hong, Zhi; Markowitz, Martin; Ho, David D.

    2015-01-01

    GSK1265744 (GSK744) is an integrase strand-transfer inhibitor that has been formulated as a long-acting (LA) injectable suitable for monthly to quarterly clinical administration. GSK744 LA was administered at two time points 4 weeks apart beginning 1 week before virus administration, and macaques were challenged weekly for 8 weeks. GSK744 LA, at plasma concentrations achievable with quarterly injections in humans, protected all animals against repeated low-dose challenges. In a second experiment, macaques were given GSK744 LA 1 week before virus administration and challenged repeatedly until infection occurred. Protection decreased over time and correlated with the plasma drug levels. With a quarterly dosing schedule in humans, our results suggest that GSK744 LA could potentially decrease adherence problems associated with daily preexposure prophylaxis (PrEP). PMID:24594934

  1. Successful Prevention of Transmission of Integrase Resistance in the Swiss HIV Cohort Study.

    PubMed

    Scherrer, Alexandra U; Yang, Wan-Lin; Kouyos, Roger D; Böni, Jürg; Yerly, Sabine; Klimkait, Thomas; Aubert, Vincent; Cavassini, Matthias; Battegay, Manuel; Hauser, Christoph; Calmy, Alexandra; Schmid, Patrick; Bernasconi, Enos; Günthard, Huldrych F

    2016-08-01

    The prevalence of integrase strand transfer inhibitor (INSTI)-transmitted drug resistance (TDR) may increase with the increasing use of INSTIs. We analyzed the prevalence of INSTI TDR in the Swiss HIV Cohort Study (2008-2014). In 1 of 1316 drug-naive samples (0.1%), a major INSTI TDR mutation was detected. Prevalence was stable, although INSTIs were increasingly used. We showed that this is in contrast to the introduction of previous drug classes, in which more treatment failures with resistant strains occurred and TDR was observed more rapidly. We demonstrated on a population-level that it is possible to avoid TDR to a new drug class for years. PMID:27130429

  2. HIV-1 Integrase Binds the Viral RNA Genome and Is Essential during Virion Morphogenesis.

    PubMed

    Kessl, Jacques J; Kutluay, Sebla B; Townsend, Dana; Rebensburg, Stephanie; Slaughter, Alison; Larue, Ross C; Shkriabai, Nikoloz; Bakouche, Nordine; Fuchs, James R; Bieniasz, Paul D; Kvaratskhelia, Mamuka

    2016-08-25

    While an essential role of HIV-1 integrase (IN) for integration of viral cDNA into human chromosome is established, studies with IN mutants and allosteric IN inhibitors (ALLINIs) have suggested that IN can also influence viral particle maturation. However, it has remained enigmatic as to how IN contributes to virion morphogenesis. Here, we demonstrate that IN directly binds the viral RNA genome in virions. These interactions have specificity, as IN exhibits distinct preference for select viral RNA structural elements. We show that IN substitutions that selectively impair its binding to viral RNA result in eccentric, non-infectious virions without affecting nucleocapsid-RNA interactions. Likewise, ALLINIs impair IN binding to viral RNA in virions of wild-type, but not escape mutant, virus. These results reveal an unexpected biological role of IN binding to the viral RNA genome during virion morphogenesis and elucidate the mode of action of ALLINIs. PMID:27565348

  3. Comparative docking and CoMFA analysis of curcumine derivatives as HIV-1 integrase inhibitors.

    PubMed

    Gupta, Pawan; Garg, Prabha; Roy, Nilanjan

    2011-08-01

    The docking studies and comparative molecular field analysis (CoMFA) were performed on highly active molecules of curcumine derivatives against 3' processing activity of HIV-1 integrase (IN) enzyme. The optimum CoMFA model was selected with statistically significant cross-validated r(2) value of 0.815 and non-cross validated r (2) value of 0.99. The common pharmacophore of highly active molecules was used for screening of HIV-1 IN inhibitors. The high contribution of polar interactions in pharmacophore mapping is well supported by docking and CoMFA results. The results of docking, CoMFA, and pharmacophore mapping give structural insights as well as important binding features of curcumine derivatives as HIV-1 IN inhibitors which can provide guidance for the rational design of novel HIV-1 IN inhibitors. PMID:21327540

  4. 6,7-Dihydroxy-1-oxoisoindoline-4-sulfonamide-containing HIV-1 Integrase Inhibitors

    PubMed Central

    Zhao, Xue Zhi; Maddali, Kasthuraiah; Smith, Steven J.; Métifiot, Mathieu; Johnson, Barry C.; Marchand, Christophe; Hughes, Stephen H.; Pommier, Yves; Burke, Terrence R.

    2012-01-01

    Although an extensive body of scientific and patent literature exists describing the development of HIV-1 integrase (IN) inhibitors, Merck’s raltegravir and Gilead’s elvitegravir remain the only IN inhibitors FDA-approved for the treatment of AIDS. The emergence of raltegravir-resistant strains of HIV-1 containing mutated forms of IN underlies the need for continued efforts to enhance the efficacy of IN inhibitors against resistant mutants. We have previously described bicyclic 6,7-dihydroxyoxoisoindolin-1-ones that show good IN inhibitory potency. This report describes the effects of introducing substituents into the 4- and 5- positions of the parent 6,7-dihydroxyoxoisoindolin-1-one platform. We have developed several sulfonamide-containing analogs that enhance potency in cell-based HIV assays by more than two orders-of-magnitude and we describe several compounds that are more potent than raltegravir against the clinically relevant Y143R IN mutant. PMID:23149229

  5. 6,7-Dihydroxy-1-oxoisoindoline-4-sulfonamide-containing HIV-1 integrase inhibitors.

    PubMed

    Zhao, Xue Zhi; Maddali, Kasthuraiah; Smith, Steven J; Métifiot, Mathieu; Johnson, Barry C; Marchand, Christophe; Hughes, Stephen H; Pommier, Yves; Burke, Terrence R

    2012-12-15

    Although an extensive body of scientific and patent literature exists describing the development of HIV-1 integrase (IN) inhibitors, Merck's raltegravir and Gilead's elvitegravir remain the only IN inhibitors FDA-approved for the treatment of AIDS. The emergence of raltegravir-resistant strains of HIV-1 containing mutated forms of IN underlies the need for continued efforts to enhance the efficacy of IN inhibitors against resistant mutants. We have previously described bicyclic 6,7-dihydroxyoxoisoindolin-1-ones that show good IN inhibitory potency. This report describes the effects of introducing substituents into the 4- and 5-positions of the parent 6,7-dihydroxyoxoisoindolin-1-one platform. We have developed several sulfonamide-containing analogs that enhance potency in cell-based HIV assays by more than two orders-of-magnitude and we describe several compounds that are more potent than raltegravir against the clinically relevant Y143R IN mutant. PMID:23149229

  6. LEDGINs inhibit late stage HIV-1 replication by modulating integrase multimerization in the virions

    PubMed Central

    2013-01-01

    Background LEDGINs are novel allosteric HIV integrase (IN) inhibitors that target the lens epithelium-derived growth factor (LEDGF)/p75 binding pocket of IN. They block HIV-1 integration by abrogating the interaction between LEDGF/p75 and IN as well as by allosterically inhibiting the catalytic activity of IN. Results Here we demonstrate that LEDGINs reduce the replication capacity of HIV particles produced in their presence. We systematically studied the molecular basis of this late effect of LEDGINs and demonstrate that HIV virions produced in their presence display a severe replication defect. Both the late effect and the previously described, early effect on integration contribute to LEDGIN antiviral activity as shown by time-of-addition, qPCR and infectivity assays. The late effect phenotype requires binding of LEDGINs to integrase without influencing proteolytic cleavage or production of viral particles. LEDGINs augment IN multimerization during virion assembly or in the released viral particles and severely hamper the infectivity of progeny virions. About 70% of the particles produced in LEDGIN-treated cells do not form a core or display aberrant empty cores with a mislocalized electron-dense ribonucleoprotein. The LEDGIN-treated virus displays defective reverse transcription and nuclear import steps in the target cells. The LEDGIN effect is possibly exerted at the level of the Pol precursor polyprotein. Conclusion Our results suggest that LEDGINs modulate IN multimerization in progeny virions and impair the formation of regular cores during the maturation step, resulting in a decreased infectivity of the viral particles in the target cells. LEDGINs thus profile as unique antivirals with combined early (integration) and late (IN assembly) effects on the HIV replication cycle. PMID:23721378

  7. Natural polymorphism S119R of HIV-1 integrase enhances primary INSTI resistance.

    PubMed

    Hachiya, Atsuko; Ode, Hirotaka; Matsuda, Masakazu; Kito, Yumiko; Shigemi, Urara; Matsuoka, Kazuhiro; Imamura, Junji; Yokomaku, Yoshiyuki; Iwatani, Yasumasa; Sugiura, Wataru

    2015-07-01

    Integrase strand transfer inhibitors (INSTIs), which block proviral DNA integration into the host chromosome, are clinically effective against HIV-1 isolates exhibiting resistance to other classes of antiretroviral agents. Although naturally occurring amino acid variation has been less frequently observed in the integrase region, the functional constraints of this variation on primary INSTI resistance-associated mutations are not fully understood. In the present study, we focused on the S119G/R/P/T (S119X) polymorphisms, which are frequently observed in HIV-1 sequences derived from clinical specimens (naïve, n=458, 26%). The frequency of the S119X polymorphism together with Q148H/R (n=8, 63%) or N155H (n=12, 83%) was relatively high compared with that of naïve group. Our in vitro assays revealed that S119G/P/T alone exerted no effect on the susceptibility to INSTIs, whereas S119R enhanced the level of INSTI resistance induced by well-known INSTI resistance-associated mutations (Y143C, Q148H or N155H). Notably, the S119R polymorphism contributed to a significant (5.9-fold) increase in dolutegravir resistance caused by G140S/Q148H. Analysis of two cases of virological failure during raltegravir-based therapy showed that the accumulation and the rapid evolution of primary INSTI resistance-associated mutations coincided with the S119R mutation. These data highlight the role of the S119X polymorphism in INSTI resistance, and this polymorphism might be linked to the potential treatment outcome with INSTI-based therapy. PMID:25956162

  8. The R262K substitution combined with H51Y in HIV-1 subtype B integrase confers low-level resistance against dolutegravir.

    PubMed

    Cutillas, Vincent; Mesplede, Thibault; Anstett, Kaitlin; Hassounah, Said; Wainberg, Mark A

    2015-01-01

    Clinical studies have shown that integrase strand transfer inhibitors (INSTIs) can be used effectively against HIV-1 infection. To date, no resistance substitution has been found in INSTI-naive patients treated with the new integrase inhibitor dolutegravir (DTG). In a recent selection study with DTG, using a virus bearing the H51Y substitution in integrase, the emergence of an R to K substitution at position 262 (R262K) was observed. We characterized this double mutant with respect to integrase strand transfer activity and susceptibility to DTG both biochemically and in tissue culture. We showed that the addition of R262K to H51Y decreased recombinant integrase strand transfer activity but improved integrase DNA-binding affinity, compared to wild-type or H51Y-containing enzymes. The defect in strand transfer activity did not translate into a decrease in HIV-1 infectivity. The combination of H51Y and R262K substitutions slightly decreased susceptibility to DTG (fold change = 1.87) in cell-based resistance assays. Although viral replication was not affected and enzyme efficiency was impaired by the addition of R262K to H51Y, there was an overall increase in the level of biochemical drug resistance against DTG. Our findings suggest that the R at position 262 plays an important role in DNA binding. PMID:25348535

  9. Incorporation of SemiSpan SuperSonic Transport (S4T) Aeroservoelastic Models into SAREC-ASV Simulation

    NASA Technical Reports Server (NTRS)

    Christhilf, David M.; Pototzky, Anthony S.; Stevens, William L.

    2010-01-01

    The Simulink-based Simulation Architecture for Evaluating Controls for Aerospace Vehicles (SAREC-ASV) was modified to incorporate linear models representing aeroservoelastic characteristics of the SemiSpan SuperSonic Transport (S4T) wind-tunnel model. The S4T planform is for a Technology Concept Aircraft (TCA) design from the 1990s. The model has three control surfaces and is instrumented with accelerometers and strain gauges. Control laws developed for wind-tunnel testing for Ride Quality Enhancement, Gust Load Alleviation, and Flutter Suppression System functions were implemented in the simulation. The simulation models open- and closed-loop response to turbulence and to control excitation. It provides time histories for closed-loop stable conditions above the open-loop flutter boundary. The simulation is useful for assessing the potential impact of closed-loop control rate and position saturation. It also provides a means to assess fidelity of system identification procedures by providing time histories for a known plant model, with and without unmeasured turbulence as a disturbance. Sets of linear models representing different Mach number and dynamic pressure conditions were implemented as MATLAB Linear Time Invariant (LTI) objects. Configuration changes were implemented by selecting which LTI object to use in a Simulink template block. A limited comparison of simulation versus wind-tunnel results is shown.

  10. Adsorption of As(III), As(V) and Cu(II) on zirconium oxide immobilized alginate beads in aqueous phase.

    PubMed

    Kwon, Oh-Hun; Kim, Jong-Oh; Cho, Dong-Wan; Kumar, Rahul; Baek, Seung Han; Kurade, Mayur B; Jeon, Byong-Hun

    2016-10-01

    A composite adsorbent to remove arsenite [As(III)], arsenate [As(V)], and copper [Cu(II)] from aqueous phase was synthesized by immobilizing zirconium oxide on alginate beads (ZOAB). The composition (wt%) of ZOAB (Zr-34.0; O-32.7; C-21.3; Ca-1.0) was confirmed by energy dispersive X-ray (EDX) analysis. Sorption studies were conducted on single and binary sorbate systems, and the effects of contact time, initial adsorbate concentration, and pH on the adsorption performance of ZOAB (pHPZC = 4.3) were monitored. The sorption process for As(III)/As(V) and Cu(II) reached an equilibrium state within 240 h and 24 h, respectively, with maximum sorption capacities of 32.3, 28.5, and 69.9 mg g(-1), respectively. The addition of Cu(II) was favorable for As(V) sorption in contrast to As(III). In the presence of 48.6 mg L(-1) Cu(II), the sorption capacity of As(V) increased from 1.5 to 3.8 mg g(-1) after 240 h. The sorption data for As(III)/As(V) and Cu(II) conformed the Freundlich and Langmuir isotherm models, respectively. The adsorption of As(III), As(V), and Cu(II) followed pseudo second order kinetics. The effect of arsenic species on Cu(II) sorption was insignificant. The results of present study demonstrated that the synthesized sorbent could be useful for the simultaneous removal of both anionic and cationic contaminants from wastewaters. PMID:27372261

  11. Speciation of As(III) and As(V) in fruit juices by dispersive liquid-liquid microextraction and hydride generation-atomic fluorescence spectrometry.

    PubMed

    Lai, Guoxin; Chen, Guoying; Chen, Tuanwei

    2016-01-01

    A sensitive method was developed to speciate and quantify As(III) and As(V) in fruit juices. At pH 3.0, As(III) and ammonium pyrrolidine dithiocarbamate (APDC) formed a complex, which was extracted into CCl4 by dispersive liquid-liquid microextraction (DLLME) and subsequently quantified by hydride generation-atomic fluorescence spectrometry (HG-AFS). After As(V) was reduced by thiosulphate at pH 1.7-1.8, total inorganic arsenic (iAs) was determined following the same protocol and As(V) was calculated from the difference. Interference from methylarsonic acid (MMA) was managed at <10% by controlling the pH of the reduction reaction. This procedure achieved 1.2 μg L(-1) limit of detection (3σ) and 92-102% recovery at 10 μg L(-1), and is applicable to most fruit juices except certain pear juice that may contain considerable MMA. PMID:26212955

  12. New calcareous soil-alginate composites for efficient uptake of Fe(III), Mn(II) and As(V) from water.

    PubMed

    El-Sherbiny, Ibrahim M; Abdel-Hamid, Mohammed I; Rashad, Mohamed; Ali, Abdelnaser S M; Azab, Yehia A

    2013-07-25

    In the present study, various grades of sodium alginates were extracted from different brown macro-algae and their characteristics were investigated using FTIR, UV-vis and EA. The alginates were used in combination with different proportions of calcareous soil to develop new composite microparticles as potential sorbents for efficient uptake of Fe(III), Mn(II) and As(V) from water. Under the investigated conditions (1g of composite equilibrated in 100ml of standard metal ion solution), the composites have removed almost 100% of Fe(III) in the concentration range of 0.5-16.0 mg l(-1). Soil, alginate and composites exhibited the highest removal (about 89%) of Mn(II) at 0.5 mg l(-1). Reasonable removal efficiency (50-60%) was recorded at 0.5 mg l(-1) of As(V) whereas, increasing the initial As(V) concentration resulted in marked decrease in removal efficiency. The collected equilibrium data were also fitted to both Langmuir and Freundlich isotherms for all the developed composites. PMID:23768586

  13. Biochar pyrolytically produced from municipal solid wastes for aqueous As(V) removal: adsorption property and its improvement with KOH activation.

    PubMed

    Jin, Hongmei; Capareda, Sergio; Chang, Zhizhou; Gao, Jun; Xu, Yueding; Zhang, Jianying

    2014-10-01

    Biochar converted from waste products is being considered as an alternative adsorbent for removal of aqueous heavy metal(loid)s. In this work, experimental and modeling investigations were conducted to examine the effect of biochars pyrolytically produced from municipal solid wastes on removing aqueous As(V) before and after activated by 2M KOH solution. Results showed that the highest adsorption capacity of pristine biochars was 24.49 mg/g. The pseudo-second-order model and Langmuir adsorption isotherm model can preferably describe the adsorption process. The activated biochar showed enhanced As(V) adsorption ability with an adsorption capacity of 30.98 mg/g, which was more than 1.3 times of pristine biochars, and 2-10 times of modified biochars reported by other literatures. Increase of surface area and changes of porous texture, especially the functional groups on the surface of activated biochars are the major contributors to its more efficient adsorption of As(V). PMID:25103038

  14. Dual inhibition of HIV-1 replication by integrase-LEDGF allosteric inhibitors is predominant at the post-integration stage

    PubMed Central

    2013-01-01

    Background LEDGF/p75 (LEDGF) is the main cellular cofactor of HIV-1 integrase (IN). It acts as a tethering factor for IN, and targets the integration of HIV in actively transcribed gene regions of chromatin. A recently developed class of IN allosteric inhibitors can inhibit the LEDGF-IN interaction. Results We describe a new series of IN-LEDGF allosteric inhibitors, the most active of which is Mut101. We determined the crystal structure of Mut101 in complex with IN and showed that the compound binds to the LEDGF-binding pocket, promoting conformational changes of IN which explain at the atomic level the allosteric effect of the IN/LEDGF interaction inhibitor on IN functions. In vitro, Mut101 inhibited both IN-LEDGF interaction and IN strand transfer activity while enhancing IN-IN interaction. Time of addition experiments indicated that Mut101 behaved as an integration inhibitor. Mut101 was fully active on HIV-1 mutants resistant to INSTIs and other classes of anti-HIV drugs, indicative that this compound has a new mode of action. However, we found that Mut101 also displayed a more potent antiretroviral activity at a post-integration step. Infectivity of viral particles produced in presence of Mut101 was severely decreased. This latter effect also required the binding of the compound to the LEDGF-binding pocket. Conclusion Mut101 has dual anti-HIV-1 activity, at integration and post-integration steps of the viral replication cycle, by binding to a unique target on IN (the LEDGF-binding pocket). The post-integration block of HIV-1 replication in virus-producer cells is the mechanism by which Mut101 is most active as an antiretroviral. To explain this difference between Mut101 antiretroviral activity at integration and post-integration stages, we propose the following model: LEDGF is a nuclear, chromatin-bound protein that is absent in the cytoplasm. Therefore, LEDGF can outcompete compound binding to IN in the nucleus of target cells lowering its antiretroviral

  15. HIV-2 Integrase Polymorphisms and Longitudinal Genotypic Analysis of HIV-2 Infected Patients Failing a Raltegravir-Containing Regimen

    PubMed Central

    Cavaco-Silva, Joana; Abecasis, Ana; Miranda, Ana Cláudia; Poças, José; Narciso, Jorge; Águas, Maria João; Maltez, Fernando; Almeida, Isabel; Germano, Isabel; Diniz, António; Gonçalves, Maria de Fátima; Gomes, Perpétua; Cunha, Celso; Camacho, Ricardo Jorge

    2014-01-01

    To characterize the HIV-2 integrase gene polymorphisms and the pathways to resistance of HIV-2 patients failing a raltegravir-containing regimen, we studied 63 integrase strand transfer inhibitors (INSTI)-naïve patients, and 10 heavily pretreated patients exhibiting virological failure while receiving a salvage raltegravir-containing regimen. All patients were infected by HIV-2 group A. 61.4% of the integrase residues were conserved, including the catalytic motif residues. No INSTI-major resistance mutations were detected in the virus population from naïve patients, but two amino acids that are secondary resistance mutations to INSTIs in HIV-1 were observed. The 10 raltegravir-experienced patients exhibited resistance mutations via three main genetic pathways: N155H, Q148R, and eventually E92Q - T97A. The 155 pathway was preferentially used (7/10 patients). Other mutations associated to raltegravir resistance in HIV-1 were also observed in our HIV-2 population (V151I and D232N), along with several novel mutations previously unreported. Data retrieved from this study should help build a more robust HIV-2-specific algorithm for the genotypic interpretation of raltegravir resistance, and contribute to improve the clinical monitoring of HIV-2-infected patients. PMID:24681625

  16. Secondary mutations in viruses resistant to HIV-1 integrase inhibitors that restore viral infectivity and replication kinetics.

    PubMed

    Nakahara, Koichiro; Wakasa-Morimoto, Chiaki; Kobayashi, Masanori; Miki, Shigeru; Noshi, Takeshi; Seki, Takahiro; Kanamori-Koyama, Mikiko; Kawauchi, Shinobu; Suyama, Akemi; Fujishita, Toshio; Yoshinaga, Tomokazu; Garvey, Edward P; Johns, Brian A; Foster, Scott A; Underwood, Mark R; Sato, Akihiko; Fujiwara, Tamio

    2009-02-01

    Passage of HIV-1 in the presence of integrase inhibitors (INIs) generates resistant viruses that have mutations in the integrase region. Integrase-resistant mutations Q148K and Q148R were identified as primary mutations with the passage of HIV-1 IIIB in the presence of INIs S-1360 or S/GSK-364735, respectively. Secondary amino acid substitutions E138K or G140S were observed when passage with INI was continued. The role of these mutations was investigated with molecular clones. Relative to Q148K alone, Q148K/E138K had 2- and >6-fold increases in resistance to S-1360 and S/GSK-364735, respectively, and the double mutant had slightly better infectivity and replication kinetics. In contrast, Q148K/G140S and Q148R/E138K had nearly equivalent or slightly reduced fold resistance to the INI compared with their respective Q148 primary mutants, and had increases in infectivity and replication kinetics. Recovery of these surrogates of viral fitness coincided with the recovery of integration efficiency of viral DNA into the host cell chromosome for these double mutants. These data show that recovery of viral integration efficiency can be an important factor for the emergence and maintenance of INI-resistant mutations. PMID:19027039

  17. Differential divalent cation requirements uncouple the assembly and catalytic reactions of human immunodeficiency virus type 1 integrase.

    PubMed Central

    Hazuda, D J; Felock, P J; Hastings, J C; Pramanik, B; Wolfe, A L

    1997-01-01

    Previous in vitro analyses have shown that the human immunodeficiency virus type 1 (HIV-1) integrase uses either manganese or magnesium to assemble as a stable complex on the donor substrate and to catalyze strand transfer. We now demonstrate that subsequent to assembly, catalysis of both 3' end processing and strand transfer requires a divalent cation cofactor and that the divalent cation requirements for assembly and catalysis can be functionally distinguished based on the ability to utilize calcium and cobalt, respectively. The different divalent cation requirements manifest by these processes are exploited to uncouple assembly and catalysis, thus staging the reaction. Staged 3' end processing and strand transfer assays are then used in conjunction with exonuclease III protection analysis to investigate the effects of integrase inhibitors on each step in the reaction. Analysis of a series of related inhibitors demonstrates that these types of compounds affect assembly and not either catalytic process, therefore reconciling the apparent disparate results obtained for such inhibitors in assays using isolated preintegration complexes. These studies provide evidence for a distinct role of the divalent cation cofactor in assembly and catalysis and have implications for both the identification and characterization of integrase inhibitors. PMID:9261430

  18. L-chicoric acid inhibits human immunodeficiency virus type 1 integration in vivo and is a noncompetitive but reversible inhibitor of HIV-1 integrase in vitro.

    PubMed

    Reinke, Ryan A; Lee, Deborah J; McDougall, Brenda R; King, Peter J; Victoria, Joseph; Mao, Yingqun; Lei, Xiangyang; Reinecke, Manfred G; Robinson, W Edward

    2004-09-01

    The human immunodeficiency virus (HIV) integrase (IN) must covalently join the viral cDNA into a host chromosome for productive HIV infection. l-Chicoric acid (l-CA) enters cells poorly but is a potent inhibitor of IN in vitro. Using quantitative real-time polymerase chain reaction (PCR), l-CA inhibits integration at concentrations from 500 nM to 10 microM but also inhibits entry at concentrations above 1 microM. Using recombinant HIV IN, steady-state kinetic analyses with l-CA were consistent with a noncompetitive or irreversible mechanism of inhibition. IN, in the presence or absence of l-CA, was successively washed. Inhibition of IN diminished, demonstrating that l-CA was reversibly bound to the protein. These data demonstrate that l-CA is a noncompetitive but reversible inhibitor of IN in vitro and of HIV integration in vivo. Thus, l-CA likely interacts with amino acids other than those which bind substrate. PMID:15302207

  19. Site-specific T-DNA integration in Arabidopsis thaliana mediated by the combined action of CRE recombinase and ϕC31 integrase.

    PubMed

    De Paepe, Annelies; De Buck, Sylvie; Nolf, Jonah; Van Lerberge, Els; Depicker, Ann

    2013-07-01

    Random T-DNA integration into the plant host genome can be problematic for a variety of reasons, including potentially variable transgene expression as a result of different integration positions and multiple T-DNA copies, the risk of mutating the host genome and the difficulty of stacking well-defined traits. Therefore, recombination systems have been proposed to integrate the T-DNA at a pre-selected site in the host genome. Here, we demonstrate the capacity of the ϕC31 integrase (INT) for efficient targeted T-DNA integration. Moreover, we show that the iterative site-specific integration system (ISSI), which combines the activities of the CRE recombinase and INT, enables the targeting of genes to a pre-selected site with the concomitant removal of the resident selectable marker. To begin, plants expressing both the CRE and INT recombinase and containing the target attP site were constructed. These plants were supertransformed with a T-DNA vector harboring the loxP site, the attB sites, a selectable marker and an expression cassette encoding a reporter protein. Three out of the 35 transformants obtained (9%) showed transgenerational site-specific integration (SSI) of this T-DNA and removal of the resident selectable marker, as demonstrated by PCR, Southern blot and segregation analysis. In conclusion, our results show the applicability of the ISSI system for precise and targeted Agrobacterium-mediated integration, allowing the serial integration of transgenic DNA sequences in plants. PMID:23574114

  20. Adsorption of As(III) and As(V) onto colloidal microparticles of commercial cross-linked polyallylamine (Sevelamer) from single and binary ion solutions.

    PubMed

    Kyzas, George Z; Siafaka, Panoraia I; Kostoglou, Margaritis; Bikiaris, Dimitrios N

    2016-07-15

    This work investigates the removal of arsenic ions in trivalent (As(III)) or pentavalent form (As(V)) from single-component and binary (equal initial ion concentrations) aqueous solutions using commercial cross-linked polyallylamine (namely as Sevelamer) as adsorbent. This is the first work in literature regarding the application of that commercial material as adsorbent for ions. Sevelamer (SVL) is a widely known pharmaceutical compound and the existence of primary and secondary amino groups (with different ratios) in its molecule increases its adsorption potential. For this purpose can be easily proposed as potential sorbent. The adsorption evaluation was based on the pH-effect (optimum pH=6, where As(III) and As(V) removal was 69 and 86%, respectively), isotherms and kinetic curves. The maximum theoretical adsorption capacity (Qm) was 86 and 133mg/g for single-component solutions of As(III) and As(V), respectively. The respective values for binary mixtures of the same concentration (100mg/L) were 84 and 116mg/g, respectively (calculated after fitting to Langmuir-Freundlich isotherm model at 20°C). A novel kinetic interpretation based on the raw experimental kinetics data was also developed. Although adsorption of As(III) and As(V) occurs mainly at different sites, there is an interdependence in their adsorption kinetics. It was found that adsorption from the binary mixtures is a two-stage process. The adsorption mechanism of SVL and arsenic ions interaction was elucidated using FTIR spectroscopy before and after adsorption. SEM images and XRD patterns (the material was amorphous both before and after arsenic adsorption indicating that the mechanism did not alter its physical state) were also taken for the characterization of SVL before and after arsenic adsorption. The adsorption mechanism was mainly attributed to the electrostatic interactions between negatively As ions and positively charged amino groups of SVL. For this reason, As(V) adsorption is higher than

  1. A new perovskite-type NdFeO3 adsorbent: synthesis, characterization, and As(V) adsorption

    NASA Astrophysics Data System (ADS)

    Luu, Minh Dai; Nhiem Dao, Ngoc; Van Nguyen, Duc; Chuc Pham, Ngoc; Ninh Vu, The; Dung Doan, Trung

    2016-06-01

    Nanocrystalline NdFeO3 perovskite oxide was prepared by the combustion method using polyvinyl alcohol (PVA) and corresponding metal nitrate precursors under optimum process conditions, using a solution with a pH of 2, a metal/PVA molar ratio of 1:3, and a calcination temperature of 600 °C, and was characterized by x-ray diffraction, scanning electron microscopy, transmission electron microscopy, Brunauer–Emmett–Teller nitrogen adsorption and desorption, energy dispersive x-ray spectroscopy, Fourier transform infrared spectroscopy, laser Raman spectroscopy, and thermogravimetric and differential thermal analysis. The synthesized perovskite NdFeO3, which had an average size of 20 nm and a relatively high surface area of 20 m2 g‑1, was investigated for adsorbing hazardous arsenate from aqueous solution. Arsenate adsorption by perovskite NdFeO3 is a pH-dependent process with a high adsorption capacity at pH levels between 4 and 7 and a maximum As(V) adsorption capacity of 126.58 mg g‑1, higher than most arsenate adsorbents reported in the literature. Kinetic and equilibrium data of reaction under the experimental conditions are best described by a pseudo-second-order and the Langmuir isotherm equation. The values of enthalpy, Gibbs free energy and entropy changes (ΔH0 = +63.916 kJ mol‑1, ΔG0 = ‑6.551 kJ mol‑1 to ‑14.021 kJ mol‑1 at T = 283‑313 K, ΔS0 = +0.249 kJ mol‑1 K‑1) suggested that the reaction was endothermic, spontaneous, and took place with increasing entropy.

  2. Determination of traces of Sb(III) using ASV in Sb-rich water samples affected by mining.

    PubMed

    Cidu, Rosa; Biddau, Riccardo; Dore, Elisabetta

    2015-01-01

    Chemical speciation [Sb(V) and Sb(III)] affects the mobility, bioavailability and toxicity of antimony. In oxygenated environments Sb(V) dominates whereas thermodynamically unstable Sb(III) may occur. In this study, a simple method for the determination of Sb(III) in non acidic, oxygenated water contaminated with antimony is proposed. The determination of Sb(III) was performed by anodic stripping voltammetry (ASV, 1-20 μg L(-1) working range), the total antimony, Sb(tot), was determined either by inductively coupled plasma mass spectrometry (ICP-MS, 1-100μgL(-1) working range) or inductively coupled plasma optical emission spectrometry (ICP-OES, 100-10,000 μg L(-1) working range) depending on concentration. Water samples were filtered on site through 0.45 μm pore size filters. The aliquot for determination of Sb(tot) was acidified with 1% (v/v) HNO3. Different preservatives, namely HCl, L(+) ascorbic acid or L(+) tartaric acid plus HNO3, were used to assess the stability of Sb(III) in synthetic solutions. The method was tested on groundwater and surface water draining the abandoned mine of Su Suergiu (Sardinia, Italy), an area heavily contaminated with Sb. The waters interacting with Sb-rich mining residues were non acidic, oxygenated, and showed extreme concentrations of Sb(tot) (up to 13,000 μg L(-1)), with Sb(III) <10% of total antimony. The stabilization with L(+) tartaric acid plus HNO3 appears useful for the determination of Sb(III) in oxygenated, Sb-rich waters. Due to the instability of Sb(III), analyses should be carried out within 7 days upon the water collection. The main advantage of the proposed method is that it does not require time-consuming preparation steps prior to analysis of Sb(III). PMID:25479865

  3. Sorption and redox reactions of As(III) and As(V) within secondary mineral coatings on aquifer sediment grains.

    PubMed

    Singer, David M; Fox, Patricia M; Guo, Hua; Marcus, Matthew A; Davis, James A

    2013-10-15

    Important reactive phenomena that affect the transport and fate of many elements occur at the mineral-water interface (MWI), including sorption and redox reactions. Fundamental knowledge of these phenomena are often based on observations of ideal mineral-water systems, for example, studies of molecular scale reactions on single crystal faces or the surfaces of pure mineral powders. Much less is understood about MWI in natural environments, which typically have nanometer to micrometer scale secondary mineral coatings on the surfaces of primary mineral grains. We examined sediment grain coatings from a well-characterized field site to determine the causes of rate limitations for arsenic (As) sorption and redox processes within the coatings. Sediments were obtained from the USGS field research site on Cape Cod, MA, and exposed to synthetic contaminated groundwater solutions. Uptake of As(III) and As(V) into the coatings was studied with a combination of electron microscopy and synchrotron techniques to assess concentration gradients and reactive processes, including electron transfer reactions. Transmission electron microscopy (TEM) and X-ray microprobe (XMP) analyses indicated that As was primarily associated with micrometer- to submicrometer aggregates of Mn-bearing nanoparticulate goethite. As(III) oxidation by this phase was observed but limited by the extent of exposed surface area of the goethite grains to the exterior of the mineral coatings. Secondary mineral coatings are potentially both sinks and sources of contaminants depending on the history of a contaminated site, and may need to be included explicitly in reactive transport models. PMID:24041305

  4. Interaction between Reverse Transcriptase and Integrase Is Required for Reverse Transcription during HIV-1 Replication

    PubMed Central

    Tekeste, Shewit S.; Wilkinson, Thomas A.; Weiner, Ethan M.; Xu, Xiaowen; Miller, Jennifer T.; Le Grice, Stuart F. J.; Clubb, Robert T.

    2015-01-01

    ABSTRACT Human immunodeficiency virus type 1 (HIV-1) replication requires reverse transcription of its RNA genome into a double-stranded cDNA copy, which is then integrated into the host cell chromosome. The essential steps of reverse transcription and integration are catalyzed by the viral enzymes reverse transcriptase (RT) and integrase (IN), respectively. In vitro, HIV-1 RT can bind with IN, and the C-terminal domain (CTD) of IN is necessary and sufficient for this binding. To better define the RT-IN interaction, we performed nuclear magnetic resonance (NMR) spectroscopy experiments to map a binding surface on the IN CTD in the presence of RT prebound to a duplex DNA construct that mimics the primer-binding site in the HIV-1 genome. To determine the biological significance of the RT-IN interaction during viral replication, we used the NMR chemical shift mapping information as a guide to introduce single amino acid substitutions of nine different residues on the putative RT-binding surface in the IN CTD. We found that six viral clones bearing such IN substitutions (R231E, W243E, G247E, A248E, V250E, and I251E) were noninfectious. Further analyses of the replication-defective IN mutants indicated that the block in replication took place specifically during early reverse transcription. The recombinant INs purified from these mutants, though retaining enzymatic activities, had diminished ability to bind RT in a cosedimentation assay. The results indicate that the RT-IN interaction is functionally relevant during the reverse transcription step of the HIV-1 life cycle. IMPORTANCE To establish a productive infection, human immunodeficiency virus type 1 (HIV-1) needs to reverse transcribe its RNA genome to create a double-stranded DNA copy and then integrate this viral DNA genome into the chromosome of the host cell. These two essential steps are catalyzed by the HIV-1 enzymes reverse transcriptase (RT) and integrase (IN), respectively. We have shown previously that IN

  5. Sequential Deletion of the Integrase (Gag-Pol) Carboxyl Terminus Reveals Distinct Phenotypic Classes of Defective HIV-1 ▿ † §

    PubMed Central

    Mohammed, Kevin D.; Topper, Michael B.; Muesing, Mark A.

    2011-01-01

    A requisite step in the life cycle of human immunodeficiency virus type 1 (HIV-1) is the insertion of the viral genome into that of the host cell, a process catalyzed by the 288-amino-acid (32-kDa) viral integrase (IN). IN recognizes and cleaves the ends of reverse-transcribed viral DNA and directs its insertion into the chromosomal DNA of the target cell. IN function, however, is not limited to integration, as the protein is required for other aspects of viral replication, including assembly, virion maturation, and reverse transcription. Previous studies demonstrated that IN is comprised of three domains: the N-terminal domain (NTD), catalytic core domain (CCD), and C-terminal domain (CTD). Whereas the CCD is mainly responsible for providing the structural framework for catalysis, the roles of the other two domains remain enigmatic. This study aimed to elucidate the primary and subsidiary roles that the CTD has in protein function. To this end, we generated and tested a nested set of IN C-terminal deletion mutants in measurable assays of virologic function. We discovered that removal of up to 15 residues (IN 273) resulted in incremental diminution of enzymatic function and infectivity and that removal of the next three residues resulted in a loss of infectivity. However, replication competency was surprisingly reestablished with one further truncation, corresponding to IN 269 and coinciding with partial restoration of integration activity, but it was lost permanently for all truncations extending N terminal to this position. Our analyses of these replication-competent and -incompetent truncation mutants suggest potential roles for the IN CTD in precursor protein processing, reverse transcription, integration, and IN multimerization. PMID:21367893

  6. New Class of HIV-1 Integrase (IN) Inhibitors with a Dual Mode of Action

    PubMed Central

    Tsiang, Manuel; Jones, Gregg S.; Niedziela-Majka, Anita; Kan, Elaine; Lansdon, Eric B.; Huang, Wayne; Hung, Magdeleine; Samuel, Dharmaraj; Novikov, Nikolai; Xu, Yili; Mitchell, Michael; Guo, Hongyan; Babaoglu, Kerim; Liu, Xiaohong; Geleziunas, Romas; Sakowicz, Roman

    2012-01-01

    tert-Butoxy-(4-phenyl-quinolin-3-yl)-acetic acids (tBPQA) are a new class of HIV-1 integrase (IN) inhibitors that are structurally distinct from IN strand transfer inhibitors but analogous to LEDGINs. LEDGINs are a class of potent antiviral compounds that interacts with the lens epithelium-derived growth factor (LEDGF) binding pocket on IN and were identified through competition binding against LEDGF. LEDGF tethers IN to the host chromatin and enables targeted integration of viral DNA. The prevailing understanding of the antiviral mechanism of LEDGINs is that they inhibit LEDGF binding to IN, which prevents targeted integration of HIV-1. We showed that in addition to the properties already known for LEDGINs, the binding of tBPQAs to the IN dimer interface inhibits IN enzymatic activity in a LEDGF-independent manner. Using the analysis of two long terminal repeat junctions in HIV-infected cells, we showed that the inhibition by tBPQAs occurs at or prior to the viral DNA 3′-processing step. Biochemical studies revealed that this inhibition operates by compound-induced conformational changes in the IN dimer that prevent proper assembly of IN onto viral DNA. For the first time, tBPQAs were demonstrated to be allosteric inhibitors of HIV-1 IN displaying a dual mode of action: inhibition of IN-viral DNA assembly and inhibition of IN-LEDGF interaction. PMID:22535962

  7. New class of HIV-1 integrase (IN) inhibitors with a dual mode of action.

    PubMed

    Tsiang, Manuel; Jones, Gregg S; Niedziela-Majka, Anita; Kan, Elaine; Lansdon, Eric B; Huang, Wayne; Hung, Magdeleine; Samuel, Dharmaraj; Novikov, Nikolai; Xu, Yili; Mitchell, Michael; Guo, Hongyan; Babaoglu, Kerim; Liu, Xiaohong; Geleziunas, Romas; Sakowicz, Roman

    2012-06-15

    tert-Butoxy-(4-phenyl-quinolin-3-yl)-acetic acids (tBPQA) are a new class of HIV-1 integrase (IN) inhibitors that are structurally distinct from IN strand transfer inhibitors but analogous to LEDGINs. LEDGINs are a class of potent antiviral compounds that interacts with the lens epithelium-derived growth factor (LEDGF) binding pocket on IN and were identified through competition binding against LEDGF. LEDGF tethers IN to the host chromatin and enables targeted integration of viral DNA. The prevailing understanding of the antiviral mechanism of LEDGINs is that they inhibit LEDGF binding to IN, which prevents targeted integration of HIV-1. We showed that in addition to the properties already known for LEDGINs, the binding of tBPQAs to the IN dimer interface inhibits IN enzymatic activity in a LEDGF-independent manner. Using the analysis of two long terminal repeat junctions in HIV-infected cells, we showed that the inhibition by tBPQAs occurs at or prior to the viral DNA 3'-processing step. Biochemical studies revealed that this inhibition operates by compound-induced conformational changes in the IN dimer that prevent proper assembly of IN onto viral DNA. For the first time, tBPQAs were demonstrated to be allosteric inhibitors of HIV-1 IN displaying a dual mode of action: inhibition of IN-viral DNA assembly and inhibition of IN-LEDGF interaction. PMID:22535962

  8. A Symmetric Region of the HIV-1 Integrase Dimerization Interface Is Essential for Viral Replication

    PubMed Central

    Serrao, Erik; Thys, Wannes; Demeulemeester, Jonas; Al-Mawsawi, Laith Q.; Christ, Frauke; Debyser, Zeger; Neamati, Nouri

    2012-01-01

    HIV-1 integrase (IN) is an important target for contemporary antiretroviral drug design research. Historically, efforts at inactivating the enzyme have focused upon blocking its active site. However, it has become apparent that new classes of allosteric inhibitors will be necessary to advance the antiretroviral field in light of the emergence of viral strains resistant to contemporary clinically used IN drugs. In this study we have characterized the importance of a close network of IN residues, distant from the active site, as important for the obligatory multimerization of the enzyme and viral replication as a whole. Specifically, we have determined that the configuration of six residues within a highly symmetrical region at the IN dimerization interface, composed of a four-tiered aromatic interaction flanked by two salt bridges, significantly contributes to proper HIV-1 replication. Additionally, we have utilized a quantitative luminescence assay to examine IN oligomerization and have determined that there is a very low tolerance for amino acid substitutions along this region. Even conservative residue substitutions negatively impacted IN multimerization, resulting in an inactive viral enzyme and a non-replicative virus. We have shown that there is a very low tolerance for amino acid variation at the symmetrical dimeric interface region characterized in this study, and therefore drugs designed to target the amino acid network detailed here could be expected to yield a significantly reduced number of drug-resistant escape mutations compared to contemporary clinically-evaluated antiretrovirals. PMID:23028829

  9. Identifying and Characterizing a Functional HIV-1 Reverse Transcriptase-binding Site on Integrase*

    PubMed Central

    Wilkinson, Thomas A.; Januszyk, Kurt; Phillips, Martin L.; Tekeste, Shewit S.; Zhang, Min; Miller, Jennifer T.; Le Grice, Stuart F. J.; Clubb, Robert T.; Chow, Samson A.

    2009-01-01

    Integrase (IN) from human immunodeficiency virus, type 1 (HIV-1) exerts pleiotropic effects in the viral replication cycle. Besides integration, IN mutations can impact nuclear import, viral maturation, and reverse transcription. IN and reverse transcriptase (RT) interact in vitro, and the IN C-terminal domain (CTD) is both necessary and sufficient for binding RT. We used nuclear magnetic resonance spectroscopy to identify a putative RT-binding surface on the IN CTD, and surface plasmon resonance to obtain kinetic parameters and the binding affinity for the IN-RT interaction. An IN K258A substitution that disrupts reverse transcription in infected cells is located at the putative RT-binding surface, and we found that this substitution substantially weakens IN CTD-RT interactions. We also identified two additional IN amino acid substitutions located at the putative RT-binding surface (W243E and V250E) that significantly impair viral replication in tissue culture. These results strengthen the notion that IN-RT interactions are biologically relevant during HIV-1 replication and also provide insights into this interaction at the molecular level. PMID:19150986

  10. Initial Characterization of Integrase-Defective Lentiviral Vectors for Pancreatic Cancer Gene Therapy.

    PubMed

    Hanoun, Naima; Gayral, Marion; Pointreau, Adeline; Buscail, Louis; Cordelier, Pierre

    2016-02-01

    The vast majority (85%) of pancreatic ductal adenocarcinomas (PDACs) are discovered at too of a late stage to allow curative surgery. In addition, PDAC is highly resistant to conventional methods of chemotherapy and radiotherapy, which only offer a marginal clinical benefit. Consequently, the prognosis of this cancer is devastating, with a 5-year survival rate of less than 5%. In this dismal context, we recently demonstrated that PDAC gene therapy using nonviral vectors is safe and feasible, with early signs of efficacy in selected patients. Our next step is to transfer to the clinic HIV-1-based lentiviral vectors (LVs) that outshine other therapeutic vectors to treat experimental models of PDAC. However, a primary safety issue presented by LVs that may delay their use in patients is the risk of oncogenesis after vector integration in the host's cell DNA. Thus, we developed a novel anticancerous approach based on integrase-defective lentiviral vectors (IDLVs) and demonstrated that IDLVs can be successfully engineered to transiently deliver therapeutic genes to inhibit pancreatic cancer cells proliferation. This work stems for the use of therapeutic IDLVs for the management of PDAC, in forthcoming early phase gene therapy clinical trial for this disease with no cure. PMID:26731312