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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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Bastys T, Gapsys V, Walter H, Heger E, Doncheva NT, Kaiser R, de Groot BL, Kalinina OV. Non-active site mutants of HIV-1 protease influence resistance and sensitisation towards protease inhibitors. Retrovirology 2020; 17:13. [PMID: 32430025 PMCID: PMC7236880 DOI: 10.1186/s12977-020-00520-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/04/2020] [Indexed: 02/07/2023] Open
Abstract
Background HIV-1 can develop resistance to antiretroviral drugs, mainly through mutations within the target regions of the drugs. In HIV-1 protease, a majority of resistance-associated mutations that develop in response to therapy with protease inhibitors are found in the protease’s active site that serves also as a binding pocket for the protease inhibitors, thus directly impacting the protease-inhibitor interactions. Some resistance-associated mutations, however, are found in more distant regions, and the exact mechanisms how these mutations affect protease-inhibitor interactions are unclear. Furthermore, some of these mutations, e.g. N88S and L76V, do not only induce resistance to the currently administered drugs, but contrarily induce sensitivity towards other drugs. In this study, mutations N88S and L76V, along with three other resistance-associated mutations, M46I, I50L, and I84V, are analysed by means of molecular dynamics simulations to investigate their role in complexes of the protease with different inhibitors and in different background sequence contexts. Results Using these simulations for alchemical calculations to estimate the effects of mutations M46I, I50L, I84V, N88S, and L76V on binding free energies shows they are in general in line with the mutations’ effect on \documentclass[12pt]{minimal}
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\begin{document}$$IC_{50}$$\end{document}IC50 values. For the primary mutation L76V, however, the presence of a background mutation M46I in our analysis influences whether the unfavourable effect of L76V on inhibitor binding is sufficient to outweigh the accompanying reduction in catalytic activity of the protease. Finally, we show that L76V and N88S changes the hydrogen bond stability of these residues with residues D30/K45 and D30/T31/T74, respectively. Conclusions We demonstrate that estimating the effect of both binding pocket and distant mutations on inhibitor binding free energy using alchemical calculations can reproduce their effect on the experimentally measured \documentclass[12pt]{minimal}
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\begin{document}$$IC_{50}$$\end{document}IC50 values. We show that distant site mutations L76V and N88S affect the hydrogen bond network in the protease’s active site, which offers an explanation for the indirect effect of these mutations on inhibitor binding. This work thus provides valuable insights on interplay between primary and background mutations and mechanisms how they affect inhibitor binding.
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Affiliation(s)
- Tomas Bastys
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123, Saarbrücken, Germany.,Saarbrücken Graduate School of Computer Science, University of Saarland, 66123, Saarbrücken, Germany
| | - Vytautas Gapsys
- Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Hauke Walter
- Medizinisches Labor Stendal, 39576, Stendal, Germany
| | - Eva Heger
- Institute of Virology, University of Cologne, 50935, Cologne, Germany
| | - Nadezhda T Doncheva
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123, Saarbrücken, Germany.,Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Rolf Kaiser
- Institute of Virology, University of Cologne, 50935, Cologne, Germany
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Olga V Kalinina
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123, Saarbrücken, Germany. .,Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), 66123, Saarbrücken, Germany. .,Faculty of Medicine, Saarland University, 66421, Homburg, Germany.
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Nayak C, Chandra I, Singh SK. An
in silico
pharmacological approach toward the discovery of potent inhibitors to combat drug resistance HIV‐1 protease variants. J Cell Biochem 2018; 120:9063-9081. [DOI: 10.1002/jcb.28181] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 11/08/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Chirasmita Nayak
- Computer Aided Drug Design and Molecular Modeling, Department of Bioinformatics Alagappa University Karaikudi India
| | - Ishwar Chandra
- Computer Aided Drug Design and Molecular Modeling, Department of Bioinformatics Alagappa University Karaikudi India
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modeling, Department of Bioinformatics Alagappa University Karaikudi India
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Flor-Parra F, Pérez-Pulido AJ, Pachón J, Pérez-Romero P. The HIV type 1 protease L10I minor mutation decreases replication capacity and confers resistance to protease inhibitors. AIDS Res Hum Retroviruses 2011; 27:65-70. [PMID: 21142921 DOI: 10.1089/aid.2010.0072] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The effect of minor mutations in PR on treatment outcome has not been well established. We characterized the HIV protease minor mutations, L10I, compared to the minor mutation, L63P, and the major mutation D30N and their impact on viral fitness and resistance to protease inhibitors. Mutations were introduced individually and in combination by site-directed mutagenesis into the provirus pNL4.3ren and constructs used for replication capacity (RC) and resistance assays. A structure prediction of the protease carrying the L10I mutation was determined. The prevalence of the minor mutation L10I had a pattern similar to that found for major mutations D30N, with a low prevalence (4.9%) in naive patients and significantly higher prevalence in treated patients. Furthermore, viruses carrying the major mutation D30N or the minor mutation L10I showed a significant decrease in RC (p-value <0.05), whereas viruses carrying the minor mutation L63P had RC similar to wild-type virus. In addition, the L10I mutation conferred resistance to saquinavir, which was supported by the higher prevalence in the cohort of the L10I mutation among patients with SQV resistance. The molecular modeling suggests that L10I may affect the conformation of Leu-23, a critical residue in the substrate binding site. In conclusion, the L10I mutation impairs RC and confers resistance to SQV, similarly to other major mutations, which may be related with changes in the conformation in the protease binding site. The presence of this mutation in the genotype of HIV from patients should be taken into consideration when designing new optimize treatments.
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Affiliation(s)
- Fernando Flor-Parra
- Institute of Biomedicine of Sevilla, University Hospital Virgen del Rocío/CSIC/University of Sevilla, Spain
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Asahchop EL, Oliveira M, Brenner BG, Martinez-Cajas JL, Toni TD, Ntemgwa M, Moisi D, Dandache S, Stranix B, Tremblay CL, Wainberg MA. Tissue culture drug resistance analysis of a novel HIV-1 protease inhibitor termed PL-100 in non-B HIV-1 subtypes. Antiviral Res 2010; 87:367-72. [PMID: 20541566 DOI: 10.1016/j.antiviral.2010.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2010] [Revised: 05/31/2010] [Accepted: 06/01/2010] [Indexed: 10/19/2022]
Abstract
PL-100 is a novel HIV-1 protease inhibitor (PI) that maintains activity against viruses that are resistant to other PIs. To further characterize this compound, we used it to select for drug resistance in tissue culture, using two non-B HIV-1 subtypes, viz. subtype C and a CRF01_AE recombinant virus. PL-100 selected for both minor and major PI resistance mutations along either of two distinct pathways. One of these involved the V82A and L90M resistance mutations while the other involved a mutation at position T80I, with other mutations being observed at positions M46I/L, I54M, K55R, L76F, P81S and I85V. The resistance patterns in both subtype C and CRF01_AE were similar and an accumulation of at least three mutations in the flap and active sites were required in each case for high-level resistance to occur, demonstrating that PL-100 has a high genetic barrier against the development of drug resistance.
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Affiliation(s)
- Eugene L Asahchop
- McGill University AIDS Centre, Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada
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