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Rodríguez-López E, Lopez P, Rodriguez Y, Sanchez R, Acevedo VS, Encarnación J, Tirado G, Ortiz-Sáchez C, Mesplède T, Rivera-Amill V. HIV-1 integrase T218I/S polymorphisms do not reduce HIV-1 integrase inhibitors' phenotypic susceptibility. AIDS Res Hum Retroviruses 2024. [PMID: 39086253 DOI: 10.1089/aid.2023.0128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2024] Open
Abstract
The recently FDA-approved cabotegravir has demonstrated efficacy as an antiretroviral agent for HIV treatment and prevention, becoming an important tool to stop the epidemic in the USA. However, the effectiveness of cabotegravir can be compromised by the presence of specific integrase natural polymorphisms, including T97A, L74M, M50I, S119P, and E157Q, particularly when coupled with the primary drug resistance mutations G140S and Q148H. Cabotegravir's recent approval as a pre-exposure prophylaxis may increase the number of individuals taking cabotegravir, which, at the same time, could increase the number of epidemiological implications. In this context, where resistance mutations, natural polymorphisms, and the lack of drug-susceptibility studies prevail, it becomes imperative to comprehensively investigate concerns related to the use of cabotegravir. We used molecular and cell-based assays to assess the impact of T218I and T218S in the context of major resistance mutations G140S/Q148H on infectivity, integration, and resistance to cabotegravir. Our findings revealed that T218I and T218S, either individually or in combination with G140S/Q148H, did not significantly affect infectivity, integration, or resistance to cabotegravir. Notably, these polymorphisms also exhibited neutrality concerning other widely used integrase inhibitors, namely raltegravir, elvitegravir, and dolutegravir. Thus, our study suggests that the T218I and T218S natural polymorphisms are unlikely to undermine the effectiveness of cabotegravir as a treatment and pre-exposure prophylaxis strategy.
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Affiliation(s)
| | - Pablo Lopez
- Ponce Health Sciences University, Research Centers in Minority Institutions Center for Research Resources, Ponce, Puerto Rico;
| | - Yadira Rodriguez
- Ponce Health Sciences University, Research Centers in Minority Institutions Center for Research Resources, Ponce, Puerto Rico;
| | - Raphael Sanchez
- Ponce Health Sciences University, Research Centers in Minority Institutions Center for Research Resources, Ponce, Puerto Rico;
| | - Van Sergei Acevedo
- Ponce Health Sciences University, School of Medicine, Ponce, Puerto Rico;
| | | | - Girssell Tirado
- Ponce Health Sciences University, Research Centers in Minority Institutions Center for Research Resources, Ponce, Puerto Rico;
| | | | - Thibault Mesplède
- Erasmus University Medical Center Rotterdam Division of Obstetrics and Fetal Medicine, Viroscience, Rotterdam, Zuid-Holland, Netherlands;
| | - Vanessa Rivera-Amill
- Ponce Health Sciences University, Microbiology Division; Research Centers in Minority Institutions Center for Research Resources, Ponce, Puerto Rico;
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2
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Sebastião CS, Abecasis AB, Jandondo D, Sebastião JMK, Vigário J, Comandante F, Pingarilho M, Pocongo B, Cassinela E, Gonçalves F, Gomes P, Giovanetti M, Francisco NM, Sacomboio E, Brito M, Neto de Vasconcelos J, Morais J, Pimentel V. HIV-1 diversity and pre-treatment drug resistance in the era of integrase inhibitor among newly diagnosed ART-naïve adult patients in Luanda, Angola. Sci Rep 2024; 14:15893. [PMID: 38987263 PMCID: PMC11237101 DOI: 10.1038/s41598-024-66905-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 07/05/2024] [Indexed: 07/12/2024] Open
Abstract
The surveillance of drug resistance in the HIV-1 naïve population remains critical to optimizing the effectiveness of antiretroviral therapy (ART), mainly in the era of integrase strand transfer inhibitor (INSTI) regimens. Currently, there is no data regarding resistance to INSTI in Angola since Dolutegravir-DTG was included in the first-line ART regimen. Herein, we investigated the HIV-1 genetic diversity and pretreatment drug resistance (PDR) profile against nucleoside/tide reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTIs), protease inhibitors (PIs), and INSTIs, using a next-generation sequencing (NGS) approach with MinION, established to track and survey DRMs in Angola. This was a cross-sectional study comprising 48 newly HIV-diagnosed patients from Luanda, Angola, screened between March 2022 and May 2023. PR, RT, and IN fragments were sequenced for drug resistance and molecular transmission cluster analysis. A total of 45 out of the 48 plasma samples were successfully sequenced. Of these, 10/45 (22.2%) presented PDR to PIs/NRTIs/NNRTIs. Major mutations for NRTIs (2.2%), NNRTIs (20%), PIs (2.2%), and accessory mutations against INSTIs (13.3%) were detected. No major mutations against INSTIs were detected. M41L (2%) and I85V (2%) mutations were detected for NRTI and PI, respectively. K103N (7%), Y181C (7%), and K101E (7%) mutations were frequently observed in NNRTI. The L74M (9%) accessory mutation was frequently observed in the INSTI class. HIV-1 pure subtypes C (33%), F1 (17%), G (15%), A1 (10%), H (6%), and D (4%), CRF01_AG (4%) were observed, while about 10% were recombinant strains. About 31% of detected HIV-1C sequences were in clusters, suggesting small-scale local transmission chains. No major mutations against integrase inhibitors were detected, supporting the continued use of INSTI in the country. Further studies assessing the HIV-1 epidemiology in the era of INSTI-based ART regimens are needed in Angola.
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Affiliation(s)
- Cruz S Sebastião
- Centro de Investigação em Saúde de Angola (CISA), Caxito, Angola.
- Instituto Nacional de Investigação em Saúde (INIS), Luanda, Angola.
- Instituto de Ciências da Saúde (ICISA), Universidade Agostinho Neto (UAN), Luanda, Angola.
- Global Health and Tropical Medicine, GHTM, Associate Laboratory in Translation and Innovation Towards Global Health, LA-REAL, Instituto de Higiene e Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Rua da Junqueira 100, 1349-008, Lisboa, Portugal.
| | - Ana B Abecasis
- Global Health and Tropical Medicine, GHTM, Associate Laboratory in Translation and Innovation Towards Global Health, LA-REAL, Instituto de Higiene e Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Rua da Junqueira 100, 1349-008, Lisboa, Portugal
| | | | | | - João Vigário
- Instituto Nacional de Sangue (INS), Ministério da Saúde, Luanda, Angola
| | | | - Marta Pingarilho
- Global Health and Tropical Medicine, GHTM, Associate Laboratory in Translation and Innovation Towards Global Health, LA-REAL, Instituto de Higiene e Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Rua da Junqueira 100, 1349-008, Lisboa, Portugal
| | - Bárbara Pocongo
- Instituto Nacional de Luta contra SIDA (INLS), Ministério da Saúde, Luanda, Angola
| | - Edson Cassinela
- Centro Nacional de Investigação Científica (CNIC), Luanda, Angola
| | - Fátima Gonçalves
- Laboratório de Biologia Molecular (LMCBM, SPC, CHLO-HEM), 1349-019, Lisbon, Portugal
| | - Perpétua Gomes
- Laboratório de Biologia Molecular (LMCBM, SPC, CHLO-HEM), 1349-019, Lisbon, Portugal
- Egas Moniz Center for Interdisciplinary Research (CiiEM), Egas Moniz School of Health & Sicence, Caparica, Almada, Portugal
| | - Marta Giovanetti
- Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, Rome, Italy
| | | | - Euclides Sacomboio
- Instituto de Ciências da Saúde (ICISA), Universidade Agostinho Neto (UAN), Luanda, Angola
| | - Miguel Brito
- Centro de Investigação em Saúde de Angola (CISA), Caxito, Angola
- H&TRC-Health & Technology Research Center, ESTeSL-Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, Lisbon, Portugal
| | | | - Joana Morais
- Instituto Nacional de Investigação em Saúde (INIS), Luanda, Angola
| | - Victor Pimentel
- Global Health and Tropical Medicine, GHTM, Associate Laboratory in Translation and Innovation Towards Global Health, LA-REAL, Instituto de Higiene e Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Rua da Junqueira 100, 1349-008, Lisboa, Portugal.
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3
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Zhang RH, Chen GQ, Wang W, Wang YC, Zhang WL, Chen T, Xiong QQ, Zhao YL, Liao SG, Li YJ, Yan GY, Zhou M. Design, synthesis and biological evaluation of indole-2-carboxylic acid derivatives as novel HIV-1 integrase strand transfer inhibitors. RSC Adv 2024; 14:9020-9031. [PMID: 38500630 PMCID: PMC10945512 DOI: 10.1039/d3ra08320a] [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: 12/06/2023] [Accepted: 03/08/2024] [Indexed: 03/20/2024] Open
Abstract
Integrase plays an important role in the life cycle of HIV-1, and integrase strand transfer inhibitors (INSTIs) can effectively impair the viral replication. However, drug resistance mutations have been confirmed to decrease the efficacy of INSTI during the antiviral therapy. Herein, indole-2-carboxylic acid (1) was found to inhibit the strand transfer of integrase, and the indole nucleus of compound 1 was observed to chelate with two Mg2+ ions within the active site of integrase. Through optimization of compound 1, a series of indole-2-carboxylic acid derivatives were designed and synthesized, and compound 17a was proved to markedly inhibit the effect of integrase, with IC50 value of 3.11 μM. Binding mode analysis of 17a demonstrated that the introduced C6 halogenated benzene ring could effectively bind with the viral DNA (dC20) through π-π stacking interaction. These results indicated that indole-2-carboxylic acid is a promising scaffold for the development of integrase inhibitors.
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Affiliation(s)
- Rong-Hong Zhang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Medical University Guiyang 550004 P. R. China
- Center for Tissue Engineering and Stem Cell Research, Key Laboratory of Regenerative Medicine of Guizhou Province, School of Basic Medical Sciences, Guizhou Medical University Guiyang 550004 P. R. China
| | - Guo-Qi Chen
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Medical University Guiyang 550004 P. R. China
- School of Pharmacy, Guizhou Medical University Guian New District Guizhou 550025 P. R. China
| | - Weilin Wang
- State Key Laboratory of Biotherapy, Collaborative Innovation of Biotherapy and Cancer Center, West China Hospital of Sichuan University Chengdu 610041 Sichuan China
| | - Yu-Chan Wang
- School of Pharmacy, Guizhou Medical University Guian New District Guizhou 550025 P. R. China
| | - Wen-Li Zhang
- School of Pharmacy, Guizhou Medical University Guian New District Guizhou 550025 P. R. China
| | - Ting Chen
- School of Pharmacy, Guizhou Medical University Guian New District Guizhou 550025 P. R. China
| | - Qian-Qian Xiong
- School of Pharmacy, Guizhou Medical University Guian New District Guizhou 550025 P. R. China
| | - Yong-Long Zhao
- School of Pharmacy, Guizhou Medical University Guian New District Guizhou 550025 P. R. China
| | - Shang-Gao Liao
- School of Pharmacy, Guizhou Medical University Guian New District Guizhou 550025 P. R. China
| | - Yong-Jun Li
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Medical University Guiyang 550004 P. R. China
| | - Guo-Yi Yan
- School of Pharmacy, Xinxiang University Xinxiang 453000 P. R. China
| | - Meng Zhou
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Medical University Guiyang 550004 P. R. China
- School of Pharmacy, Guizhou Medical University Guian New District Guizhou 550025 P. R. China
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4
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Mahajan PS, Smith SJ, Li M, Craigie R, Hughes SH, Zhao XZ, Burke TR. N-Substituted Bicyclic Carbamoyl Pyridones: Integrase Strand Transfer Inhibitors that Potently Inhibit Drug-Resistant HIV-1 Integrase Mutants. ACS Infect Dis 2024; 10:917-927. [PMID: 38346249 PMCID: PMC10928719 DOI: 10.1021/acsinfecdis.3c00525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 01/16/2024] [Accepted: 01/23/2024] [Indexed: 03/09/2024]
Abstract
HIV-1 integrase (IN) is an important molecular target for the development of anti-AIDS drugs. A recently FDA-approved second-generation integrase strand transfer inhibitor (INSTI) cabotegravir (CAB, 2021) is being marketed for use in long-duration antiviral formulations. However, missed doses during extended therapy can potentially result in persistent low levels of CAB that could select for resistant mutant forms of IN, leading to virological failure. We report a series of N-substituted bicyclic carbamoyl pyridones (BiCAPs) that are simplified analogs of CAB. Several of these potently inhibit wild-type HIV-1 in single-round infection assays in cultured cells and retain high inhibitory potencies against a panel of viral constructs carrying resistant mutant forms of IN. Our lead compound, 7c, proved to be more potent than CAB against the therapeutically important resistant double mutants E138K/Q148K (>12-fold relative to CAB) and G140S/Q148R (>36-fold relative to CAB). A significant number of the BiCAPs also potently inhibit the drug-resistant IN mutant R263K, which has proven to be problematic for the FDA-approved second-generation INSTIs.
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Affiliation(s)
- Pankaj S Mahajan
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Steven J Smith
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Min Li
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Robert Craigie
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Stephen H Hughes
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Xue Zhi Zhao
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Terrence R Burke
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
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5
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Wang YC, Zhang WL, Zhang RH, Liu CH, Zhao YL, Yan GY, Liao SG, Li YJ, Zhou M. The Discovery of Indole-2-carboxylic Acid Derivatives as Novel HIV-1 Integrase Strand Transfer Inhibitors. Molecules 2023; 28:8020. [PMID: 38138510 PMCID: PMC10745497 DOI: 10.3390/molecules28248020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 11/26/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
As an important antiviral target, HIV-1 integrase plays a key role in the viral life cycle, and five integrase strand transfer inhibitors (INSTIs) have been approved for the treatment of HIV-1 infections so far. However, similar to other clinically used antiviral drugs, resistance-causing mutations have appeared, which have impaired the efficacy of INSTIs. In the current study, to identify novel integrase inhibitors, a set of molecular docking-based virtual screenings were performed, and indole-2-carboxylic acid was developed as a potent INSTI scaffold. Indole-2-carboxylic acid derivative 3 was proved to effectively inhibit the strand transfer of HIV-1 integrase, and binding conformation analysis showed that the indole core and C2 carboxyl group obviously chelated the two Mg2+ ions within the active site of integrase. Further structural optimizations on compound 3 provided the derivative 20a, which markedly increased the integrase inhibitory effect, with an IC50 value of 0.13 μM. Binding mode analysis revealed that the introduction of a long branch on C3 of the indole core improved the interaction with the hydrophobic cavity near the active site of integrase, indicating that indole-2-carboxylic acid is a promising scaffold for the development of integrase inhibitors.
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Affiliation(s)
- Yu-Chan Wang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Medical University, Guiyang 550004, China; (Y.-C.W.); (W.-L.Z.); (R.-H.Z.); (Y.-J.L.)
- Center for Tissue Engineering and Stem Cell Research, Key Laboratory of Regenerative Medicine of Guizhou Province, School of Basic Medical Sciences, Guizhou Medical University, Guiyang 550004, China
- School of Pharmacy, Guizhou Medical University, Guian New District, Guiyang 550025, China; (Y.-L.Z.); (S.-G.L.)
| | - Wen-Li Zhang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Medical University, Guiyang 550004, China; (Y.-C.W.); (W.-L.Z.); (R.-H.Z.); (Y.-J.L.)
- School of Pharmacy, Guizhou Medical University, Guian New District, Guiyang 550025, China; (Y.-L.Z.); (S.-G.L.)
| | - Rong-Hong Zhang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Medical University, Guiyang 550004, China; (Y.-C.W.); (W.-L.Z.); (R.-H.Z.); (Y.-J.L.)
- Center for Tissue Engineering and Stem Cell Research, Key Laboratory of Regenerative Medicine of Guizhou Province, School of Basic Medical Sciences, Guizhou Medical University, Guiyang 550004, China
| | - Chun-Hua Liu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Medical University, Guiyang 550004, China; (Y.-C.W.); (W.-L.Z.); (R.-H.Z.); (Y.-J.L.)
| | - Yong-Long Zhao
- School of Pharmacy, Guizhou Medical University, Guian New District, Guiyang 550025, China; (Y.-L.Z.); (S.-G.L.)
| | - Guo-Yi Yan
- School of Pharmacy, Xinxiang University, Xinxiang 453000, China;
| | - Shang-Gao Liao
- School of Pharmacy, Guizhou Medical University, Guian New District, Guiyang 550025, China; (Y.-L.Z.); (S.-G.L.)
| | - Yong-Jun Li
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Medical University, Guiyang 550004, China; (Y.-C.W.); (W.-L.Z.); (R.-H.Z.); (Y.-J.L.)
| | - Meng Zhou
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Medical University, Guiyang 550004, China; (Y.-C.W.); (W.-L.Z.); (R.-H.Z.); (Y.-J.L.)
- School of Pharmacy, Guizhou Medical University, Guian New District, Guiyang 550025, China; (Y.-L.Z.); (S.-G.L.)
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6
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Rivera CG, Zeuli JD, Smith BL, Johnson TM, Bhatia R, Otto AO, Temesgen Z. HIV Pre-Exposure Prophylaxis: New and Upcoming Drugs to Address the HIV Epidemic. Drugs 2023; 83:1677-1698. [PMID: 38079092 DOI: 10.1007/s40265-023-01963-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2023] [Indexed: 12/20/2023]
Abstract
Human immunodeficiency virus (HIV) pre-exposure prophylaxis (PrEP) provides a critical intervention toward ending the HIV epidemic and protecting people with reasons to utilize PrEP. PrEP options continue to expand as new administration modalities offer the potential to tailor PrEP use for individual success. We have provided the evidence for new and emerging antiretroviral agents for PrEP (cabotegravir, lenacapavir, dapivirine, and broadly neutralizing antibodies), divided into pharmacology, animal model, and human data, accompanied by a summary and suggested place in therapy. Cabotegravir is a US Food and Drug Administration (FDA)-approved intramuscular injection given every 2 months with a strong body of evidence demonstrating efficacy for HIV PrEP, lenacapavir administered subcutaneously every 6 months is currently under investigation for HIV PrEP, dapivirine vaginal ring is an available PrEP option for women in certain areas of Africa, and broadly neutralizing monoclonal antibodies have been challenged in demonstrating efficacy in phase 1-2 study for HIV PrEP to date. Clinical literature for individual agents is discussed with data from major studies summarized in tables. This review provides a detailed overview of recently available and premier candidate PrEP drugs.
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Affiliation(s)
- Christina G Rivera
- Section of Infectious Diseases, HIV Program, Mayo Clinic, Rochester, MN, USA
- Department of Pharmacy, Mayo Clinic, Rochester, MN, USA
| | - John D Zeuli
- Section of Infectious Diseases, HIV Program, Mayo Clinic, Rochester, MN, USA
- Department of Pharmacy, Mayo Clinic, Rochester, MN, USA
| | - Bradley L Smith
- Department of Pharmacy, Grady Health System, Atlanta, GA, USA
| | - Tanner M Johnson
- Section of Infectious Diseases, HIV Program, Mayo Clinic, Rochester, MN, USA
- Department of Pharmacy, Mayo Clinic, Rochester, MN, USA
| | - Ramona Bhatia
- Division of Infectious Diseases, Department of Medicine, University of Illinois at Chicago, Chicago, USA
| | - Ashley O Otto
- Department of Pharmacy, Mayo Clinic, Rochester, MN, USA
| | - Zelalem Temesgen
- Section of Infectious Diseases, HIV Program, Mayo Clinic, Rochester, MN, USA.
- Section of Infectious Diseases, Mayo Clinic and Foundation, 200 First St. SW, Rochester, MN, 55905, USA.
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7
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Li M, Oliveira Passos D, Shan Z, Smith SJ, Sun Q, Biswas A, Choudhuri I, Strutzenberg TS, Haldane A, Deng N, Li Z, Zhao XZ, Briganti L, Kvaratskhelia M, Burke TR, Levy RM, Hughes SH, Craigie R, Lyumkis D. Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants. SCIENCE ADVANCES 2023; 9:eadg5953. [PMID: 37478179 DOI: 10.1126/sciadv.adg5953] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 06/16/2023] [Indexed: 07/23/2023]
Abstract
HIV-1 infection depends on the integration of viral DNA into host chromatin. Integration is mediated by the viral enzyme integrase and is blocked by integrase strand transfer inhibitors (INSTIs), first-line antiretroviral therapeutics widely used in the clinic. Resistance to even the best INSTIs is a problem, and the mechanisms of resistance are poorly understood. Here, we analyze combinations of the mutations E138K, G140A/S, and Q148H/K/R, which confer resistance to INSTIs. The investigational drug 4d more effectively inhibited the mutants compared with the approved drug Dolutegravir (DTG). We present 11 new cryo-EM structures of drug-resistant HIV-1 intasomes bound to DTG or 4d, with better than 3-Å resolution. These structures, complemented with free energy simulations, virology, and enzymology, explain the mechanisms of DTG resistance involving E138K + G140A/S + Q148H/K/R and show why 4d maintains potency better than DTG. These data establish a foundation for further development of INSTIs that potently inhibit resistant forms in integrase.
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Affiliation(s)
- Min Li
- National Institute of Diabetes and Digestive Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | | | - Zelin Shan
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Steven J Smith
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Qinfang Sun
- Center for Biophysics and Computational Biology, and Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
| | - Avik Biswas
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Center for Biophysics and Computational Biology and Department of Physics, Temple University, Philadelphia, PA 19122, USA
| | - Indrani Choudhuri
- Center for Biophysics and Computational Biology, and Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
| | | | - Allan Haldane
- Center for Biophysics and Computational Biology and Department of Physics, Temple University, Philadelphia, PA 19122, USA
| | - Nanjie Deng
- Department of Chemistry and Physical Sciences, Pace University, New York, NY, 10038, USA
| | - Zhaoyang Li
- National Institute of Diabetes and Digestive Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Xue Zhi Zhao
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Lorenzo Briganti
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Terrence R Burke
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Ronald M Levy
- Center for Biophysics and Computational Biology and Department of Physics, Temple University, Philadelphia, PA 19122, USA
| | - Stephen H Hughes
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Robert Craigie
- National Institute of Diabetes and Digestive Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Dmitry Lyumkis
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Graduate School of Biological Sciences, Section of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
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8
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Singer MR, Dinh T, Levintov L, Annamalai AS, Rey JS, Briganti L, Cook NJ, Pye VE, Taylor IA, Kim K, Engelman AN, Kim B, Perilla JR, Kvaratskhelia M, Cherepanov P. The Drug-Induced Interface That Drives HIV-1 Integrase Hypermultimerization and Loss of Function. mBio 2023; 14:e0356022. [PMID: 36744954 PMCID: PMC9973045 DOI: 10.1128/mbio.03560-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 01/03/2023] [Indexed: 02/07/2023] Open
Abstract
Allosteric HIV-1 integrase (IN) inhibitors (ALLINIs) are an emerging class of small molecules that disrupt viral maturation by inducing the aberrant multimerization of IN. Here, we present cocrystal structures of HIV-1 IN with two potent ALLINIs, namely, BI-D and the drug candidate Pirmitegravir. The structures reveal atomistic details of the ALLINI-induced interface between the HIV-1 IN catalytic core and carboxyl-terminal domains (CCD and CTD). Projecting from their principal binding pocket on the IN CCD dimer, the compounds act as molecular glue by engaging a triad of invariant HIV-1 IN CTD residues, namely, Tyr226, Trp235, and Lys266, to nucleate the CTD-CCD interaction. The drug-induced interface involves the CTD SH3-like fold and extends to the beginning of the IN carboxyl-terminal tail region. We show that mutations of HIV-1 IN CTD residues that participate in the interface with the CCD greatly reduce the IN-aggregation properties of Pirmitegravir. Our results explain the mechanism of the ALLINI-induced condensation of HIV-1 IN and provide a reliable template for the rational development of this series of antiretrovirals through the optimization of their key contacts with the viral target. IMPORTANCE Despite the remarkable success of combination antiretroviral therapy, HIV-1 remains among the major causes of human suffering and loss of life in poor and developing nations. To prevail in this drawn-out battle with the pandemic, it is essential to continue developing advanced antiviral agents to fight drug resistant HIV-1 variants. Allosteric integrase inhibitors (ALLINIs) are an emerging class of HIV-1 antagonists that are orthogonal to the current antiretroviral drugs. These small molecules act as highly specific molecular glue, which triggers the aggregation of HIV-1 integrase. In this work, we present high-resolution crystal structures that reveal the crucial interactions made by two potent ALLINIs, namely, BI-D and Pirmitegravir, with HIV-1 integrase. Our results explain the mechanism of drug action and will inform the development of this promising class of small molecules for future use in antiretroviral regimens.
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Affiliation(s)
- Matthew R. Singer
- Chromatin Structure & Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Tung Dinh
- Division of Infectious Diseases, School of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Lev Levintov
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
| | - Arun S. Annamalai
- Division of Infectious Diseases, School of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Juan S. Rey
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
| | - Lorenzo Briganti
- Division of Infectious Diseases, School of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Nicola J. Cook
- Chromatin Structure & Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Valerie E. Pye
- Chromatin Structure & Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Ian A. Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, London, United Kingdom
| | | | - Alan N. Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Baek Kim
- Center for Drug Discovery, Children’s Healthcare of Atlanta, Atlanta, Georgia, USA
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Juan R. Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, School of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Peter Cherepanov
- Chromatin Structure & Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
- Department of Infectious Disease, St-Mary's Campus, Imperial College London, London, United Kingdom
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9
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Charpentier C, Le Hingrat Q, Ferré VM, Damond F, Descamps D. Future of Antiretroviral Drugs and Evolution of HIV-1 Drug Resistance. Viruses 2023; 15:v15020540. [PMID: 36851754 PMCID: PMC9967014 DOI: 10.3390/v15020540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/12/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023] Open
Abstract
Highly active antiretroviral (ARV) therapy has been used for many years, but the use in low- and middle-income countries of antiretroviral drugs with low genetic barrier to resistance, combined with limited availability of viral load testing, has led to higher rates of acquired drug resistance, sustaining the rate of transmitted drug resistance. Here, we describe the evolution of ARV drugs with the ongoing development of injectable long-acting forms and the requirements regarding all new ARV drugs (i.e., no transmitted drug resistance, no cross-resistance and high genetic barrier to resistance). Then, we report the evolution of both transmitted and acquired resistance regarding new ARV drugs. The WHO has set very ambitious but motivating goals for HIV testing, treatment and viral suppression, aiming to achieve rates of 95% for all three by 2025. Reaching these goals requires a wide implementation and use of close virological monitoring in LMICs.
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10
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Zhu Y, Huang Y, Zheng C, Tang J, Zeng G, Xie W, Wang H, Zhang L, Liu S, Zhang Y, Tan W, Tan J, Jiang L, He Y, Xu L, Yang Z, Zhao J. Primary resistance to integrase inhibitors in Shenzhen. J Antimicrob Chemother 2023; 78:546-549. [PMID: 36585770 DOI: 10.1093/jac/dkac442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 12/12/2022] [Indexed: 01/01/2023] Open
Abstract
OBJECTIVES In recent years, integrase strand transfer inhibitor (INSTI)-containing regimens have been increasingly adopted in treatment for HIV/AIDS and promoted as non-occupational post-exposure prophylaxis in China. This study aims to describe the prevalence of resistance to integrase and drug resistance mutations (DRMs) among ART-naive patients in Shenzhen, China. METHODS Serum samples and demographic information were collected from newly reported ART-naive patients in Shenzhen in 2020. The study sequenced the coding sequence of the HIV-1 integrase gene and determined the DRMs.. RESULTS In this study, 1682 newly reported cases were included and 1071 of them were successfully sequenced finally. The prevalence of primary drug resistance was 1.77%, with 19 samples showing varying degrees of resistance to INSTIs. The study detected six major DRMs in 16 individuals and eight accessory DRMs in 24 individuals. The prevalence of transmitted drug resistance (TDR) mutations was 1.21%, with five transmitted mutations detected in 13 individuals. The prevalence of drug resistance to raltegravir and elvitegravir was statistically higher than to bictegravir, cabotegravir and dolutegravir. CONCLUSIONS The prevalence of INSTI resistance in Shenzhen in 2020 was relatively high. Continued surveillance for resistance to INSTIs is recommended and treatment regimens should be adopted based on the pattern of resistance to INSTIs. Dolutegravir or bictegravir is first recommended when considering INSTIs as treatment regimens.
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Affiliation(s)
- Yue Zhu
- School of Public Health, Shantou University, Shantou, China.,Department of HIV/AIDS Control and Prevention, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Yuanmei Huang
- Department of HIV/AIDS Control and Prevention, Shenzhen Center for Disease Control and Prevention, Shenzhen, China.,School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Chenli Zheng
- Department of HIV/AIDS Control and Prevention, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Jie Tang
- Department of HIV/AIDS Control and Prevention, Shenzhen Center for Disease Control and Prevention, Shenzhen, China.,School of Public Health, University of South China, Hengyang, China
| | - Guang Zeng
- Department of HIV/AIDS Control and Prevention, Shenzhen Center for Disease Control and Prevention, Shenzhen, China.,School of Public Health, University of South China, Hengyang, China
| | - Wei Xie
- Department of HIV/AIDS Control and Prevention, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Hui Wang
- Department of Infectious Diseases, The Third People's Hospital of Shenzhen, Shenzhen, China
| | - Lukun Zhang
- Department of Infectious Diseases, The Third People's Hospital of Shenzhen, Shenzhen, China
| | - Shaochu Liu
- Department of HIV/AIDS Control and Prevention, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Yan Zhang
- Department of HIV/AIDS Control and Prevention, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Wei Tan
- Department of HIV/AIDS Control and Prevention, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Jingguang Tan
- Department of HIV/AIDS Control and Prevention, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Lijuan Jiang
- Department of HIV/AIDS Control and Prevention, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Yun He
- Department of Infectious Diseases, The Third People's Hospital of Shenzhen, Shenzhen, China
| | - Liumei Xu
- Department of Infectious Diseases, The Third People's Hospital of Shenzhen, Shenzhen, China
| | - Zhengrong Yang
- Department of HIV/AIDS Control and Prevention, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Jin Zhao
- School of Public Health, Shantou University, Shantou, China.,Department of HIV/AIDS Control and Prevention, Shenzhen Center for Disease Control and Prevention, Shenzhen, China.,School of Public Health, Shanxi Medical University, Taiyuan, China
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11
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Ndashimye E, Reyes PS, Arts EJ. New antiretroviral inhibitors and HIV-1 drug resistance: more focus on 90% HIV-1 isolates? FEMS Microbiol Rev 2023; 47:fuac040. [PMID: 36130204 PMCID: PMC9841967 DOI: 10.1093/femsre/fuac040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/13/2022] [Accepted: 09/18/2022] [Indexed: 01/21/2023] Open
Abstract
Combined HIV antiretroviral therapy (cART) has been effective except if drug resistance emerges. As cART has been rolled out in low-income countries, drug resistance has emerged at higher rates than observed in high income countries due to factors including initial use of these less tolerated cART regimens, intermittent disruptions in drug supply, and insufficient treatment monitoring. These socioeconomic factors impacting drug resistance are compounded by viral mechanistic differences by divergent HIV-1 non-B subtypes compared to HIV-1 subtype B that largely infects the high-income countries (just 10% of 37 million infected). This review compares the inhibition and resistance of diverse HIV-1 subtypes and strains to the various approved drugs as well as novel inhibitors in clinical trials. Initial sequence variations and differences in replicative fitness between HIV-1 subtypes pushes strains through different fitness landscapes to escape from drug selective pressure. The discussions here provide insight to patient care givers and policy makers on how best to use currently approved ART options and reduce the emergence of drug resistance in ∼33 million individuals infected with HIV-1 subtype A, C, D, G, and recombinants forms. Unfortunately, over 98% of the literature on cART resistance relates to HIV-1 subtype B.
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Affiliation(s)
- Emmanuel Ndashimye
- Department of Microbiology and Immunology, Western University Schulich School of Medicine & Dentistry, Western University, N6A 3K7, London, Ontario, Canada
- Joint Clinical Research Centre, -Center for AIDS Research Laboratories, 256, Kampala, Uganda
| | - Paul S Reyes
- Department of Microbiology and Immunology, Western University Schulich School of Medicine & Dentistry, Western University, N6A 3K7, London, Ontario, Canada
| | - Eric J Arts
- Department of Microbiology and Immunology, Western University Schulich School of Medicine & Dentistry, Western University, N6A 3K7, London, Ontario, Canada
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12
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Johnson MM, Jones CE, Clark DN. The Effect of Treatment-Associated Mutations on HIV Replication and Transmission Cycles. Viruses 2022; 15:107. [PMID: 36680147 PMCID: PMC9861436 DOI: 10.3390/v15010107] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/21/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022] Open
Abstract
HIV/AIDS mortality has been decreasing over the last decade. While promising, this decrease correlated directly with increased use of antiretroviral drugs. As a natural consequence of its high mutation rate, treatments provide selection pressure that promotes the natural selection of escape mutants. Individuals may acquire drug-naive strains, or those that have already mutated due to treatment. Even within a host, mutation affects HIV tropism, where initial infection begins with R5-tropic virus, but the clinical transition to AIDS correlates with mutations that lead to an X4-tropic switch. Furthermore, the high mutation rate of HIV has spelled failure for all attempts at an effective vaccine. Pre-exposure drugs are currently the most effective drug-based preventatives, but their effectiveness is also threatened by viral mutation. From attachment and entry to assembly and release, the steps in the replication cycle are also discussed to describe the drug mechanisms and mutations that arise due to those drugs. Revealing the patterns of HIV-1 mutations, their effects, and the coordinated attempt to understand and control them will lead to effective use of current preventative measures and treatment options, as well as the development of new ones.
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Affiliation(s)
- Madison M. Johnson
- Department of Microbiology, Weber State University, Ogden, UT 84408, USA
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13
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Subramanian R, Wang J, Murray B, Custodio J, Hao J, Lazerwith S, MacLennan Staiger K, Mwangi J, Sun H, Tang J, Wang K, Rhodes G, Wijaya S, Zhang H, Smith BJ. Human pharmacokinetics prediction with an in vitro- in vivo correction factor approach and in vitro drug-drug interaction profile of bictegravir, a potent integrase-strand transfer inhibitor component in approved biktarvy ® for the treatment of HIV-1 infection. Xenobiotica 2022; 52:1020-1030. [PMID: 36701274 DOI: 10.1080/00498254.2023.2169207] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Bictegravir (BIC) is a potent small-molecule integrase strand-transfer inhibitor (INSTI) and a component of Biktarvy®, a single-tablet combination regimen that is currently approved for the treatment of human immunodeficiency virus type 1 (HIV-1) infection. The in vitro properties, pharmacokinetics (PK), and drug-drug interaction (DDI) profile of BIC were characterised in vitro and in vivo.BIC is a weakly acidic, ionisable, lipophilic, highly plasma protein-bound BCS class 2 molecule, which makes it difficult to predict human PK using standard methods. Its systemic plasma clearance is low, and the volume of distribution is approximately the volume of extracellular water in nonclinical species. BIC metabolism is predominantly mediated by cytochrome P450 enzyme (CYP) 3A and UDP-glucuronosyltransferase 1A1. BIC shows a low potential to perpetrate clinically meaningful DDIs via known drug metabolising enzymes or transporters.The human PK of BIC was predicted using a combination of bioavailability and volume of distribution scaled from nonclinical species and a modified in vitro-in vivo correlation (IVIVC) correction for clearance. Phase 1 studies in healthy subjects largely bore out the prediction and supported the methods used. The approach presented herein could be useful for other drug molecules where standard projections are not sufficiently accurate. .
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Affiliation(s)
| | | | | | | | - Jia Hao
- Gilead Sciences, Inc, Foster City, CA, USA
| | | | | | | | | | | | - Kelly Wang
- Gilead Sciences, Inc, Foster City, CA, USA
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14
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Rhee SY, Parkin N, Harrigan PR, Holmes S, Shafer RW. Genotypic correlates of resistance to the HIV-1 strand transfer integrase inhibitor cabotegravir. Antiviral Res 2022; 208:105427. [PMID: 36191692 PMCID: PMC11015861 DOI: 10.1016/j.antiviral.2022.105427] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/22/2022] [Accepted: 09/25/2022] [Indexed: 11/15/2022]
Abstract
Cabotegravir (CAB) is an integrase strand transfer inhibitor (INSTI) formulated as a long-acting injectable drug approved for pre-exposure prophylaxis and use with a long acting rilpivirine formulation for therapy in patients with virological suppression. However, there has been no comprehensive review of the genetic mechanisms of CAB resistance. Studies reporting the selection of drug resistance mutations (DRMs) by CAB and the results of in vitro CAB susceptibility testing were reviewed. The impact of integrase mutations on CAB susceptibility was assessed using regularized regression analysis. The most commonly selected mutations in the 24 persons developing virological failure while receiving CAB included Q148R (n = 15), N155H (n = 7), and E138K (n = 5). T97A, G118R, G140 A/R/S, and R263K each developed in 1-2 persons. With the exception of T97A, G118R, and G140 A/R, these DRMs were also selected in vitro while G140R was selected in the SIV macaque model. Although these DRMs are similar to those occurring in persons receiving the related INSTI dolutegravir, Q148R was more likely to occur with CAB while G118R and R263K were more likely to occur with dolutegravir. Regularized regression analysis identified 14 DRMs significantly associated with reduced CAB susceptibility including six primary DRMs which reduced susceptibility on their own including G118R, Q148 H/K/R, N155H, and R263K, and eight accessory DRMs including M50I, L74 F/M, T97A, E138K, and G140 A/C/S. Isolates with Q148 H/K/R in combination with L74M, E138 A/K, G140 A/S, and N155H often had >10-fold reduced CAB susceptibility. M50I, L74M, and T97A are polymorphic mutations that alone did not appear to increase the risk of virological failure in persons receiving a CAB-containing regimen. Careful patient screening is required to prevent CAB from being used during active virus replication. Close virological monitoring is required to minimize CAB exposure to active replication to prevent the emergence of DRMs associated with cross-resistance to other INSTIs.
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Affiliation(s)
- Soo-Yon Rhee
- Division of Infectious Diseases, Department of Medicine, Stanford, CA, USA.
| | - Neil Parkin
- Data First Consulting Inc., Sebastopol, CA, USA
| | - P Richard Harrigan
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | | | - Robert W Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford, CA, USA
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15
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Shema Mugisha C, Dinh T, Kumar A, Tenneti K, Eschbach JE, Davis K, Gifford R, Kvaratskhelia M, Kutluay SB. Emergence of Compensatory Mutations Reveals the Importance of Electrostatic Interactions between HIV-1 Integrase and Genomic RNA. mBio 2022; 13:e0043122. [PMID: 35975921 PMCID: PMC9601147 DOI: 10.1128/mbio.00431-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/27/2022] [Indexed: 01/11/2023] Open
Abstract
HIV-1 integrase (IN) has a noncatalytic function in virion maturation through its binding to the viral RNA genome (gRNA). Class II IN substitutions inhibit IN-gRNA binding and result in the formation of virions with aberrant morphologies marked by mislocalization of the gRNA between the capsid lattice and the lipid envelope. These viruses are noninfectious due to a block at an early reverse transcription stage in target cells. HIV-1 IN utilizes basic residues within its C-terminal domain (CTD) to bind to the gRNA; however, the molecular nature of how these residues mediate gRNA binding and whether other regions of IN are involved remain unknown. To address this, we have isolated compensatory substitutions in the background of a class II IN mutant virus bearing R269A/K273A substitutions within the IN-CTD. We found that the nearby D256N and D270N compensatory substitutions restored the ability of IN to bind gRNA and led to the formation of mature infectious virions. Reinstating the local positive charge of the IN-CTD through individual D256R, D256K, D278R, and D279R substitutions was sufficient to specifically restore IN-gRNA binding and reverse transcription for the IN R269A/K273A as well as the IN R262A/R263A class II mutants. Structural modeling suggested that compensatory substitutions in the D256 residue created an additional interaction interface for gRNA binding, whereas other substitutions acted locally within the unstructured C-terminal tail of IN. Taken together, our findings highlight the essential role of CTD in gRNA binding and reveal the importance of pliable electrostatic interactions between the IN-CTD and the gRNA. IMPORTANCE In addition to its catalytic function, HIV-1 integrase (IN) binds to the viral RNA genome (gRNA) through positively charged residues (i.e., R262, R263, R269, K273) within its C-terminal domain (CTD) and regulates proper virion maturation. Mutation of these residues results in the formation of morphologically aberrant viruses blocked at an early reverse transcription stage in cells. Here we show that compensatory substitutions in nearby negatively charged aspartic acid residues (i.e., D256N, D270N) restore the ability of IN to bind gRNA for these mutant viruses and result in the formation of accurately matured infectious virions. Similarly, individual charge reversal substitutions at D256 as well as other nearby positions (i.e., D278, D279) are all sufficient to enable the respective IN mutants to bind gRNA, and subsequently restore reverse transcription and virion infectivity. Taken together, our findings reveal the importance of highly pliable electrostatic interactions in IN-gRNA binding.
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Affiliation(s)
- Christian Shema Mugisha
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Tung Dinh
- Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Abhishek Kumar
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Kasyap Tenneti
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Jenna E. Eschbach
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Keanu Davis
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Robert Gifford
- MRC-University of Glasgow Centre for Virus Research, Bearsden, Glasgow, United Kingdom
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Sebla B. Kutluay
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA
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16
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A clinical review of HIV integrase strand transfer inhibitors (INSTIs) for the prevention and treatment of HIV-1 infection. Retrovirology 2022; 19:22. [PMID: 36273165 PMCID: PMC9588231 DOI: 10.1186/s12977-022-00608-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/26/2022] [Indexed: 12/13/2022] Open
Abstract
Integrase strand transfer inhibitors (INSTIs) have improved the treatment of human immunodeficiency virus (HIV). There are currently four approved for use in treatment-naïve individuals living with HIV; these include first generation raltegravir, elvitegravir, and second generation dolutegravir and bictegravir. The most recent INSTI, cabotegravir, is approved for (1) treatment of HIV infection in adults to replace current antiretroviral therapy in individuals who maintain virologic suppression on a stable antiretroviral regimen without history of treatment failure and no known resistance to its components and (2) pre-exposure prophylaxis in individuals at risk of acquiring HIV-1 infection. Cabotegravir can be administered intramuscularly as a monthly or bi-monthly injection depending on the indication. This long-acting combination has been associated with treatment satisfaction in clinical studies and may be helpful for individuals who have difficulty taking daily oral medications. Worldwide, second generation INSTIs are preferred for treatment-naïve individuals. Advantages of these INSTIs include their high genetic barrier to resistance, limited drug-drug interactions, excellent rates of virologic suppression, and favorable tolerability. Few INSTI resistance-associated mutations have been reported in clinical trials involving dolutegravir, bictegravir and cabotegravir. Other advantages of specific INSTIs include their use in various populations such as infants and children, acute HIV infection, and individuals of childbearing potential. The most common adverse events observed in clinical studies involving INSTIs included diarrhea, nausea, insomnia, fatigue, and headache, with very low rates of treatment discontinuation versus comparator groups. The long-term clinical implications of weight gain associated with second generation INSTIs dolutegravir and bictegravir warrants further study. This review summarizes key clinical considerations of INSTIs in terms of clinical pharmacology, drug-drug interactions, resistance, and provides perspective on clinical decision-making. Additionally, we summarize major clinical trials evaluating the efficacy and safety of INSTIs in treatment-naïve patients living with HIV as well as individuals at risk of acquiring HIV infection.
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17
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Parikh UM, Koss CA, Mellors JW. Long-Acting Injectable Cabotegravir for HIV Prevention: What Do We Know and Need to Know about the Risks and Consequences of Cabotegravir Resistance? Curr HIV/AIDS Rep 2022; 19:384-393. [PMID: 36112336 PMCID: PMC9508028 DOI: 10.1007/s11904-022-00616-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2022] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Cabotegravir is a potent integrase strand transfer inhibitor (INSTI) recently approved as a long-acting injectable formulation for HIV prevention (CAB-LA). We summarize what is known about cabotegravir pharmacokinetics, activity, and emergence of resistance from in vitro, macaque and clinical studies, and we evaluate the risk of resistance from CAB-LA with on-time injections and after CAB-LA discontinuation. RECENT FINDINGS The accumulation of multiple INSTI mutations is required for high-level cabotegravir resistance, and the same mutation combinations may cause cross-resistance to dolutegravir, which is widely used for first-line antiretroviral therapy in low- and middle-income countries. Though CAB-LA was highly effective in preventing HIV, breakthrough infections did occur in trials of CAB-LA despite on-time injections, resulting in selection of single and combinations of INSTI resistance mutations. As CAB-LA is scaled-up, prompt HIV diagnosis to prevent resistance, and resistance monitoring could help preserve the effectiveness of INSTIs for both HIV treatment and prevention.
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Affiliation(s)
- Urvi M Parikh
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, USA.
| | - Catherine A Koss
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco, San Francisco, USA
| | - John W Mellors
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, USA
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Allosteric Integrase Inhibitor Influences on HIV-1 Integration and Roles of LEDGF/p75 and HDGFL2 Host Factors. Viruses 2022; 14:v14091883. [PMID: 36146690 PMCID: PMC9502684 DOI: 10.3390/v14091883] [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: 07/28/2022] [Revised: 08/11/2022] [Accepted: 08/24/2022] [Indexed: 02/01/2023] Open
Abstract
Allosteric integrase (IN) inhibitors (ALLINIs), which are promising preclinical compounds that engage the lens epithelium-derived growth factor (LEDGF)/p75 binding site on IN, can inhibit different aspects of human immunodeficiency virus 1 (HIV-1) replication. During the late phase of replication, ALLINIs induce aberrant IN hyper-multimerization, the consequences of which disrupt IN binding to genomic RNA and virus particle morphogenesis. During the early phase of infection, ALLINIs can suppress HIV-1 integration into host genes, which is also observed in LEDGF/p75-depelted cells. Despite this similarity, the roles of LEDGF/p75 and its paralog hepatoma-derived growth factor like 2 (HDGFL2) in ALLINI-mediated integration retargeting are untested. Herein, we mapped integration sites in cells knocked out for LEDGF/p75, HDGFL2, or both factors, which revealed that these two proteins in large part account for ALLINI-mediated integration retargeting during the early phase of infection. We also determined that ALLINI-treated viruses are defective during the subsequent round of infection for integration into genes associated with speckle-associated domains, which are naturally highly targeted for HIV-1 integration. Class II IN mutant viruses with alterations distal from the LEDGF/p75 binding site moreover shared this integration retargeting phenotype. Altogether, our findings help to inform the molecular bases and consequences of ALLINI action.
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19
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Sawant AA, Jadav SS, Nayani K, Mainkar PS. Development of Synthetic Approaches Towards HIV Integrase Strand Transfer Inhibitors (INSTIs). ChemistrySelect 2022. [DOI: 10.1002/slct.202201915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ashwini Amol Sawant
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
| | - Surender Singh Jadav
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
- Department of Applied Biology CSIR-Indian Institute of Chemical Technology Tarnaka Uppal Road Hyderabad 500037 India
| | - Kiranmai Nayani
- Department of Organic Synthesis and Process Chemistry CSIR-Indian Institute of Chemical Technology Tarnaka Uppal Road Hyderabad 500037 India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
| | - Prathama S. Mainkar
- Department of Organic Synthesis and Process Chemistry CSIR-Indian Institute of Chemical Technology Tarnaka Uppal Road Hyderabad 500037 India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
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20
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Ozhmegova EN, Bobkova MR. [HIV drug resistance: past and current trends]. Vopr Virusol 2022; 67:193-205. [PMID: 35831962 DOI: 10.36233/0507-4088-113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
HIV infection is incurable, but effective antiretroviral therapy (ART) makes it possible to achieve an undetectable viral load (VL), to preserve the function of the immune system and to prevent the patient's health. Due to the constant increase in the use of ART and the high variability of HIV, especially in patients receiving so-called suboptimal therapy for various reasons, the incidence of drug resistance (DR) is increasing. In turn, the presence of DR in an HIV-infected patient affects the effectiveness of therapy, which leads to a limited choice and an increase in the cost of treatment regimens, disease progression and, consequently, an increased risk of death, as well as transmission of infection to partners. The main problems of drug resistance, its types and causes, as well as factors associated with its development are considered. The main drug resistance mutations for each of the drug classes are described.
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Affiliation(s)
- E N Ozhmegova
- FSBI «National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - M R Bobkova
- FSBI «National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya» of the Ministry of Health of Russia
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21
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Ghasabi F, Hashempour A, Khodadad N, Bemani S, Keshani P, Shekiba MJ, Hasanshahi Z. First report of computational protein-ligand docking to evaluate susceptibility to HIV integrase inhibitors in HIV-infected Iranian patients. Biochem Biophys Rep 2022; 30:101254. [PMID: 35368742 PMCID: PMC8968007 DOI: 10.1016/j.bbrep.2022.101254] [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: 01/15/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 12/04/2022] Open
Abstract
Background Iran has recently included integrase (INT) inhibitors (INTIs) in the first-line treatment regimen in human immunodeficiency virus (HIV)-infected patients. However, there is no bioinformatics data to elaborate the impact of resistance-associated mutations (RAMs) and naturally occurring polymorphisms (NOPs) on INTIs treatment outcome in Iranian patients. Method In this cross-sectional survey, 850 HIV-1-infected patients enrolled; of them, 78 samples had successful sequencing results for INT gene. Several analyses were performed including docking screening, genotypic resistance, secondary/tertiary structures, post-translational modification (PTM), immune epitopes, etc. Result The average docking energy (E value) of different samples with elvitegravir (EVG) and raltegravir (RAL) was more than other INTIs. Phylogenetic tree analysis and Stanford HIV Subtyping program revealed HIV-1 CRF35-AD was the predominant subtype (94.9%) in our cases; in any event, online subtyping tools confirmed A1 as the most frequent subtype. For the first time, CRF-01B and BF were identified as new subtypes in Iran. Decreased CD4 count was associated with several factors: poor or unstable adherence, naïve treatment, and drug user status. Conclusion As the first bioinformatic report on HIV-integrase from Iran, this study indicates that EVG and RAL are the optimal INTIs in first-line antiretroviral therapy (ART) in Iranian patients. Some conserved motifs and specific amino acids in INT-protein binding sites have characterized that mutation(s) in them may disrupt INT-drugs interaction and cause a significant loss in susceptibility to INTIs. Good adherence, treatment of naïve patients, and monitoring injection drug users are fundamental factors to control HIV infection in Iran effectively.
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Key Words
- Antiretroviral therapy, ART
- Behavioral Diseases Consultation Center, BDCC
- Bictegravir, BIC
- C-terminal domain, CTD
- CRF35-AD
- Cabotegravir, CBT
- Catalytic core domain, CCD
- Dolutegravir, DTG
- Drug resistance
- Elvitegravir, EVG
- Grand average hydropathy, GRAVY
- HIV
- Human immunodeficiency virus, HIV
- INT, Integrase
- INTIs, Integrase inhibitors (INTIs)
- Injecting drug users, IDUs
- Integrase
- Integrase inhibitors
- Molecular docking
- N-terminal domain, NTD
- Naturally occurring polymorphisms, NOPs
- Post-translational modification, PTM
- Raltegravir, RAL
- Resistance-associated mutations, RAMs
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Affiliation(s)
- Farzane Ghasabi
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ava Hashempour
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nastaran Khodadad
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Soudabeh Bemani
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Parisa Keshani
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohamad Javad Shekiba
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Hasanshahi
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
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22
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Taki E, Soleimani F, Asadi A, Ghahramanpour H, Namvar A, Heidary M. Cabenuva: the last FDA-approved drug to treat HIV. Expert Rev Anti Infect Ther 2022; 20:1135-1147. [PMID: 35596583 DOI: 10.1080/14787210.2022.2081153] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION The conventional combination antiretroviral therapy (cART) besides all its benefits, exhibited poor adherence to daily pill administration, life-long treatment period and emergence of viral resistance. The development of long-acting (LA) drugs have changed the management of common medical conditions for human immunodeficiency virus (HIV). Cabenuva is the first LA antiretroviral injectable drug composed of nano-formulation of cabotegravir (CAB) and rilpivirine (RPV). AREAS COVERED In this review article, we aim to have a brief overview of results of major clinical trials which administrated cabenuva for patients considering the efficacy and safety profiles. Moreover, we discuss about CAB and RPV chemical structure, mechanism of action, activity against drug-sensitive and resistant HIV and pharmacodynamics/ pharmacokinetics properties. EXPERT OPINION Based on the results of the ATLAS and FLAIR trials, cabenuva regimen once-monthly has shown equal effectivity to oral cART in maintaining HIV-1 suppression in patients. Furthermore, ATLAS-2M study revealed the non-inferiority of cabenuva regimen every 8 weeks compared to every 4 weeks. The injectable LA ART, reduces the number of treatment intake as well as increases adherence especially in patients with HIV-related stigma. Administration of extended-release agents probably minimize the risk of treatment-related toxicity and resistance related to sub-optimal adherence to oral ART, so cabenuva can be suggested as a suitable alternative for HIV infection control in current era.
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Affiliation(s)
- Elahe Taki
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Faezeh Soleimani
- Department of Chemistry, Medicinal Chemistry Research Laboratory, Shiraz University of Technology, Shiraz, Iran
| | - Arezoo Asadi
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hossein Ghahramanpour
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ali Namvar
- Student Research Committee, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Mohsen Heidary
- Department of Laboratory Sciences, School of Paramedical Sciences, Sabzevar University of Medical Sciences, Sabzevar, Iran.,Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar, Iran
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23
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Schneiderman BS, Barski MS, Maertens GN. Cabotegravir, the Long-Acting Integrase Strand Transfer Inhibitor, Potently Inhibits Human T-Cell Lymphotropic Virus Type 1 Transmission in vitro. Front Med (Lausanne) 2022; 9:889621. [PMID: 35547224 PMCID: PMC9082600 DOI: 10.3389/fmed.2022.889621] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 03/31/2022] [Indexed: 11/28/2022] Open
Abstract
Human T-cell lymphotropic virus type 1 (HTLV-1) is a deltaretrovirus most prevalent in southwestern Japan, sub-Saharan Africa, Australia, South America, and the Caribbean. Latest figures approximate 10 million people worldwide to be infected with HTLV-1. This is likely a significant underestimation due to lack of screening in endemic areas and absence of seroconversion symptoms. The two primary diseases associated with HTLV-1 infection are adult T cell leukaemia-lymphoma, a malignant and, sometimes, aggressive cancer; and HTLV-1 associated myelopathy/tropical spastic paraparesis, a debilitating neurological degenerative disease. Unfortunately, despite the poor prognosis, there is currently no effective treatment for HTLV-1 infection. We previously showed that integrase strand transfer inhibitors (INSTIs) clinically used for human immunodeficiency virus type 1 (HIV-1) prophylaxis and treatment are also effective against HTLV-1 transmission in vitro. In 2021 a new INSTI, cabotegravir, was approved by the FDA for HIV-1 treatment. We thus set out to evaluate its efficacy against HTLV-1 infection in vitro. Strand transfer assays performed using recombinant HTLV-1 integrase treated with increasing concentrations of cabotegravir, effectively inhibited strand transfer activity, displaying an IC50 of 77.8 ± 22.4 nM. Furthermore, cabotegravir blocked HTLV-1 transmission in tissue culture; we determined an EC50 of 0.56 ± 0.26 nM, similar to bictegravir. Alu-PCR confirmed the block in integration. Thus, there are four INSTIs and one reverse transcriptase inhibitor approved by the FDA for HIV-1 treatment, that potently block HTLV-1 infection in vitro. This should strongly encourage the establishment of a new standard of HTLV-1 treatment – particularly for pre-exposure prophylaxis and prevention of mother-to-child transmission.
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Affiliation(s)
| | - Michal S Barski
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Goedele N Maertens
- Department of Infectious Disease, Imperial College London, London, United Kingdom
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24
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Forgiveness of INSTI-Containing Regimens at Drug Concentrations Simulating Variable Adherence In Vitro. Antimicrob Agents Chemother 2022; 66:e0203821. [PMID: 35389236 PMCID: PMC9112893 DOI: 10.1128/aac.02038-21] [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] [Indexed: 12/02/2022] Open
Abstract
The integrase strand transfer inhibitor (INSTI)-based regimens bictegravir/emtricitabine/tenofovir alafenamide (BIC/FTC/TAF), dolutegravir (DTG)+FTC/TAF, DTG/lamivudine (3TC), and DTG/rilpivirine (RPV) are all approved for treatment of HIV-infected patients, with various limitations. Here, time to in vitro viral breakthrough (VB) and resistance barrier using simulated human drug exposures at either full or suboptimal treatment adherence to each regimen were compared. At drug concentrations corresponding to full adherence and 1 missed dose (Cmin and Cmin−1), no VB occurred with any regimen. At Cmin−2, VB occurred only with DTG+3TC, with emergent resistance to both drugs. At Cmin−3, VB occurred with all regimens: 100% of DTG+3TC cultures had VB by day 12, and <15% of BIC+FTC+TAF, DTG+FTC+TAF, and DTG+RPV cultures had VB. Emergent reverse transcriptase (RT) or integrase (IN) resistance was seen with DTG+RPV and DTG+3TC but not with BIC+FTC+TAF or DTG+FTC+TAF. At Cmin−4, 100% VB occurred with DTG+3TC and DTG+FTC+TAF by day 12, while 94% VB occurred with DTG+RPV by day 25 and only 50% VB occurred with BIC+FTC+TAF by day 35. Emergent Cmin−4 drug resistance was seen with all regimens but at differing frequencies; DTG+RPV had the most cultures with resistance. Emergent resistance was consistent with clinical observations. Overall, under high adherence conditions, no in vitro VB or resistance development occurred with these INSTI-based regimens. However, when multiple missed doses were simulated in vitro, BIC+FTC+TAF had the highest forgiveness and barrier to resistance of all tested regimens. Compared to DTG+3TC and DTG+FTC+TAF, DTG+RPV had higher forgiveness but lower resistance barrier after several simulated missed doses.
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25
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D'Antoni ML, Andreatta K, Acosta R, Martin H, Chang S, Martin R, White KL. Brief Report: Bictegravir/Emtricitabine/Tenofovir Alafenamide Efficacy in Participants With Preexisting Primary Integrase Inhibitor Resistance Through 48 Weeks of Phase 3 Clinical Trials. J Acquir Immune Defic Syndr 2022; 89:433-440. [PMID: 34897227 PMCID: PMC8860220 DOI: 10.1097/qai.0000000000002888] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 11/15/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND Preexisting drug resistance limits the utility of HIV antiretroviral therapy. Studies have demonstrated safety and efficacy of bictegravir/emtricitabine/tenofovir alafenamide (B/F/TAF), including in patients with M184V/I substitutions. SETTING We investigated virologic outcomes through 48 weeks of B/F/TAF treatment in individuals with preexisting primary integrase strand transfer inhibitor resistance (INSTI-R). METHODS Preexisting INSTI-R was retrospectively evaluated from 7 B/F/TAF studies. INSTI-R was assessed by historical genotypes and/or baseline RNA or DNA sequencing. Viral loads were measured at all visits. RESULTS Preexisting primary INSTI-R substitutions were detected in 20 of the 1907 participants (1.0%). The 20 participants were predominantly male (75%), were Black (65%), had HIV-1 subtype B (85%), and had baseline median CD4 counts of 594 cells/mm3 and median age of 52 years. Most of the participants (n = 19) were virologically suppressed at baseline and had one primary INSTI-R substitution, E92G, Y143C/H, S147G, Q148H/K/R, N155S, or R263K, +/-secondary substitutions. All suppressed participants maintained virologic suppression throughout 48 weeks without any viral blips. One treatment-naive participant had virus with Q148H+G140S that was fully sensitive to bictegravir but only partially to dolutegravir (phenotype <2.5-fold change and >4-fold change, respectively). With a baseline viral load of 30,000 copies/mL, this participant was virologically suppressed by week 4 and maintained <50 copies/mL through week 48. CONCLUSIONS This small cohort with primary INSTI-R achieved and/or maintained virologic suppression through 48 weeks of B/F/TAF treatment. Consistent with the potent in vitro activity of bictegravir against most INSTI-R patterns, B/F/TAF may be a potential treatment option for patients with select preexisting INSTI-R, if confirmed by further studies.
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26
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Adu-Ampratwum D, Pan Y, Koneru PC, Antwi J, Hoyte AC, Kessl J, Griffin PR, Kvaratskhelia M, Fuchs JR, Larue RC. Identification and Optimization of a Novel HIV-1 Integrase Inhibitor. ACS OMEGA 2022; 7:4482-4491. [PMID: 35155940 PMCID: PMC8829933 DOI: 10.1021/acsomega.1c06378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/13/2022] [Indexed: 05/17/2023]
Abstract
Human immunodeficiency virus-1 (HIV-1) is the causative agent of acquired immunodeficiency syndrome (AIDS). HIV-1, like all retroviruses, stably integrates its vDNA copy into host chromatin, a process allowing for permanent infection. This essential step for HIV-1 replication is catalyzed by viral integrase (IN) and aided by cellular protein LEDGF/p75. In addition, IN is also crucial for proper virion maturation as it interacts with the viral RNA genome to ensure encapsulation of ribonucleoprotein complexes within the protective capsid core. These key functions make IN an attractive target for the development of inhibitors with various mechanisms of action. We conducted a high-throughput screen (HTS) of ∼370,000 compounds using a homogeneous time-resolved fluorescence-based assay capable of capturing diverse inhibitors targeting multifunctional IN. Our approach revealed chemical scaffolds containing diketo acid moieties similar to IN strand transfer inhibitors (INSTIs) as well as novel compounds distinct from all current IN inhibitors including INSTIs and allosteric integrase inhibitors (ALLINIs). Specifically, our HTS resulted in the discovery of compound 12, with a novel IN inhibitor scaffold amenable for chemical modification. Its more potent derivative 14e similarly inhibited catalytic activities of WT and mutant INs containing archetypical INSTI- and ALLINI-derived resistant substitutions. Further SAR-based optimization resulted in compound 22 with an antiviral EC50 of ∼58 μM and a selectivity index of >8500. Thus, our studies identified a novel small-molecule scaffold for inhibiting HIV-1 IN, which provides a promising platform for future development of potent antiviral agents to complement current HIV-1 therapies.
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Affiliation(s)
- Daniel Adu-Ampratwum
- Division
of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Yuhan Pan
- Division
of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Pratibha C. Koneru
- Division
of Infectious Diseases, School of Medicine, University of Colorado, Aurora, Colorado 80045, United States
| | - Janet Antwi
- Division
of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Ashley C. Hoyte
- Division
of Infectious Diseases, School of Medicine, University of Colorado, Aurora, Colorado 80045, United States
| | - Jacques Kessl
- Department
of Chemistry & Biochemistry, The University
of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Patrick R. Griffin
- Department
of Molecular Medicine, The Scripps Research
Institute, Jupiter, Florida 33458, United
States
| | - Mamuka Kvaratskhelia
- Division
of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
- Division
of Infectious Diseases, School of Medicine, University of Colorado, Aurora, Colorado 80045, United States
| | - James R. Fuchs
- Division
of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Ross C. Larue
- Division
of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
- Department
of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
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27
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Smith RA, Wu VH, Song J, Raugi DN, Diallo Mbaye K, Seydi M, Gottlieb GS. Spectrum of Activity of Raltegravir and Dolutegravir Against Novel Treatment-Associated Mutations in HIV-2 Integrase: A Phenotypic Analysis Using an Expanded Panel of Site-Directed Mutants. J Infect Dis 2022; 226:497-509. [PMID: 35134180 PMCID: PMC9417127 DOI: 10.1093/infdis/jiac037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/28/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Integrase inhibitors (INIs) are a key component of antiretroviral therapy for human immunodeficiency virus-1 (HIV-1) and HIV-2 infection. Although INI resistance pathways are well-defined for HIV-1, mutations that emerge in HIV-2 in response to INIs are incompletely characterized. METHODS We performed systematic searches of GenBank and HIV-2 drug resistance literature to identify treatment-associated mutations for phenotypic evaluation. We then constructed a library of 95 mutants of HIV-2ROD9 that contained single or multiple amino acid changes in the integrase protein. Each variant was tested for susceptibility to raltegravir and dolutegravir using a single-cycle indicator cell assay. RESULTS We observed extensive cross-resistance between raltegravir and dolutegravir in HIV-2ROD9. HIV-2-specific integrase mutations Q91R, E92A, A153G, and H157Q/S, which have not been previously characterized, significantly increased the half maximum effective concentration (EC50) for raltegravir when introduced into 1 or more mutational backgrounds; mutations E92A/Q, T97A, and G140A/S conferred similar enhancements of dolutegravir resistance. HIV-2ROD9 variants encoding G118R alone, or insertions of residues SREGK or SREGR at position 231, were resistant to both INIs. CONCLUSIONS Our analysis demonstrates the contributions of novel INI-associated mutations to raltegravir and dolutegravir resistance in HIV-2. These findings should help to improve algorithms for genotypic drug resistance testing in HIV-2-infected individuals.
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Affiliation(s)
- Robert A Smith
- Correspondence: Robert A. Smith, PhD, Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, 750 Republican Street, Building E, Box 358061, Seattle, WA 98109 ()
| | - Vincent H Wu
- Center for Emerging and Reemerging Infectious Diseases, University of Washington, Seattle, Washington, USA,Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - Jennifer Song
- Center for Emerging and Reemerging Infectious Diseases, University of Washington, Seattle, Washington, USA,Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - Dana N Raugi
- Center for Emerging and Reemerging Infectious Diseases, University of Washington, Seattle, Washington, USA,Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - Khardiata Diallo Mbaye
- Service des Maladies Infectieuses et Tropicales, Centre Hospitalier National Universitaire de Fann, Dakar, Senegal
| | - Moussa Seydi
- Service des Maladies Infectieuses et Tropicales, Centre Hospitalier National Universitaire de Fann, Dakar, Senegal
| | - Geoffrey S Gottlieb
- Center for Emerging and Reemerging Infectious Diseases, University of Washington, Seattle, Washington, USA,Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA,Department of Global Health, University of Washington, Seattle, Washington, USA
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Impact of Integrase Sequences From HIV-1 Subtypes A6/A1 on the
In Vitro
Potency of Cabotegravir or Rilpivirine. Antimicrob Agents Chemother 2022; 66:e0170221. [PMID: 34978890 PMCID: PMC8923183 DOI: 10.1128/aac.01702-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The FLAIR study demonstrated noninferiority of monthly long-acting cabotegravir + rilpivirine versus daily oral dolutegravir/abacavir/lamivudine for maintaining virologic suppression. Three participants who received long-acting therapy had confirmed virologic failure (CVF) at Week 48, and all had HIV-1 that was originally classified as subtype A1 and contained the baseline integrase polymorphism L74I; updated classification algorithms reclassified all 3 as HIV-1 subtype A6. Retrospectively, the impact of L74I on in vitro sensitivity and durability of response to cabotegravir in HIV-1 subtype B and A6 backgrounds was studied. Site-directed L74I and mutations observed in participants with CVF were generated in HIV-1 subtype B and a consensus integrase derived from 3 subtype A6 CVF baseline sequences. Rilpivirine susceptibility was assessed in HIV-1 subtype B and A1 containing reverse transcriptase mutations observed in participants with CVF. HIV-1 subtype B L74I and L74I/G140R mutants and HIV-1 subtype A6 I74L and I74/G140R mutants remained susceptible to cabotegravir; L74I/Q148R double mutants exhibited reduced susceptibility in HIV-1 subtypes B and A6 (half maximal effective capacity fold change, 4.4 and 4.1, respectively). Reduced rilpivirine susceptibility was observed across HIV-1 subtypes B and A1 with resistance-associated mutations K101E or E138K (half maximal effective capacity fold change, 2.21 to 3.09). In cabotegravir breakthrough experiments, time to breakthrough was similar between L74 and I74 viruses across HIV-1 subtypes B and A6; Q148R was selected at low cabotegravir concentrations. Therefore, the L74I integrase polymorphism did not differentially impact in vitro sensitivity to cabotegravir across HIV-1 subtype B and A6 integrase genes (ClinicalTrials.gov identifier: NCT02938520).
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Abstract
A hallmark of retroviral replication is establishment of the proviral state, wherein a DNA copy of the viral RNA genome is stably incorporated into a host cell chromosome. Integrase is the viral enzyme responsible for the catalytic steps involved in this process, and integrase strand transfer inhibitors are widely used to treat people living with HIV. Over the past decade, a series of X-ray crystallography and cryogenic electron microscopy studies have revealed the structural basis of retroviral DNA integration. A variable number of integrase molecules congregate on viral DNA ends to assemble a conserved intasome core machine that facilitates integration. The structures additionally informed on the modes of integrase inhibitor action and the means by which HIV acquires drug resistance. Recent years have witnessed the development of allosteric integrase inhibitors, a highly promising class of small molecules that antagonize viral morphogenesis. In this Review, we explore recent insights into the organization and mechanism of the retroviral integration machinery and highlight open questions as well as new directions in the field.
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30
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Wagner T, Zuckerman NS, Halperin T, Chemtob D, Levy I, Elbirt D, Shachar E, Olshtain-Pops K, Elinav H, Chowers M, Itsomin V, Riesenberg K, Wax M, Shirazi R, Gozlan Y, Matus N, Girshengorn S, Marom R, Mendelson E, Turner D, Mor O. Epidemiology and Transmitted HIV-1 Drug Resistance among Treatment-Naïve Individuals in Israel, 2010-2018. Viruses 2021; 14:v14010071. [PMID: 35062274 PMCID: PMC8779053 DOI: 10.3390/v14010071] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 12/27/2021] [Accepted: 12/28/2021] [Indexed: 01/22/2023] Open
Abstract
Despite the low prevalence of HIV-1 in Israel, continuous waves of immigration may have impacted the local epidemic. We characterized all people diagnosed with HIV-1 in Israel in 2010–2018. The demographics and clinical data of all individuals (n = 3639) newly diagnosed with HIV-1 were retrieved. Subtypes, transmitted drug-resistance mutations (TDRM), and phylogenetic relations, were determined in >50% of them. In 39.1%, HIV-1 transmission was through heterosexual contact; 34.3% were men who have sex with men (MSM); and 10.4% were people who inject drugs. Many (>65%) were immigrants. Israeli-born individuals were mostly (78.3%) MSM, whereas only 9% of those born in Sub-Saharan Africa (SSA), Eastern Europe and Central Asia (EEU/CA), were MSM. The proportion of individuals from SSA decreased through the years 2010–2018 (21.1% in 2010–2012; 16.8% in 2016–2018) whereas those from EEU/CA increased significantly (21% in 2010–2012; 27.8% in 2016–2018, p < 0.001). TDRM were identified in 12.1%; 3.7, 3.3 and 6.6% had protease inhibitors (PI), nucleotide reverse transcriptase inhibitors (NRTI), and non-nucleoside reverse transcriptase inhibitors (NNRTI) TDRM, respectively, with the overall proportion remaining stable in the studied years. None had integrase TDRM. Subtype B was present in 43.9%, subtype A in 25.2% (A6 in 22.8 and A1 in 2.4%) and subtype C in 17.1% of individuals. Most MSM had subtype B. Subtype C carriers formed small clusters (with one unexpected MSM cluster), A1 formed a cluster mainly of locally-born patients with NNRTI mutations, and A6 formed a looser cluster of individuals mainly from EEU. Israelis, <50 years old, carrying A1, had the highest risk for having TDRM. In conclusion, an increase in immigrants from EEU/CA and a decrease in those from SSA characterized the HIV-1 epidemic in 2010–2018. Baseline resistance testing should still be recommended to identify TDRM, and improve surveillance and care.
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Affiliation(s)
- Tali Wagner
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel; (T.W.); (I.L.); (M.C.); (E.M.); (D.T.)
- Chaim Sheba Medical Center, National HIV-1 and Viral Hepatitis Reference Laboratory, Ramat Gan 5262112, Israel; (N.S.Z.); (M.W.); (R.S.); (Y.G.)
| | - Neta S. Zuckerman
- Chaim Sheba Medical Center, National HIV-1 and Viral Hepatitis Reference Laboratory, Ramat Gan 5262112, Israel; (N.S.Z.); (M.W.); (R.S.); (Y.G.)
| | - Tami Halperin
- Tel-Aviv Sourasky Medical Center, Crusaid Kobler AIDS Center, Tel Aviv 6423906, Israel; (T.H.); (N.M.); (S.G.); (R.M.)
| | - Daniel Chemtob
- Faculty of Medicine, Braun School of Public Health & Community Medicine, Hebrew University-Hadassah Medical School, Jerusalem 9112102, Israel; (D.C.); (D.E.); (H.E.)
- Tuberculosis and AIDS Department, Ministry of Health, Jerusalem 9101002, Israel
| | - Itzchak Levy
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel; (T.W.); (I.L.); (M.C.); (E.M.); (D.T.)
- Chaim Sheba Medical Center, Infectious Disease Unit, Ramat Gan 5262112, Israel
| | - Daniel Elbirt
- Faculty of Medicine, Braun School of Public Health & Community Medicine, Hebrew University-Hadassah Medical School, Jerusalem 9112102, Israel; (D.C.); (D.E.); (H.E.)
- Immunology, Kaplan Medical Center, Rehovot 76100, Israel
| | - Eduardo Shachar
- Immunology Unit, Rambam Health Care Campus, Haifa 3109601, Israel;
- Rappaport Faculty of Medicine, Institute of Technology, Technion, Haifa 3200003, Israel
| | | | - Hila Elinav
- Faculty of Medicine, Braun School of Public Health & Community Medicine, Hebrew University-Hadassah Medical School, Jerusalem 9112102, Israel; (D.C.); (D.E.); (H.E.)
- Hadassah Medical Center, Jerusalem 9112102, Israel;
| | - Michal Chowers
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel; (T.W.); (I.L.); (M.C.); (E.M.); (D.T.)
- Infectious Diseases, Meir Medical Center, Kfar Saba 4428164, Israel
| | | | - Klaris Riesenberg
- Faculty of Health Sciences, Goldman Medical School, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel;
- Soroka Medical Center, Infectious Disease Institute, Beer-Sheva 84101, Israel
| | - Marina Wax
- Chaim Sheba Medical Center, National HIV-1 and Viral Hepatitis Reference Laboratory, Ramat Gan 5262112, Israel; (N.S.Z.); (M.W.); (R.S.); (Y.G.)
| | - Rachel Shirazi
- Chaim Sheba Medical Center, National HIV-1 and Viral Hepatitis Reference Laboratory, Ramat Gan 5262112, Israel; (N.S.Z.); (M.W.); (R.S.); (Y.G.)
| | - Yael Gozlan
- Chaim Sheba Medical Center, National HIV-1 and Viral Hepatitis Reference Laboratory, Ramat Gan 5262112, Israel; (N.S.Z.); (M.W.); (R.S.); (Y.G.)
| | - Natasha Matus
- Tel-Aviv Sourasky Medical Center, Crusaid Kobler AIDS Center, Tel Aviv 6423906, Israel; (T.H.); (N.M.); (S.G.); (R.M.)
| | - Shirley Girshengorn
- Tel-Aviv Sourasky Medical Center, Crusaid Kobler AIDS Center, Tel Aviv 6423906, Israel; (T.H.); (N.M.); (S.G.); (R.M.)
| | - Rotem Marom
- Tel-Aviv Sourasky Medical Center, Crusaid Kobler AIDS Center, Tel Aviv 6423906, Israel; (T.H.); (N.M.); (S.G.); (R.M.)
| | - Ella Mendelson
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel; (T.W.); (I.L.); (M.C.); (E.M.); (D.T.)
- Chaim Sheba Medical Center, National HIV-1 and Viral Hepatitis Reference Laboratory, Ramat Gan 5262112, Israel; (N.S.Z.); (M.W.); (R.S.); (Y.G.)
| | - Dan Turner
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel; (T.W.); (I.L.); (M.C.); (E.M.); (D.T.)
- Tel-Aviv Sourasky Medical Center, Crusaid Kobler AIDS Center, Tel Aviv 6423906, Israel; (T.H.); (N.M.); (S.G.); (R.M.)
| | - Orna Mor
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel; (T.W.); (I.L.); (M.C.); (E.M.); (D.T.)
- Chaim Sheba Medical Center, National HIV-1 and Viral Hepatitis Reference Laboratory, Ramat Gan 5262112, Israel; (N.S.Z.); (M.W.); (R.S.); (Y.G.)
- Correspondence: ; Tel.: +972-3-530-2458
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Smith SJ, Ferris A, Zhao X, Pauly G, Schneider JP, Burke TR, Hughes SH. INSTIs and NNRTIs Potently Inhibit HIV-1 Polypurine Tract Mutants in a Single Round Infection Assay. Viruses 2021; 13:v13122501. [PMID: 34960770 PMCID: PMC8705849 DOI: 10.3390/v13122501] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/30/2021] [Accepted: 12/04/2021] [Indexed: 01/25/2023] Open
Abstract
Integrase strand transfer inhibitors (INSTIs) are a class of antiretroviral compounds that prevent the insertion of a DNA copy of the viral genome into the host genome by targeting the viral enzyme integrase (IN). Dolutegravir (DTG) is a leading INSTI that is given, usually in combination with nucleoside reverse transcriptase inhibitors (NRTIs), to treat HIV-1 infections. The emergence of resistance to DTG and other leading INSTIs is rare. However, there are recent reports suggesting that drug resistance mutations can occur at positions outside the integrase gene either in the HIV-1 polypurine tract (PPT) or in the envelope gene (env). Here, we used single round infectivity assays to measure the antiviral potencies of several FDA-approved INSTIs and non-nucleoside reverse transcriptase inhibitors (NNRTIs) against a panel of HIV-1 PPT mutants. We also tested several of our promising INSTIs and NNRTIs in these assays. No measurable loss in potency was observed for either INSTIs or NNRTIs against the HIV-1 PPT mutants. This suggests that HIV-1 PPT mutants are not able, by themselves, to confer resistance to INSTIs or NNRTIs.
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Affiliation(s)
- Steven J. Smith
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; (S.J.S.); (A.F.)
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; (X.Z.); (G.P.); (J.P.S.); (T.R.B.J.)
| | - Andrea Ferris
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; (S.J.S.); (A.F.)
| | - Xuezhi Zhao
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; (X.Z.); (G.P.); (J.P.S.); (T.R.B.J.)
| | - Gary Pauly
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; (X.Z.); (G.P.); (J.P.S.); (T.R.B.J.)
| | - Joel P. Schneider
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; (X.Z.); (G.P.); (J.P.S.); (T.R.B.J.)
| | - Terrence R. Burke
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; (X.Z.); (G.P.); (J.P.S.); (T.R.B.J.)
| | - Stephen H. Hughes
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; (S.J.S.); (A.F.)
- Correspondence:
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32
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Advances in the development of HIV integrase strand transfer inhibitors. Eur J Med Chem 2021; 225:113787. [PMID: 34425310 DOI: 10.1016/j.ejmech.2021.113787] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 08/05/2021] [Accepted: 08/05/2021] [Indexed: 12/30/2022]
Abstract
HIV-1 integrase (IN) is a key enzyme in viral replication that catalyzes the covalent integration of viral cDNA into the host genome. Currently, five HIV-1 IN strand transfer inhibitors (INSTIs) are approved for clinical use. These drugs represent an important addition to the armamentarium for antiretroviral therapy. This review briefly illustrates the development history of INSTIs. The characteristics of the currently approved INSTIs, as well as their future perspectives, are critically discussed.
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Passos DO, Li M, Craigie R, Lyumkis D. Retroviral integrase: Structure, mechanism, and inhibition. Enzymes 2021; 50:249-300. [PMID: 34861940 DOI: 10.1016/bs.enz.2021.06.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The retroviral protein Integrase (IN) catalyzes concerted integration of viral DNA into host chromatin to establish a permanent infection in the target cell. We learned a great deal about the mechanism of catalytic integration through structure/function studies over the previous four decades of IN research. As one of three essential retroviral enzymes, IN has also been targeted by antiretroviral drugs to treat HIV-infected individuals. Inhibitors blocking the catalytic integration reaction are now state-of-the-art drugs within the antiretroviral therapy toolkit. HIV-1 IN also performs intriguing non-catalytic functions that are relevant to the late stages of the viral replication cycle, yet this aspect remains poorly understood. There are also novel allosteric inhibitors targeting non-enzymatic functions of IN that induce a block in the late stages of the viral replication cycle. In this chapter, we will discuss the function, structure, and inhibition of retroviral IN proteins, highlighting remaining challenges and outstanding questions.
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Affiliation(s)
| | - Min Li
- National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, United States
| | - Robert Craigie
- National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, United States
| | - Dmitry Lyumkis
- The Salk Institute for Biological Studies, La Jolla, CA, United States; The Scripps Research Institute, La Jolla, CA, United States.
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Ndashimye E, Li Y, Reyes PS, Avino M, Olabode AS, Kityo CM, Kyeyune F, Nankya I, Quiñones-Mateu ME, Barr SD, Arts EJ. High-level resistance to bictegravir and cabotegravir in subtype A- and D-infected HIV-1 patients failing raltegravir with multiple resistance mutations. J Antimicrob Chemother 2021; 76:2965-2974. [PMID: 34453542 DOI: 10.1093/jac/dkab276] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 07/02/2021] [Indexed: 01/15/2023] Open
Abstract
OBJECTIVES The second-generation integrase strand transfer inhibitor (INSTI) bictegravir is becoming accessible in low- and middle-income countries (LMICs), and another INSTI, cabotegravir, has recently been approved as a long-acting injectable. Data on bictegravir and cabotegravir susceptibility in raltegravir-experienced HIV-1 subtype A- and D-infected patients carrying drug resistance mutations (DRMs) remain very scarce in LMICs. PATIENTS AND METHODS HIV-1 integrase (IN)-recombinant viruses from eight patients failing raltegravir-based third-line therapy in Uganda were genotypically and phenotypically tested for susceptibility to bictegravir and cabotegravir. Ability of these viruses to integrate into human genomes was assessed in MT-4 cells. RESULTS HIV-1 IN-recombinant viruses harbouring single primary mutations (N155H or Y143R/S) or in combination with secondary INSTI mutations (T97A, M50I, L74IM, E157Q, G163R or V151I) were susceptible to both bictegravir and cabotegravir. However, combinations of primary INSTI-resistance mutations such as E138A/G140A/G163R/Q148R or E138K/G140A/S147G/Q148K led to decreased susceptibility to both cabotegravir (fold change in EC50 values from 429 to 1000×) and bictegravir (60 to 100×), exhibiting a high degree of cross-resistance. However, these same IN-recombinant viruses showed impaired integration capacity (14% to 48%) relative to the WT HIV-1 NL4-3 strain in the absence of drug. CONCLUSIONS Though not currently widely accessible in most LMICs, bictegravir and cabotegravir offer a valid alternative to HIV-infected individuals harbouring subtype A and D HIV-1 variants with reduced susceptibility to first-generation INSTIs but previous exposure to raltegravir may reduce efficacy, more so with cabotegravir.
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Affiliation(s)
- Emmanuel Ndashimye
- Department of Microbiology and Immunology, Western University, London, Canada.,Joint Clinical Research Centre, Kampala, Uganda.,Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Yue Li
- Department of Microbiology and Immunology, Western University, London, Canada
| | - Paul S Reyes
- Department of Microbiology and Immunology, Western University, London, Canada
| | - Mariano Avino
- Department of Pathology and Laboratory Medicine, Western University, London, Canada
| | - Abayomi S Olabode
- Department of Pathology and Laboratory Medicine, Western University, London, Canada
| | | | - Fred Kyeyune
- Joint Clinical Research Centre, Kampala, Uganda.,Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Immaculate Nankya
- Joint Clinical Research Centre, Kampala, Uganda.,Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | | | - Stephen D Barr
- Department of Microbiology and Immunology, Western University, London, Canada
| | - Eric J Arts
- Department of Microbiology and Immunology, Western University, London, Canada
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Menéndez-Arias L, Martín-Alonso S, Frutos-Beltrán E. An Update on Antiretroviral Therapy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1322:31-61. [PMID: 34258736 DOI: 10.1007/978-981-16-0267-2_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Human immunodeficiency virus (HIV) infection and acquired immune deficiency syndrome (AIDS) still claim many lives across the world. However, research efforts during the last 40 years have led to the approval of over 30 antiretroviral drugs and the introduction of combination therapies that have turned HIV infection into a chronic but manageable disease. In this chapter, we provide an update on current available drugs and treatments, as well as future prospects towards reducing pill burden and developing long-acting drugs and novel antiretroviral therapies. In addition, we summarize efforts to cure HIV, including pharmaceutical strategies focused on the elimination of the virus.
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Affiliation(s)
- Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid, Spain.
| | - Samara Martín-Alonso
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid, Spain
| | - Estrella Frutos-Beltrán
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid, Spain
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36
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Yang F, Yang J, Zhang Z, Tu G, Yao X, Xue W, Zhu F. Recent Advances in Computer-aided Antiviral Drug Design Targeting HIV-1 Integrase and Reverse Transcriptase Associated Ribonuclease H. Curr Med Chem 2021; 29:1664-1676. [PMID: 34238145 DOI: 10.2174/0929867328666210708090123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/29/2021] [Accepted: 05/06/2021] [Indexed: 11/22/2022]
Abstract
Acquired immunodeficiency syndrome (AIDS) has been a chronic, life-threatening disease for a long time. However, a broad range of antiretroviral drug regimens are applicable for the successful suppression of virus replication in human immunodeficiency virus type 1 (HIV-1) infected people. The mutation-induced drug resistance problems during the treatment of AIDS forced people to continuously look for new antiviral agents. HIV-1 integrase (IN) and reverse transcriptase associated ribonuclease (RT-RNase H), two pivotal enzymes in HIV-1 replication progress, has gain popularity as drug-able targets for designing novel HIV-1 antiviral drugs. During the development of HIV-1 IN and/or RT-RNase H inhibitors, computer-aided drug design (CADD), including homology modeling, pharmacophore, docking, molecular dynamics (MD) simulation, and binding free energy calculation, represents a significant tool to accelerate the discovery of new drug candidates and reduce costs in antiviral drug development. In this review, we summarized the recent advances in the design of single-and dual-target inhibitors against HIV-1 IN or/and RT-RNase H as well as the prediction of mutation-induced drug resistance based on computational methods. We highlighted the results of the reported literature and proposed some perspectives on the design of novel and more effective antiviral drugs in the future.
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Affiliation(s)
- Fengyuan Yang
- School of Pharmaceutical Sciences, Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chongqing University, Chongqing 401331, China
| | - Jingyi Yang
- School of Pharmaceutical Sciences, Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chongqing University, Chongqing 401331, China
| | - Zhao Zhang
- School of Pharmaceutical Sciences, Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chongqing University, Chongqing 401331, China
| | - Gao Tu
- School of Pharmaceutical Sciences, Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chongqing University, Chongqing 401331, China
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, China
| | - Weiwei Xue
- School of Pharmaceutical Sciences, Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chongqing University, Chongqing 401331, China
| | - Feng Zhu
- School of Pharmaceutical Sciences, Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chongqing University, Chongqing 401331, China
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Smith SJ, Zhao XZ, Passos DO, Pye VE, Cherepanov P, Lyumkis D, Burke TR, Hughes SH. HIV-1 Integrase Inhibitors with Modifications That Affect Their Potencies against Drug Resistant Integrase Mutants. ACS Infect Dis 2021; 7:1469-1482. [PMID: 33686850 PMCID: PMC8205226 DOI: 10.1021/acsinfecdis.0c00819] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
![]()
Integrase strand transfer inhibitors
(INSTIs) block the integration
step of the retroviral lifecycle and are first-line drugs used for
the treatment of HIV-1/AIDS. INSTIs have a polycyclic core with heteroatom
triads, chelate the metal ions at the active site, and have a halobenzyl
group that interacts with viral DNA attached to the core by a flexible
linker. The most broadly effective INSTIs inhibit both wild-type (WT)
integrase (IN) and a variety of well-known mutants. However, because
there are mutations that reduce the potency of all of the available
INSTIs, new and better compounds are needed. Models based on recent
structures of HIV-1 and red-capped mangabey SIV INs suggest modifications
in the INSTI structures that could enhance interactions with the 3′-terminal
adenosine of the viral DNA, which could improve performance against
INSTI resistant mutants. We designed and tested a series of INSTIs
having modifications to their naphthyridine scaffold. One of the new
compounds retained good potency against an expanded panel of HIV-1
IN mutants that we tested. Our results suggest the possibility of
designing inhibitors that combine the best features of the existing
compounds, which could provide additional efficacy against known HIV-1
IN mutants.
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Affiliation(s)
- Steven J. Smith
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Xue Zhi Zhao
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Dario Oliveira Passos
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Valerie E. Pye
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London NW1 1AT, U.K
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London NW1 1AT, U.K
- St Mary’s Hospital, Department of Infectious Disease, Imperial College London, Section of Virology, Norfolk Place, London W2 1PG, U.K
| | - Dmitry Lyumkis
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Terrence R. Burke
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Stephen H. Hughes
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
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Smith SJ, Zhao XZ, Passos DO, Pye VE, Cherepanov P, Lyumkis D, Burke TR, Hughes SH. HIV-1 Integrase Inhibitors with Modifications That Affect Their Potencies against Drug Resistant Integrase Mutants. ACS Infect Dis 2021. [PMID: 33686850 DOI: 10.1021/acsinfecdis.0c00819/suppl_file/id0c00819_liveslides.mp4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2023]
Abstract
Integrase strand transfer inhibitors (INSTIs) block the integration step of the retroviral lifecycle and are first-line drugs used for the treatment of HIV-1/AIDS. INSTIs have a polycyclic core with heteroatom triads, chelate the metal ions at the active site, and have a halobenzyl group that interacts with viral DNA attached to the core by a flexible linker. The most broadly effective INSTIs inhibit both wild-type (WT) integrase (IN) and a variety of well-known mutants. However, because there are mutations that reduce the potency of all of the available INSTIs, new and better compounds are needed. Models based on recent structures of HIV-1 and red-capped mangabey SIV INs suggest modifications in the INSTI structures that could enhance interactions with the 3'-terminal adenosine of the viral DNA, which could improve performance against INSTI resistant mutants. We designed and tested a series of INSTIs having modifications to their naphthyridine scaffold. One of the new compounds retained good potency against an expanded panel of HIV-1 IN mutants that we tested. Our results suggest the possibility of designing inhibitors that combine the best features of the existing compounds, which could provide additional efficacy against known HIV-1 IN mutants.
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Affiliation(s)
- Steven J Smith
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Xue Zhi Zhao
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Dario Oliveira Passos
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Valerie E Pye
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London NW1 1AT, U.K
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London NW1 1AT, U.K
- St Mary's Hospital, Department of Infectious Disease, Imperial College London, Section of Virology, Norfolk Place, London W2 1PG, U.K
| | - Dmitry Lyumkis
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Terrence R Burke
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Stephen H Hughes
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
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39
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Abstract
The HIV integrase (IN) strand transfer inhibitor (INSTI) bictegravir (BIC) has a long dissociation half-life (t1/2) from wild-type IN-DNA complexes: BIC 163 hr > dolutegravir (DTG) 96 hr > raltegravir (RAL) 10 hr > elvitegravir (EVG) 3.3 hr. In cells, BIC had more durable antiviral activity against wild-type HIV after drug washout than RAL or EVG. BIC also had a longer t1/2 and maintained longer antiviral activity after drug washout than DTG with the clinically relevant resistance IN mutant G140S+Q148H. Structural analyses indicate that BIC makes more contacts with the IN-DNA complex than DTG mainly via its bicyclic ring system which may contribute to more prolonged residence time and resilience against many resistance mutations.
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Tzou PL, Rhee SY, Descamps D, Clutter DS, Hare B, Mor O, Grude M, Parkin N, Jordan MR, Bertagnolio S, Schapiro JM, Harrigan PR, Geretti AM, Marcelin AG, Shafer RW. Integrase strand transfer inhibitor (INSTI)-resistance mutations for the surveillance of transmitted HIV-1 drug resistance. J Antimicrob Chemother 2021; 75:170-182. [PMID: 31617907 DOI: 10.1093/jac/dkz417] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/03/2019] [Accepted: 09/06/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Integrase strand transfer inhibitors (INSTIs) are expected to be widely adopted globally, requiring surveillance of resistance emergence and transmission. OBJECTIVES We therefore sought to develop a standardized list of INSTI-resistance mutations suitable for the surveillance of transmitted INSTI resistance. METHODS To characterize the suitability of the INSTI-resistance mutations for transmitted HIV-1 drug resistance (TDR) surveillance, we classified them according to their presence on published expert lists, conservation in INSTI-naive persons, frequency in INSTI-treated persons and contribution to reduced in vitro susceptibility. Mutation prevalences were determined using integrase sequences from 17302 INSTI-naive and 2450 INSTI-treated persons; 53.3% of the INSTI-naive sequences and 20.0% of INSTI-treated sequences were from non-B subtypes. Approximately 10% of sequences were from persons who received dolutegravir alone or a first-generation INSTI followed by dolutegravir. RESULTS Fifty-nine previously recognized (or established) INSTI-resistance mutations were present on one or more of four published expert lists. They were classified into three main non-overlapping groups: 29 relatively common non-polymorphic mutations, occurring in five or more individuals and significantly selected by INSTI treatment; 8 polymorphic mutations; and 22 rare mutations. Among the 29 relatively common INSTI-selected mutations, 24 emerged as candidates for inclusion on a list of INSTI surveillance drug-resistance mutations: T66A/I/K, E92G/Q, G118R, F121Y, E138A/K/T, G140A/C/S, Y143C/H/R/S, S147G, Q148H/R/K, N155H, S230R and R263K. CONCLUSIONS A set of 24 non-polymorphic INSTI-selected mutations is likely to be useful for quantifying INSTI-associated TDR. This list may require updating as more sequences become available from INSTI-experienced persons infected with HIV-1 non-subtype B viruses and/or receiving dolutegravir.
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Affiliation(s)
- Philip L Tzou
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Soo-Yon Rhee
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Diane Descamps
- Université de Paris, IAME, INSERM, F-75018, Paris, France; AP-HP, Hôpital Bichat, Laboratoire de Virologie, F-75018, Paris, France
| | - Dana S Clutter
- Kaiser-Permanente Medical Care Program - Northern California, South San Francisco, CA, USA
| | - Bradley Hare
- Kaiser-Permanente Medical Care Program - Northern California, San Francisco, CA, USA
| | - Orna Mor
- Central Virology Laboratory, Sheba Medical Center, Ministry of Health, Ramat-Gan, Israel and Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv, Israel
| | - Maxime Grude
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Department of Virology, F-75013, Paris, France
| | - Neil Parkin
- Data First Consulting Inc., Sebastopol, CA, USA
| | | | - Silvia Bertagnolio
- Department of HIV and Global Hepatitis Programme, WHO, Geneva, Switzerland
| | | | - P Richard Harrigan
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Anna Maria Geretti
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Anne-Geneviève Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Department of Virology, F-75013, Paris, France
| | - Robert W Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
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Mbhele N, Chimukangara B, Gordon M. HIV-1 integrase strand transfer inhibitors: a review of current drugs, recent advances and drug resistance. Int J Antimicrob Agents 2021; 57:106343. [PMID: 33852932 DOI: 10.1016/j.ijantimicag.2021.106343] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 03/30/2021] [Accepted: 04/03/2021] [Indexed: 12/22/2022]
Abstract
Antiretroviral therapy has been imperative in controlling the human immunodeficiency virus (HIV) epidemic. Most low- and middle-income countries have used nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTIs) and protease inhibitors extensively in the treatment of HIV. However, integrase strand transfer inhibitors (INSTIs) are becoming more common. Since their identification as a promising therapeutic drug, significant progress has been made that has led to the approval of five INSTIs by the US Food and Drug Administration (FDA), i.e. dolutegravir (DTG), raltegravir (RAL), elvitegravir (EVG), bictegravir (BIC) and cabotegravir (CAB). INSTIs have been shown to effectively halt HIV-1 replication and are commended for having a higher genetic barrier to resistance compared with NRTIs and NNRTIs. More interestingly, DTG has shown a higher genetic barrier to resistance compared with RAL and EVG, and CAB is being used as the first long-acting agent in HIV-1 treatment. Considering the increasing interest in INSTIs for HIV-1 treatment, we focus our review on the retroviral integrase, development of INSTIs and their mode of action. We also discuss each of the INSTI drugs, including potential drug resistance and known side effects.
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Affiliation(s)
- Nokuzola Mbhele
- KwaZulu-Natal Research, Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Doris Duke Medical Research Institute, Durban, South Africa
| | - Benjamin Chimukangara
- KwaZulu-Natal Research, Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Doris Duke Medical Research Institute, Durban, South Africa; Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa; Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, Durban, South Africa
| | - Michelle Gordon
- KwaZulu-Natal Research, Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Doris Duke Medical Research Institute, Durban, South Africa.
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López P, Tirado G, Arias A, Sánchez R, Rodríguez-López ER, Rivera-Amill V. Short Communication: Integrase Strand Transfer Inhibitors Drug Resistance Mutations in Puerto Rico HIV-Positive Individuals. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18052719. [PMID: 33800269 PMCID: PMC7967446 DOI: 10.3390/ijerph18052719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/29/2021] [Accepted: 02/02/2021] [Indexed: 11/16/2022]
Abstract
The HIV-1 integrase viral protein is responsible for incorporating the viral DNA into the genomic DNA. The inhibition of viral integration into host cell DNA is part of recent therapeutic procedures. Combination therapy with protease and reverse transcriptase inhibitors has demonstrated good synergistic results in reducing viral replication. The purpose of this study is to assess the occurrence of integrase drug resistance mutations from the period comprising 2013 through 2018 in Puerto Rico (PR). We analyzed 131 nucleotide sequences available in our HIV genotyping database, and we performed drug resistance mutation analyses using the Stanford HIV Drug Resistance Database. Twenty-one sequences (16.03%) harbored major or resistance-associated mutations. We identified the Q148HKR, G140S, Y143R, N155H, S147G, and E138EA major drug resistance mutations and the D232DN, T97TA, E157Q, G163GART accessory mutations. We detected high-level drug resistance to Elvitegravir and Raltegravir (76.19% and 85.71%). Moreover, we identified sequences harboring drug resistance mutations that could provide resistance to Dolutegravir. The transmission of strains with integrase antiretroviral resistance has been previously documented in treatment naïve patients. Given the increase of patients treated with integrase inhibitors, surveillance of drug resistance mutations is an essential aspect of PR's clinical management of HIV infection.
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Mulato A, Acosta R, Chang S, Martin R, Yant SR, Cihlar T, White K. Simulating HIV Breakthrough and Resistance Development During Variable Adherence to Antiretroviral Treatment. J Acquir Immune Defic Syndr 2021; 86:369-377. [PMID: 33196554 DOI: 10.1097/qai.0000000000002562] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 10/26/2020] [Indexed: 01/04/2023]
Abstract
BACKGROUND Barriers to lifelong HIV-1 suppression by antiretrovirals include poor adherence and drug resistance; regimens with higher tolerance to missed doses (forgiveness) would be beneficial to patients. To model short-term nonadherence, in vitro experiments monitoring viral breakthrough (VB) and resistance development were conducted. METHODS HIV breakthrough experiments simulated drug exposures at full adherence or suboptimal adherence to bictegravir+emtricitabine+tenofovir alafenamide (BIC+FTC+TAF) or dolutegravir + lamivudine (DTG+3TC). MT-2 cells were infected with wild-type or low frequency M184V HIV-1, exposed to drug combinations, monitored for VB, and rebound virus was deep sequenced. Drug concentrations were determined using human plasma-free adjusted clinical trough concentrations (Cmin), at simulated Cmin after missing 1 to 3 consecutive doses (Cmin - 1 or Cmin - 2, and Cmin - 3) based on drug or active metabolite half-lives. RESULTS Cultures infected with wild-type or low frequency M184V HIV-1 showed no VB with BIC+FTC+TAF at drug concentrations corresponding to Cmin, Cmin - 1, or Cmin - 2 but breakthrough did occur in 26 of 36 cultures at Cmin - 3, where the M184V variant emerged in one culture. Experiments using DTG + 3TC prevented most breakthrough at Cmin concentrations (9/60 had breakthrough) but showed more breakthroughs as drug concentrations decreased (up to 36/36) and variants associated with resistance to both drugs emerged in some cases. CONCLUSIONS These in vitro VB results suggest that the high potency, long half-lives, and antiviral synergy provided by the BIC/FTC/TAF triple therapy regimen may protect from viral rebound and resistance development after short-term lapses in drug adherence.
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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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Aquaro S, Borrajo A, Pellegrino M, Svicher V. Mechanisms underlying of antiretroviral drugs in different cellular reservoirs with a focus on macrophages. Virulence 2021; 11:400-413. [PMID: 32375558 PMCID: PMC7219522 DOI: 10.1080/21505594.2020.1760443] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Ongoing with current combinations of antiretroviral drugs for the treatment of Human Immunodeficiency Virus (HIV) infection can successfully maintain long-term suppression of HIV-1 replication in plasma. Still, none of these therapies is capable of extinguishing the virus from the long-lived cellular reservoir, including monocyte-derived macrophages (MDM), that means the principal obstacle to HIV cure. MDM are widely distributed in all tissues and organs, including central system nervous (CNS) where they represent the most frequent HIV-infected cells that means the principal obstacle to HIV cure. Current FDA-approved antiretroviral drugs target viral reverse transcriptase, protease, integrase, and entry processes (coreceptor or fusion blockade). It is desirable to continue to develop new antiretrovirals directed against alternative targets in the virus lifecycle in order to further optimize therapeutic options, overcome resistance to existing medications, and potentially contribute to the elimination of viral reservoirs.This review provides a comprehensive overview of the activity of antiretroviral drugs (classical and upcoming) in monocytes-derived macrophages (MDM). Defining the antiviral activity of these drugs in this important cellular HIV-1 reservoir provides crucial hints about their efficacy in HIV-1 infected patients.
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Affiliation(s)
- Stefano Aquaro
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Ana Borrajo
- Department of Experimental Medicine, University of Rome Tor Vergata, Roma, Italy.,Department of Microbiology and Parasitology, Faculty of Pharmacy, Complutense University of Madrid, Madrid, Spain
| | - Michele Pellegrino
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Valentina Svicher
- Department of Experimental Medicine, University of Rome Tor Vergata, Roma, Italy
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Smith SJ, Zhao XZ, Passos DO, Lyumkis D, Burke TR, Hughes SH. Integrase Strand Transfer Inhibitors Are Effective Anti-HIV Drugs. Viruses 2021; 13:v13020205. [PMID: 33572956 PMCID: PMC7912079 DOI: 10.3390/v13020205] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/20/2021] [Accepted: 01/25/2021] [Indexed: 12/12/2022] Open
Abstract
Integrase strand transfer inhibitors (INSTIs) are currently recommended for the first line treatment of human immunodeficiency virus type one (HIV-1) infection. The first-generation INSTIs are effective but can select for resistant viruses. Recent advances have led to several potent second-generation INSTIs that are effective against both wild-type (WT) HIV-1 integrase and many of the first-generation INSTI-resistant mutants. The emergence of resistance to these new second-generation INSTIs has been minimal, which has resulted in alternative treatment strategies for HIV-1 patients. Moreover, because of their high antiviral potencies and, in some cases, their bioavailability profiles, INSTIs will probably have prominent roles in pre-exposure prophylaxis (PrEP). Herein, we review the current state of the clinically relevant INSTIs and discuss the future outlook for this class of antiretrovirals.
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Affiliation(s)
- Steven J. Smith
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA;
| | - Xue Zhi Zhao
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; (X.Z.Z.); (T.R.B.J.)
| | - Dario Oliveira Passos
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; (D.O.P.); (D.L.)
| | - Dmitry Lyumkis
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; (D.O.P.); (D.L.)
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Terrence R. Burke
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; (X.Z.Z.); (T.R.B.J.)
| | - Stephen H. Hughes
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA;
- Correspondence:
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Abstract
A regimen comprising extended release injectable suspensions of cabotegravir and rilpivirine for concurrent administration (CABENUVA™) is being developed by ViiV Healthcare and Janssen Pharmaceutica (Janssen) as a complete regimen for HIV infection. Based on the results of the ATLAS and FLAIR trials, the regimen was recently approved in Canada for the treatment of HIV-1 infection in adults to replace current antiretroviral therapy in patients who are virologically stable and suppressed. This article summarizes the milestones in the development of co-packaged cabotegravir and rilpivirine leading to this first approval.
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Affiliation(s)
- A Markham
- Springer Nature, Private Bag 65901, Mairangi Bay, Auckland, 0754, New Zealand.
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Perazzolo S, Mandal S, Prathipati PK, Destache CJ. Bictegravir Plus Tenofovir Alafenamide Nanoformulation as a Long-Acting Pre-Exposure Prophylaxis Regimen: Application of Modeling to Design Non-Human Primate Pharmacokinetic Experiments. Front Pharmacol 2020; 11:603242. [PMID: 33390993 PMCID: PMC7775496 DOI: 10.3389/fphar.2020.603242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 11/24/2020] [Indexed: 12/13/2022] Open
Abstract
Bictegravir (BIC) and tenofovir alafenamide fumarate (TAF), two potent anti-HIV drugs, had been nanoformulated (nBIC-TAF) to achieve once-a-month PrEP coverage. In-vivo mouse experiments for nBIC-TAF exhibited favorable subcutaneous (SC) pharmacokinetics. To probe the clinical suitability of the nBIC-TAF, as the next step, we intend to study nBIC-TAF in non-human primates (NHP), as the best preclinical model to foster clinical trials. Before entering an expensive NHP study, however, we seek to improve our a priori understanding about nBIC-TAF in higher species, having just mouse data. The mechanism-based pharmacokinetic modeling (MBPK) has been used as an appropriate method for pharmacokinetic modeling and interspecies scaling for nanoformulations. Via the use of MBPK, in this work, we created a model for nBIC-TAF able to predict plasma concentration-time curves in NHP. BIKTARVY is a daily oral combination of BIC, TAF, and emtricitabine (Gilead Science, CA), approved for HIV therapy. Using BIKTARVY equivalent dosages (from their NHP studies), we predicted that, following just one SC dose of nBIC-TAF in NHP, both BIC and tenofovir will have detectable and above in vitro efficacy levels for 28 days. Furthermore, the MBPK was able to provide a mechanistic explanation regarding the long-acting mechanism characterizing nBIC-TAF: nanoparticles stores in the SC space from which drugs slowly dissociate. Dissociated drugs in the SC space then buffer the plasma pool over time, yielding an extended-release effect in the plasma. Overall, we predicted for nBIC-TAF a promising long-acting pharmacokinetic in NHP, potentially usable as monthly PrEP. These results will help investigators to gain confidence for facing regulatory submissions at early stages.
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Affiliation(s)
- Simone Perazzolo
- Nanomath LLC and University of Washington, Seattle, WA, United States
| | - Subhra Mandal
- School of Pharmacy, Creighton University, Omaha, NE, United States
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Canetti D, Spagnuolo V. An evaluation of cabotegravir for HIV treatment and prevention. Expert Opin Pharmacother 2020; 22:403-414. [PMID: 33112699 DOI: 10.1080/14656566.2020.1843635] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Introduction: Oral pre-exposure prophylaxis (PrEP) and antiretroviral therapy (ART) represent the cornerstones of HIV infection prevention and treatment. However, despite their high efficacy, the need to take daily oral pill(s) negatively impacts long-term patient adherence. In some cases, it can also be associated with drug-drug interactions and adverse gastrointestinal effects, as well as being a constant reminder to individuals of their HIV status. The availability of long-acting non-orally administered antiretroviral drugs could, therefore, be extremely useful. Cabotegravir (CAB) is a second-generation integrase strand transfer inhibitor, characterized by a relatively high genetic barrier and good antiretroviral potency, which is administrable as a long-acting injectable suspension (LAI CAB).Areas covered: The authors present and discuss the efficacy and available safety data of LAI CAB, either when co-administered with rilpivirine (RPV; LAI CAB + RPV) for the treatment of HIV infection, or when used as single agent for PrEP.Expert opinion: Cabotegravir has the potential to play a primary role in the treatment and prevention of HIV infection. The future availability of LAI CAB + RPV and LAI CAB may mark the beginning of an era of LAI ART and PrEP, respectively.
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Affiliation(s)
- Diana Canetti
- Division of Infectious Diseases, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
| | - Vincenzo Spagnuolo
- Division of Infectious Diseases, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy.,School of Medicine, Vita-Salute San Raffaele University, Milan, Italy
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