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Pirkl M, Büch J, Devaux C, Böhm M, Sönnerborg A, Incardona F, Abecasis A, Vandamme AM, Zazzi M, Kaiser R, Lengauer T, The EuResist Network Study Group. Analysis of mutational history of multidrug-resistant genotypes with a mutagenetic tree model. J Med Virol 2023; 95:e28389. [PMID: 36484375 DOI: 10.1002/jmv.28389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/24/2022] [Accepted: 12/01/2022] [Indexed: 12/14/2022]
Abstract
Human immunodeficiency virus (HIV) can develop resistance to all antiretroviral drugs. Multidrug resistance, however, is a rare event in modern HIV treatment, but can be life-threatening, particular in patients with very long therapy histories and in areas with limited access to novel drugs. To understand the evolution of multidrug resistance, we analyzed the EuResist database to uncover the accumulation of mutations over time. We hypothesize that the accumulation of resistance mutations is not acquired simultaneously and randomly across viral genotypes but rather tends to follow a predetermined order. The knowledge of this order might help to elucidate potential mechanisms of multidrug resistance. Our evolutionary model shows an almost monotonic increase of resistance with each acquired mutation, including less well-known nucleoside reverse transcriptase (RT) inhibitor-related mutations like K223Q, L228H, and Q242H. Mutations within the integrase (IN) (T97A, E138A/K G140S, Q148H, N155H) indicate high probability of multidrug resistance. Hence, these IN mutations also tend to be observed together with mutations in the protease (PR) and RT. We followed up with an analysis of the mutation-specific error rates of our model given the data. We identified several mutations with unusual rates (PR: M41L, L33F, IN: G140S). This could imply the existence of previously unknown virus variants in the viral quasispecies. In conclusion, our bioinformatics model supports the analysis and understanding of multidrug resistance.
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Affiliation(s)
- Martin Pirkl
- Institute of Virology, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Joachim Büch
- Institute of Virology, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Carole Devaux
- Department of Infection and Immunity, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Michael Böhm
- Institute of Virology, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Anders Sönnerborg
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institute, Solna, Sweden
| | | | - Ana Abecasis
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Anne-Mieke Vandamme
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal.,Department of Microbiology, Immunology and Transplantation, Clinical and Epidemiological Virology, Institute for the Future, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Rolf Kaiser
- Institute of Virology, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Thomas Lengauer
- Institute of Virology, University Hospital Cologne, University of Cologne, Cologne, Germany
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Pironti A, Pfeifer N, Walter H, Jensen BEO, Zazzi M, Gomes P, Kaiser R, Lengauer T. Using drug exposure for predicting drug resistance - A data-driven genotypic interpretation tool. PLoS One 2017; 12:e0174992. [PMID: 28394945 PMCID: PMC5386274 DOI: 10.1371/journal.pone.0174992] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 03/17/2017] [Indexed: 01/31/2023] Open
Abstract
Antiretroviral treatment history and past HIV-1 genotypes have been shown to be useful predictors for the success of antiretroviral therapy. However, this information may be unavailable or inaccurate, particularly for patients with multiple treatment lines often attending different clinics. We trained statistical models for predicting drug exposure from current HIV-1 genotype. These models were trained on 63,742 HIV-1 nucleotide sequences derived from patients with known therapeutic history, and on 6,836 genotype-phenotype pairs (GPPs). The mean performance regarding prediction of drug exposure on two test sets was 0.78 and 0.76 (ROC-AUC), respectively. The mean correlation to phenotypic resistance in GPPs was 0.51 (PhenoSense) and 0.46 (Antivirogram). Performance on prediction of therapy-success on two test sets based on genetic susceptibility scores was 0.71 and 0.63 (ROC-AUC), respectively. Compared to geno2pheno[resistance], our novel models display a similar or superior performance. Our models are freely available on the internet via www.geno2pheno.org. They can be used for inferring which drug compounds have previously been used by an HIV-1-infected patient, for predicting drug resistance, and for selecting an optimal antiretroviral therapy. Our data-driven models can be periodically retrained without expert intervention as clinical HIV-1 databases are updated and therefore reduce our dependency on hard-to-obtain GPPs.
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Affiliation(s)
- Alejandro Pironti
- Department of Computational Biology and Applied Algorithmics, Max-Planck-Institut für Informatik, Saarbrücken, Germany
- * E-mail:
| | - Nico Pfeifer
- Department of Computational Biology and Applied Algorithmics, Max-Planck-Institut für Informatik, Saarbrücken, Germany
| | - Hauke Walter
- Medizinisches Infektiologiezentrum Berlin, Berlin, Germany
- Medizinisches Labor Stendal, Stendal, Germany
| | - Björn-Erik O. Jensen
- Clinic for Gastroenterology, Hepatology, and Infectiology, University Clinic of Düsseldorf, Düsseldorf, Germany
| | - Maurizio Zazzi
- Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Perpétua Gomes
- Laboratorio de Biologia Molecular, LMCBM, SPC, HEM - Centro Hospitalar de Lisboa Ocidental, Lisbon, Portugal
- Centro de Investigacao Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciencias da Saude Sul, Caparica, Portugal
| | - Rolf Kaiser
- Institute for Virology, University Clinic of Cologne, Cologne, Germany
| | - Thomas Lengauer
- Department of Computational Biology and Applied Algorithmics, Max-Planck-Institut für Informatik, Saarbrücken, Germany
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Schneider A, Corona A, Spöring I, Jordan M, Buchholz B, Maccioni E, Di Santo R, Bodem J, Tramontano E, Wöhrl BM. Biochemical characterization of a multi-drug resistant HIV-1 subtype AG reverse transcriptase: antagonism of AZT discrimination and excision pathways and sensitivity to RNase H inhibitors. Nucleic Acids Res 2016; 44:2310-22. [PMID: 26850643 PMCID: PMC4797301 DOI: 10.1093/nar/gkw060] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 01/24/2016] [Indexed: 11/27/2022] Open
Abstract
We analyzed a multi-drug resistant (MR) HIV-1 reverse transcriptase (RT), subcloned from a patient-derived subtype CRF02_AG, harboring 45 amino acid exchanges, amongst them four thymidine analog mutations (TAMs) relevant for high-level AZT (azidothymidine) resistance by AZTMP excision (M41L, D67N, T215Y, K219E) as well as four substitutions of the AZTTP discrimination pathway (A62V, V75I, F116Y and Q151M). In addition, K65R, known to antagonize AZTMP excision in HIV-1 subtype B was present. Although MR-RT harbored the most significant amino acid exchanges T215Y and Q151M of each pathway, it exclusively used AZTTP discrimination, indicating that the two mechanisms are mutually exclusive and that the Q151M pathway is obviously preferred since it confers resistance to most nucleoside inhibitors. A derivative was created, additionally harboring the TAM K70R and the reversions M151Q as well as R65K since K65R antagonizes excision. MR-R65K-K70R-M151Q was competent of AZTMP excision, whereas other combinations thereof with only one or two exchanges still promoted discrimination. To tackle the multi-drug resistance problem, we tested if the MR-RTs could still be inhibited by RNase H inhibitors. All MR-RTs exhibited similar sensitivity toward RNase H inhibitors belonging to different inhibitor classes, indicating the importance of developing RNase H inhibitors further as anti-HIV drugs.
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Affiliation(s)
- Anna Schneider
- Universität Bayreuth, Lehrstuhl Biopolymere und Forschungszentrum für Bio-Makromoleküle, Universitätsstrasse 30, 95447 Bayreuth, Germany
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS 554, 09042, Monserrato, Cagliari, Italy
| | - Imke Spöring
- Julius-Maximilians-Universität Würzburg, Institut für Virologie und Immunbiologie, Versbacher Strasse 7, 97078 Würzburg, Germany
| | - Mareike Jordan
- Universität Bayreuth, Lehrstuhl Biopolymere und Forschungszentrum für Bio-Makromoleküle, Universitätsstrasse 30, 95447 Bayreuth, Germany
| | - Bernd Buchholz
- Universität Heidelberg, Medizinische Fakultät Mannheim, Klinik für Kinder- und Jugendmedizin, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
| | - Elias Maccioni
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS 554, 09042, Monserrato, Cagliari, Italy
| | - Roberto Di Santo
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, Rome, I-00185, Italy
| | - Jochen Bodem
- Julius-Maximilians-Universität Würzburg, Institut für Virologie und Immunbiologie, Versbacher Strasse 7, 97078 Würzburg, Germany
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS 554, 09042, Monserrato, Cagliari, Italy
| | - Birgitta M Wöhrl
- Universität Bayreuth, Lehrstuhl Biopolymere und Forschungszentrum für Bio-Makromoleküle, Universitätsstrasse 30, 95447 Bayreuth, Germany
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Singh K, Flores JA, Kirby KA, Neogi U, Sonnerborg A, Hachiya A, Das K, Arnold E, McArthur C, Parniak M, Sarafianos SG. Drug resistance in non-B subtype HIV-1: impact of HIV-1 reverse transcriptase inhibitors. Viruses 2014; 6:3535-62. [PMID: 25254383 PMCID: PMC4189038 DOI: 10.3390/v6093535] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 09/09/2014] [Accepted: 09/09/2014] [Indexed: 01/20/2023] Open
Abstract
Human immunodeficiency virus (HIV) causes approximately 2.5 million new infections every year, and nearly 1.6 million patients succumb to HIV each year. Several factors, including cross-species transmission and error-prone replication have resulted in extraordinary genetic diversity of HIV groups. One of these groups, known as group M (main) contains nine subtypes (A-D, F-H and J-K) and causes ~95% of all HIV infections. Most reported data on susceptibility and resistance to anti-HIV therapies are from subtype B HIV infections, which are prevalent in developed countries but account for only ~12% of all global HIV infections, whereas non-B subtype HIV infections that account for ~88% of all HIV infections are prevalent primarily in low and middle-income countries. Although the treatments for subtype B infections are generally effective against non-B subtype infections, there are differences in response to therapies. Here, we review how polymorphisms, transmission efficiency of drug-resistant strains, and differences in genetic barrier for drug resistance can differentially alter the response to reverse transcriptase-targeting therapies in various subtypes.
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Affiliation(s)
- Kamalendra Singh
- Christopher Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
| | - Jacqueline A Flores
- Christopher Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
| | - Karen A Kirby
- Christopher Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm 141 86, Sweden.
| | - Anders Sonnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm 141 86, Sweden.
| | - Atsuko Hachiya
- Clinical Research Center, Department of Infectious Diseases and Immunology, National Hospital Organization, Nagoya Medical Center, Nagoya 460-0001, Japan.
| | - Kalyan Das
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ 08854, USA.
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ 08854, USA.
| | - Carole McArthur
- Department of Oral and Craniofacial Science , School of Dentistry, University of Missouri, Kansas City, MO 64108, USA.
| | - Michael Parniak
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
| | - Stefan G Sarafianos
- Christopher Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
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Wang J, Li D, Bambara RA, Dykes C. Reverse transcriptase backbone can alter the polymerization and RNase activities of non-nucleoside reverse transcriptase mutants K101E+G190S. J Gen Virol 2013; 94:2297-2308. [PMID: 23804564 DOI: 10.1099/vir.0.054999-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Previous work by our group showed that human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) containing non-nucleoside RT inhibitor (NNRTI) drug resistance mutations has defects in RNase H activity as well as reduced amounts of RT protein in virions. These deficits correlate with replication fitness in the absence of NNRTIs. Viruses with the mutant combination K101E+G190S replicated better in the presence of NNRTIs than in the absence of drug. Stimulation of virus growth by NNRTIs occurred during the early steps of the virus life cycle and was modulated by the RT backbone sequence in which the resistance mutations arose. We wanted to determine what effects RT backbone sequence would have on RT content and polymerization and RNase H activities in the absence of NNRTIs. We compared a NL4-3 RT with K101E+G190S to a patient-isolate RT sequence D10 with K101E+G190S. We show here that, unlike the NL4-3 backbone, the D10 backbone sequence decreased the RNA-dependent DNA polymerization activity of purified recombinant RT compared to WT. In contrast, RTs with the D10 backbone had increased RNase H activity compared to WT and K101E+G190S in the NL4-3 backbone. D10 virions also had increased amounts of RT compared to K101E+G190S in the NL4-3 backbone. We conclude that the backbone sequence of RT can alter the activities of the NNRTI drug-resistant mutant K101E+G190S, and that identification of the amino acids responsible will aid in understanding the mechanism by which NNRTI drug-resistant mutants alter fitness and NNRTIs stimulate HIV-1 virus replication.
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Affiliation(s)
- Jiong Wang
- University of Rochester, School of Medicine and Dentistry, Department of Medicine, Rochester, NY, USA
| | - Dongge Li
- University of Rochester, School of Medicine and Dentistry, Department of Medicine, Rochester, NY, USA
| | - Robert A Bambara
- University of Rochester, School of Medicine and Dentistry, Department of Microbiology and Immunology, Rochester, NY, USA
| | - Carrie Dykes
- University of Rochester, School of Medicine and Dentistry, Department of Medicine, Rochester, NY, USA
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Michailidis E, Ryan EM, Hachiya A, Kirby KA, Marchand B, Leslie MD, Huber AD, Ong YT, Jackson JC, Singh K, Kodama EN, Mitsuya H, Parniak MA, Sarafianos SG. Hypersusceptibility mechanism of Tenofovir-resistant HIV to EFdA. Retrovirology 2013; 10:65. [PMID: 23800377 PMCID: PMC3695782 DOI: 10.1186/1742-4690-10-65] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 06/13/2013] [Indexed: 11/28/2022] Open
Abstract
Background The K65R substitution in human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) is the major resistance mutation selected in patients treated with first-line antiretroviral tenofovir disoproxil fumarate (TDF). 4'-ethynyl-2-fluoro-2'-deoxyadenosine (EFdA), is the most potent nucleoside analog RT inhibitor (NRTI) that unlike all approved NRTIs retains a 3'-hydroxyl group and has remarkable potency against wild-type (WT) and drug-resistant HIVs. EFdA acts primarily as a chain terminator by blocking translocation following its incorporation into the nascent DNA chain. EFdA is in preclinical development and its effect on clinically relevant drug resistant HIV strains is critically important for the design of optimal regimens prior to initiation of clinical trials. Results Here we report that the K65R RT mutation causes hypersusceptibility to EFdA. Specifically, in single replication cycle experiments we found that EFdA blocks WT HIV ten times more efficiently than TDF. Under the same conditions K65R HIV was inhibited over 70 times more efficiently by EFdA than TDF. We determined the molecular mechanism of this hypersensitivity using enzymatic studies with WT and K65R RT. This substitution causes minor changes in the efficiency of EFdA incorporation with respect to the natural dATP substrate and also in the efficiency of RT translocation following incorporation of the inhibitor into the nascent DNA. However, a significant decrease in the excision efficiency of EFdA-MP from the 3’ primer terminus appears to be the primary cause of increased susceptibility to the inhibitor. Notably, the effects of the mutation are DNA-sequence dependent. Conclusion We have elucidated the mechanism of K65R HIV hypersusceptibility to EFdA. Our findings highlight the potential of EFdA to improve combination strategies against TDF-resistant HIV-1 strains.
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Affiliation(s)
- Eleftherios Michailidis
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology & Immunology, University of Missouri, Columbia, MO 65211, USA
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Menéndez-Arias L. Molecular basis of human immunodeficiency virus type 1 drug resistance: overview and recent developments. Antiviral Res 2013; 98:93-120. [PMID: 23403210 DOI: 10.1016/j.antiviral.2013.01.007] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 01/26/2013] [Accepted: 01/29/2013] [Indexed: 12/15/2022]
Abstract
The introduction of potent combination therapies in the mid-90s had a tremendous effect on AIDS mortality. However, drug resistance has been a major factor contributing to antiretroviral therapy failure. Currently, there are 26 drugs approved for treating human immunodeficiency virus (HIV) infections, although some of them are no longer prescribed. Most of the available antiretroviral drugs target HIV genome replication (i.e. reverse transcriptase inhibitors) and viral maturation (i.e. viral protease inhibitors). Other drugs in clinical use include a viral coreceptor antagonist (maraviroc), a fusion inhibitor (enfuvirtide) and two viral integrase inhibitors (raltegravir and elvitegravir). Elvitegravir and the nonnucleoside reverse transcriptase inhibitor rilpivirine have been the most recent additions to the antiretroviral drug armamentarium. An overview of the molecular mechanisms involved in antiretroviral drug resistance and the role of drug resistance-associated mutations was previously presented (Menéndez-Arias, L., 2010. Molecular basis of human immunodeficiency virus drug resistance: an update. Antiviral Res. 85, 210-231). This article provides now an updated review that covers currently approved drugs, new experimental agents (e.g. neutralizing antibodies) and selected drugs in preclinical or early clinical development (e.g. experimental integrase inhibitors). Special attention is dedicated to recent research on resistance to reverse transcriptase and integrase inhibitors. In addition, recently discovered interactions between HIV and host proteins and novel strategies to block HIV assembly or viral entry emerge as promising alternatives for the development of effective antiretroviral treatments.
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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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Izumi K, Kawaji K, Miyamoto F, Shimane K, Shimura K, Sakagami Y, Hattori T, Watanabe K, Oishi S, Fujii N, Matsuoka M, Kaku M, Sarafianos SG, Kodama EN. Mechanism of resistance to S138A substituted enfuvirtide and its application to peptide design. Int J Biochem Cell Biol 2013; 45:908-15. [PMID: 23357451 DOI: 10.1016/j.biocel.2013.01.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 01/15/2013] [Accepted: 01/20/2013] [Indexed: 11/19/2022]
Abstract
T-20 (enfuvirtide) resistance is caused by the N43D primary resistance mutation at its presumed binding site at the N-terminal heptad repeat (N-HR) of gp41, accompanied by the S138A secondary mutation at the C-terminal HR of gp41 (C-HR). We have discovered that modifying T-20 to include S138A (T-20S138A) allows it to efficiently block wild-type and T20-resistant viruses, by a mechanism that involves improved binding of T-20S138A to the N-HR that contains the N43D primary mutation. To determine how HIV-1 in turn escapes T-20S138A we used a dose escalation method to select T-20S138A-resistant HIV-1 starting with either wild-type (HIV-1WT) or T-20-resistant (HIV-1N43D/S138A) virus. We found that when starting with WT background, I37N and L44M emerged in the N-HR of gp41, and N126K in the C-HR. However, when starting with HIV-1N43D/S138A, L33S and I69L emerged in N-HR, and E137K in C-HR. T-20S138A-resistant recombinant HIV-1 showed cross-resistance to other T-20 derivatives, but not to C34 derivatives, suggesting that T-20S138A suppressed HIV-1 replication by a similar mechanism to T-20. Furthermore, E137K enhanced viral replication kinetics and restored binding affinity with N-HR containing N43D, indicating that it acts as a secondary, compensatory mutation. We therefore introduced E137K into T-20S138A (T-20E137K/S138A) and revealed that T-20E137K/S138A moderately suppressed replication of T-20S138A-resistant HIV-1. T-20E137K/S138A retained activity to HIV-1 without L33S, which seems to be a key mutation for T-20 derivatives. Our data demonstrate that secondary mutations can be consistently used for the design of peptide inhibitors that block replication of HIV resistant to fusion inhibitors.
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Affiliation(s)
- Kazuki Izumi
- Laboratory of Virus Control, Institute for Virus Research, Kyoto University, 53 Shogoin Kawaramachi, Kyoto 606-8507, Japan
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