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Troyano-Hernáez P, Reinosa R, Holguín A. Genetic Diversity and Low Therapeutic Impact of Variant-Specific Markers in HIV-1 Pol Proteins. Front Microbiol 2022; 13:866705. [PMID: 35910645 PMCID: PMC9330395 DOI: 10.3389/fmicb.2022.866705] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
The emergence and spread of new HIV-1 variants pose a challenge for the effectiveness of antiretrovirals (ARV) targeting Pol proteins. During viral evolution, non-synonymous mutations have fixed along the viral genome, leading to amino acid (aa) changes that can be variant-specific (V-markers). Those V-markers fixed in positions associated with drug resistance mutations (DRM), or R-markers, can impact drug susceptibility and resistance pathways. All available HIV-1 Pol sequences from ARV-naïve subjects were downloaded from the United States Los Alamos HIV Sequence Database, selecting 59,733 protease (PR), 6,437 retrotranscriptase (RT), and 6,059 integrase (IN) complete sequences ascribed to the four HIV-1 groups and group M subtypes and circulating recombinant forms (CRFs). Using a bioinformatics tool developed in our laboratory (EpiMolBio), we inferred the consensus sequences for each Pol protein and HIV-1 variant to analyze the aa conservation in Pol. We analyzed the Wu–Kabat protein variability coefficient (WK) in PR, RT, and IN group M to study the susceptibility of each site to evolutionary replacements. We identified as V-markers the variant-specific aa changes present in >75% of the sequences in variants with >5 available sequences, considering R-markers those V-markers that corresponded to DRM according to the IAS-USA2019 and Stanford-Database 9.0. The mean aa conservation of HIV-1 and group M consensus was 82.60%/93.11% in PR, 88.81%/94.07% in RT, and 90.98%/96.02% in IN. The median group M WK was 10 in PR, 4 in RT, and 5 in IN. The residues involved in binding or catalytic sites showed a variability <0.5%. We identified 106 V-markers: 31 in PR, 28 in RT, and 47 in IN, present in 11, 12, and 13 variants, respectively. Among them, eight (7.5%) were R-markers, present in five variants, being minor DRM with little potential effect on ARV susceptibility. We present a thorough analysis of Pol variability among all HIV-1 variants circulating to date. The relatively high aa conservation observed in Pol proteins across HIV-1 variants highlights their critical role in the viral cycle. However, further studies are needed to understand the V-markers’ impact on the Pol proteins structure, viral cycle, or treatment strategies, and periodic variability surveillance studies are also required to understand PR, RT, and IN evolution.
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Gaballah A, Ghazal A, Metwally D, Emad R, Essam G, Attia NM, Amer AN. Mutation patterns, cross resistance and virological failure among HIV type-1 patients in Alexandria, Egypt. Future Virol 2022. [DOI: 10.2217/fvl-2021-0279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: The main purpose of this cross-sectional study was to detect the prevalence of drug resistance mutations related to nonnucleoside/nucleoside reverse transcriptase inhibitors (NNRTIs/NRTIs) and protease inhibitors (PIs). Patients & methods: Patients (n = 45) with HIV type-1 were recruited, 30 of whom were treatment naive and 15 treatment experienced. A partial pol gene covering the protease/reverse transcriptase (PRRT) region was amplified and then sequenced by the Sanger method. Results & conclusion: The most common NNRTI/NRTI-related mutations were ‘V179I (24%) and K103N (14.3%)’ and ‘M41L and V75M’ (14.3% each). M36I and H69K were the most prevalent PI-related mutations (86% each). The results of the current study serve as an initial crucial step in defining the overall prevalence of HIV type-1 drug resistance in Egypt.
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Affiliation(s)
- Ahmed Gaballah
- Microbiology Department, Medical Research Institute, Alexandria University, Egypt
| | - Abeer Ghazal
- Microbiology Department, Medical Research Institute, Alexandria University, Egypt
| | - Dalia Metwally
- Microbiology Department, Medical Research Institute, Alexandria University, Egypt
| | - Rasha Emad
- Alexandria Main University Hospital, Alexandria University, Egypt
| | - Ghada Essam
- Microbiology & Immunology Department, Faculty of Pharmacy & Drug Manufacturing, Pharos University, Egypt
| | - Nancy M Attia
- Microbiology Department, Medical Research Institute, Alexandria University, Egypt
| | - Ahmed N Amer
- Microbiology & Immunology Department, Faculty of Pharmacy & Drug Manufacturing, Pharos University, Egypt
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Yu YX, Liu WT, Li HY, Wang W, Sun HB, Zhang LL, Wu SL. Decoding molecular mechanism underlying binding of drugs to HIV-1 protease with molecular dynamics simulations and MM-GBSA calculations. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:889-915. [PMID: 34551634 DOI: 10.1080/1062936x.2021.1979647] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/08/2021] [Indexed: 06/13/2023]
Abstract
HIV-1 protease (PR) is thought to be efficient targets of anti-AIDS drug design. Molecular dynamics (MD) simulations and multiple post-processing analysis technologies were applied to decipher molecular mechanism underlying binding of three drugs Lopinavir (LPV), Nelfinavir (NFV) and Atazanavir (ATV) to the PR. Binding free energies calculated by molecular mechanics generalized Born surface area (MM-GBSA) suggest that compensation between binding enthalpy and entropy plays a vital role in binding of drugs to PR. Dynamics analyses show that binding of LPV, NFV and ATV highly affects structural flexibility, motion modes and dynamics behaviour of the PR, especially for two flaps. Computational alanine scanning and interaction network analysis verify that although three drugs have structural difference, they share similar binding modes to the PR and common interaction clusters with the PR. The current findings also confirm that residues located interaction clusters, such as Asp25/Asp25', Gly27/Gly27', Ala28/Ala28', Asp29, Ile47/Ile47', Gly49/Gly49', Ile50/Ile50', Val82/Val82' and Ile84/Ile84, can be used as efficient targets of clinically available inhibitors towards the PR.
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Affiliation(s)
- Y X Yu
- School of Science, Shandong Jiaotong University, Jinan, China
| | - W T Liu
- Shuifa Qilu Cultural Tourism Development Co., Ltd, Shuifa Ecological Industry Group, Jinan, China
| | - H Y Li
- School of Science, Shandong Jiaotong University, Jinan, China
| | - W Wang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - H B Sun
- School of Science, Shandong Jiaotong University, Jinan, China
| | - L L Zhang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - S L Wu
- School of Science, Shandong Jiaotong University, Jinan, China
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Tran TT, Liu Z, Fanucci GE. Conformational landscape of non-B variants of HIV-1 protease: A pulsed EPR study. Biochem Biophys Res Commun 2020; 532:219-224. [PMID: 32863004 DOI: 10.1016/j.bbrc.2020.08.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 08/12/2020] [Indexed: 02/02/2023]
Abstract
HIV infection is a global health epidemic with current FDA-approved HIV-1 Protease inhibitors (PIs) designed against subtype B protease, yet they are used in HIV treatment world-wide regardless of patient HIV classification. In this study, double electron-electron resonance (DEER) electron paramagnetic resonance (EPR) spectroscopy was utilized to gain insights in how natural polymorphisms in several African and Brazilian protease (PR) variants affect the conformational landscape both in the absence and presence of inhibitors. Findings show that Subtypes F and H HIV-1 PR adopt a primarily closed conformation in the unbound state with two secondary mutations, D60E and I62V, postulated to be responsible for the increased probability for closed conformation. In contrast, subtype D, CRF_AG, and CRF_BF HIV-1 PR adopt a primarily semi-open conformation, as observed for PI-naïve-subtype B when unbound by substrate or inhibitor. The impact that inhibitor binding has on shifting the conformational land scape of these variants is also characterized, where analysis provides classification of inhibitor induced shifts away from the semi-open state into weak, moderate and strong effects. The findings are compared to those for prior studies of inhibitor induced conformational shifts in PI-naïve Subtype B, C and CRF_AE.
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Affiliation(s)
- Trang T Tran
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611, USA
| | - Zhanglong Liu
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611, USA
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611, USA.
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Perrier M, Castain L, Regad L, Todesco E, Landman R, Visseaux B, Yazdanpanah Y, Rodriguez C, Joly V, Calvez V, Marcelin AG, Descamps D, Charpentier C. HIV-1 protease, Gag and gp41 baseline substitutions associated with virological response to a PI-based regimen. J Antimicrob Chemother 2020; 74:1679-1692. [PMID: 30768160 DOI: 10.1093/jac/dkz043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 01/04/2019] [Accepted: 01/08/2019] [Indexed: 12/29/2022] Open
Abstract
OBJECTIVES To assess, at ART initiation, the impact of baseline substitutions in protease, Gag and gp41 regions on the virological response to a first-line PI-based regimen. PATIENTS AND METHODS One hundred and fifty-four HIV-infected ART-naive patients initiating a PI-based regimen including darunavir (n = 129) or atazanavir (n = 25) were assessed, including 36 experiencing virological failure (VF). Whole pol, gag and gp41 genes were sequenced at ART baseline by ultra-deep sequencing (UDS) using Illumina® technology. Supervised data-mining analyses were performed to identify mutations associated with virological response. Structural analyses were performed to assess the impact of mutations on protease conformation. RESULTS UDS was successful in 127, 138 and 134 samples for protease, Gag and gp41, respectively (31% subtype B and 38% CRF02_AG). Overall, T4A and S37T mutations in protease were identified as being associated with VF (P = 0.02 and P = 0.005, respectively). Among CRF02_AG sequences, I72M and E21D mutations were associated with VF (P = 0.03 for both). They all induced some conformational changes of some protease side-chain residues located near mutated residues. In Gag, mutations associated with VF were G62D, N315H and Y441S (P = 0.005, P = 0.007 and P = 0.0003, respectively). All were localized outside Gag cleavage sites (G62D, matrix; N315H, capsid; and Y441S, p1). In gp41, the I270T mutation, localized in the cytoplasmic tail, was associated with VF (P = 0.003), and the I4L mutation, in the fusion peptide, was associated with virological success (P = 0.004). CONCLUSIONS In this study, new baseline substitutions in Gag, protease and g41, potentially impacting PI-based regimen outcome, were evidenced. Phenotypic analyses are required to confirm their role in the PI-resistance mechanism.
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Affiliation(s)
- Marine Perrier
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat, AP-HP, Paris, France
| | - Louise Castain
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de Virologie, F-75013 Paris, France
| | - Leslie Regad
- Sorbonne Paris Cité, Université Paris-Diderot, CNRS, INSERM, Biologie Fonctionnelle et Adaptative UMR 8251, Computational Modeling of Protein Ligand Interactions U1133, Paris, France
| | - Eve Todesco
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de Virologie, F-75013 Paris, France
| | - Roland Landman
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Service de Maladies Infectieuses et Tropicales, Hôpital Bichat, AP-HP, Paris, France
| | - Benoit Visseaux
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat, AP-HP, Paris, France
| | - Yazdan Yazdanpanah
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Service de Maladies Infectieuses et Tropicales, Hôpital Bichat, AP-HP, Paris, France
| | - Christophe Rodriguez
- INSERM U955 Eq18, CNR hépatites virales B, C et delta, Laboratoire de Virologie, Hôpital Henri Mondor, AP-HP, Paris, France
| | - Véronique Joly
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Service de Maladies Infectieuses et Tropicales, Hôpital Bichat, AP-HP, Paris, France
| | - Vincent Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de Virologie, F-75013 Paris, France
| | - Anne-Geneviève Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de Virologie, F-75013 Paris, France
| | - Diane Descamps
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat, AP-HP, Paris, France
| | - Charlotte Charpentier
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat, AP-HP, Paris, France
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Zarei M, Ravanshad M, Bagban A, Fallahi S. A Molecular Approach to Nested RT-PCR Using a New Set of Primers for the Detection of the Human Immunodeficiency Virus Protease Gene. Jundishapur J Microbiol 2016; 9:e30365. [PMID: 27679699 PMCID: PMC5035394 DOI: 10.5812/jjm.30365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 06/08/2016] [Accepted: 06/18/2016] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The human immunodeficiency virus (HIV-1) is the etiologic agent of AIDS. The disease can be transmitted via blood in the window period prior to the development of antibodies to the disease. Thus, an appropriate method for the detection of HIV-1 during this window period is very important. OBJECTIVES This descriptive study proposes a sensitive, efficient, inexpensive, and easy method to detect HIV-1. PATIENTS AND METHODS In this study 25 serum samples of patients under treatment and also 10 positive and 10 negative control samples were studied. Twenty-five blood samples were obtained from HIV-1-infected individuals who were receiving treatment at the acquired immune deficiency syndrome (AIDS) research center of Imam Khomeini hospital in Tehran. The identification of HIV-1-positive samples was done by using reverse transcription to produce copy deoxyribonucleic acid (cDNA) and then optimizing the nested polymerase chain reaction (PCR) method. Two pairs of primers were then designed specifically for the protease gene fragment of the nested real time-PCR (RT-PCR) samples. Electrophoresis was used to examine the PCR products. The results were analyzed using statistical tests, including Fisher's exact test, and SPSS17 software. RESULTS The 325 bp band of the protease gene was observed in all the positive control samples and in none of the negative control samples. The proposed method correctly identified HIV-1 in 23 of the 25 samples. CONCLUSIONS These results suggest that, in comparison with viral cultures, antibody detection by enzyme linked immunosorbent assay (ELISAs), and conventional PCR methods, the proposed method has high sensitivity and specificity for the detection of HIV-1.
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Affiliation(s)
- Mohammad Zarei
- Shirvan Center of Higher Health Education, North Khorasan University of Medical Sciences, Bojnurd, IR Iran
| | - Mehrdad Ravanshad
- Department of Medical Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, IR Iran
| | - Ashraf Bagban
- Department of Medical Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, IR Iran
- Corresponding author: Ashraf Bagban, Department of Medical Virology, Tarbiat Modares University, Tehran, IR Iran. Tel: +98-9153865400, Fax: +98-5147235031, E-mail:
| | - Shahab Fallahi
- Department of Medical Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, IR Iran
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7
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Costa MGS, Benetti-Barbosa TG, Desdouits N, Blondel A, Bisch PM, Pascutti PG, Batista PR. Impact of M36I polymorphism on the interaction of HIV-1 protease with its substrates: insights from molecular dynamics. BMC Genomics 2014; 15 Suppl 7:S5. [PMID: 25573486 PMCID: PMC4243740 DOI: 10.1186/1471-2164-15-s7-s5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Background Over the last decades, a vast structural knowledge has been gathered on the HIV-1 protease (PR). Noticeably, most of the studies focused the B-subtype, which has the highest prevalence in developed countries. Accordingly, currently available anti-HIV drugs target this subtype, with considerable benefits for the corresponding patients. However, in developing countries, there is a wide variety of HIV-1 subtypes carrying PR polymorphisms related to reduced drug susceptibility. The non-active site mutation, M36I, is the most frequent polymorphism, and is considered as a non-B subtype marker. Yet, the structural impact of this substitution on the PR structure and on the interaction with natural substrates remains poorly documented. Results Herein, we used molecular dynamics simulations to investigate the role of this polymorphism on the interaction of PR with six of its natural cleavage-sites substrates. Free energy analyses by MMPB/SA calculations showed an affinity decrease of M36I-PR for the majority of its substrates. The only exceptions were the RT-RH, with equivalent affinity, and the RH-IN, for which an increased affinity was found. Furthermore, molecular simulations suggest that, unlike other peptides, RH-IN induced larger structural fluctuations in the wild-type enzyme than in the M36I variant. Conclusions With multiple approaches and analyses we identified structural and dynamical determinants associated with the changes found in the binding affinity of the M36I variant. This mutation influences the flexibility of both PR and its complexed substrate. The observed impact of M36I, suggest that combination with other non-B subtype polymorphisms, could lead to major effects on the interaction with the 12 known cleavage sites, which should impact the virion maturation.
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Inhibitors of the Human Immunodeficiency Virus Protease. Antiviral Res 2014. [DOI: 10.1128/9781555815493.ch7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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9
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Huang X, Britto MD, Kear-Scott JL, Boone CD, Rocca JR, Simmerling C, Mckenna R, Bieri M, Gooley PR, Dunn BM, Fanucci GE. The role of select subtype polymorphisms on HIV-1 protease conformational sampling and dynamics. J Biol Chem 2014; 289:17203-14. [PMID: 24742668 DOI: 10.1074/jbc.m114.571836] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
HIV-1 protease is an essential enzyme for viral particle maturation and is a target in the fight against HIV-1 infection worldwide. Several natural polymorphisms are also associated with drug resistance. Here, we utilized both pulsed electron double resonance, also called double electron-electron resonance, and NMR (15)N relaxation measurements to characterize equilibrium conformational sampling and backbone dynamics of an HIV-1 protease construct containing four specific natural polymorphisms commonly found in subtypes A, F, and CRF_01 A/E. Results show enhanced backbone dynamics, particularly in the flap region, and the persistence of a novel conformational ensemble that we hypothesize is an alternative flap orientation of a curled open state or an asymmetric configuration when interacting with inhibitors.
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Affiliation(s)
- Xi Huang
- From the Department of Chemistry, University of Florida, Gainesville, Florida 32611
| | - Manuel D Britto
- From the Department of Chemistry, University of Florida, Gainesville, Florida 32611
| | - Jamie L Kear-Scott
- From the Department of Chemistry, University of Florida, Gainesville, Florida 32611
| | - Christopher D Boone
- the Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610
| | - James R Rocca
- the Advanced Magnetic Resonance Imaging and Spectroscopy Facility, McKnight Brain Institute, University of Florida, Gainesville, Florida 32610
| | - Carlos Simmerling
- the Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, and
| | - Robert Mckenna
- the Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610
| | - Michael Bieri
- the Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Paul R Gooley
- the Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Ben M Dunn
- the Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610
| | - Gail E Fanucci
- From the Department of Chemistry, University of Florida, Gainesville, Florida 32611,
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Huang X, de Vera IMS, Veloro AM, Rocca JR, Simmerling C, Dunn BM, Fanucci GE. Backbone ¹H, ¹³C, and ¹⁵N chemical shift assignment for HIV-1 protease subtypes and multi-drug resistant variant MDR 769. BIOMOLECULAR NMR ASSIGNMENTS 2013; 7:199-202. [PMID: 22752791 PMCID: PMC3518686 DOI: 10.1007/s12104-012-9409-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Accepted: 06/21/2012] [Indexed: 06/01/2023]
Abstract
HIV-1 protease (HIV-1PR) is an essential drug target in the treatment of patients infected with HIV-1. Mutations are found to arise in over 38 of 99 amino acid sites in this protein in response to drug therapy or natural selection, where many are found combinations that alter enzyme kinetics or inhibitor susceptibility without a clear structural mechanism. In efforts to understand how these mutations alter the flexibility and dynamics of HIV-1PR, we report the backbone (1)H, (13)C, and (15)N chemical shift assignments for subtypes C, circulating recombinant form CRF01_AE and a multi-drug resistant variant MDR 769. These assignments are essential for future work aimed at characterizing backbone dynamics, exchange dynamics and dynamics of protein/substrate or protein/inhibitor interactions.
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Affiliation(s)
- Xi Huang
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, Florida 32611, USA
| | | | - Angelo M. Veloro
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, Florida 32611, USA
| | - James R. Rocca
- Advanced Magnetic Resonance and Imaging, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA
| | - Carlos Simmerling
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, USA
| | - Ben M. Dunn
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Gail E. Fanucci
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, Florida 32611, USA
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Mutations in HIV-1 gag and pol compensate for the loss of viral fitness caused by a highly mutated protease. Antimicrob Agents Chemother 2012; 56:4320-30. [PMID: 22644035 DOI: 10.1128/aac.00465-12] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
During the last few decades, the treatment of HIV-infected patients by highly active antiretroviral therapy, including protease inhibitors (PIs), has become standard. Here, we present results of analysis of a patient-derived, multiresistant HIV-1 CRF02_AG recombinant strain with a highly mutated protease (PR) coding sequence, where up to 19 coding mutations have accumulated in the PR. The results of biochemical analysis in vitro showed that the patient-derived PR is highly resistant to most of the currently used PIs and that it also exhibits very poor catalytic activity. Determination of the crystal structure revealed prominent changes in the flap elbow region and S1/S1' active site subsites. While viral loads in the patient were found to be high, the insertion of the patient-derived PR into a HIV-1 subtype B backbone resulted in reduction of infectivity by 3 orders of magnitude. Fitness compensation was not achieved by elevated polymerase (Pol) expression, but the introduction of patient-derived gag and pol sequences in a CRF02_AG backbone rescued viral infectivity to near wild-type (wt) levels. The mutations that accumulated in the vicinity of the processing sites spanning the p2/NC, NC/p1, and p6pol/PR proteins lead to much more efficient hydrolysis of corresponding peptides by patient-derived PR in comparison to the wt enzyme. This indicates a very efficient coevolution of enzyme and substrate maintaining high viral loads in vivo under constant drug pressure.
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Agniswamy J, Shen CH, Aniana A, Sayer JM, Louis JM, Weber IT. HIV-1 protease with 20 mutations exhibits extreme resistance to clinical inhibitors through coordinated structural rearrangements. Biochemistry 2012; 51:2819-28. [PMID: 22404139 PMCID: PMC3328860 DOI: 10.1021/bi2018317] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The escape mutant of HIV-1 protease (PR) containing 20 mutations (PR20) undergoes efficient polyprotein processing even in the presence of clinical protease inhibitors (PIs). PR20 shows >3 orders of magnitude decreased affinity for PIs darunavir (DRV) and saquinavir (SQV) relative to PR. Crystal structures of PR20 crystallized with yttrium, substrate analogue p2-NC, DRV, and SQV reveal three distinct conformations of the flexible flaps and diminished interactions with inhibitors through the combination of multiple mutations. PR20 with yttrium at the active site exhibits widely separated flaps lacking the usual intersubunit contacts seen in other inhibitor-free dimers. Mutations of residues 35-37 in the hinge loop eliminate interactions and perturb the flap conformation. Crystals of PR20/p2-NC contain one uninhibited dimer with one very open flap and one closed flap and a second inhibitor-bound dimer in the closed form showing six fewer hydrogen bonds with the substrate analogue relative to wild-type PR. PR20 complexes with PIs exhibit expanded S2/S2' pockets and fewer PI interactions arising from coordinated effects of mutations throughout the structure, in agreement with the strikingly reduced affinity. In particular, insertion of the large aromatic side chains of L10F and L33F alters intersubunit interactions and widens the PI binding site through a network of hydrophobic contacts. The two very open conformations of PR20 as well as the expanded binding site of the inhibitor-bound closed form suggest possible approaches for modifying inhibitors to target extreme drug-resistant HIV.
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Affiliation(s)
- Johnson Agniswamy
- Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, Georgia 30303, United States
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13
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Effect of natural polymorphisms in the HIV-1 CRF02_AG protease on protease inhibitor hypersusceptibility. Antimicrob Agents Chemother 2012; 56:2719-25. [PMID: 22330918 DOI: 10.1128/aac.06079-11] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Hypersusceptibility (HS) to inhibition by different antiretroviral drugs (ARVs) among diverse HIV-infected individuals may be a misnomer because clinical response to treatment is evaluated in relation to subtype B infections while drug susceptibility of the infecting virus, regardless of subtype, is compared to a subtype B HIV-1 laboratory strain (NL4-3 or IIIB). Mounting evidence suggests that HS to different ARVs may result in better treatment outcome just as drug resistance leads to treatment failure. We have identified key amino acid polymorphisms in the protease coding region of a non-B HIV-1 subtype linked to protease inhibitor HS, namely, 17E and 64M in CRF02_AG. These HS-linked polymorphisms were introduced in the BD6-15 CRF02_AG molecular clone and tested for inhibition using a panel of protease inhibitors. In general, suspected HS-linked polymorphisms did increase susceptibility to specific protease inhibitors such as amprenavir and atazanavir, but the combination of the 17E/64M polymorphisms showed greater HS. These two mutations were found at low frequencies but linked in a sequence database of over 700 protease sequences of CRF02_AG. In direct head-to-head virus competitions, CRF02_AG harboring the 17E/64M polymorphisms also had higher replicative fitness than did the 17E or the 64M polymorphism in the CFR02_AG clone. These findings suggest that subtype-specific, linked polymorphisms can result in hypersusceptibility to ARVs. Considering the potential benefit of HS to treatment outcome, screening for potential HS-linked polymorphisms as well as preexisting drug resistance mutations in treatment-naïve patients may guide the choice of ARVs for the best treatment outcome.
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14
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Yan GW, Chen Y, Li Y, Chen HF. Revealing interaction mode between HIV-1 protease and mannitol analog inhibitor. Chem Biol Drug Des 2012; 79:916-25. [PMID: 22296911 DOI: 10.1111/j.1747-0285.2012.01348.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
HIV protease is a key enzyme to play a key role in the HIV-1 replication cycle and control the maturation from HIV viruses to an infectious virion. HIV-1 protease has become an important target for anti-HIV-1 drug development. Here, we used molecular dynamics simulation to study the binding mode between mannitol derivatives and HIV-1 protease. The results suggest that the most active compound (M35) has more stable hydrogen bonds and stable native contacts than the less active one (M17). These mannitol derivatives might have similar interaction mode with HIV-1 protease. Then, 3D-QSAR was used to construct quantitative structure-activity models. The cross-validated q(2) values are found as 0.728 and 0.611 for CoMFA and CoMSIA, respectively. And the non-cross-validated r(2) values are 0.973 and 0.950. Nine test set compounds validate the model. The results show that this model possesses better prediction ability than the previous work. This model can be used to design new chemical entities and make quantitative prediction of the bioactivities for HIV-1 protease inhibitors before resorting to in vitro and in vivo experiment.
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Affiliation(s)
- Guan-Wen Yan
- State Key Laboratory of Microbial metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China
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15
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Tie Y, Wang YF, Boross PI, Chiu TY, Ghosh AK, Tozser J, Louis JM, Harrison RW, Weber IT. Critical differences in HIV-1 and HIV-2 protease specificity for clinical inhibitors. Protein Sci 2012; 21:339-50. [PMID: 22238126 DOI: 10.1002/pro.2019] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 12/13/2011] [Accepted: 12/13/2011] [Indexed: 11/12/2022]
Abstract
Clinical inhibitor amprenavir (APV) is less effective on HIV-2 protease (PR₂) than on HIV-1 protease (PR₁). We solved the crystal structure of PR₂ with APV at 1.5 Å resolution to identify structural changes associated with the lowered inhibition. Furthermore, we analyzed the PR₁ mutant (PR(1M) ) with substitutions V32I, I47V, and V82I that mimic the inhibitor binding site of PR₂. PR(1M) more closely resembled PR₂ than PR₁ in catalytic efficiency on four substrate peptides and inhibition by APV, whereas few differences were seen for two other substrates and inhibition by saquinavir (SQV) and darunavir (DRV). High resolution crystal structures of PR(1M) with APV, DRV, and SQV were compared with available PR₁ and PR₂ complexes. Val/Ile32 and Ile/Val47 showed compensating interactions with SQV in PR(1M) and PR₁, however, Ile82 interacted with a second SQV bound in an extension of the active site cavity of PR(1M). Residues 32 and 82 maintained similar interactions with DRV and APV in all the enzymes, whereas Val47 and Ile47 had opposing effects in the two subunits. Significantly diminished interactions were seen for the aniline of APV bound in PR₁ (M) and PR₂ relative to the strong hydrogen bonds observed in PR₁, consistent with 15- and 19-fold weaker inhibition, respectively. Overall, PR(1M) partially replicates the specificity of PR₂ and gives insight into drug resistant mutations at residues 32, 47, and 82. Moreover, this analysis provides a structural explanation for the weaker antiviral effects of APV on HIV-2.
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Affiliation(s)
- Yunfeng Tie
- Department of Biology, Georgia State University, Atlanta, Georgia 30303, USA
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16
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Champenois K, Baras A, Choisy P, Ajana F, Melliez H, Bocket L, Yazdanpanah Y. Lopinavir/ritonavir resistance in patients infected with HIV-1: two divergent resistance pathways? J Med Virol 2011; 83:1677-81. [DOI: 10.1002/jmv.22161] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2011] [Indexed: 11/10/2022]
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17
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Sayer JM, Agniswamy J, Weber IT, Louis JM. Autocatalytic maturation, physical/chemical properties, and crystal structure of group N HIV-1 protease: relevance to drug resistance. Protein Sci 2011; 19:2055-72. [PMID: 20737578 DOI: 10.1002/pro.486] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The mature protease from Group N human immunodeficiency virus Type 1 (HIV-1) (PR1(N)) differs in 20 amino acids from the extensively studied Group M protease (PR1(M)) at positions corresponding to minor drug-resistance mutations (DRMs). The first crystal structure (1.09 Å resolution) of PR1(N) with the clinical inhibitor darunavir (DRV) reveals the same overall structure as PR1(M), but with a slightly larger inhibitor-binding cavity. Changes in the 10s loop and the flap hinge propagate to shift one flap away from the inhibitor, whereas L89F and substitutions in the 60s loop perturb inhibitor-binding residues 29-32. However, kinetic parameters of PR1(N) closely resemble those of PR1(M), and calorimetric results are consistent with similar binding affinities for DRV and two other clinical PIs, suggesting that minor DRMs coevolve to compensate for the detrimental effects of drug-specific major DRMs. A miniprecursor (TFR 1-61-PR1(N)) comprising the transframe region (TFR) fused to the N-terminus of PR1(N) undergoes autocatalytic cleavage at the TFR/PR1(N) site concomitant with the appearance of catalytic activity characteristic of the dimeric, mature enzyme. This cleavage is inhibited at an equimolar ratio of precursor to DRV (∼6 μM), which partially stabilizes the precursor dimer from a monomer. However, cleavage at L34/W35 within the TFR, which precedes the TFR 1-61/PR1(N) cleavage at pH ≤ 5, is only partially inhibited. Favorable properties of PR1(N) relative to PR1(M) include its suitability for column fractionation by size under native conditions and >10-fold higher dimer dissociation constant (150 nM). Exploiting these properties may facilitate testing of potential dimerization inhibitors that perturb early precursor processing steps.
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Affiliation(s)
- Jane M Sayer
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland 20892-0520, USA
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18
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Chaplin B, Eisen G, Idoko J, Onwujekwe D, Idigbe E, Adewole I, Gashau W, Meloni S, Sarr A, Sankalé J, Ekong E, Murphy R, Kanki P. Impact of HIV type 1 subtype on drug resistance mutations in Nigerian patients failing first-line therapy. AIDS Res Hum Retroviruses 2011; 27:71-80. [PMID: 20964479 DOI: 10.1089/aid.2010.0050] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A diverse array of non-subtype B HIV-1 viruses circulates in Africa and dominates the global pandemic. It is important to understand how drug resistance mutations in non-B subtypes may develop differently from the patterns described in subtype B. HIV-1 reverse transcriptase and protease sequences from 338 patients with treatment failure to first-line ART regimens were evaluated. Multivariate logistic regression was used to examine the effect of subtype on each mutation controlling for regimen, time on therapy, and total mutations. The distribution of HIV-1 subtypes included CRF02_AG (45.0%), G (37.9%), CRF06_cpx (4.4%), A (3.6%), and other subtypes or recombinant sequences (9.2%). The most common NRTI mutations were M184V (89.1%) and thymidine analog mutations (TAMs). The most common NNRTI mutations were Y181C (49.7%), K103N (36.4%), G190A (26.3%), and A98G (19.5%). Multivariate analysis showed that CRF02_AG was less likely to have the M41L mutation compared to other subtypes [adjusted odds ratio (AOR) = 0.35; p = 0.022]. Subtype A patients showed a 42.5-fold increased risk (AOR = 42.5, p = 0.001) for the L210W mutation. Among NNRTI mutations, subtype G patients had an increased risk for A98G (AOR = 2.40, p = 0.036) and V106I (AOR = 6.15, p = 0.010), whereas subtype CRF02_AG patients had an increased risk for V90I (AOR = 3.16; p = 0.003) and a decreased risk for A98G (AOR = 0.48, p = 0.019). Five RT mutations were found to vary significantly between different non-B West African subtypes. Further study to understand the clinical impact of subtype-specific diversity on drug resistance will be critically important to the continued success of ART scale-up in resource-limited settings.
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Affiliation(s)
- B. Chaplin
- Harvard School of Public Health, Boston, Massachusetts
| | - G. Eisen
- Harvard School of Public Health, Boston, Massachusetts
| | - J. Idoko
- Jos University Teaching Hospital, Plateau State, Nigeria
| | - D. Onwujekwe
- National Institute of Medical Research, Lagos, Nigeria
| | - E. Idigbe
- National Institute of Medical Research, Lagos, Nigeria
| | - I. Adewole
- University College Hospital, Ibadan, Nigeria
| | - W. Gashau
- University Maiduguri Teaching Hospital, Maiduguri, Nigeria
| | - S. Meloni
- Harvard School of Public Health, Boston, Massachusetts
| | - A.D. Sarr
- Harvard School of Public Health, Boston, Massachusetts
| | - J.L. Sankalé
- Harvard School of Public Health, Boston, Massachusetts
| | - E. Ekong
- Harvard School of Public Health, Boston, Massachusetts
| | | | - P. Kanki
- Harvard School of Public Health, Boston, Massachusetts
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19
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Gu H, Chen H, Wei D, Wang J. Molecular dynamics simulations exploring drug resistance in HIV-1 proteases. ACTA ACUST UNITED AC 2010. [DOI: 10.1007/s11434-010-3257-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Genoni A, Morra G, Merz KM, Colombo G. Computational study of the resistance shown by the subtype B/HIV-1 protease to currently known inhibitors. Biochemistry 2010; 49:4283-95. [PMID: 20415450 DOI: 10.1021/bi100569u] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Human immunodeficiency virus type 1 protease (HIV-1 PR) is an essential enzyme in the HIV-1 life cycle. As such, this protein represents a major drug target in AIDS therapy, but emerging resistance to antiretroviral inhibitor cocktails, caused by high viral mutation rates, represents a significant challenge in AIDS treatment. Many mutations are not located within the active site or binding pocket, nor they do significantly modify the three-dimensional structural organization of the enzyme; hence, the mechanism(s) by which they alter inhibitor affinity for the protease remains uncertain. In this article, we present an all-atom computational analysis of the dynamic residue-residue coordination between the active site residues and the rest of the protein and of the energetic properties of different HIV-1 PR complexes. We analyze both the wild-type form and mutated forms that induce drug resistance. In particular, the results show differences between the wild type and the mutants in their mechanism of dynamic coordination, in the signal propagation between the active site residues and the rest of the protein, and in the energy networks responsible for the stabilization of the bound inhibitor conformation. Finally, we propose a dynamic and energetic explanation for HIV-1 protease drug resistance, and, through this model, we identify a possible new site that could be helpful in the design of a new family of HIV-1 PR allosteric inhibitors.
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Affiliation(s)
- Alessandro Genoni
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
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21
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Robbins AH, Coman RM, Bracho-Sanchez E, Fernandez MA, Gilliland CT, Li M, Agbandje-McKenna M, Wlodawer A, Dunn BM, McKenna R. Structure of the unbound form of HIV-1 subtype A protease: comparison with unbound forms of proteases from other HIV subtypes. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:233-42. [PMID: 20179334 PMCID: PMC2827345 DOI: 10.1107/s0907444909054298] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Accepted: 12/16/2009] [Indexed: 04/06/2023]
Abstract
The crystal structure of the unbound form of HIV-1 subtype A protease (PR) has been determined to 1.7 A resolution and refined as a homodimer in the hexagonal space group P6(1) to an R(cryst) of 20.5%. The structure is similar in overall shape and fold to the previously determined subtype B, C and F PRs. The major differences lie in the conformation of the flap region. The flaps in the crystal structures of the unbound subtype B and C PRs, which were crystallized in tetragonal space groups, are either semi-open or wide open. In the present structure of subtype A PR the flaps are found in the closed position, a conformation that would be more anticipated in the structure of HIV protease complexed with an inhibitor. The amino-acid differences between the subtypes and their respective crystal space groups are discussed in terms of the differences in the flap conformations.
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Affiliation(s)
- Arthur H. Robbins
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Roxana M. Coman
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Edith Bracho-Sanchez
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Marty A. Fernandez
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - C. Taylor Gilliland
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Mi Li
- Basic Research Program, SAIC-Frederick, Frederick, Maryland, USA
- Macromolecular Crystallography Laboratory, NCI-Frederick, Frederick, Maryland, USA
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Alexander Wlodawer
- Macromolecular Crystallography Laboratory, NCI-Frederick, Frederick, Maryland, USA
| | - Ben M. Dunn
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
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22
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Kear JL, Blackburn ME, Veloro AM, Dunn BM, Fanucci GE. Subtype polymorphisms among HIV-1 protease variants confer altered flap conformations and flexibility. J Am Chem Soc 2010; 131:14650-1. [PMID: 19788299 DOI: 10.1021/ja907088a] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) protease plays a fundamental role in the maturation and life cycle of the retrovirus HIV-1, as it functions in regulating post-translational processing of the viral polyproteins gag and gag-pol; thus, it is a key target of AIDS antiviral therapy. Accessibility of substrate to the active site is mediated by two flaps, which must undergo a large conformational change from an open to a closed conformation during substrate binding and catalysis. The electron paramagnetic resonance (EPR) method of site-directed spin labeling (SDSL) with double electron-electron resonance (DEER) spectroscopy was utilized to monitor the conformations of the flaps in apo HIV-1 protease (HIV-1PR), subtypes B, C, and F, CRF01_A/E, and patient isolates V6 and MDR 769. The distance distribution profiles obtained from analysis of the dipolar modulated echo curves were reconstructed to yield a set of Gaussian-shaped populations, which provide an analysis of the flap conformations sampled. The relative percentages of each conformer population described as "tucked/curled", "closed", "semi-open", and "wide-open" were determined and compared for various constructs. The results and analyses show that sequence variations among subtypes, CRFs, and patient isolates of apo HIV-1PR alter the average flap conformation in a way that can be understood as inducing shifts in the relative populations, or conformational sampling, of the previously described four conformations for HIV-1PR.
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Affiliation(s)
- Jamie L Kear
- Department of Chemistry, P.O. Box 117200, University of Florida, Gainesville, Florida 32611-7200, USA
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23
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Krauchenco S, Martins NH, Sanches M, Polikarpov I. Effectiveness of commercial inhibitors against subtype F HIV-1 protease. J Enzyme Inhib Med Chem 2009; 24:638-45. [DOI: 10.1080/14756360802321740] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Sandra Krauchenco
- Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador São-carlense, 400CEP 13560-970, São Carlos, SP, Brazil
| | - Nadia H. Martins
- Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador São-carlense, 400CEP 13560-970, São Carlos, SP, Brazil
| | - Mario Sanches
- Laboratório Nacional de Luz Síncrotron, Caixa Postal 6192CEP 13084-971, Campinas, SP, Brazil
| | - Igor Polikarpov
- Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador São-carlense, 400CEP 13560-970, São Carlos, SP, Brazil
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24
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Loizidou EZ, Zeinalipour-Yazdi CD, Christofides T, Kostrikis LG. Analysis of binding parameters of HIV-1 integrase inhibitors: correlates of drug inhibition and resistance. Bioorg Med Chem 2009; 17:4806-18. [PMID: 19450984 DOI: 10.1016/j.bmc.2009.04.058] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Revised: 04/07/2009] [Accepted: 04/09/2009] [Indexed: 12/19/2022]
Abstract
This study undertook an exploratory data analysis of the binding parameters of HIV-1 integrase inhibitors. The study group involved inhibitors in preclinical development from the diketo acid, pyrroloquinoline and naphthyridine carboxamide families and the most advanced inhibitors Raltegravir and Elvitegravir. Distinct differences were observed in the energetics of binding between the studied classes of inhibitors that also correlated with drug resistant patterns. Quantitative-property-activity-relationships correlated experimental IC(50) values to the binding energy and the logarithm of the partition coefficient between n-octanol and water (clogP). The approach followed here serves as an improved basis for the development of 'second generation' integrase inhibitors.
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Affiliation(s)
- Eriketi Z Loizidou
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus.
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25
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Ishizaki A, Cuong NH, Thuc PV, Trung NV, Saijoh K, Kageyama S, Ishigaki K, Tanuma J, Oka S, Ichimura H. Profile of HIV type 1 infection and genotypic resistance mutations to antiretroviral drugs in treatment-naive HIV type 1-infected individuals in Hai Phong, Viet Nam. AIDS Res Hum Retroviruses 2009; 25:175-82. [PMID: 19239356 DOI: 10.1089/aid.2008.0193] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We evaluated the prevalence and profile of antiretroviral treatment (ART)-associated resistance mutations among HIV-1 strains in northern Vietnam by genotypically analyzing strains isolated from ART-naive individuals in Hai Phong, a city in which HIV-1 is highly prevalent. Plasma samples were collected from injecting drug users (IDU, n = 760), female sex workers (FSW, n = 91), seafarers (n = 94), pregnant women (n = 200), and blood donors (n = 210), and screened for HIV-1 antibodies. Plasma viral RNA was extracted from HIV-1-positive samples, amplified by reverse transcriptase (RT)-PCR of protease and RT genes, and analyzed for genotypes and ART-associated resistance mutations. HIV-1 prevalence among IDU, FSW, seafarers, pregnant women, and blood donors was 35.9%, 23.1%, 0%, 0.5%, and 2.9%, respectively. Phylogenetic analyses revealed that the most prevalent HIV-1 subtype was CRF01_AE (98.3%), similar to strains prevalent in southern China. Four (1.4%) subtype B strains and one (0.3%) unique recombinant between subtypes B and C were also identified. We found protease inhibitor-associated major resistance mutations in one of the 294 cases analyzed (0.3%; mutation M46I). We found RT inhibitor-associated major resistance mutations in 7/273 cases (2.6%; one occurrence each of L74I, M184I, and K219E; three cases of K103N; and two cases of G190E). One CRF01_AE strain harboring a protease codon 35 insertion was first identified in Vietnam. Thus, monitoring of drug-resistant HIV-1 and establishment of a database are required for the proper selection of ART in Vietnam.
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Affiliation(s)
- Azumi Ishizaki
- Department of Hygiene, Kanazawa University, Graduate School of Medical Science, Kanazawa, Japan
- Department of Viral Infection and International Health, Kanazawa University, Graduate School of Medical Science, Kanazawa, Japan
| | | | | | - Nguyen Vu Trung
- Department of Medical microbiology, Hanoi Medical University, Hanoi, Viet Nam
| | - Kiyofumi Saijoh
- Department of Hygiene, Kanazawa University, Graduate School of Medical Science, Kanazawa, Japan
| | - Seiji Kageyama
- Department of Viral Infection and International Health, Kanazawa University, Graduate School of Medical Science, Kanazawa, Japan
| | - Kyoko Ishigaki
- AIDS Research and Clinical Center, International Medical Center of Japan, Tokyo, Japan
| | - Junko Tanuma
- AIDS Research and Clinical Center, International Medical Center of Japan, Tokyo, Japan
| | - Shinichi Oka
- AIDS Research and Clinical Center, International Medical Center of Japan, Tokyo, Japan
| | - Hiroshi Ichimura
- Department of Viral Infection and International Health, Kanazawa University, Graduate School of Medical Science, Kanazawa, Japan
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26
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Wase NV, Wright PC. Systems biology of cyanobacterial secondary metabolite production and its role in drug discovery. Expert Opin Drug Discov 2008; 3:903-29. [DOI: 10.1517/17460441.3.8.903] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Nishikant V Wase
- The University of Sheffield, Biological and Environmental Systems Group, Department of Chemical and Process Engineering, Mappin St., Sheffield, S1 3JD, UK ;
| | - Phillip C Wright
- The University of Sheffield, Biological and Environmental Systems Group, Department of Chemical and Process Engineering, Mappin St., Sheffield, S1 3JD, UK ;
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27
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Effect of flap mutations on structure of HIV-1 protease and inhibition by saquinavir and darunavir. J Mol Biol 2008; 381:102-15. [PMID: 18597780 DOI: 10.1016/j.jmb.2008.05.062] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2008] [Revised: 05/13/2008] [Accepted: 05/14/2008] [Indexed: 11/20/2022]
Abstract
HIV-1 (human immunodeficiency virus type 1) protease (PR) and its mutants are important antiviral drug targets. The PR flap region is critical for binding substrates or inhibitors and catalytic activity. Hence, mutations of flap residues frequently contribute to reduced susceptibility to PR inhibitors in drug-resistant HIV. Structural and kinetic analyses were used to investigate the role of flap residues Gly48, Ile50, and Ile54 in the development of drug resistance. The crystal structures of flap mutants PR(I50V) (PR with I50V mutation), PR(I54V) (PR with I54V mutation), and PR(I54M) (PR with I54M mutation) complexed with saquinavir (SQV) as well as PR(G48V) (PR with G48V mutation), PR(I54V), and PR(I54M) complexed with darunavir (DRV) were determined at resolutions of 1.05-1.40 A. The PR mutants showed changes in flap conformation, interactions with adjacent residues, inhibitor binding, and the conformation of the 80s loop relative to the wild-type PR. The PR contacts with DRV were closer in PR(G48V)-DRV than in the wild-type PR-DRV, whereas they were longer in PR(I54M)-DRV. The relative inhibition of PR(I54V) and that of PR(I54M) were similar for SQV and DRV. PR(G48V) was about twofold less susceptible to SQV than to DRV, whereas the opposite was observed for PR(I50V). The observed inhibition was in agreement with the association of G48V and I50V with clinical resistance to SQV and DRV, respectively. This analysis of structural and kinetic effects of the mutants will assist in the development of more effective inhibitors for drug-resistant HIV.
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28
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Coming and going: Some aspects of care for migrants with HIV in the UK. J Infect 2008; 57:11-5. [DOI: 10.1016/j.jinf.2008.05.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2008] [Accepted: 05/08/2008] [Indexed: 11/20/2022]
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29
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Structural analysis of human immunodeficiency virus type 1 CRF01_AE protease in complex with the substrate p1-p6. J Virol 2008; 82:6762-6. [PMID: 18434392 DOI: 10.1128/jvi.00018-08] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The effect of amino acid variability between human immunodeficiency virus type 1 (HIV-1) clades on structure and the emergence of resistance mutations in HIV-1 protease has become an area of significant interest in recent years. We determined the first crystal structure of the HIV-1 CRF01_AE protease in complex with the p1-p6 substrate to a resolution of 2.8 A. Hydrogen bonding between the flap hinge and the protease core regions shows significant structural rearrangements in CRF01_AE protease compared to the clade B protease structure.
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30
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Coman RM, Robbins AH, Fernandez MA, Gilliland CT, Sochet AA, Goodenow MM, McKenna R, Dunn BM. The contribution of naturally occurring polymorphisms in altering the biochemical and structural characteristics of HIV-1 subtype C protease. Biochemistry 2007; 47:731-43. [PMID: 18092815 DOI: 10.1021/bi7018332] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fourteen subtype B and C protease variants have been engineered in an effort to study whether the preexistent baseline polymorphisms, by themselves or in combination with drug resistance mutations, differentially alter the biochemical and structural features of the subtype C protease when compared with those of subtype B protease. The kinetic studies performed in this work showed that the preexistent polymorphisms in subtype C protease, by themselves, do not provide for a greater level of resistance. Inhibition analysis with eight clinically used protease inhibitors revealed that the natural polymorphisms found in subtype C protease, in combination with drug resistance mutations, can influence enzymatic catalytic efficiency and inhibitor resistance. Structural analyses of the subtype C protease bound to nelfinavir and indinavir showed that these inhibitors form similar interactions with the residues in the active site of subtype B and C proteases. It also revealed that the naturally occurring polymorphisms could alter the position of the outer loops of the subtype C protease, especially the 60's loop.
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Affiliation(s)
- Roxana M Coman
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida 32610, USA
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