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Venkatachalam S, Murlidharan N, Krishnan SR, Ramakrishnan C, Setshedi M, Pandian R, Barh D, Tiwari S, Azevedo V, Sayed Y, Gromiha MM. Understanding Drug Resistance of Wild-Type and L38HL Insertion Mutant of HIV-1 C Protease to Saquinavir. Genes (Basel) 2023; 14:533. [PMID: 36833460 PMCID: PMC9957153 DOI: 10.3390/genes14020533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/25/2023] Open
Abstract
Acquired immunodeficiency syndrome (AIDS) is one of the most challenging infectious diseases to treat on a global scale. Understanding the mechanisms underlying the development of drug resistance is necessary for novel therapeutics. HIV subtype C is known to harbor mutations at critical positions of HIV aspartic protease compared to HIV subtype B, which affects the binding affinity. Recently, a novel double-insertion mutation at codon 38 (L38HL) was characterized in HIV subtype C protease, whose effects on the interaction with protease inhibitors are hitherto unknown. In this study, the potential of L38HL double-insertion in HIV subtype C protease to induce a drug resistance phenotype towards the protease inhibitor, Saquinavir (SQV), was probed using various computational techniques, such as molecular dynamics simulations, binding free energy calculations, local conformational changes and principal component analysis. The results indicate that the L38HL mutation exhibits an increase in flexibility at the hinge and flap regions with a decrease in the binding affinity of SQV in comparison with wild-type HIV protease C. Further, we observed a wide opening at the binding site in the L38HL variant due to an alteration in flap dynamics, leading to a decrease in interactions with the binding site of the mutant protease. It is supported by an altered direction of motion of flap residues in the L38HL variant compared with the wild-type. These results provide deep insights into understanding the potential drug resistance phenotype in infected individuals.
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Affiliation(s)
- Sankaran Venkatachalam
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Nisha Murlidharan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Sowmya R. Krishnan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - C. Ramakrishnan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Mpho Setshedi
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - Ramesh Pandian
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - Debmalya Barh
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil
- Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur 721172, West Bengal, India
| | - Sandeep Tiwari
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil
- Institute of Biology, Federal University of Bahia, Salvador, BA 40110-909, Brazil
- Institute of Health Sciences, Federal University of Bahia, Salvador, BA 40110-909, Brazil
| | - Vasco Azevedo
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil
| | - Yasien Sayed
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - M. Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
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Petkov S, Kilpeläinen A, Bayurova E, Latanova A, Mezale D, Fridrihsone I, Starodubova E, Jansons J, Dudorova A, Gordeychuk I, Wahren B, Isaguliants M. HIV-1 Protease as DNA Immunogen against Drug Resistance in HIV-1 Infection: DNA Immunization with Drug Resistant HIV-1 Protease Protects Mice from Challenge with Protease-Expressing Cells. Cancers (Basel) 2022; 15:cancers15010238. [PMID: 36612231 PMCID: PMC9818955 DOI: 10.3390/cancers15010238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/12/2022] [Accepted: 12/20/2022] [Indexed: 01/04/2023] Open
Abstract
DNA immunization with HIV-1 protease (PR) is advanced for immunotherapy of HIV-1 infection to reduce the number of infected cells producing drug-resistant virus. A consensus PR of the HIV-1 FSU_A strain was designed, expression-optimized, inactivated (D25N), and supplemented with drug resistance (DR) mutations M46I, I54V, and V82A common for FSU_A. PR variants with D25N/M46I/I54V (PR_Ai2mut) and with D25N/M46I/I54V/V82A (PR_Ai3mut) were cloned into the DNA vaccine vector pVAX1, and PR_Ai3mut, into a lentiviral vector for the transduction of murine mammary adenocarcinoma cells expressing luciferase 4T1luc2. BALB/c mice were DNA-immunized by intradermal injections of PR_Ai, PR_Ai2mut, PR_Ai3mut, vector pVAX1, or PBS with electroporation. All PR variants induced specific CD8+ T-cell responses revealed after splenocyte stimulation with PR-derived peptides. Splenocytes of mice DNA-immunized with PR_Ai and PR_Ai2mut were not activated by peptides carrying V82A, whereas splenocytes of PR_Ai3mut-immunized mice recognized both peptides with and without V82A mutation. Mutations M46I and I54V were immunologically silent. In the challenge study, DNA immunization with PR_Ai3mut protected mice from the outgrowth of subcutaneously implanted adenocarcinoma 4T1luc2 cells expressing PR_Ai3mut; a tumor was formed only in 1/10 implantation sites and no metastases were detected. Immunizations with other PR variants were not protective; all mice formed tumors and multiple metastasis in the lungs, liver, and spleen. CD8+ cells of PR_Ai3mut DNA-immunized mice exhibited strong IFN-γ/IL-2 responses against PR peptides, while the splenocytes of mice in other groups were nonresponsive. Thus, immunization with a DNA plasmid encoding inactive HIV-1 protease with DR mutations suppressed the growth and metastatic activity of tumor cells expressing PR identical to the one encoded by the immunogen. This demonstrates the capacity of T-cell response induced by DNA immunization to recognize single DR mutations, and supports the concept of the development of immunotherapies against drug resistance in HIV-1 infection. It also suggests that HIV-1-infected patients developing drug resistance may have a reduced natural immune response against DR HIV-1 mutations causing an immune escape.
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Affiliation(s)
- Stefan Petkov
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Athina Kilpeläinen
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Ekaterina Bayurova
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Stockholm, Sweden
- Department of Research, Riga Stradins University, LV-1007 Riga, Latvia
- Chumakov Federal Scientific Center for Research and Development of Immune and Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia
| | - Anastasia Latanova
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Stockholm, Sweden
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Dzeina Mezale
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Stockholm, Sweden
- Department of Research, Riga Stradins University, LV-1007 Riga, Latvia
| | - Ilse Fridrihsone
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Stockholm, Sweden
- Department of Research, Riga Stradins University, LV-1007 Riga, Latvia
| | - Elizaveta Starodubova
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Stockholm, Sweden
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Juris Jansons
- Department of Research, Riga Stradins University, LV-1007 Riga, Latvia
- Latvian Research and Study Centre, LV-1067 Riga, Latvia
| | - Alesja Dudorova
- Department of Research, Riga Stradins University, LV-1007 Riga, Latvia
- Paul Stradins University Hospital, LV-1002 Riga, Latvia
| | - Ilya Gordeychuk
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Stockholm, Sweden
- Department of Research, Riga Stradins University, LV-1007 Riga, Latvia
- Chumakov Federal Scientific Center for Research and Development of Immune and Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia
| | - Britta Wahren
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Maria Isaguliants
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Stockholm, Sweden
- Department of Research, Riga Stradins University, LV-1007 Riga, Latvia
- Correspondence:
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Chimukangara B, Lessells RJ, Sartorius B, Gounder L, Manyana S, Pillay M, Singh L, Giandhari J, Govender K, Samuel R, Msomi N, Naidoo K, de Oliveira T, Moodley P, Parboosing R. HIV-1 drug resistance in adults and adolescents on protease inhibitor-based antiretroviral treatment in KwaZulu-Natal Province, South Africa. J Glob Antimicrob Resist 2021; 29:468-475. [PMID: 34785393 DOI: 10.1016/j.jgar.2021.10.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 08/19/2021] [Accepted: 10/26/2021] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND In low- and middle-income countries, increasing levels of HIV drug resistance (HIVDR) on second-line protease inhibitor (PI)-based regimens are a cause for concern, given limited drug options for third-line antiretroviral therapy (ART). OBJECTIVES We conducted a retrospective analysis of routine HIV-1 genotyping laboratory data from KwaZulu-Natal, in South Africa, to describe the frequency and patterns of HIVDR mutations and their consequent impact on standardized third-line regimens. METHODS This was a cross-sectional analysis of all HIV-1 genotypic resistance tests conducted by the National Health Laboratory Service in KwaZulu-Natal, South Africa (Jan 2015 - Dec 2016), for adults and adolescents (age ≥10 years) on second-line PI-based ART with virological failure. We assigned a third-line regimen to each record, based on a national treatment algorithm and calculated the genotypic susceptibility score (GSS) for that regimen. RESULTS Of 348 samples analyzed, 287 (83%) had at least one drug resistance mutation (DRM) and 114 (33%) had at least one major PI DRM. Major PI resistance was associated with longer duration on second-line ART (aOR per 6-months, 1.11, 95% CI 1.04-1.19) and older age (aOR 1.03, 95% CI 1.01-1.05). Of 112 patients requiring third-line ART, 12 (11%) had a GSS of <2 for the algorithm-assigned third-line regimen. CONCLUSIONS One in three people failing second-line ART had significant PI DRMs. A subgroup of these individuals had extensive HIVDR, where the predicted activity of third-line ART was suboptimal, highlighting the need for continuous evaluation of outcomes on third-line regimens and close monitoring for emergent HIV-1 integrase-inhibitor resistance.
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Affiliation(s)
- Benjamin Chimukangara
- Department of Virology, University of KwaZulu-Natal/National Health Laboratory Service, Durban, South Africa; Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa; Critical Care Medicine Department, NIH Clinical Center, Bethesda, MD, USA.
| | - Richard J Lessells
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Benn Sartorius
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Lilishia Gounder
- Department of Virology, University of KwaZulu-Natal/National Health Laboratory Service, Durban, South Africa
| | - Sontaga Manyana
- Department of Virology, University of KwaZulu-Natal/National Health Laboratory Service, Durban, South Africa
| | - Melendhran Pillay
- Department of Virology, University of KwaZulu-Natal/National Health Laboratory Service, Durban, South Africa
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Kerusha Govender
- Department of Virology, University of KwaZulu-Natal/National Health Laboratory Service, Durban, South Africa
| | - Reshmi Samuel
- Department of Virology, University of KwaZulu-Natal/National Health Laboratory Service, Durban, South Africa
| | - Nokukhanya Msomi
- Department of Virology, University of KwaZulu-Natal/National Health Laboratory Service, Durban, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa; South African Medical Research Council (SAMRC), CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Tulio de Oliveira
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Department of Global Health, University of Washington, Seattle, United States
| | - Pravi Moodley
- Department of Virology, University of KwaZulu-Natal/National Health Laboratory Service, Durban, South Africa
| | - Raveen Parboosing
- Department of Virology, University of KwaZulu-Natal/National Health Laboratory Service, Durban, South Africa
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Posada-Céspedes S, Van Zyl G, Montazeri H, Kuipers J, Rhee SY, Kouyos R, Günthard HF, Beerenwinkel N. Comparing mutational pathways to lopinavir resistance in HIV-1 subtypes B versus C. PLoS Comput Biol 2021; 17:e1008363. [PMID: 34491984 DOI: 10.1371/journal.pcbi.1008363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 09/17/2021] [Accepted: 08/09/2021] [Indexed: 11/19/2022] Open
Abstract
Although combination antiretroviral therapies seem to be effective at controlling HIV-1 infections regardless of the viral subtype, there is increasing evidence for subtype-specific drug resistance mutations. The order and rates at which resistance mutations accumulate in different subtypes also remain poorly understood. Most of this knowledge is derived from studies of subtype B genotypes, despite not being the most abundant subtype worldwide. Here, we present a methodology for the comparison of mutational networks in different HIV-1 subtypes, based on Hidden Conjunctive Bayesian Networks (H-CBN), a probabilistic model for inferring mutational networks from cross-sectional genotype data. We introduce a Monte Carlo sampling scheme for learning H-CBN models for a larger number of resistance mutations and develop a statistical test to assess differences in the inferred mutational networks between two groups. We apply this method to infer the temporal progression of mutations conferring resistance to the protease inhibitor lopinavir in a large cross-sectional cohort of HIV-1 subtype C genotypes from South Africa, as well as to a data set of subtype B genotypes obtained from the Stanford HIV Drug Resistance Database and the Swiss HIV Cohort Study. We find strong support for different initial mutational events in the protease, namely at residue 46 in subtype B and at residue 82 in subtype C. The inferred mutational networks for subtype B versus C are significantly different sharing only five constraints on the order of accumulating mutations with mutation at residue 54 as the parental event. The results also suggest that mutations can accumulate along various alternative paths within subtypes, as opposed to a unique total temporal ordering. Beyond HIV drug resistance, the statistical methodology is applicable more generally for the comparison of inferred mutational networks between any two groups. There is a disparity in the distribution of infections by HIV-1 subtype in the world. Subtype B is predominant in America, Australia and western and central Europe, and most therapeutic strategies are based on research and clinical studies on this subtype. However, non-B subtypes represent the majority of global HIV-1 infections; e.g., subtype C alone accounts for nearly half of all HIV-1 infections. We present a statistical framework enabling the comparison of patterns of accumulating mutations in different HIV-1 subtypes. Specifically, we compare the temporal ordering of lopinavir resistance mutations in HIV-1 subtypes B versus C. To this end, we combine the Hidden Conjunctive Bayesian Network (H-CBN) model with an approximate inference scheme enabling comparisons of larger networks. We show that the development of resistance to lopinavir differs significantly between subtypes B and C, such that findings based on subtype B sequences can not always be applied to sybtype C. The described methodology is suitable for comparing different subgroups in the context of other evolutionary processes.
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