101
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Assessment of the susceptibility of mutant HIV-1 to antiviral agents. J Virol Methods 2010; 165:230-7. [DOI: 10.1016/j.jviromet.2010.02.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2009] [Revised: 01/29/2010] [Accepted: 02/03/2010] [Indexed: 11/17/2022]
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102
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Reigadas S, Anies G, Masquelier B, Calmels C, Stuyver LJ, Parissi V, Fleury H, Andreola ML. The HIV-1 integrase mutations Y143C/R are an alternative pathway for resistance to Raltegravir and impact the enzyme functions. PLoS One 2010; 5:e10311. [PMID: 20436677 PMCID: PMC2859942 DOI: 10.1371/journal.pone.0010311] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Accepted: 03/28/2010] [Indexed: 11/21/2022] Open
Abstract
Resistance to HIV-1 integrase (IN) inhibitor raltegravir (RAL), is encoded by mutations in the IN region of the pol gene. The emergence of the N155H mutation was replaced by a pattern including the Y143R/C/H mutations in three patients with anti-HIV treatment failure. Cloning analysis of the IN gene showed an independent selection of the mutations at loci 155 and 143. Characterization of the phenotypic evolution showed that the switch from N155H to Y143C/R was linked to an increase in resistance to RAL. Wild-type (WT) IN and IN with mutations Y143C or Y143R were assayed in vitro in 3′end-processing, strand transfer and concerted integration assays. Activities of mutants were moderately impaired for 3′end-processing and severely affected for strand transfer. Concerted integration assay demonstrated a decrease in mutant activities using an uncleaved substrate. With 3′end-processing assay, IC50 were 0.4 µM, 0.9 µM (FC = 2.25) and 1.2 µM (FC = 3) for WT, IN Y143C and IN Y143R, respectively. An FC of 2 was observed only for IN Y143R in the strand transfer assay. In concerted integration, integrases were less sensitive to RAL than in ST or 3′P but mutants were more resistant to RAL than WT.
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Affiliation(s)
- Sandrine Reigadas
- Laboratoire de Virologie, CHU de Bordeaux, EA 2968, Université Victor Segalen, Bordeaux, France
| | - Guerric Anies
- Laboratoire de Virologie, CHU de Bordeaux, EA 2968, Université Victor Segalen, Bordeaux, France
| | - Bernard Masquelier
- Laboratoire de Virologie, CHU de Bordeaux, EA 2968, Université Victor Segalen, Bordeaux, France
| | | | | | | | - Herve Fleury
- Laboratoire de Virologie, CHU de Bordeaux, EA 2968, Université Victor Segalen, Bordeaux, France
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103
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Goethals O, Vos A, Van Ginderen M, Geluykens P, Smits V, Schols D, Hertogs K, Clayton R. Primary mutations selected in vitro with raltegravir confer large fold changes in susceptibility to first-generation integrase inhibitors, but minor fold changes to inhibitors with second-generation resistance profiles. Virology 2010; 402:338-46. [PMID: 20421122 DOI: 10.1016/j.virol.2010.03.034] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Revised: 02/09/2010] [Accepted: 03/18/2010] [Indexed: 10/19/2022]
Abstract
Emergence of resistance to raltegravir reduces its treatment efficacy in HIV-1-infected patients. To delineate the effect of resistance mutations on viral susceptibility to integrase inhibitors, in vitro resistance selections with raltegravir and with MK-2048, an integrase inhibitor with a second-generation-like resistance profile, were performed. Mutation Q148R arose in four out of six raltegravir-selected resistant viruses. In addition, mutations Q148K and N155H were selected. In the same time frame, no mutations were selected with MK-2048. Q148H/K/R and N155H conferred resistance to raltegravir, but only minor changes in susceptibility to MK-2048. V54I, a previously unreported mutation, selected with raltegravir, was identified as a possible compensation mutation. Mechanisms by which N155H, Q148H/K/R, Y143R and E92Q confer resistance are proposed based on a structural model of integrase. These data improve the understanding of resistance against raltegravir and cross-resistance to MK-2048 and other integrase inhibitors, which will aid in the discovery of second-generation integrase inhibitors.
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Affiliation(s)
- Olivia Goethals
- Tibotec Virco Virology BVBA, Gen De Wittelaan L 11B 3, 2800 Mechelen, Belgium
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104
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Abstract
Similar to all antiretroviral drugs, failure of raltegravirbased treatment regimens to fully supress HIV replication almost invariably results in emergence of HIV resistance to this new drug. HIV resistance to raltegravir is the consequence of mutations located close to the integrase active site, which can be divided into three main evolutionary pathways: the N155H, the Q148R/H/K and the Y143R/C pathways. Each of these primary mutations can be accompanied by a variety of secondary mutations that both increase resistance and compensate for the variable loss of viral replicative capacity that is often associated with primary resistance mutations. One unique property of HIV resistance to raltegravir is that each of these different resistance pathways are mutually exclusive and appear to evolve separately on distinct viral genomes. Resistance is frequently initiated by viruses carrying mutations of the N155H pathway, followed by emergence and further dominance of viral genomes carrying mutations of the Q148R/H/K or of the Y143R/C pathways, which express higher levels of resistance. Even if some natural integrase polymorphisms can be part of this evolution process, these polymorphisms do not affect HIV susceptibility in the absence of primary mutations. Therefore, all HIV-1 subtypes and groups, together with HIV-2, are naturally susceptible to raltegravir. Finally, because interaction of integrase strand transfer inhibitors with the HIV integrase active site is comparable from one compound to another, raltegravir-resistant viruses express significant cross resistance to most other compounds of this new class of antiretroviral drugs.
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Affiliation(s)
- Francois Clavel
- Inserm U941, Institut Universitaire d'Hematologie, Hopital Saint-Louis, Paris, France.
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105
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Abstract
Integration of the HIV-1 viral DNA generated by reverse transcription of the RNA genome into the host cell chromosomes is a key step of viral replication, catalyzed by the viral integrase. In October 2007, the first integrase inhibitor, raltegravir, was approved for clinical use under the name of Isentress™. The results of the various clinical trials that have evaluated raltegravir have been very encouraging with regard to the immunological and virological efficacy and tolerance. However, as observed for other anti-retrovirals, specific resistance mutations have been identified in patients failing to respond to treatment with raltegravir. Although knowledge of the integrase structural biology remains fragmentary, the structures and modeling data available might provide relevant clues on the origin of the emergence of these resistance mutations. In this review, we describe the mechanism of action of this drug and the main data relating to its use in vivo, together with recent structural data important to our understanding of the origin of viral resistance.
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Affiliation(s)
- Jean-Francois Mouscadet
- LBPA, CNRS UMR8113, Ecole Normale Superieure de Cachan, 61 avenue du President Wilson, 94235 Cachan Cedex, France.
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106
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A single-center cohort experience of raltegravir in salvage patients failing therapy. J Acquir Immune Defic Syndr 2010; 53:666-7. [PMID: 20335744 DOI: 10.1097/qai.0b013e3181ba4845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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107
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da Silva D, Van Wesenbeeck L, Breilh D, Reigadas S, Anies G, Van Baelen K, Morlat P, Neau D, Dupon M, Wittkop L, Fleury H, Masquelier B. HIV-1 resistance patterns to integrase inhibitors in antiretroviral-experienced patients with virological failure on raltegravir-containing regimens. J Antimicrob Chemother 2010; 65:1262-9. [DOI: 10.1093/jac/dkq099] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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108
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Carayon K, Leh H, Henry E, Simon F, Mouscadet JF, Deprez E. A cooperative and specific DNA-binding mode of HIV-1 integrase depends on the nature of the metallic cofactor and involves the zinc-containing N-terminal domain. Nucleic Acids Res 2010; 38:3692-708. [PMID: 20164093 PMCID: PMC2887959 DOI: 10.1093/nar/gkq087] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
HIV-1 integrase catalyzes the insertion of the viral genome into chromosomal DNA. We characterized the structural determinants of the 3′-processing reaction specificity—the first reaction of the integration process—at the DNA-binding level. We found that the integrase N-terminal domain, containing a pseudo zinc-finger motif, plays a key role, at least indirectly, in the formation of specific integrase–DNA contacts. This motif mediates a cooperative DNA binding of integrase that occurs only with the cognate/viral DNA sequence and the physiologically relevant Mg2+ cofactor. The DNA-binding was essentially non-cooperative with Mn2+ or using non-specific/random sequences, regardless of the metallic cofactor. 2,2′-Dithiobisbenzamide-1 induced zinc ejection from integrase by covalently targeting the zinc-finger motif, and significantly decreased the Hill coefficient of the Mg2+-mediated integrase–DNA interaction, without affecting the overall affinity. Concomitantly, 2,2′-dithiobisbenzamide-1 severely impaired 3′-processing (IC50 = 11–15 nM), suggesting that zinc ejection primarily perturbs the nature of the active integrase oligomer. A less specific and weaker catalytic effect of 2,2′-dithiobisbenzamide-1 is mediated by Cys 56 in the catalytic core and, notably, accounts for the weaker inhibition of the non-cooperative Mn2+-dependent 3′-processing. Our data show that the cooperative DNA-binding mode is strongly related to the sequence-specific DNA-binding, and depends on the simultaneous presence of the Mg2+ cofactor and the zinc effector.
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Affiliation(s)
- Kevin Carayon
- LBPA, CNRS, Ecole Normale Supérieure de Cachan, 61 av. du Président Wilson, 94235 Cachan, France
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109
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Tschochner M, Chopra A, Maiden TM, Ahmad IF, James I, Furrer H, Günthard HF, Mallal S, Rauch A, John M. Effects of HIV type-1 immune selection on susceptability to integrase inhibitor resistance. Antivir Ther 2010; 14:953-64. [PMID: 19918099 DOI: 10.3851/imp1419] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND All site-specific interactions between HIV type-1 (HIV-1) subtype, human leukocyte antigen (HLA)-associated immune selection and integrase inhibitor resistance are not completely understood. We examined naturally occurring polymorphisms in HIV-1 integrase sequences from 342 antiretroviral-naive individuals from the Western Australian HIV Cohort Study and the Swiss HIV Cohort Study. METHODS Standard bulk sequencing and sequence-based typing were used to generate integrase sequences and high-resolution HLA genotypes, respectively. Viral residues were examined with respect to drug resistance mutations and CD8(+) T-cell escape mutations. RESULTS In both predominantly subtype B cohorts, 12 of 38 sites that mediate integrase inhibitor resistance mutations were absolutely conserved, and these included the primary resistance mutations. There were 18 codons with non-primary drug resistance-associated substitutions at rates of up to 58.8% and eight sites with alternative polymorphisms. Five viral residues were potentially subject to dual-drug and HLA-associated immune selection in which both selective pressures either drove the same amino acid substitution (codons 72, 157 and 163) or HLA alleles were associated with an alternative polymorphism that would alter the genetic barrier to resistance (codons 125 and 193). The common polymorphism T125A, which was characteristic of non-subtype B and was also associated with carriage of HLA-B*57/*5801, increased the mutational barrier to the resistance mutation T125K. CONCLUSIONS Primary integrase inhibitor resistance mutations were not detected in the absence of drug exposure in keeping with sites of high constraint. Viral polymorphisms caused by immune selection and/or associated with non-subtype B might alter the genetic barrier to some non-primary resistance-associated mutations.
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Affiliation(s)
- Monika Tschochner
- Institute for Immunology and Infectious Diseases, Royal Perth Hospital and Murdoch University, Perth, Australia
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110
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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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111
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Perryman AL, Forli S, Morris GM, Burt C, Cheng Y, Palmer MJ, Whitby K, McCammon JA, Phillips C, Olson AJ. A dynamic model of HIV integrase inhibition and drug resistance. J Mol Biol 2010; 397:600-15. [PMID: 20096702 DOI: 10.1016/j.jmb.2010.01.033] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Revised: 01/13/2010] [Accepted: 01/14/2010] [Indexed: 11/19/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) integrase is one of three virally encoded enzymes essential for replication and, therefore, a rational choice as a drug target for the treatment of HIV-1-infected individuals. In 2007, raltegravir became the first integrase inhibitor approved for use in the treatment of HIV-infected patients, more than a decade since the approval of the first protease inhibitor (saquinavir, Hoffman La-Roche, 1995) and two decades since the approval of the first reverse transcriptase inhibitor (retrovir, GlaxoSmithKline, 1987). The slow progress toward a clinically effective HIV-1 integrase inhibitor can at least in part be attributed to a poor structural understanding of this key viral protein. Here we describe the development of a restrained molecular dynamics protocol that produces a more accurate model of the active site of this drug target. This model provides an advance on previously described models as it ensures that the catalytic DDE motif makes correct, monodentate interactions with the two active-site magnesium ions. Dynamic restraints applied to this coordination state create models with the correct solvation sphere for the metal ion complex and highlight the coordination sites available for metal-binding ligands. Application of appropriate dynamic flexibility to the core domain allowed the inclusion of multiple conformational states in subsequent docking studies. These models have allowed us to (1) explore the effects of key drug resistance mutations on the dynamic flexibility and conformational preferences of HIV integrase and to (2) study raltegravir binding in the context of these dynamic models of both wild type and the G140S/Q148H drug-resistant enzyme.
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Affiliation(s)
- Alex L Perryman
- Department of Molecular Biology, The Scripps Research Institute, MB5, 10550 N Torrey Pines Road, La Jolla, CA 92037, USA
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112
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Marchand C, Maddali K, Métifiot M, Pommier Y. HIV-1 IN inhibitors: 2010 update and perspectives. Curr Top Med Chem 2010; 9:1016-37. [PMID: 19747122 DOI: 10.2174/156802609789630910] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2009] [Accepted: 06/13/2009] [Indexed: 12/29/2022]
Abstract
Integrase (IN) is the newest validated target against AIDS and retroviral infections. The remarkable activity of raltegravir (Isentress((R))) led to its rapid approval by the FDA in 2007 as the first IN inhibitor. Several other IN strand transfer inhibitors (STIs) are in development with the primary goal to overcome resistance due to the rapid occurrence of IN mutations in raltegravir-treated patients. Thus, many scientists and drug companies are actively pursuing clinically useful IN inhibitors. The objective of this review is to provide an update on the IN inhibitors reported in the last two years, including second generation STI, recently developed hydroxylated aromatics, natural products, peptide, antibody and oligonucleotide inhibitors. Additionally, the targeting of IN cofactors such as LEDGF and Vpr will be discussed as novel strategies for the treatment of AIDS.
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Affiliation(s)
- Christophe Marchand
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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113
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Reigadas S, Andréola ML, Wittkop L, Cosnefroy O, Anies G, Recordon-Pinson P, Thiébaut R, Masquelier B, Fleury H. Evolution of 2-long terminal repeat (2-LTR) episomal HIV-1 DNA in raltegravir-treated patients and in in vitro infected cells. J Antimicrob Chemother 2010; 65:434-7. [PMID: 20051476 DOI: 10.1093/jac/dkp473] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Our aim was to analyse the evolution of HIV-1 2-long terminal repeat (2-LTR) circular DNA in vitro and ex vivo in the presence of raltegravir. PATIENTS AND METHODS Twenty-five patients starting a raltegravir-based regimen were included. Total HIV-1 DNA and 2-LTR DNA were quantified at baseline and in follow-up samples up to month 12. The effect of raltegravir on the formation of 2-LTR circles was evaluated in HeLa P4 cells. The effect of raltegravir was also investigated by sequence analysis of the 2-LTR circle junctions. RESULTS Among 21 patients with undetectable 2-LTR DNA at baseline, 7 had detectable 2-LTR DNA during the follow-up. Three of four patients with detectable 2-LTR DNA at baseline had undetectable 2-LTR DNA during the follow-up (P = 0.27). The mean 2-LTR level increased significantly (+0.07 log(10)/month, P = 0.02) in raltegravir-treated patients, and a 2-LTR increase was also observed in raltegravir-treated HeLa P4 cells, with a peak at 3 days post-infection. 2-LTR DNA showed a high prevalence of deletions ex vivo (64.5%) and in vitro (50%) in the presence of raltegravir, which was not statistically different from the prevalence in untreated patients or cells. CONCLUSIONS In antiretroviral-experienced patients receiving raltegravir, 2-LTR DNA increased while total HIV-1 DNA decreased over time. The frequent rearrangements found in 2-LTR sequences warrant further investigations to determine the dynamics of evolution of unintegrated HIV-1 DNA.
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Affiliation(s)
- Sandrine Reigadas
- Laboratory of Virology, EA2968, University of Bordeaux 2, Bordeaux, France.
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114
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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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115
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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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116
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Dunn LL, McWilliams MJ, Das K, Arnold E, Hughes SH. Mutations in the thumb allow human immunodeficiency virus type 1 reverse transcriptase to be cleaved by protease in virions. J Virol 2009; 83:12336-44. [PMID: 19759158 PMCID: PMC2786724 DOI: 10.1128/jvi.00676-09] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Accepted: 09/04/2009] [Indexed: 02/07/2023] Open
Abstract
Although human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) has been extensively studied, there are still significant questions about the effects of mutations on the maturation and stability of RT. We show here that a significant fraction (>80%) of the single point mutations we generated in the thumb subdomain of HIV-1 (RT) affect the stability of RT in virions. Fragments of the unstable mutant RTs can be detected in Western blots of virion proteins; however, the degree of degradation varies. The titers of the mutants whose virions contain degraded RTs are reduced. Some, but not all, of the unstable RT thumb subdomain mutants we analyzed have a temperature-sensitive phenotype. A preliminary survey of mutations in other subdomains of RT shows that some of these mutations also destabilize RT. The stability of the RT mutants is enhanced by the addition of a protease inhibitor, suggesting that the viral protease plays an important role in the degradation of the mutant RTs. These results confirm and extend earlier reports of mutations that affect the stability of RT in virions. The data suggest that the stability of a mutant RT in virions could be a major factor in determining the virus titer and, by extension, viral fitness, which could affect whether a mutation in RT is acceptable to the virus.
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Affiliation(s)
- Linda L. Dunn
- HIV-Drug Resistance Program, NCI-Frederick, Frederick, Maryland 21701, Rutgers University, Department of Chemistry and Chemical Biology, Piscataway, New Jersey 08854
| | - Mary Jane McWilliams
- HIV-Drug Resistance Program, NCI-Frederick, Frederick, Maryland 21701, Rutgers University, Department of Chemistry and Chemical Biology, Piscataway, New Jersey 08854
| | - Kalyan Das
- HIV-Drug Resistance Program, NCI-Frederick, Frederick, Maryland 21701, Rutgers University, Department of Chemistry and Chemical Biology, Piscataway, New Jersey 08854
| | - Eddy Arnold
- HIV-Drug Resistance Program, NCI-Frederick, Frederick, Maryland 21701, Rutgers University, Department of Chemistry and Chemical Biology, Piscataway, New Jersey 08854
| | - Stephen H. Hughes
- HIV-Drug Resistance Program, NCI-Frederick, Frederick, Maryland 21701, Rutgers University, Department of Chemistry and Chemical Biology, Piscataway, New Jersey 08854
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117
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Sakkhachornphop S, Jiranusornkul S, Kodchakorn K, Nangola S, Sirisanthana T, Tayapiwatana C. Designed zinc finger protein interacting with the HIV-1 integrase recognition sequence at 2-LTR-circle junctions. Protein Sci 2009; 18:2219-30. [PMID: 19701937 PMCID: PMC2788277 DOI: 10.1002/pro.233] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2009] [Accepted: 08/13/2009] [Indexed: 12/16/2022]
Abstract
Integration of HIV-1 cDNA into the host genome is a crucial step for viral propagation. Two nucleotides, cytosine and adenine (CA), conserved at the 3' end of the viral cDNA genome, are cleaved by the viral integrase (IN) enzyme. As IN plays a crucial role in the early stages of the HIV-1 life cycle, substrate blockage of IN is an attractive strategy for therapeutic interference. In this study, we used the 2-LTR-circle junctions of HIV-1 DNA as a model to design zinc finger protein (ZFP) targeting at the end terminal portion of HIV-1 LTR. A six-contiguous ZFP, namely 2LTRZFP was designed using zinc finger tools. The designed motif was expressed and purified from E. coli to determine its binding properties. Surface plasmon resonance (SPR) was used to determine the binding affinity of 2LTRZFP to its target DNA. The level of dissociation constant (K(d)) was 12.0 nM. The competitive SPR confirmed that 2LTRZFP specifically interacted with its target DNA. The qualitative binding activity was subsequently determined by EMSA and demonstrated the aforementioned correlation. In addition, molecular modeling and binding energy analyses were carried out to provide structural insight into the binding of 2LTRZFP to the specific and nonspecific DNA target. It is suggested that hydrogen-bonding interactions play a key role in the DNA recognition mechanisms of the designed ZFP. Our study suggested an alternative HIV therapeutic strategy using ZFP interference of the HIV integration process.
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Affiliation(s)
- Supachai Sakkhachornphop
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai UniversityChiang Mai 50200, Thailand
- Research Institute for Health Sciences, Chiang Mai UniversityChiang Mai 50200, Thailand
| | - Supat Jiranusornkul
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai UniversityChiang Mai 50200, Thailand
| | - Kanchanok Kodchakorn
- Thailand Excellence Center for Tissue Engineering, Department of Biochemistry, Faculty of Medicine, Chiang Mai UniversityChiang Mai 50200, Thailand
| | - Sawitree Nangola
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai UniversityChiang Mai 50200, Thailand
| | - Thira Sirisanthana
- Research Institute for Health Sciences, Chiang Mai UniversityChiang Mai 50200, Thailand
| | - Chatchai Tayapiwatana
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai UniversityChiang Mai 50200, Thailand
- Biomedical Technology Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency at the Faculty of Associated Medical Sciences, Chiang Mai UniversityChiang Mai 50200, Thailand
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118
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Wirden M, Simon A, Schneider L, Tubiana R, Malet I, Ait-Mohand H, Peytavin G, Katlama C, Calvez V, Marcelin AG. Raltegravir has no residual antiviral activity in vivo against HIV-1 with resistance-associated mutations to this drug. J Antimicrob Chemother 2009; 64:1087-90. [PMID: 19717396 DOI: 10.1093/jac/dkp310] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Emergence of major resistance mutations has already been associated with raltegravir regimen failure. Because of few remaining therapeutic options, the maintenance of raltegravir in the salvage regimen is often considered despite the risk of worsening resistance to integrase inhibitors. We determined whether raltegravir retains residual antiretroviral activity in vivo against viruses harbouring raltegravir mutations, and thus whether the drug can contribute to the subsequent regimen. METHODS This retrospective observational study reports the changes in the viral load (VL) after the withdrawal of raltegravir from patients carrying virus with resistance mutations. We selected patients under stable treatment and with stable VL during at least the previous 2 months before the withdrawal. RESULTS Five patients (A-E) were selected. The median changes in VL and CD4 counts at the end of the raltegravir interruption were -0.04 log copies/mL (range, -0.20 to +0.19) and +58 cells/mm(3) (range, -56 to +252), respectively. CONCLUSIONS All VL changes were well below the clinically relevant variation of 0.5 log copies/mL at the end of the interruption. Thus, this study indicates that, for viruses harbouring one of the two main resistance pathways described for raltegravir, no relevant antiviral activity seems to persist in vivo. Even if further observations would be useful to reinforce this conclusion, the cost/benefit and risk/benefit of maintaining raltegravir as part of a salvage regimen in the presence of raltegravir mutations seem debatable, especially in the absence of relevant antiretroviral activity in this context.
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Affiliation(s)
- Marc Wirden
- Department of Virology, AP-HP, Pitié-Salpêtrière Hospital, 83 boulevard de l'Hopital, Paris, France.
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119
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Menéndez-Arias L. Molecular basis of human immunodeficiency virus drug resistance: an update. Antiviral Res 2009; 85:210-31. [PMID: 19616029 DOI: 10.1016/j.antiviral.2009.07.006] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2009] [Revised: 06/26/2009] [Accepted: 07/03/2009] [Indexed: 11/25/2022]
Abstract
Antiretroviral therapy has led to a significant decrease in human immunodeficiency virus (HIV)-related mortality. Approved antiretroviral drugs target different steps of the viral life cycle including viral entry (coreceptor antagonists and fusion inhibitors), reverse transcription (nucleoside and non-nucleoside inhibitors of the viral reverse transcriptase), integration (integrase inhibitors) and viral maturation (protease inhibitors). Despite the success of combination therapies, the emergence of drug resistance is still a major factor contributing to therapy failure. Viral resistance is caused by mutations in the HIV genome coding for structural changes in the target proteins that can affect the binding or activity of the antiretroviral drugs. This review provides an overview of the molecular mechanisms involved in the acquisition of resistance to currently used and promising investigational drugs, emphasizing the structural role of drug resistance mutations. The optimization of current antiretroviral drug regimens and the development of new drugs are still challenging issues in HIV chemotherapy. This article forms part of a special issue of Antiviral Research marking the 25th anniversary of antiretroviral drug discovery and development, Vol 85, issue 1, 2010.
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Affiliation(s)
- Luis Menéndez-Arias
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid), c/Nicolás Cabrera 1, Campus de Cantoblanco, 28049 Madrid, Spain.
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120
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Serrao E, Odde S, Ramkumar K, Neamati N. Raltegravir, elvitegravir, and metoogravir: the birth of "me-too" HIV-1 integrase inhibitors. Retrovirology 2009; 6:25. [PMID: 19265512 PMCID: PMC2660292 DOI: 10.1186/1742-4690-6-25] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2009] [Accepted: 03/05/2009] [Indexed: 11/10/2022] Open
Abstract
Merck's MK-0518, known as raltegravir, has recently become the first FDA-approved HIV-1 integrase (IN) inhibitor and has since risen to blockbuster drug status. Much research has in turn been conducted over the last few years aimed at recreating but optimizing the compound's interactions with the protein. Resulting me-too drugs have shown favorable pharmacokinetic properties and appear drug-like but, as expected, most have a highly similar interaction with IN to that of raltegravir. We propose that, based upon conclusions drawn from our docking studies illustrated herein, most of these me-too MK-0518 analogues may experience a low success rate against raltegravir-resistant HIV strains. As HIV has a very high mutational competence, the development of drugs with new mechanisms of inhibitory action and/or new active substituents may be a more successful route to take in the development of second- and third-generation IN inhibitors.
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Affiliation(s)
- Erik Serrao
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, School of Pharmacy, Los Angeles, CA 90089, USA.
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121
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van Hal SJ, Herring B, Deris Z, Wang B, Saksena NK, Dwyer DE. HIV-1 integrase polymorphisms are associated with prior antiretroviral drug exposure. Retrovirology 2009; 6:12. [PMID: 19203393 PMCID: PMC2649883 DOI: 10.1186/1742-4690-6-12] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2008] [Accepted: 02/09/2009] [Indexed: 11/30/2022] Open
Abstract
In a recent summary of integrase sequences, primary integrase inhibitor mutations were rare. In a review of integrase inhibitor-naïve Australian HIV-1 sequences, primary mutations were not identified, although the accessory mutation G140S was detected. A link with previous antiretroviral therapy, intra-subtype B divergence across the integrase gene and transmission of integrase polymorphisms were also noted. Based on these findings, we would recommend ongoing surveillance of integrase mutations, and integrase region sequencing for patients prior to commencement of integrase inhibitors.
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Affiliation(s)
- Sebastiaan J van Hal
- Centre for Infectious Diseases and Microbiology, ICPMR Westmead Hospital, University of Sydney, Westmead 2145, NSW, Australia.
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