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Zhang X, Niu W, Tang T, Hou C, Guo Y, Kong R. A Strategy to Find Novel Candidate DKAs Inhibitors Using Modified QSAR Model with Favorable Druggability Properties. Chem Res Chin Univ 2019. [DOI: 10.1007/s40242-019-9183-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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2
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Balasubramanian S, Rajagopalan M, Bojja RS, Skalka AM, Andrake MD, Ramaswamy A. The conformational feasibility for the formation of reaching dimer in ASV and HIV integrase: a molecular dynamics study. J Biomol Struct Dyn 2016; 35:3469-3485. [PMID: 27835934 DOI: 10.1080/07391102.2016.1257955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Retroviral integrases are reported to form alternate dimer assemblies like the core-core dimer and reaching dimer. The core-core dimer is stabilized predominantly by an extensive interface between two catalytic core domains. The reaching dimer is stabilized by N-terminal domains that reach to form intermolecular interfaces with the other subunit's core and C-terminal domains (CTD), as well as CTD-CTD interactions. In this study, molecular dynamics (MD), Brownian dynamics (BD) simulations, and free energy analyses, were performed to elucidate determinants for the stability of the reaching dimer forms of full-length Avian Sarcoma Virus (ASV) and Human Immunodeficiency Virus (HIV) IN, and to examine the role of the C-tails (the last ~16-18 residues at the C-termini) in their structural dynamics. The dynamics of an HIV reaching dimer derived from small angle X-ray scattering and protein crosslinking data, was compared with the dynamics of a core-core dimer model derived from combining the crystal structures of two-domain fragments. The results showed that the core domains in the ASV reaching dimer express free dynamics, whereas those in the HIV reaching dimer are highly stable. BD simulations suggest a higher rate of association for the HIV core-core dimer than the reaching dimer. The predicted stability of these dimers was therefore ranked in the following order: ASV reaching dimer < HIV reaching dimer < composite core-core dimer. Analyses of MD trajectories have suggested residues that are critical for intermolecular contacts in each reaching dimer. Tests of these predictions and insights gained from these analyses could reveal a potential pathway for the association and dissociation of full-length IN multimers.
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Affiliation(s)
- Sangeetha Balasubramanian
- a Centre for Bioinformatics, School of Life Sciences , Pondicherry University , Puducherry 605014 , India
| | - Muthukumaran Rajagopalan
- a Centre for Bioinformatics, School of Life Sciences , Pondicherry University , Puducherry 605014 , India
| | - Ravi Shankar Bojja
- b Institute for Cancer Research , Fox Chase Cancer Center , Philadelphia , PA 19111 , USA
| | - Anna Marie Skalka
- b Institute for Cancer Research , Fox Chase Cancer Center , Philadelphia , PA 19111 , USA
| | - Mark D Andrake
- b Institute for Cancer Research , Fox Chase Cancer Center , Philadelphia , PA 19111 , USA
| | - Amutha Ramaswamy
- a Centre for Bioinformatics, School of Life Sciences , Pondicherry University , Puducherry 605014 , India
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Roberts VA. C-Terminal Domain of Integrase Binds between the Two Active Sites. J Chem Theory Comput 2015; 11:4500-11. [PMID: 26575940 DOI: 10.1021/ct501125r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
HIV integrase (HIV-IN), one of three HIV enzymes, is a target for the treatment of AIDS, but the full biological assembly has been difficult to characterize, hampering inhibitor design. The recent crystallographic structures of integrase from prototype foamy virus (PFV-IN) with bound DNA were a breakthrough, revealing how viral DNA organizes two integrase dimers into a tetramer that has the two active sites appropriately spaced for insertion of the viral DNA into host DNA. The organization of domains within each PFV-IN protein chain, however, varies significantly from that found in HIV-IN structures. With the goal of identifying shared structural characteristics, the interactions among components of the PFV-IN and HIV-IN assemblies were investigated with the macromolecular docking program DOT. DOT performs an exhaustive, rigid-body search between two macromolecules. Computational docking reproduced the crystallographic interactions of the PFV-IN catalytic and N-terminal domains with viral DNA and found similar viral DNA interactions for HIV-IN. Computational docking did not reproduce the crystallographic interactions of the PFV-IN C-terminal domain (CTD). Instead, two symmetry-related positions were found for the PFV-IN CTD that indicate formation of a CTD dimer between the two active sites. Our predicted CTD dimer is consistent with cross-linking studies showing interactions of the CTD with viral DNA that appear to be blocked in the PFV-IN structures. The CTD dimer can insert two arginine-rich loops between the two bound vDNA molecules and the host DNA, a region that is unoccupied in the PFV-IN crystallographic structures. The positive potential from these two loops would alleviate the large negative potential created by the close proximity of two viral vDNA ends, helping to bring together the two active sites and assisting host DNA binding. This study demonstrates the ability of computational docking to evaluate complex crystallographic assemblies, identify interactions that are influenced by the crystal environment, and provide plausible alternatives.
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Affiliation(s)
- Victoria A Roberts
- San Diego Supercomputer Center, University of California, San Diego , La Jolla, California 92093, United States
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4
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Structural dynamics of native and V260E mutant C-terminal domain of HIV-1 integrase. J Comput Aided Mol Des 2015; 29:371-85. [PMID: 25586721 DOI: 10.1007/s10822-015-9830-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 01/06/2015] [Indexed: 12/22/2022]
Abstract
The C-terminal domain (CTD) of HIV-1 integrase is a five stranded β-barrel resembling an SH3 fold. Mutational studies on isolated CTD and full-length IN have reported V260E mutant as either homo-dimerization defective or affecting the stability and folding of CTD. In this study, molecular dynamics simulation techniques were used to unveil the effect of V260E mutation on isolated CTD monomer and dimer. Both monomeric and dimeric forms of wild type and V260E mutant are highly stable during the simulated period. However, the stabilizing π-stacking interaction between Trp243 and Trp243' at the dimer interface is highly disturbed in CTD-V260E (>6 Å apart). The loss in entropy for dimerization is -30 and -25 kcal/mol for CTD-wt and CTD-V260E respectively signifying a weak hydrophobic interaction and its perturbation in CTD-V260E. The mutant Glu260 exhibits strong attraction/repulsion with all the basic/acidic residues of CTD. In addition to this, the dynamics of CTD-wild type and V260E monomers at 498 K was analyzed to elucidate the effect of V260E mutation on CTD folding. Increase in SASA and reduction in the number of contacts in CTD-V260E during simulation highlights the instability caused by the mutation. In general, V260E mutation affects both multimerization and protein folding with a pronounced effect on protein folding rather than multimerization. This study emphasizes the importance of the hydrophobic nature and SH3 fold of CTD in proper functioning of HIV integrase and perturbing this nature would be a rational approach toward designing more selective and potent allosteric anti-HIV inhibitors.
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Sangeetha B, Muthukumaran R, Amutha R. The dynamics of interconverting D- and E-forms of the HIV-1 integrase N-terminal domain. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2014; 43:485-98. [DOI: 10.1007/s00249-014-0979-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 06/23/2014] [Accepted: 07/21/2014] [Indexed: 12/19/2022]
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6
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Quevedo MA, Ribone SR, Briñón MC, Dehaen W. Development of a receptor model for efficient in silico screening of HIV-1 integrase inhibitors. J Mol Graph Model 2014; 52:82-90. [PMID: 25023663 DOI: 10.1016/j.jmgm.2014.06.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 06/19/2014] [Accepted: 06/20/2014] [Indexed: 12/01/2022]
Abstract
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 inhibitors. In conclusion, we report an exhaustively validated receptor model if IN that is useful for the efficient screening of large chemical compounds databases in the search of potent HIV-1 IN inhibitors.
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Affiliation(s)
- Mario A Quevedo
- Departamento de Farmacia, Facultad de Ciencias Químicas, Ciudad Universitaria, Universidad Nacional de Córdoba, 5000 Córdoba, Argentina.
| | - Sergio R Ribone
- Departamento de Farmacia, Facultad de Ciencias Químicas, Ciudad Universitaria, Universidad Nacional de Córdoba, 5000 Córdoba, Argentina
| | - Margarita C Briñón
- Departamento de Farmacia, Facultad de Ciencias Químicas, Ciudad Universitaria, Universidad Nacional de Córdoba, 5000 Córdoba, Argentina
| | - Wim Dehaen
- Molecular Design and Synthesis, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
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DeAnda F, Hightower KE, Nolte RT, Hattori K, Yoshinaga T, Kawasuji T, Underwood MR. Dolutegravir interactions with HIV-1 integrase-DNA: structural rationale for drug resistance and dissociation kinetics. PLoS One 2013; 8:e77448. [PMID: 24146996 PMCID: PMC3797783 DOI: 10.1371/journal.pone.0077448] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 09/10/2013] [Indexed: 01/12/2023] Open
Abstract
Signature HIV-1 integrase mutations associated with clinical raltegravir resistance involve 1 of 3 primary genetic pathways, Y143C/R, Q148H/K/R and N155H, the latter 2 of which confer cross-resistance to elvitegravir. In accord with clinical findings, in vitro drug resistance profiling studies with wild-type and site-directed integrase mutant viruses have shown significant fold increases in raltegravir and elvitegravir resistance for the specified viral mutants relative to wild-type HIV-1. Dolutegravir, in contrast, has demonstrated clinical efficacy in subjects failing raltegravir therapy due to integrase mutations at Y143, Q148 or N155, which is consistent with its distinct in vitro resistance profile as dolutegravir's antiviral activity against these viral mutants is equivalent to its activity against wild-type HIV-1. Kinetic studies of inhibitor dissociation from wild-type and mutant integrase-viral DNA complexes have shown that dolutegravir also has a distinct off-rate profile with dissociative half-lives substantially longer than those of raltegravir and elvitegravir, suggesting that dolutegravir's prolonged binding may be an important contributing factor to its distinct resistance profile. To provide a structural rationale for these observations, we constructed several molecular models of wild-type and clinically relevant mutant HIV-1 integrase enzymes in complex with viral DNA and dolutegravir, raltegravir or elvitegravir. Here, we discuss our structural models and the posited effects that the integrase mutations and the structural and electronic properties of the integrase inhibitors may have on the catalytic pocket and inhibitor binding and, consequently, on antiviral potency in vitro and in the clinic.
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Affiliation(s)
- Felix DeAnda
- Chemical Sciences, GlaxoSmithKline, Research Triangle Park, North Carolina, United States of America
| | - Kendra E. Hightower
- Biological Sciences, GlaxoSmithKline, Research Triangle Park, North Carolina, United States of America
| | - Robert T. Nolte
- Chemical Sciences, GlaxoSmithKline, Research Triangle Park, North Carolina, United States of America
| | | | | | - Takashi Kawasuji
- Chemistry Infectious Diseases, Shionogi & Co., Ltd., Osaka, Japan
| | - Mark R. Underwood
- Medicines Development Infectious Diseases, GlaxoSmithKline, Research Triangle Park, North Carolina, United States of America
- * E-mail:
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8
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Veith N, Feldman-Salit A, Cojocaru V, Henrich S, Kummer U, Wade RC. Organism-adapted specificity of the allosteric regulation of pyruvate kinase in lactic acid bacteria. PLoS Comput Biol 2013; 9:e1003159. [PMID: 23946717 PMCID: PMC3738050 DOI: 10.1371/journal.pcbi.1003159] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 06/11/2013] [Indexed: 11/19/2022] Open
Abstract
Pyruvate kinase (PYK) is a critical allosterically regulated enzyme that links glycolysis, the primary energy metabolism, to cellular metabolism. Lactic acid bacteria rely almost exclusively on glycolysis for their energy production under anaerobic conditions, which reinforces the key role of PYK in their metabolism. These organisms are closely related, but have adapted to a huge variety of native environments. They include food-fermenting organisms, important symbionts in the human gut, and antibiotic-resistant pathogens. In contrast to the rather conserved inhibition of PYK by inorganic phosphate, the activation of PYK shows high variability in the type of activating compound between different lactic acid bacteria. System-wide comparative studies of the metabolism of lactic acid bacteria are required to understand the reasons for the diversity of these closely related microorganisms. These require knowledge of the identities of the enzyme modifiers. Here, we predict potential allosteric activators of PYKs from three lactic acid bacteria which are adapted to different native environments. We used protein structure-based molecular modeling and enzyme kinetic modeling to predict and validate potential activators of PYK. Specifically, we compared the electrostatic potential and the binding of phosphate moieties at the allosteric binding sites, and predicted potential allosteric activators by docking. We then made a kinetic model of Lactococcus lactis PYK to relate the activator predictions to the intracellular sugar-phosphate conditions in lactic acid bacteria. This strategy enabled us to predict fructose 1,6-bisphosphate as the sole activator of the Enterococcus faecalis PYK, and to predict that the PYKs from Streptococcus pyogenes and Lactobacillus plantarum show weaker specificity for their allosteric activators, while still having fructose 1,6-bisphosphate play the main activator role in vivo. These differences in the specificity of allosteric activation may reflect adaptation to different environments with different concentrations of activating compounds. The combined computational approach employed can readily be applied to other enzymes.
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Affiliation(s)
- Nadine Veith
- Molecular and Cellular Modelling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
- Department of Modelling Biological Processes, Centre for Organismal Studies (COS)/BIOQUANT, Heidelberg University, Heidelberg, Germany
| | - Anna Feldman-Salit
- Molecular and Cellular Modelling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
- Department of Modelling Biological Processes, Centre for Organismal Studies (COS)/BIOQUANT, Heidelberg University, Heidelberg, Germany
- Center for Modelling and Simulation in the Biosciences (BIOMS), Heidelberg, Germany
| | - Vlad Cojocaru
- Molecular and Cellular Modelling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - Stefan Henrich
- Molecular and Cellular Modelling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - Ursula Kummer
- Department of Modelling Biological Processes, Centre for Organismal Studies (COS)/BIOQUANT, Heidelberg University, Heidelberg, Germany
| | - Rebecca C. Wade
- Molecular and Cellular Modelling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
- Center for Molecular Biology (ZMBH), Heidelberg University, Heidelberg, Germany
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Abstract
Integrase (IN) is a clinically validated target for the treatment of human immunodeficiency virus infections and raltegravir exhibits remarkable clinical activity. The next most advanced IN inhibitor is elvitegravir. However, mutant viruses lead to treatment failure and mutations within the IN coding sequence appear to confer cross-resistance. The characterization of those mutations is critical for the development of second generation IN inhibitors to overcome resistance. This review focuses on IN resistance based on structural and biochemical data, and on the role of the IN flexible loop i.e., between residues G140-G149 in drug action and resistance.
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Affiliation(s)
| | | | | | - Yves Pommier
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-301-496-5944; Fax: +1-301-402-0752
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Balasubramanian S, Rajagopalan M, Ramaswamy A. Structural dynamics of full-length retroviral integrase: a molecular dynamics analysis. J Biomol Struct Dyn 2012; 29:659-70. [DOI: 10.1080/07391102.2011.672630] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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11
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Xue W, Liu H, Yao X. Molecular mechanism of HIV-1 integrase-vDNA interactions and strand transfer inhibitor action: A molecular modeling perspective. J Comput Chem 2011; 33:527-36. [DOI: 10.1002/jcc.22887] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 09/25/2011] [Accepted: 10/20/2011] [Indexed: 01/03/2023]
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12
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HU JP, LIU W, TANG DY, ZHANG YQ, CHANG S. Study on The Binding Mode and Mobility of HIV-1 Integrase With L708, 906 Inhibitor*. PROG BIOCHEM BIOPHYS 2011. [DOI: 10.3724/sp.j.1206.2010.00438] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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13
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Structure-based modeling of the functional HIV-1 intasome and its inhibition. Proc Natl Acad Sci U S A 2010; 107:15910-5. [PMID: 20733078 DOI: 10.1073/pnas.1002346107] [Citation(s) in RCA: 173] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The intasome is the basic recombination unit of retroviral integration, comprising the integrase protein and the ends of the viral DNA made by reverse transcription. Clinical inhibitors preferentially target the DNA-bound form of integrase as compared with the free protein, highlighting the critical requirement for detailed understanding of HIV-1 intasome structure and function. Although previous biochemical studies identified integrase residues that contact the DNA, structural details of protein-protein and protein-DNA interactions within the functional intasome were lacking. The recent crystal structure of the prototype foamy virus (PFV) integrase-viral DNA complex revealed numerous details of this related integration machine. Structures of drug-bound PFV intasomes moreover elucidated the mechanism of inhibitor action. Herein we present a model for the HIV-1 intasome assembled using the PFV structure as template. Our results pinpoint previously identified protein-DNA contacts within the quaternary structure and reveal hitherto unknown roles for Arg20 and Lys266 in DNA binding and integrase function. Models for clinical inhibitors bound at the HIV-1 integrase active site were also constructed and compared with previous studies. Our findings highlight the structural basis for HIV-1 integration and define the mechanism of its inhibition, which should help in formulating new drugs to inhibit viruses resistant to first-in-class compounds.
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Abstract
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-1 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-1 integrase inhibitors. Different structurally diverse integrase inhibitors have been identified by, or with significant help from, various CADD tools.
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Affiliation(s)
- Chenzhong Liao
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, NCI-Frederick, 376 Boyles Street, Frederick, MD 21702, USA
| | - Marc C Nicklaus
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, NCI-Frederick, 376 Boyles Street, Frederick, MD 21702, USA
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Crystal structure of the HIV-1 integrase core domain in complex with sucrose reveals details of an allosteric inhibitory binding site. FEBS Lett 2010; 584:1455-62. [DOI: 10.1016/j.febslet.2010.03.016] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Revised: 03/05/2010] [Accepted: 03/09/2010] [Indexed: 01/15/2023]
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Hobaika Z, Zargarian L, Boulard Y, Maroun RG, Mauffret O, Fermandjian S. Specificity of LTR DNA recognition by a peptide mimicking the HIV-1 integrase {alpha}4 helix. Nucleic Acids Res 2010; 37:7691-700. [PMID: 19808934 PMCID: PMC2794180 DOI: 10.1093/nar/gkp824] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
HIV-1 integrase integrates retroviral DNA through 3′-processing and strand transfer reactions in the presence of a divalent cation (Mg2+ or Mn2+). The α4 helix exposed at the catalytic core surface is essential to the specific recognition of viral DNA. To define group determinants of recognition, we used a model composed of a peptide analogue of the α4 helix, oligonucleotides mimicking processed and unprocessed U5 LTR end and 5 mM Mg2+. Circular dichroism, fluorescence and NMR experiments confirmed the implication of the α4 helix polar/charged face in specific and non-specific bindings to LTR ends. The specific binding requires unprocessed LTR ends—i.e. an unaltered 3′-processing site CA↓GT3′—and is reinforced by Mg2+ (Kd decreases from 2 to 0.8 nM). The latter likely interacts with the ApG and GpT3′ steps of the 3′-processing site. With deletion of GT3′, only persists non-specific binding (Kd of 100 μM). Proton chemical shift deviations showed that specific binding need conserved amino acids in the α4 helix and conserved nucleotide bases and backbone groups at LTR ends. We suggest a conserved recognition mechanism based on both direct and indirect readout and which is subject to evolutionary pressure.
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Affiliation(s)
- Zeina Hobaika
- Laboratoire de Biotechnologies et Pharmacologie génétique Appliquée (LBPA), UMR 8113 CNRS, Ecole Normale Supérieure de Cachan, 61 Avenue du Président Wilson, 94235 Cachan Cedex, France
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Mouscadet JF, Arora R, André J, Lambry JC, Delelis O, Malet I, Marcelin AG, Calvez V, Tchertanov L. HIV-1 IN alternative molecular recognition of DNA induced by raltegravir resistance mutations. J Mol Recognit 2010; 22:480-94. [PMID: 19623602 DOI: 10.1002/jmr.970] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Virologic failure during treatment with raltegravir, the first effective drug targeting HIV integrase, is associated with two exclusive pathways involving either Q148H/R/K, G140S/A or N155H mutations. We carried out a detailed analysis of the molecular and structural effects of these mutations. We observed no topological change in the integrase core domain, with conservation of a newly identified Omega-shaped hairpin containing the Q148 residue, in particular. In contrast, the mutations greatly altered the specificity of DNA recognition by integrase. The native residues displayed a clear preference for adenine, whereas the mutant residues strongly favored pyrimidines. Raltegravir may bind to N155 and/or Q148 residues as an adenine bioisoster. This may account for the selected mutations impairing raltegravir binding while allowing alternative DNA recognition by integrase. This study opens up new opportunities for the design of integrase inhibitors active against raltegravir-resistant viruses.
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Affiliation(s)
- Jean-François Mouscadet
- LBPA, CNRS, Ecole Normale Supérieure de Cachan, 61 Avenue du Président Wilson, 94235 Cachan, France
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18
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Delelis O, Thierry S, Subra F, Simon F, Malet I, Alloui C, Sayon S, Calvez V, Deprez E, Marcelin AG, Tchertanov L, Mouscadet JF. Impact of Y143 HIV-1 integrase mutations on resistance to raltegravir in vitro and in vivo. Antimicrob Agents Chemother 2010; 54:491-501. [PMID: 19901095 PMCID: PMC2798554 DOI: 10.1128/aac.01075-09] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Revised: 09/10/2009] [Accepted: 10/28/2009] [Indexed: 11/20/2022] Open
Abstract
Integrase (IN), the HIV-1 enzyme responsible for the integration of the viral genome into the chromosomes of infected cells, is the target of the recently approved antiviral raltegravir (RAL). Despite this drug's activity against viruses resistant to other antiretrovirals, failures of raltegravir therapy were observed, in association with the emergence of resistance due to mutations in the integrase coding region. Two pathways involving primary mutations on residues N155 and Q148 have been characterized. It was suggested that mutations at residue Y143 might constitute a third primary pathway for resistance. The aims of this study were to investigate the susceptibility of HIV-1 Y143R/C mutants to raltegravir and to determine the effects of these mutations on the IN-mediated reactions. Our observations demonstrate that Y143R/C mutants are strongly impaired for both of these activities in vitro. However, Y143R/C activity can be kinetically restored, thereby reproducing the effect of the secondary G140S mutation that rescues the defect associated with the Q148R/H mutants. A molecular modeling study confirmed that Y143R/C mutations play a role similar to that determined for Q148R/H mutations. In the viral replicative context, this defect leads to a partial block of integration responsible for a weak replicative capacity. Nevertheless, the Y143 mutant presented a high level of resistance to raltegravir. Furthermore, the 50% effective concentration (EC(50)) determined for Y143R/C mutants was significantly higher than that obtained with G140S/Q148R mutants. Altogether our results not only show that the mutation at position Y143 is one of the mechanisms conferring resistance to RAL but also explain the delayed emergence of this mutation.
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Affiliation(s)
- Olivier Delelis
- LBPA, CNRS, Ecole Normale Supérieure de Cachan, Cachan, France, Université Pierre et Marie Curie—Paris, UMR S-943, Paris, France, INSERM, U943, Paris, France, AP-HP, Groupe Hospitalier Pitié Salpêtrière, Laboratoire de Virologie, Paris, France, Service de Bactériologie, Virologie-Hygiène, Hôpital Avicennes EA 3406, AP-HP, Université Paris 13, Bobigny, Paris, France
| | - Sylvain Thierry
- LBPA, CNRS, Ecole Normale Supérieure de Cachan, Cachan, France, Université Pierre et Marie Curie—Paris, UMR S-943, Paris, France, INSERM, U943, Paris, France, AP-HP, Groupe Hospitalier Pitié Salpêtrière, Laboratoire de Virologie, Paris, France, Service de Bactériologie, Virologie-Hygiène, Hôpital Avicennes EA 3406, AP-HP, Université Paris 13, Bobigny, Paris, France
| | - Frédéric Subra
- LBPA, CNRS, Ecole Normale Supérieure de Cachan, Cachan, France, Université Pierre et Marie Curie—Paris, UMR S-943, Paris, France, INSERM, U943, Paris, France, AP-HP, Groupe Hospitalier Pitié Salpêtrière, Laboratoire de Virologie, Paris, France, Service de Bactériologie, Virologie-Hygiène, Hôpital Avicennes EA 3406, AP-HP, Université Paris 13, Bobigny, Paris, France
| | - Françoise Simon
- LBPA, CNRS, Ecole Normale Supérieure de Cachan, Cachan, France, Université Pierre et Marie Curie—Paris, UMR S-943, Paris, France, INSERM, U943, Paris, France, AP-HP, Groupe Hospitalier Pitié Salpêtrière, Laboratoire de Virologie, Paris, France, Service de Bactériologie, Virologie-Hygiène, Hôpital Avicennes EA 3406, AP-HP, Université Paris 13, Bobigny, Paris, France
| | - Isabelle Malet
- LBPA, CNRS, Ecole Normale Supérieure de Cachan, Cachan, France, Université Pierre et Marie Curie—Paris, UMR S-943, Paris, France, INSERM, U943, Paris, France, AP-HP, Groupe Hospitalier Pitié Salpêtrière, Laboratoire de Virologie, Paris, France, Service de Bactériologie, Virologie-Hygiène, Hôpital Avicennes EA 3406, AP-HP, Université Paris 13, Bobigny, Paris, France
| | - Chakib Alloui
- LBPA, CNRS, Ecole Normale Supérieure de Cachan, Cachan, France, Université Pierre et Marie Curie—Paris, UMR S-943, Paris, France, INSERM, U943, Paris, France, AP-HP, Groupe Hospitalier Pitié Salpêtrière, Laboratoire de Virologie, Paris, France, Service de Bactériologie, Virologie-Hygiène, Hôpital Avicennes EA 3406, AP-HP, Université Paris 13, Bobigny, Paris, France
| | - Sophie Sayon
- LBPA, CNRS, Ecole Normale Supérieure de Cachan, Cachan, France, Université Pierre et Marie Curie—Paris, UMR S-943, Paris, France, INSERM, U943, Paris, France, AP-HP, Groupe Hospitalier Pitié Salpêtrière, Laboratoire de Virologie, Paris, France, Service de Bactériologie, Virologie-Hygiène, Hôpital Avicennes EA 3406, AP-HP, Université Paris 13, Bobigny, Paris, France
| | - Vincent Calvez
- LBPA, CNRS, Ecole Normale Supérieure de Cachan, Cachan, France, Université Pierre et Marie Curie—Paris, UMR S-943, Paris, France, INSERM, U943, Paris, France, AP-HP, Groupe Hospitalier Pitié Salpêtrière, Laboratoire de Virologie, Paris, France, Service de Bactériologie, Virologie-Hygiène, Hôpital Avicennes EA 3406, AP-HP, Université Paris 13, Bobigny, Paris, France
| | - Eric Deprez
- LBPA, CNRS, Ecole Normale Supérieure de Cachan, Cachan, France, Université Pierre et Marie Curie—Paris, UMR S-943, Paris, France, INSERM, U943, Paris, France, AP-HP, Groupe Hospitalier Pitié Salpêtrière, Laboratoire de Virologie, Paris, France, Service de Bactériologie, Virologie-Hygiène, Hôpital Avicennes EA 3406, AP-HP, Université Paris 13, Bobigny, Paris, France
| | - Anne-Geneviève Marcelin
- LBPA, CNRS, Ecole Normale Supérieure de Cachan, Cachan, France, Université Pierre et Marie Curie—Paris, UMR S-943, Paris, France, INSERM, U943, Paris, France, AP-HP, Groupe Hospitalier Pitié Salpêtrière, Laboratoire de Virologie, Paris, France, Service de Bactériologie, Virologie-Hygiène, Hôpital Avicennes EA 3406, AP-HP, Université Paris 13, Bobigny, Paris, France
| | - Luba Tchertanov
- LBPA, CNRS, Ecole Normale Supérieure de Cachan, Cachan, France, Université Pierre et Marie Curie—Paris, UMR S-943, Paris, France, INSERM, U943, Paris, France, AP-HP, Groupe Hospitalier Pitié Salpêtrière, Laboratoire de Virologie, Paris, France, Service de Bactériologie, Virologie-Hygiène, Hôpital Avicennes EA 3406, AP-HP, Université Paris 13, Bobigny, Paris, France
| | - Jean-François Mouscadet
- LBPA, CNRS, Ecole Normale Supérieure de Cachan, Cachan, France, Université Pierre et Marie Curie—Paris, UMR S-943, Paris, France, INSERM, U943, Paris, France, AP-HP, Groupe Hospitalier Pitié Salpêtrière, Laboratoire de Virologie, Paris, France, Service de Bactériologie, Virologie-Hygiène, Hôpital Avicennes EA 3406, AP-HP, Université Paris 13, Bobigny, Paris, France
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19
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Barreca ML, Iraci N, De Luca L, Chimirri A. Induced-fit docking approach provides insight into the binding mode and mechanism of action of HIV-1 integrase inhibitors. ChemMedChem 2009; 4:1446-56. [PMID: 19544345 DOI: 10.1002/cmdc.200900166] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A three-dimensional model of a complex between HIV-1 integrase (IN), viral DNA, and metal ions that we recently built was used as a target for a docking method (induced-fit docking, IFD) that accurately predicts ligand binding modes and concomitant structural changes in the receptor. Six different well-known integrase strand transfer inhibitors (INSTIs): L-708,906, L-731,988, S-1360, L-870,810, raltegravir, and elvitegravir were thus used as ligands for our docking simulations. The obtained IFD results are consistent with the mechanism of action proposed for this class of IN inhibitors, that is, metal chelating/binding agents. This study affords new insight into the possible mechanism of inhibition and binding conformations for INSTIs. The impact on our hypothesis of specific mutations associated with IN inhibitor resistance was also evaluated. All these findings might have implications for integrase-directed HIV-1 drug discovery efforts.
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Affiliation(s)
- Maria Letizia Barreca
- Dipartimento di Chimica e Tecnologia del Farmaco, Facoltà di Farmacia, Università di Perugia, Via del Liceo 1, 06123 Perugia, Italy.
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20
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Acevedo ML, Arbildúa JJ, Monasterio O, Toledo H, León O. Role of the 207-218 peptide region of Moloney murine leukemia virus integrase in enzyme catalysis. Arch Biochem Biophys 2009; 495:28-34. [PMID: 20026028 DOI: 10.1016/j.abb.2009.12.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 12/11/2009] [Accepted: 12/13/2009] [Indexed: 11/18/2022]
Abstract
X-ray diffraction data on a few retroviral integrases show a flexible loop near the active site. By sequence alignment, the peptide region 207-218 of Mo-MLV IN appears to correspond to this flexible loop. In this study, residues H208, Y211, R212, Q214, S215 and S216 of Mo-MLV IN were mutated to determine their role on enzyme activity. We found that Y211A, R212A, R212K and Q214A decreased integration activity, while disintegration and 3'-processing were not significantly affected. By contrast H208A was completely inactive in all the assays. The core domain of Mo-MLV integrase was modeled and the flexibility of the region 207-216 was analyzed. Substitutions with low integration activity showed a lower flexibility than wild type integrase. We propose that the peptide region 207-216 is a flexible loop and that H208, Y211, R212 and Q214 of this loop are involved in the correct assembly of the DNA-integrase complex during integration.
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Affiliation(s)
- Mónica L Acevedo
- Programa de Virología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile.
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21
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Kessl JJ, McKee CJ, Eidahl JO, Shkriabai N, Katz A, Kvaratskhelia M. HIV-1 Integrase-DNA Recognition Mechanisms. Viruses 2009; 1:713-36. [PMID: 21994566 PMCID: PMC3185514 DOI: 10.3390/v1030713] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 11/03/2009] [Accepted: 11/04/2009] [Indexed: 01/24/2023] Open
Abstract
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.
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Affiliation(s)
- Jacques J Kessl
- Center for Retrovirus Research and Comprehensive Cancer Center, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA; E-Mails: (J.J.K.); (C.J.M.); (J.O.E.), (N.S.); (A.K.)
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22
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Mirambeau G. [How proviral DNA is integrated into the host cell DNA and how this process can be inhibited]. Enferm Infecc Microbiol Clin 2009; 26 Suppl 12:11-6. [PMID: 19572420 DOI: 10.1016/s0213-005x(08)76567-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The HIV replication cycle passes through a stage of integrating proviral DNA into the cell's DNA. In this process, the viral enzyme, integrase, catalyses two reactions. The first reaction, which seems to occur in the cytoplasm, involves 3'-end processing, in which two nucleotides are removed from the 3' ends of the viral DNA by integrase. The second reaction, which occurs in the nucleus, involves the strand transfer reaction, catalyzed by integrase, in which the recessed 3' ends of the viral DNA are joined to the protruding 5' ends in the target DNA. Although this activity has not yet been completely defined and the structure of the active form of integrase, probably a tetramer, has not been resolved, drugs of the diketoacid (DKA) family have been found. These drugs are highly potent inhibitors of the second phase, the strand transfer reaction. Through a series of optimizations, a highly effective molecule for clinical use, raltegravir, has been achieved. The present article provides a summary of basic knowledge on integrase, as well as the activity and the modes of inhibition of this enzyme. Also discussed is the reduced, but nevertheless real, development of resistance to raltegravir, requiring second-generation integrase inhibitors to be designed.
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Affiliation(s)
- Gilles Mirambeau
- Unitat de Recerca de la Sida, Fundació Clinic-IDIBAPS, Pare Cientific de Barcelona, Universidad de Barcelona, Barcelona, España.
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23
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Paxman JJ, Borg NA, Horne J, Thompson PE, Chin Y, Sharma P, Simpson JS, Wielens J, Piek S, Kahler CM, Sakellaris H, Pearce M, Bottomley SP, Rossjohn J, Scanlon MJ. The structure of the bacterial oxidoreductase enzyme DsbA in complex with a peptide reveals a basis for substrate specificity in the catalytic cycle of DsbA enzymes. J Biol Chem 2009; 284:17835-45. [PMID: 19389711 PMCID: PMC2719422 DOI: 10.1074/jbc.m109.011502] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2009] [Revised: 04/22/2009] [Indexed: 11/06/2022] Open
Abstract
Oxidative protein folding in Gram-negative bacteria results in the formation of disulfide bonds between pairs of cysteine residues. This is a multistep process in which the dithiol-disulfide oxidoreductase enzyme, DsbA, plays a central role. The structure of DsbA comprises an all helical domain of unknown function and a thioredoxin domain, where active site cysteines shuttle between an oxidized, substrate-bound, reduced form and a DsbB-bound form, where DsbB is a membrane protein that reoxidizes DsbA. Most DsbA enzymes interact with a wide variety of reduced substrates and show little specificity. However, a number of DsbA enzymes have now been identified that have narrow substrate repertoires and appear to interact specifically with a smaller number of substrates. The transient nature of the DsbA-substrate complex has hampered our understanding of the factors that govern the interaction of DsbA enzymes with their substrates. Here we report the crystal structure of a complex between Escherichia coli DsbA and a peptide with a sequence derived from a substrate. The binding site identified in the DsbA-peptide complex was distinct from that observed for DsbB in the DsbA-DsbB complex. The structure revealed details of the DsbA-peptide interaction and suggested a mechanism by which DsbA can simultaneously show broad specificity for substrates yet exhibit specificity for DsbB. This mode of binding was supported by solution nuclear magnetic resonance data as well as functional data, which demonstrated that the substrate specificity of DsbA could be modified via changes at the binding interface identified in the structure of the complex.
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Affiliation(s)
- Jason J. Paxman
- From Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville, Victoria 3052
| | - Natalie A. Borg
- the Protein Crystallography Unit, Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800
| | - James Horne
- From Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville, Victoria 3052
| | - Philip E. Thompson
- From Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville, Victoria 3052
| | - Yanni Chin
- From Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville, Victoria 3052
| | - Pooja Sharma
- From Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville, Victoria 3052
| | - Jamie S. Simpson
- From Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville, Victoria 3052
| | - Jerome Wielens
- From Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville, Victoria 3052
| | - Susannah Piek
- the School of Biomedical, Biomolecular and Chemical Sciences, QEII Medical Centre, University of Western Australia, Crawley, Western Australia 6009, and
| | - Charlene M. Kahler
- the School of Biomedical, Biomolecular and Chemical Sciences, QEII Medical Centre, University of Western Australia, Crawley, Western Australia 6009, and
| | - Harry Sakellaris
- the School of Biomedical, Biomolecular and Chemical Sciences, QEII Medical Centre, University of Western Australia, Crawley, Western Australia 6009, and
| | - Mary Pearce
- the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Stephen P. Bottomley
- the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Jamie Rossjohn
- the Protein Crystallography Unit, Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800
| | - Martin J. Scanlon
- From Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville, Victoria 3052
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24
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Structural and theoretical studies of [6-bromo-1-(4-fluorophenylmethyl)-4(1H)-quinolinon-3-yl)]-4-hydroxy-2-oxo-3-butenoïc acid as HIV-1 integrase inhibitor. Bioorg Med Chem Lett 2009; 19:4806-9. [PMID: 19556126 DOI: 10.1016/j.bmcl.2009.06.044] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2009] [Revised: 06/08/2009] [Accepted: 06/11/2009] [Indexed: 11/21/2022]
Abstract
Ethyl [6-bromo-1-(4-fluorophenylmethyl)-4(1H)-quinolinon-3-yl]-4-hydroxy-2-oxo-3-butenoate 1 and [6-bromo-1-(4-fluorophenylmethyl)-4(1H)-quinolinon-3-yl)]-4-hydroxy-2-oxo-3-butenoïc acid 2 were synthesized as potential HIV-1 integrase inhibitors and evaluated for their enzymatic and antiviral activity, acidic compound 2 being more potent than ester compound 1. X-ray diffraction analyses and theoretical calculations show that the diketoacid chain of compound 2 is preferentially coplanar with the quinolinone ring (dihedral angle of 0-30 degrees ). Docking studies suggest binding modes in agreement with structure-activity relationships.
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25
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Catalytically-active complex of HIV-1 integrase with a viral DNA substrate binds anti-integrase drugs. Proc Natl Acad Sci U S A 2009; 106:8192-7. [PMID: 19416821 DOI: 10.1073/pnas.0811919106] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
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.
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26
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Bera S, Pandey KK, Vora AC, Grandgenett DP. Molecular Interactions between HIV-1 integrase and the two viral DNA ends within the synaptic complex that mediates concerted integration. J Mol Biol 2009; 389:183-98. [PMID: 19362096 DOI: 10.1016/j.jmb.2009.04.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2009] [Revised: 03/16/2009] [Accepted: 04/04/2009] [Indexed: 01/08/2023]
Abstract
A macromolecular nucleoprotein complex in retrovirus-infected cells, termed the preintegration complex, is responsible for the concerted integration of linear viral DNA genome into host chromosomes. Isolation of sufficient quantities of the cytoplasmic preintegration complexes for biochemical and biophysical analysis is difficult. We investigated the architecture of HIV-1 nucleoprotein complexes involved in the concerted integration pathway in vitro. HIV-1 integrase (IN) non-covalently juxtaposes two viral DNA termini forming the synaptic complex, a transient intermediate in the integration pathway, and shares properties associated with the preintegration complex. IN slowly processes two nucleotides from the 3' OH ends and performs the concerted insertion of two viral DNA ends into target DNA. IN remains associated with the concerted integration product, termed the strand transfer complex. The synaptic complex and strand transfer complex can be isolated by native agarose gel electrophoresis. In-gel fluorescence resonance energy transfer measurements demonstrated that the energy transfer efficiencies between the juxtaposed Cy3 and Cy5 5'-end labeled viral DNA ends in the synaptic complex (0.68+/-0.09) was significantly different from that observed in the strand transfer complex (0.07+/-0.02). The calculated distances were 46+/-3 A and 83+/-5 A, respectively. DNaseI footprint analysis of the complexes revealed that IN protects U5 and U3 DNA sequences up to approximately 32 bp from the end, suggesting two IN dimers were bound per terminus. Enhanced DNaseI cleavages were observed at nucleotide positions 6 and 9 from the terminus on U3 but not on U5, suggesting independent assembly events. Protein-protein cross-linking of IN within these complexes revealed the presence of dimers, tetramers, and a larger multimer (>120 kDa). Our results suggest a new model where two IN dimers individually assemble on U3 and U5 ends before the non-covalent juxtaposition of two viral DNA ends, producing the synaptic complex.
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Affiliation(s)
- Sibes Bera
- Saint Louis University Health Sciences Center, Institute for Molecular Virology, Doisy Research Center, St. Louis, MO 63104, USA.
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27
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Michel F, Crucifix C, Granger F, Eiler S, Mouscadet JF, Korolev S, Agapkina J, Ziganshin R, Gottikh M, Nazabal A, Emiliani S, Benarous R, Moras D, Schultz P, Ruff M. Structural basis for HIV-1 DNA integration in the human genome, role of the LEDGF/P75 cofactor. EMBO J 2009; 28:980-91. [PMID: 19229293 DOI: 10.1038/emboj.2009.41] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Accepted: 01/26/2009] [Indexed: 12/28/2022] Open
Abstract
Integration of the human immunodeficiency virus (HIV-1) cDNA into the human genome is catalysed by integrase. Several studies have shown the importance of the interaction of cellular cofactors with integrase for viral integration and infectivity. In this study, we produced a stable and functional complex between the wild-type full-length integrase (IN) and the cellular cofactor LEDGF/p75 that shows enhanced in vitro integration activity compared with the integrase alone. Mass spectrometry analysis and the fitting of known atomic structures in cryo negatively stain electron microscopy (EM) maps revealed that the functional unit comprises two asymmetric integrase dimers and two LEDGF/p75 molecules. In the presence of DNA, EM revealed the DNA-binding sites and indicated that, in each asymmetric dimer, one integrase molecule performs the catalytic reaction, whereas the other one positions the viral DNA in the active site of the opposite dimer. The positions of the target and viral DNAs for the 3' processing and integration reaction shed light on the integration mechanism, a process with wide implications for the understanding of viral-induced pathologies.
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Affiliation(s)
- Fabrice Michel
- IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Département de Biologie et de Génomique Structurales, UDS, CNRS, INSERM, Illkirch, France
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28
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Langley DR, Samanta HK, Lin Z, Walker MA, Krystal MR, Dicker IB. The terminal (catalytic) adenosine of the HIV LTR controls the kinetics of binding and dissociation of HIV integrase strand transfer inhibitors. Biochemistry 2009; 47:13481-8. [PMID: 18991395 DOI: 10.1021/bi801372d] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Specific HIV integrase strand transfer inhibitors are thought to bind to the integrase active site, positioned to coordinate with two catalytic magnesium atoms in a pocket flanked by the end of the viral LTR. A structural role for the 3' terminus of the viral LTR in the inhibitor-bound state has not previously been examined. This study describes the kinetics of binding of a specific strand transfer inhibitor to integrase variants assembled with systematic changes to the terminal 3' adenosine. Kinetic experiments are consistent with a two-step binding model in which there are different functions for the terminal adenine base and the terminal deoxyribose sugar. Adenine seems to act as a "shield" which retards the rate of inhibitor association with the integrase active site, possibly by acting as an internal competitive inhibitor. The terminal deoxyribose is responsible for retarding the rate of inhibitor dissociation, either by sterically blocking inhibitor egress or by a direct interaction with the bound inhibitor. These findings further our understanding of the details of the inhibitor binding site of specific strand transfer inhibitors.
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Affiliation(s)
- David R Langley
- Department of Computer Assisted Drug Design, Bristol-Myers Squibb Research & Development, Wallingford, Connecticut 06492, USA
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29
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Merad H, Porumb H, Zargarian L, René B, Hobaika Z, Maroun RG, Mauffret O, Fermandjian S. An unusual helix turn helix motif in the catalytic core of HIV-1 integrase binds viral DNA and LEDGF. PLoS One 2009; 4:e4081. [PMID: 19119323 PMCID: PMC2607020 DOI: 10.1371/journal.pone.0004081] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2008] [Accepted: 12/04/2008] [Indexed: 01/29/2023] Open
Abstract
Background Integrase (IN) of the type 1 human immunodeficiency virus (HIV-1) catalyzes the integration of viral DNA into host cellular DNA. We identified a bi-helix motif (residues 149–186) in the crystal structure of the catalytic core (CC) of the IN-Phe185Lys variant that consists of the α4 and α5 helices connected by a 3 to 5-residue turn. The motif is embedded in a large array of interactions that stabilize the monomer and the dimer. Principal Findings We describe the conformational and binding properties of the corresponding synthetic peptide. This displays features of the protein motif structure thanks to the mutual intramolecular interactions of the α4 and α5 helices that maintain the fold. The main properties are the binding to: 1- the processing-attachment site at the LTR (long terminal repeat) ends of virus DNA with a Kd (dissociation constant) in the sub-micromolar range; 2- the whole IN enzyme; and 3- the IN binding domain (IBD) but not the IBD-Asp366Asn variant of LEDGF (lens epidermal derived growth factor) lacking the essential Asp366 residue. In our motif, in contrast to the conventional HTH (helix-turn-helix), it is the N terminal helix (α4) which has the role of DNA recognition helix, while the C terminal helix (α5) would rather contribute to the motif stabilization by interactions with the α4 helix. Conclusion The motif, termed HTHi (i, for inverted) emerges as a central piece of the IN structure and function. It could therefore represent an attractive target in the search for inhibitors working at the DNA-IN, IN-IN and IN-LEDGF interfaces.
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Affiliation(s)
- Hayate Merad
- LBPA, CNRS (UMR 8113)–Ecole Normale Supérieure de Cachan, Cachan, France
| | - Horea Porumb
- LBPA, CNRS (UMR 8113)–Ecole Normale Supérieure de Cachan, Cachan, France
| | - Loussiné Zargarian
- LBPA, CNRS (UMR 8113)–Ecole Normale Supérieure de Cachan, Cachan, France
| | - Brigitte René
- LBPA, CNRS (UMR 8113)–Ecole Normale Supérieure de Cachan, Cachan, France
| | - Zeina Hobaika
- LBPA, CNRS (UMR 8113)–Ecole Normale Supérieure de Cachan, Cachan, France
| | - Richard G. Maroun
- Département des Sciences de la Vie et de la Terre, Faculté des Sciences, Université Saint Joseph, CST-Mar Roukos, B. P. 1514, Beyrouth, Liban
| | - Olivier Mauffret
- LBPA, CNRS (UMR 8113)–Ecole Normale Supérieure de Cachan, Cachan, France
| | - Serge Fermandjian
- LBPA, CNRS (UMR 8113)–Ecole Normale Supérieure de Cachan, Cachan, France
- * E-mail:
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30
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Ferro S, De Luca L, Barreca ML, Iraci N, De Grazia S, Christ F, Witvrouw M, Debyser Z, Chimirri A. Docking Studies on a New Human Immodeficiency Virus Integrase−Mg−DNA Complex: Phenyl Ring Exploration and Synthesis of 1H-Benzylindole Derivatives through Fluorine Substitutions. J Med Chem 2008; 52:569-73. [DOI: 10.1021/jm8009266] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stefania Ferro
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, 98168 Messina, Italy, Dipartimento di Chimica e Tecnologia del Farmaco, Via del Liceo 1, 06123 Perugia, Italy, Molecular Medicine, Katholieke Universiteit Leuven, 3000 Leuven, Belgium, and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Laura De Luca
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, 98168 Messina, Italy, Dipartimento di Chimica e Tecnologia del Farmaco, Via del Liceo 1, 06123 Perugia, Italy, Molecular Medicine, Katholieke Universiteit Leuven, 3000 Leuven, Belgium, and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Maria Letizia Barreca
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, 98168 Messina, Italy, Dipartimento di Chimica e Tecnologia del Farmaco, Via del Liceo 1, 06123 Perugia, Italy, Molecular Medicine, Katholieke Universiteit Leuven, 3000 Leuven, Belgium, and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Nunzio Iraci
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, 98168 Messina, Italy, Dipartimento di Chimica e Tecnologia del Farmaco, Via del Liceo 1, 06123 Perugia, Italy, Molecular Medicine, Katholieke Universiteit Leuven, 3000 Leuven, Belgium, and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Sara De Grazia
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, 98168 Messina, Italy, Dipartimento di Chimica e Tecnologia del Farmaco, Via del Liceo 1, 06123 Perugia, Italy, Molecular Medicine, Katholieke Universiteit Leuven, 3000 Leuven, Belgium, and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Frauke Christ
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, 98168 Messina, Italy, Dipartimento di Chimica e Tecnologia del Farmaco, Via del Liceo 1, 06123 Perugia, Italy, Molecular Medicine, Katholieke Universiteit Leuven, 3000 Leuven, Belgium, and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Myriam Witvrouw
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, 98168 Messina, Italy, Dipartimento di Chimica e Tecnologia del Farmaco, Via del Liceo 1, 06123 Perugia, Italy, Molecular Medicine, Katholieke Universiteit Leuven, 3000 Leuven, Belgium, and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Zeger Debyser
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, 98168 Messina, Italy, Dipartimento di Chimica e Tecnologia del Farmaco, Via del Liceo 1, 06123 Perugia, Italy, Molecular Medicine, Katholieke Universiteit Leuven, 3000 Leuven, Belgium, and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Alba Chimirri
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, 98168 Messina, Italy, Dipartimento di Chimica e Tecnologia del Farmaco, Via del Liceo 1, 06123 Perugia, Italy, Molecular Medicine, Katholieke Universiteit Leuven, 3000 Leuven, Belgium, and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
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31
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Integrase and integration: biochemical activities of HIV-1 integrase. Retrovirology 2008; 5:114. [PMID: 19091057 PMCID: PMC2615046 DOI: 10.1186/1742-4690-5-114] [Citation(s) in RCA: 153] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2008] [Accepted: 12/17/2008] [Indexed: 01/12/2023] Open
Abstract
Integration of retroviral DNA is an obligatory step of retrovirus replication because proviral DNA is the template for productive infection. Integrase, a retroviral enzyme, catalyses integration. The process of integration can be divided into two sequential reactions. The first one, named 3'-processing, corresponds to a specific endonucleolytic reaction which prepares the viral DNA extremities to be competent for the subsequent covalent insertion, named strand transfer, into the host cell genome by a trans-esterification reaction. Recently, a novel specific activity of the full length integrase was reported, in vitro, by our group for two retroviral integrases (HIV-1 and PFV-1). This activity of internal cleavage occurs at a specific palindromic sequence mimicking the LTR-LTR junction described into the 2-LTR circles which are peculiar viral DNA forms found during viral infection. Moreover, recent studies demonstrated the existence of a weak palindromic consensus found at the integration sites. Taken together, these data underline the propensity of retroviral integrases for binding symmetrical sequences and give perspectives for targeting specific sequences used for gene therapy.
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32
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Effects of varying the spacing within the D,D-35-E motif in the catalytic region of retroviral integrase. Virology 2008; 379:223-33. [DOI: 10.1016/j.virol.2008.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2008] [Revised: 03/05/2008] [Accepted: 07/01/2008] [Indexed: 11/20/2022]
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33
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Malet I, Soulie C, Tchertanov L, Derache A, Amellal B, Traore O, Simon A, Katlama C, Mouscadet JF, Calvez V, Marcelin AG. Structural effects of amino acid variations between B and CRF02-AG HIV-1 integrases. J Med Virol 2008; 80:754-61. [PMID: 18360887 DOI: 10.1002/jmv.21169] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
HIV-1 integrase is one of the three essential enzyme required for viral replication and has a great potential as a novel target for anti-HIV drugs. The sequence variability of the entire integrase (IN) was examined in HIV-1 subtype B and CRF02-AG antiretroviral naïve infected patients for the presence of naturally occurring polymorphisms IN gene sequences and protein structures from both subtypes were compared. The phylogenetic analysis showed a total concordance between the 3 pol gene sequences for patients identified as subtype B whereas 3% of patients identified as CRF02-AG showed a mixture of subtypes. The analysis of IN aa sequences showed that 13 positions (K/R14, V/I31, L/I101, T/V112, T/A124, T/A125, G/N134, I/V135, K/T136, V/I201, T/S206, L/I234, and S/G283) differed between subtypes B and CRF02-AG. As observed in the 3D model of the preintegration complex, these differences may impact the functional property of IN. The fact that most variations were grouped suggests that some of them are linked together through compensatory mechanisms. This comparison allowed us to identify several variations of amino acids in HIV-1 IN subtype CRF02-AG that could have a putative impact on anti-integrase sensitivity. In particular, the region formed by Thr125, Thr124, Val31 contains at least one residue, T125, which variation has been involved in eliciting resistance to the naphtyridine carboxamide L870,810 IN inhibitor. In conclusion, virological response to anti-integrase should be studied carefully, according to the subtype, in clinical trials.
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34
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Dayam R, Gundla R, Al-Mawsawi LQ, Neamati N. HIV-1 integrase inhibitors: 2005-2006 update. Med Res Rev 2008; 28:118-54. [PMID: 17979144 DOI: 10.1002/med.20116] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
HIV-1 integrase (IN) catalyzes the integration of proviral DNA into the host genome, an essential step for viral replication. Inhibition of IN catalytic activity provides an attractive strategy for antiretroviral drug design. Currently two IN inhibitors, MK-0518 and GS-9137, are in advanced stages of human clinical trials. The IN inhibitors in clinical evaluation demonstrate excellent antiretroviral efficacy alone or in combination regimens as compared to previously used clinical antiretroviral agents in naive and treatment-experienced HIV-1 infected patients. However, the emergence of viral strains resistant to clinically studied IN inhibitors and the dynamic nature of the HIV-1 genome demand a continued effort toward the discovery of novel inhibitors to keep a therapeutic advantage over the virus. Continued efforts in the field have resulted in the discovery of compounds from diverse chemical classes. In this review, we provide a comprehensive report of all IN inhibitors discovered in the years 2005 and 2006.
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Affiliation(s)
- Raveendra Dayam
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, School of Pharmacy, Los Angeles, California 90089, USA
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35
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Zhao Z, McKee CJ, Kessl JJ, Santos WL, Daigle JE, Engelman A, Verdine G, Kvaratskhelia M. Subunit-specific protein footprinting reveals significant structural rearrangements and a role for N-terminal Lys-14 of HIV-1 Integrase during viral DNA binding. J Biol Chem 2007; 283:5632-41. [PMID: 18093980 DOI: 10.1074/jbc.m705241200] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
To identify functional contacts between HIV-1 integrase (IN) and its viral DNA substrate, we devised a new experimental strategy combining the following two methodologies. First, disulfide-mediated cross-linking was used to site-specifically link select core and C-terminal domain amino acids to respective positions in viral DNA. Next, surface topologies of free IN and IN-DNA complexes were compared using Lys- and Arg-selective small chemical modifiers and mass spectrometric analysis. This approach enabled us to dissect specific contacts made by different monomers within the multimeric complex. The foot-printing studies for the first time revealed the importance of a specific N-terminal domain residue, Lys-14, in viral DNA binding. In addition, a DNA-induced conformational change involving the connection between the core and C-terminal domains was observed. Site-directed mutagenesis experiments confirmed the importance of the identified contacts for recombinant IN activities and virus infection. These new findings provided major constraints, enabling us to identify the viral DNA binding channel in the active full-length IN multimer. The experimental approach described here has general application to mapping interactions within functional nucleoprotein complexes.
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Affiliation(s)
- Zhuojun Zhao
- Center for Retrovirus Research and Comprehensive Cancer Center, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, USA
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36
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Bosserman MA, O'Quinn DF, Wong I. Loop202-208 in avian sarcoma virus integrase mediates tetramer assembly and processing activity. Biochemistry 2007; 46:11231-9. [PMID: 17845008 DOI: 10.1021/bi700197a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Integrase (IN) catalyzes insertion of the retroviral genome into the host via two sequential reactions. The processing activity cleaves the 3'-dinucleotides from the two ends of the viral DNA which are then inserted into the host DNA. Tetramers are required for the joining step. While dimers have been shown to catalyze processing, they do so inefficiently, and the oligomeric requirement for processing is unknown. We have replaced loop202-208 at the putative dimer-dimer interface of the avian sarcoma virus IN with its analogue, loop188-194, from human immunodeficiency virus IN. The mutation abolished disintegration activity and a 2 x 10(-2) s-1 fast phase during single-turnover processing. A 3 x 10(-4) s-1 slow processing phase was unaffected. Preincubation with a DNA substrate known to promote tetramerization increased products formed during the fast phase by 2.5-fold only for wild-type IN, correlating the fast and slow phases with processing by tetramers and dimers, respectively. We propose a novel tetramer model for coupling processing and integration based on efficient processing by the tetramer. We provide for the first time direct evidence of the functional relevance of a structural element, loop202-208, which appears to be required for mediating the interaction between dimer halves of the active tetramer.
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Affiliation(s)
- Mary A Bosserman
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536, USA
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37
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Cox AG, Nair V. Novel HIV integrase inhibitors with anti-HIV activity: insights into integrase inhibition from docking studies. Antivir Chem Chemother 2007; 17:343-53. [PMID: 17249248 DOI: 10.1177/095632020601700604] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The mechanism of integrase is generally accepted to be dependant on the presence of two divalent metal ions in the active site. However, the only available crystal structures of HIV-1 integrase contain either one or no metal ions, hampering structure-based design studies of integrase inhibitors. For this reason, a two-metal ion model of integrase was constructed. This model was used for computational docking studies with novel diketoacid integrase inhibitors containing pyrimidine nucleobase scaffolds. The docking protocol allowed for some steric contact between the ligand and protein during docking simulations, which implicitly accounted for potential conformational changes in the protein as a result of binding viral DNA or the ligand. The results suggest that the aromatic rings in these diketo acids bind to regions close to the viral DNA and may interfere with mobility of a vital catalytic loop. The docking data also suggest that the ligand can be prevented from adopting a favourable conformation by changes in the relative orientation of its diketo side-chain and aromatic rings. The docked pose of each of the active compounds coordinated both of the metal ions present in the active site of integrase through the diketo acid functionality of these compounds. This result is more consistent with theoretical data on inhibitor mechanism, and thus recommends this docking approach over rigid use of one-metal ion models derived from current crystal structures of integrase.
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Affiliation(s)
- Arthur G Cox
- The Center for Drug Discovery and Department of Pharmaceutical and Biomedical Sciences, The University of Georgia, Athens, GA, USA
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38
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Topper M, Luo Y, Zhadina M, Mohammed K, Smith L, Muesing MA. Posttranslational acetylation of the human immunodeficiency virus type 1 integrase carboxyl-terminal domain is dispensable for viral replication. J Virol 2006; 81:3012-7. [PMID: 17182677 PMCID: PMC1865993 DOI: 10.1128/jvi.02257-06] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
A recent report sought to demonstrate that acetylation of specific lysines within integrase (IN) by the histone acetyltransferase (HAT) p300 regulates human immunodeficiency virus type 1 (HIV-1) integration and is essential for viral replication (A. Cereseto, L. Manganaro, M. I. Gutierrez, M. Terreni, A. Fittipaldi, M. Lusic, A. Marcello, and M. Giacca, EMBO J. 24:3070-3081, 2005). We can corroborate the efficient and specific acetylation of the IN carboxyl-terminal domain (CTD) (amino acids 212 to 288) by p300 using purified recombinant components. Although arginine substitution mutagenesis of the isolated CTD confirms that the majority of p300 acetylation occurs at lysine residues 264, 266, and 273, the pattern of acetylation is not uniform and a hierarchy of reactivity can be established. Several combinatorial mutations of the CTD lysines modified by p300 in vitro were reconstructed into an otherwise infectious proviral plasmid clone and examined for viral growth and frequency of productive chromosomal integration. In contrast to the findings of Cereseto and coworkers, who used epitope-tagged viruses for their experiments, we find that an untagged mutant virus, IN K(264/266/273)R, is fully replication competent. This discrepancy may be explained by the use of an acidic epitope tag placed at the extreme carboxyl terminus of integrase, near the target site for acetylation. Although the tagged, wild-type virus is viable, the combination of this epitope tag with the RRR substitution mutation results in a replication-defective phenotype. Although IN belongs to the very small set of nonhistone proteins modified by HAT-mediated activity, an obligate role for acetylation at the reactive CTD lysines in HIV-1 IN cannot be confirmed.
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Affiliation(s)
- Michael Topper
- Aaron Diamond AIDS Research Center, Rockefeller University, 455 1st Avenue, New York, NY 10016, USA
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39
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Abstract
HIV-1 integrase, which catalyzes the joining of viral DNA to the host cell DNA, has attracted considerable attention as a target for the design and screening of novel anti-HIV drugs as it is essential for virus replication and the establishment of persistent infection. Progress in the identification of different classes of compounds that block integrase activity has been summarized recently in several excellent reviews. Here, we present a brief overview of integrase inhibition, highlighting some of the unusual properties of this protein and important considerations in searching for potential new inhibitors and their evaluation.
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Affiliation(s)
- Joseph Ramcharan
- Locus Pharmaceuticals Inc., 4 Valley Square, 512 East Township Line Road, Blue Bell, PA 19422, USA
| | - Anna Marie Skalka
- Fox Chase Cancer Center, Institute for Cancer Research, Philadelphia, PA 19111, USA
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40
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Guiot E, Carayon K, Delelis O, Simon F, Tauc P, Zubin E, Gottikh M, Mouscadet JF, Brochon JC, Deprez E. Relationship between the oligomeric status of HIV-1 integrase on DNA and enzymatic activity. J Biol Chem 2006; 281:22707-19. [PMID: 16774912 DOI: 10.1074/jbc.m602198200] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The 3'-processing of the extremities of viral DNA is the first of two reactions catalyzed by HIV-1 integrase (IN). High order IN multimers (tetramers) are required for complete integration, but it remains unclear which oligomer is responsible for the 3'-processing reaction. Moreover, IN tends to aggregate, and it is unknown whether the polymerization or aggregation of this enzyme on DNA is detrimental or beneficial for activity. We have developed a fluorescence assay based on anisotropy for monitoring release of the terminal dinucleotide product in real-time. Because the initial anisotropy value obtained after DNA binding and before catalysis depends on the fractional saturation of DNA sites and the size of IN.DNA complexes, this approach can be used to study the relationship between activity and binding/multimerization parameters in the same assay. By increasing the IN:DNA ratio, we found that the anisotropy increased but the 3'-processing activity displayed a characteristic bell-shaped behavior. The anisotropy values obtained in the first phase were predictive of subsequent activity and accounted for the number of complexes. Interestingly, activity peaked and then decreased in the second phase, whereas anisotropy continued to increase. Time-resolved fluorescence anisotropy studies showed that the most competent form for catalysis corresponds to a dimer bound to one viral DNA end, whereas higher order complexes such as aggregates predominate during the second phase when activity drops off. We conclude that a single IN dimer at each extremity of viral DNA molecules is required for 3'-processing, with a dimer of dimers responsible for the subsequent full integration.
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Affiliation(s)
- Elvire Guiot
- Laboratoire de Biotechnologie et Pharmacologie Genetique Appliquee, CNRS, UMR8113, Ecole Normale Supérieure de Cachan, 61 av du Président Wilson, 94235 Cachan, France
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