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Aulicino PC, Momin Z, Rozenszajn M, Monzon A, Arazi-Caillaud S, Bologna R, Mangano A, Kimata JT. HIV-1 subtype F integrase polymorphisms external to the catalytic core domain contribute to severe loss of replication capacity in context of the integrase inhibitor resistance mutation Q148H. J Antimicrob Chemother 2022; 77:2793-2802. [PMID: 35897124 PMCID: PMC9989736 DOI: 10.1093/jac/dkac238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/20/2022] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND In prior studies, HIV-1 BF recombinants with subtype F integrases failed to develop resistance to raltegravir through the Q148H mutational pathway. We aimed to determine the role of subtype-specific polymorphisms in integrase on drug susceptibility, viral replication and integration. METHODS Integrase sequences were retrieved from the Los Alamos Database or obtained from the Garrahan HIV cohort. HIV-1 infectious molecular clones with or without Q148H (+ G140S) resistance mutations were constructed using integrases of subtype B (NL4-3) or F1(BF) ARMA159 and URTR23. Integrase chimeras were generated by reciprocal exchanges of a 200 bp fragment spanning amino acids 85-150 of the catalytic core domain (CCD) of NL4-3-Q148H and either ARMA159-Q148H or URTR23-Q148H. Viral infections were quantified by p24 ELISA and Alu-gag integration PCR assay. RESULTS At least 18 different polymorphisms distinguish subtype B from F1(BF) recombinant integrases. In phenotypic experiments, p24 at Day 15 post-infection was high (105-106 pg/mL) for WT and NL4-3-Q148H; by contrast, it was low (102-104 pg/mL) for both F1(BF)-Q148H + G140S viruses, and undetectable for the Q148H mutants. Compared with WT viruses, integrated DNA was reduced by 5-fold for NL4-3-Q148H (P = 0.05), 9-fold for URTR23-Q148H (P = 0.01) and 16000-fold for ARMA159-Q148H (P = 0.01). Reciprocal exchange between B and F1(BF) of an integrase CCD region failed to rescue the replicative defect of F1(BF) integrase mutants. CONCLUSIONS The functional impairment of Q148H in the context of subtype F integrases from BF recombinants explains the lack of selection of this pathway in vivo. Non-B polymorphisms external to the integrase CCD may influence the pathway to integrase strand transfer inhibitor resistance.
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Affiliation(s)
- Paula C Aulicino
- Laboratory of Cellular Biology and Retroviruses, Unit of Virology and Molecular Epidemiology, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Zoha Momin
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Mijael Rozenszajn
- Laboratory of Cellular Biology and Retroviruses, Unit of Virology and Molecular Epidemiology, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Arturo Monzon
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Solange Arazi-Caillaud
- Unit of Epidemiology and Infectology, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Buenos Aires, Argentina
| | - Rosa Bologna
- Unit of Epidemiology and Infectology, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Buenos Aires, Argentina
| | - Andrea Mangano
- Laboratory of Cellular Biology and Retroviruses, Unit of Virology and Molecular Epidemiology, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Jason T Kimata
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA
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Hybrid Molecules as Potential Drugs for the Treatment of HIV: Design and Applications. Pharmaceuticals (Basel) 2022; 15:ph15091092. [PMID: 36145313 PMCID: PMC9502546 DOI: 10.3390/ph15091092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 08/23/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Human immunodeficiency virus (HIV) infection is a major problem for humanity because HIV is constantly changing and developing resistance to current drugs. This necessitates the development of new anti-HIV drugs that take new approaches to combat an ever-evolving virus. One of the promising alternatives to combination antiretroviral therapy (cART) is the molecular hybrid strategy, in which two or more pharmacophore units of bioactive scaffolds are combined into a single molecular structure. These hybrid structures have the potential to have higher efficacy and lower toxicity than their parent molecules. Given the potential advantages of the hybrid molecular approach, the development and synthesis of these compounds are of great importance in anti-HIV drug discovery. This review focuses on the recent development of hybrid compounds targeting integrase (IN), reverse transcriptase (RT), and protease (PR) proteins and provides a brief description of their chemical structures, structure–activity relationship, and binding mode.
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Vergni D, Santoni D, Bouba Y, Lemme S, Fabeni L, Carioti L, Bertoli A, Gennari W, Forbici F, Perno CF, Gagliardini R, Ceccherini-Silberstein F, Santoro MM. Evaluation of HIV-1 integrase variability by combining computational and probabilistic approaches. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 101:105294. [PMID: 35513162 DOI: 10.1016/j.meegid.2022.105294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/24/2022] [Accepted: 04/28/2022] [Indexed: 10/18/2022]
Abstract
This study aimed at updating previous data on HIV-1 integrase variability, by using effective bioinformatics methods combining different statistical instruments from simple entropy and mutation rate to more specific approaches such as Hellinger distance. A total of 2133 HIV-1 integrase sequences were analyzed in: i) 1460 samples from drug-naïve [DN] individuals; ii) 386 samples from drug-experienced but INI-naïve [IN] individuals; iii) 287 samples from INI-experienced [IE] individuals. Within the three groups, 76 amino acid positions were highly conserved (≤0.2% variation, Hellinger distance: <0.25%), with 35 fully invariant positions; while, 80 positions were conserved (>0.2% to <1% variation, Hellinger distance: <1%). The H12-H16-C40-C43 and D64-D116-E152 motifs were all well conserved. Some residues were affected by dramatic changes in their mutation distributions, especially between DN and IE samples (Hellinger distance ≥1%). In particular, 15 positions (D6, S24, V31, S39, L74, A91, S119, T122, T124, T125, V126, K160, N222, S230, C280) showed a significant decrease of mutation rate in IN and/or IE samples compared to DN samples. Conversely, 8 positions showed significantly higher mutation rate in samples from treated individuals (IN and/or IE) compared to DN. Some of these positions, such as E92, T97, G140, Y143, Q148 and N155, were already known to be associated with resistance to integrase inhibitors; other positions including S24, M154, V165 and D270 are not yet documented to be associated with resistance. Our study confirms the high conservation of HIV-1 integrase and identified highly invariant positions using robust and innovative methods. The role of novel mutations located in the critical region of HIV-1 integrase deserves further investigation.
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Affiliation(s)
- Davide Vergni
- Istituto per le Applicazioni del Calcolo "Mauro Picone" - CNR, Rome, Italy.
| | - Daniele Santoni
- Istituto di Analisi dei Sistemi ed. Informatica "Antonio Ruberti" - CNR, Rome, Italy
| | - Yagai Bouba
- Chantal BIYA International Reference Centre for research on HIV/AIDS prevention and management (CIRCB), Yaoundé, Cameroon; Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Saverio Lemme
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Lavinia Fabeni
- Laboratory of Virology, IRCCS, National Institute for Infectious Diseases "Lazzaro Spallanzani", Rome, Italy
| | - Luca Carioti
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Ada Bertoli
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy; Laboratory of Virology, University Hospital "Tor Vergata", Rome, Italy
| | - William Gennari
- Microbiology and Virology Unit, University Hospital, University of Modena and Reggio Emilia, Modena, Italy
| | - Federica Forbici
- Laboratory of Virology, IRCCS, National Institute for Infectious Diseases "Lazzaro Spallanzani", Rome, Italy
| | - Carlo Federico Perno
- Multimodal Laboratory Research Department, Children Hospital Bambino Gesù, IRCCS, Rome, Italy
| | - Roberta Gagliardini
- HIV/AIDS Department, IRCCS, National Institute for Infectious Diseases "Lazzaro Spallanzani", Rome, Italy
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Semengue ENJ, Armenia D, Inzaule S, Santoro MM, Dambaya B, Takou D, Teto G, Nka AD, Yagai B, Fabeni L, Chenwi C, Angong Beloumou G, Djupsa Ndjeyep SC, Colizzi V, Perno CF, Ceccherini-Silberstein F, Fokam J. Baseline integrase drug resistance mutations and conserved regions across HIV-1 clades in Cameroon: implications for transition to dolutegravir in resource-limited settings. J Antimicrob Chemother 2021; 76:1277-1285. [PMID: 33501504 DOI: 10.1093/jac/dkab004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/28/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Transition to dolutegravir-based regimens in resource-limited settings (RLS) requires prior understanding of HIV-1 integrase variants and conserved regions. Therefore, we evaluated integrase drug resistance mutations (DRMs) and conserved regions amongst integrase strand transfer inhibitor (INSTI)-naive patients harbouring diverse HIV-1 clades in Cameroon. METHODS A cross-sectional study was conducted amongst 918 INSTI-naive patients from Cameroon (89 ART-naive and 829 ART-experienced patients). HIV-1 sequences were interpreted regarding INSTI-DRMs using the Stanford HIVdb v8.9-1 and the 2019 IAS-USA list. Amino acid positions with <1% variability were considered as highly conserved. Subtyping was performed by phylogeny. RESULTS Overall prevalence (95% CI) of INSTI-DRMs was 0.8% (0.4-1.7), with 0.0% (0.0-4.0) amongst ART-naive versus 0.9% (0.5-1.9) amongst ART-experienced patients; P = 0.44. Accessory mutations (95% CI) were found in 33.8% (30.9-37.0), with 38.2% (28.1-49.1) amongst ART-naive versus 33.4% (30.4-36.7) amongst ART-experienced patients; P = 0.21. Of 288 HIV-1 integrase amino acid positions, 58.3% were highly conserved across subtypes in the following major regions: V75-G82, E85-P90, H114-G118, K127-W132, E138-G149, Q168-L172, T174-V180, W235-A239 and L241-D253. Wide genetic diversity was found (37 clades), including groups M (92.3%), N (1.4%), O (6.2%) and P (0.1%). Amongst group M, CRF02_AG was predominant (47.4%), with a significantly higher frequency (95% CI) of accessory mutations compared with non-AG [41.4% (36.8-46.0) versus 27.1% (23.3-31.2) respectively; P < 0.001]. CONCLUSIONS The low baseline of INSTI-DRMs (<1%) in Cameroon suggests effectiveness of dolutegravir-based regimens. In spite of high conservation across clades, the variability of accessory mutations between major circulating strains underscores the need for monitoring the selection of INSTI-DRMs while scaling up dolutegravir-based regimens in RLS.
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Affiliation(s)
- Ezechiel Ngoufack Jagni Semengue
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy.,Evangelical University of Cameroon, Bandjoun, Cameroon
| | - Daniele Armenia
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy.,Saint Camillus International University of Health and Medical Sciences, Rome, Italy
| | - Seth Inzaule
- Department of Global Health, Academic Medical Center of the University of Amsterdam and Amsterdam Institute for Global Health and Development, Amsterdam, The Netherlands
| | | | - Béatrice Dambaya
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Faculty of Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Désiré Takou
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
| | - Georges Teto
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
| | - Alex Durand Nka
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy.,Evangelical University of Cameroon, Bandjoun, Cameroon
| | - Bouba Yagai
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Lavinia Fabeni
- Laboratory of Virology, National Institute for Infectious Diseases "Lazzaro Spallanzani" - IRCCS, Rome, Italy
| | - Collins Chenwi
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Grâce Angong Beloumou
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
| | - Sandrine Claire Djupsa Ndjeyep
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
| | - Vittorio Colizzi
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy.,Evangelical University of Cameroon, Bandjoun, Cameroon
| | - Carlo-Federico Perno
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Bambino Gesu Children's Hospital, IRCCS, Rome, Italy
| | | | - Joseph Fokam
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon.,National HIV Drug Resistance Working Group, Ministry of Public Health, Cameroon.,Faculty of Health Sciences, University of Buea, Buea, Cameroon
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Pham HT, Alves BM, Yoo S, Xiao MA, Leng J, Quashie PK, Soares EA, Routy JP, Soares MA, Mesplède T. Progressive emergence of an S153F plus R263K combination of integrase mutations in the proviral DNA of one individual successfully treated with dolutegravir. J Antimicrob Chemother 2021; 76:639-647. [PMID: 33184634 DOI: 10.1093/jac/dkaa471] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/19/2020] [Indexed: 01/12/2023] Open
Abstract
OBJECTIVES The development of HIV drug resistance against the integrase strand transfer inhibitor dolutegravir is rare. We report here the transient detection, by near full-genome ultradeep sequencing, of minority HIV-1 subtype B variants bearing the S153F and R263K integrase substitutions in the proviral DNA from blood cells of one patient who successfully initiated dolutegravir-based ART, over 24 weeks. Our objective was to study the effects of these substitutions. METHODS Strand transfer and DNA-binding activities of recombinant integrase proteins were measured in cell-free assays. Cell-based resistance, infectivity and replicative capacities were measured using molecular clones. Structural modelling was performed to understand experimental results. RESULTS R263K emerged first, followed by the addition of S153F at Week 12. By Week 24, both mutations remained present, but at lower prevalence. We confirmed the coexistence of S153F and R263K on single viral genomes. Combining S153F or S153Y with R263K decreased integration and viral replicative capacity and conferred high levels of drug resistance against all integrase inhibitors. Alone, S153Y and S153F did little to infectivity or dolutegravir resistance. We identified altered DNA binding as a mechanism of resistance. The patient remained with undetectable viral loads at all timepoints. CONCLUSIONS Drug-resistant minority variants have often been reported under suppressive ART. Our study adds to these observations by unravelling a progression towards higher levels of resistance through a novel pathway despite continuous undetectable viral loads. Poorly replicative HIV drug-resistant minority proviral variants did not compromise viral suppression in one individual treated with dolutegravir.
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Affiliation(s)
- Hanh T Pham
- McGill AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Department of Microbiology and Immunology, Faculty of Medicine, McGill University, Montréal, Québec, Canada
| | - Brunna M Alves
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Sunbin Yoo
- McGill AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Department of Microbiology and Immunology, Faculty of Medicine, McGill University, Montréal, Québec, Canada
| | - Meng A Xiao
- McGill AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Department of Microbiology and Immunology, Faculty of Medicine, McGill University, Montréal, Québec, Canada
| | - Jing Leng
- McGill AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Department of Microbiology and Immunology, Faculty of Medicine, McGill University, Montréal, Québec, Canada
| | - Peter K Quashie
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
- The Francis Crick Institute, London, UK
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Esmeralda A Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Jean-Pierre Routy
- For Montreal PHI Cohort Study Group, Division of Hematology, McGill University Health Centre, Montréal, Québec, Canada
| | - Marcelo A Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Thibault Mesplède
- McGill AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Department of Microbiology and Immunology, Faculty of Medicine, McGill University, Montréal, Québec, Canada
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