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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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Corona A, Meleddu R, Delelis O, Subra F, Cottiglia F, Esposito F, Distinto S, Maccioni E, Tramontano E. 5-Nitro-3-(2-(4-phenylthiazol-2-yl)hydrazineylidene)indolin-2-one derivatives inhibit HIV-1 replication by a multitarget mechanism of action. Front Cell Infect Microbiol 2023; 13:1193280. [PMID: 37424782 PMCID: PMC10328743 DOI: 10.3389/fcimb.2023.1193280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/25/2023] [Indexed: 07/11/2023] Open
Abstract
In the effort to identify and develop new HIV-1 inhibitors endowed with innovative mechanisms, we focused our attention on the possibility to target more than one viral encoded enzymatic function with a single molecule. In this respect, we have previously identified by virtual screening a new indolinone-based scaffold for dual allosteric inhibitors targeting both reverse transcriptase-associated functions: polymerase and RNase H. Pursuing with the structural optimization of these dual inhibitors, we synthesized a series of 35 new 3-[2-(4-aryl-1,3-thiazol-2-ylidene)hydrazin-1-ylidene]1-indol-2-one and 3-[3-methyl-4-arylthiazol-2-ylidene)hydrazine-1-ylidene)indolin-2-one derivatives, which maintain their dual inhibitory activity in the low micromolar range. Interestingly, compounds 1a, 3a, 10a, and 9b are able to block HIV-1 replication with EC50 < 20 µM. Mechanism of action studies showed that such compounds could block HIV-1 integrase. In particular, compound 10a is the most promising for further multitarget compound development.
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Affiliation(s)
- Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
| | - Rita Meleddu
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
| | - Olivier Delelis
- Laboratory of Biology and Applied Pharmacology (LBPA), Ecole Normale Supérieure (ENS) Cachan, Centre National de la Recherche Scientifique (CNRS), Cachan, France
| | - Frederic Subra
- Laboratory of Biology and Applied Pharmacology (LBPA), Ecole Normale Supérieure (ENS) Cachan, Centre National de la Recherche Scientifique (CNRS), Cachan, France
| | - Filippo Cottiglia
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
| | - Simona Distinto
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
| | - Elias Maccioni
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
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Sayan M, Yildirim FS, Akhan S, Karaoglan I, Akalin H. Integrase Strand Transfer Inhibitor (INSTI) Genotypic Resistance Analysis in Treatment-nNaive, INSTI Free Antiretroviral-Experienced and INSTI-Experienced Turkish Patients Infected with HIV-1. Curr HIV Res 2022; 20:184-192. [PMID: 35240975 DOI: 10.2174/1570162x20666220303104509] [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: 10/10/2021] [Revised: 01/10/2022] [Accepted: 01/28/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND AND OBJECTIVE Integrase strand transfer inhibitors (INSTIs) are currently the standard of practice for first-line HIV therapy for most patients. We evaluated the mutations associated with INSTI resistance in naive HIV-1 infected patients and treated them with antiretrovirals (ART). METHODS The study, conducted in the 2018 - 2020 period, included 50 ART-naïve patients, 69 INSTI free ART-experienced patients, and 82 INSTI-experienced patients. INSTI resistance mutations were interpreted using the Stanford University HIVdb Program algorithm. RESULTS INSTI resistance was not detected in ART naïve patients. At least one INSTI resistance mutation was detected in 10% of the INSTI-free patients and 29% of the INSTI-treated patients. Major INSTI-mutations E138K, Y143R, S147G, Q148R, N155H, and E157Q were found in raltegravir. Additional mutations, E92Q, E138K, G140A, S147G, and Q148R were found in elvitegravir; E192Q, E138K/T, G140A/S, S147G, Q148H/R, N155H, E157Q were found in dolutegravir (DTG) experienced patients. According to all drug classes, drug resistance mutation prevalences were determined at the rate of 60%, 46%, and 46% in the RAL, EVG, and DTG groups, respectively. CONCLUSION Our findings provide data for treatment and resistance management of INSTIs and may provide feedback for INSTIs resistance surveillance consensus-building efforts. In viral rebound under INSTI treatment, INSTI-resistant mutations follow typical INSTI resistance pathways and high resistance rates. INSTI resistance genotypic analysis should be considered before any DTG-based regimes can be initiated in the future, and reduced DTG susceptibility should be carefully monitored and investigated.
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Affiliation(s)
- Murat Sayan
- Kocaeli University, Research and Education Hospital, PCR Laboratory, Kocaeli, Turkey
- Near East University, DESAM Research Institute, Nicosia, Northern Cyprus
| | - Figen Sarigul Yildirim
- Health Sciences University, Antalya Research and Education Hospital, Department of Infectious Diseases, Antalya, Turkey
| | - Sila Akhan
- Kocaeli University, Medical Faculty, Department of Infectious Diseases and Clinical Microbiology, Kocaeli, Turkey
| | - Ilkay Karaoglan
- Gaziantep University, Medical Faculty, Department of Infectious Diseases and Clinical Microbiology, Gaziantep, Turkey
| | - Halis Akalin
- Uludağ University, Medical Faculty, Department of Infectious Diseases and Clinical Microbiology, Bursa, Turkey
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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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Rhee SY, Grant PM, Tzou PL, Barrow G, Harrigan PR, Ioannidis JPA, Shafer RW. A systematic review of the genetic mechanisms of dolutegravir resistance. J Antimicrob Chemother 2020; 74:3135-3149. [PMID: 31280314 PMCID: PMC6798839 DOI: 10.1093/jac/dkz256] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/06/2019] [Accepted: 05/22/2019] [Indexed: 12/17/2022] Open
Abstract
Background Characterizing the mutations selected by the integrase strand transfer inhibitor (INSTI) dolutegravir and their effects on susceptibility is essential for identifying viruses less likely to respond to dolutegravir therapy and for monitoring persons with virological failure (VF) on dolutegravir therapy. Methods We systematically reviewed dolutegravir resistance studies to identify mutations emerging under dolutegravir selection pressure, the effect of INSTI resistance mutations on in vitro dolutegravir susceptibility, and the virological efficacy of dolutegravir in antiretroviral-experienced persons. Results and conclusions We analysed 14 studies describing 84 in vitro passage experiments, 26 studies describing 63 persons developing VF plus INSTI resistance mutations on a dolutegravir-containing regimen, 41 studies describing dolutegravir susceptibility results, and 22 clinical trials and 16 cohort studies of dolutegravir-containing regimens. The most common INSTI resistance mutations in persons with VF on a dolutegravir-containing regimen were R263K, G118R, N155H and Q148H/R, with R263K and G118R predominating in previously INSTI-naive persons. R263K reduced dolutegravir susceptibility ∼2-fold. G118R generally reduced dolutegravir susceptibility >5-fold. The highest levels of reduced susceptibility occurred in viruses containing Q148 mutations in combination with G140 and/or E138 mutations. Dolutegravir two-drug regimens were highly effective for first-line therapy and for virologically suppressed persons provided dolutegravir’s companion drug was fully active. Dolutegravir three-drug regimens were highly effective for salvage therapy in INSTI-naive persons provided one or more of dolutegravir’s companion drugs was fully active. However, dolutegravir monotherapy in virologically suppressed persons and functional dolutegravir monotherapy in persons with active viral replication were associated with a non-trivial risk of VF plus INSTI resistance mutations.
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Affiliation(s)
- Soo-Yon Rhee
- Department of Medicine, Stanford University, Stanford, CA, USA
| | - Philip M Grant
- Department of Medicine, Stanford University, Stanford, CA, USA
| | - Philip L Tzou
- Department of Medicine, Stanford University, Stanford, CA, USA
| | - Geoffrey Barrow
- Centre for HIV/AIDS Research, Education and Services (CHARES), Department of Medicine, University of the West Indies, Kingston, Jamaica
| | - P Richard Harrigan
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - John P A Ioannidis
- Department of Medicine, Stanford University, Stanford, CA, USA.,Meta-Research Innovation Center at Stanford, Stanford University, Stanford, CA, USA
| | - Robert W Shafer
- Department of Medicine, Stanford University, Stanford, CA, USA
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Orta-Resendiz A, Rodriguez-Diaz RA, Angulo-Medina LA, Hernandez-Flores M, Soto-Ramirez LE. HIV-1 acquired drug resistance to integrase inhibitors in a cohort of antiretroviral therapy multi-experienced Mexican patients failing to raltegravir: a cross-sectional study. AIDS Res Ther 2020; 17:6. [PMID: 32041622 PMCID: PMC7011548 DOI: 10.1186/s12981-020-0262-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 01/30/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In resource-limited settings, multi-experienced HIV infected patients are often prescribed raltegravir for salvage therapy. Patients failing raltegravir-containing regimens require other drugs including other integrase inhibitors. In this context, real-life data about the resistance and cross-resistance pathways between integrase inhibitors is limited. The aim of this study was to investigate integrase resistance pathways in a cohort of Mexican multi-experienced patients failing of a raltegravir-containing salvage regimen. METHODS Twenty-five plasma samples from subjects failing antiretroviral regimens which included raltegravir were obtained from various healthcare centres from 2009 to 2017 in Mexico. Antiretroviral history and demographics were collected. Samples were processed for integrase resistance genotyping testing by sequencing. The viral sequences were analysed with the Stanford HIV drug resistance database algorithm. Data was analysed with SPSS Statistics software. RESULTS We found a mean viral load of 4.17 log10 c/mL (SD 1.11) at the time of virologic failure. Forty-eight percent of the samples were raltegravir resistant. The Y143R/H/C substitutions were the most prevalent, followed by the N155H, and both Q148H/K and G140S/A in the same proportion. The Q148 + G140 combination was found in (12%) of the samples. Cross-resistance to elvitegravir was found in 83.3% and in 18.2% for both dolutegravir and bictegravir. Thirteen samples (52%) were susceptible to the four integrase strand-transfer inhibitors. CONCLUSIONS Our findings suggest a high occurrence of resistance and cross-resistance to other integrase inhibitors among multi-experienced subjects failing raltegravir. We found a modestly lower proportion of cross-resistance to dolutegravir than data from clinical trials. Likely this drug could be used for salvage therapy. Explanations for the absence of mutations in half of the samples, other than reduced adherence, should be further investigated. Close surveillance is needed.
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Achieng L, Riedel DJ. Dolutegravir Resistance and Failure in a Kenyan Patient. J Infect Dis 2019; 219:165-167. [PMID: 30165703 DOI: 10.1093/infdis/jiy436] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Loice Achieng
- Department of Clinical Medicine and Therapeutics, University of Nairobi, Kenya
| | - David J Riedel
- Institute of Human Virology and Division of Infectious Diseases, University of Maryland School of Medicine, Baltimore
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Malet I, Ambrosio FA, Subra F, Herrmann B, Leh H, Bouger MC, Artese A, Katlama C, Talarico C, Romeo I, Alcaro S, Costa G, Deprez E, Calvez V, Marcelin AG, Delelis O. Pathway involving the N155H mutation in HIV-1 integrase leads to dolutegravir resistance. J Antimicrob Chemother 2019; 73:1158-1166. [PMID: 29373677 DOI: 10.1093/jac/dkx529] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/14/2017] [Indexed: 11/13/2022] Open
Abstract
Background Dolutegravir, an integrase strand-transfer inhibitor (STI), shows a high genetic barrier to resistance. Dolutegravir is reported to be effective against viruses resistant to raltegravir and elvitegravir. In this study, we report the case of a patient treated with dolutegravir monotherapy. Failure of dolutegravir treatment was observed concomitant with the appearance of N155H-K211R-E212T mutations in the integrase (IN) gene in addition to the polymorphic K156N mutation that was present at baseline in this patient. Methods The impact of N155H-K156N-K211R-E212T mutations was studied in cell-free, culture-based assays and by molecular modelling. Results Cell-free and culture-based assays confirm that selected mutations in the patient, in the context of the polymorphic mutation K156N present at the baseline, lead to high resistance to dolutegravir requiring that the analysis be done at timepoints longer than usual to properly reveal the results. Interestingly, the association of only N155H and K156N is sufficient for significant resistance to dolutegravir. Modelling studies showed that dolutegravir is less stable in IN/DNA complexes with respect to the WT sequence. Conclusions Our results indicate that the stability of STI IN/DNA complexes is an important parameter that must be taken into account when evaluating dolutegravir resistance. This study confirms that a pathway including N155H can be selected in patients treated with dolutegravir with the help of the polymorphic K156N that acts as a secondary mutation that enhances the resistance to dolutegravir.
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Affiliation(s)
- Isabelle Malet
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP UMRS 1136), 75013 Paris, France.,Department of Virology, AP-HP, Hôpital Pitié-Salpêtrière, Paris, France
| | - Francesca A Ambrosio
- Department of Health Sciences, University "Magna Græcia" of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Frédéric Subra
- LBPA, ENS Cachan, CNRS UMR8113, IDA FR3242, Université Paris-Saclay, F-94235 Cachan, France
| | - Béatrice Herrmann
- LBPA, ENS Cachan, CNRS UMR8113, IDA FR3242, Université Paris-Saclay, F-94235 Cachan, France
| | - Hervé Leh
- LBPA, ENS Cachan, CNRS UMR8113, IDA FR3242, Université Paris-Saclay, F-94235 Cachan, France
| | - Marie-Christine Bouger
- LBPA, ENS Cachan, CNRS UMR8113, IDA FR3242, Université Paris-Saclay, F-94235 Cachan, France
| | - Anna Artese
- Department of Health Sciences, University "Magna Græcia" of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Christine Katlama
- Department of Infectious Diseases, Hôpital Pitié Salpetriere, Paris, France
| | - Carmine Talarico
- Department of Health Sciences, University "Magna Græcia" of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Isabella Romeo
- Department of Health Sciences, University "Magna Græcia" of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Stefano Alcaro
- Department of Health Sciences, University "Magna Græcia" of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Giosuè Costa
- Department of Health Sciences, University "Magna Græcia" of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Eric Deprez
- LBPA, ENS Cachan, CNRS UMR8113, IDA FR3242, Université Paris-Saclay, F-94235 Cachan, France
| | - Vincent Calvez
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP UMRS 1136), 75013 Paris, France.,Department of Virology, AP-HP, Hôpital Pitié-Salpêtrière, Paris, France
| | - Anne-Geneviève Marcelin
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP UMRS 1136), 75013 Paris, France.,Department of Virology, AP-HP, Hôpital Pitié-Salpêtrière, Paris, France
| | - Olivier Delelis
- LBPA, ENS Cachan, CNRS UMR8113, IDA FR3242, Université Paris-Saclay, F-94235 Cachan, France
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Yang F, Zheng G, Fu T, Li X, Tu G, Li YH, Yao X, Xue W, Zhu F. Prediction of the binding mode and resistance profile for a dual-target pyrrolyl diketo acid scaffold against HIV-1 integrase and reverse-transcriptase-associated ribonuclease H. Phys Chem Chem Phys 2019; 20:23873-23884. [PMID: 29947629 DOI: 10.1039/c8cp01843j] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The rapid emergence of drug-resistant variants is one of the most common causes of highly active antiretroviral therapeutic (HAART) failure in patients infected with HIV-1. Compared with the existing HAART, the recently developed pyrrolyl diketo acid scaffold targeting both HIV-1 integrase (IN) and reverse transcriptase-associated ribonuclease H (RNase H) is an efficient approach to counteract the failure of anti-HIV treatment due to drug resistance. However, the binding mode and potential resistance profile of these inhibitors with important mechanistic principles remain poorly understood. To address this issue, an integrated computational method was employed to investigate the binding mode of inhibitor JMC6F with HIV-1 IN and RNase H. By using per-residue binding free energy decomposition analysis, the following residues: Asp64, Thr66, Leu68, Asp116, Tyr143, Gln148 and Glu152 in IN, Asp443, Glu478, Trp536, Lys541 and Asp549 in RNase H were identified as key residues for JMC6F binding. And then computational alanine scanning was carried to further verify the key residues. Moreover, the resistance profile of the currently known major mutations in HIV-1 IN and 2 mutations in RNase H against JMC6F was predicted by in silico mutagenesis studies. The results demonstrated that only three mutations in HIV-1 IN (Y143C, Q148R and N155H) and two mutations in HIV-1 RNase H (Y501R and Y501W) resulted in a reduction of JMC6F potency, thus indicating their potential role in providing resistance to JMC6F. These data provided important insights into the binding mode and resistance profile of the inhibitors with a pyrrolyl diketo acid scaffold in HIV-1 IN and RNase H, which would be helpful for the development of more effective dual HIV-1 IN and RNase H inhibitors.
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Affiliation(s)
- Fengyuan Yang
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China.
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10
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Abstract
A once-daily tablet formulation (Isentress® HD; Isentress® 600 mg) of the integrase strand transfer inhibitor raltegravir is now available for the treatment of HIV-1 infection. The 600 mg tablet has improved bioavailability versus the existing twice-daily 400 mg tablet (due, at least in part, to differences in tablet dissolution) and the recommended dosage is 1200 mg (i.e. two 600 mg tablets) once daily. In combination with emtricitabine/tenofovir disoproxil fumarate in treatment-naïve adults, once-daily raltegravir 1200 mg provided virological suppression non-inferior to that seen with twice-daily raltegravir 400 mg over 48 and 96 weeks in the phase 3 ONCEMRK trial. The once-daily raltegravir regimen was also generally well tolerated in this study, displaying a tolerability profile similar to that of the twice-daily regimen. The once-daily tablet simplifies and improves the convenience of raltegravir regimens, although its impact on adherence has yet to be determined. Thus, once-daily raltegravir tablets are a convenient alternative to twice-daily raltegravir tablets for the treatment of HIV-1, further expanding the therapeutic options available to meet the diverse needs of this patient population.
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11
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Reply to Das and Berkhout, "How Polypurine Tract Changes in the HIV-1 RNA Genome Can Cause Resistance against the Integrase Inhibitor Dolutegravir". mBio 2018; 9:mBio.00623-18. [PMID: 29844110 PMCID: PMC5974467 DOI: 10.1128/mbio.00623-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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HIV drug resistance against strand transfer integrase inhibitors. Retrovirology 2017; 14:36. [PMID: 28583191 PMCID: PMC5460515 DOI: 10.1186/s12977-017-0360-7] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 05/30/2017] [Indexed: 12/03/2022] Open
Abstract
Integrase strand transfer inhibitors (INSTIs) are the newest class of antiretroviral drugs to be approved for treatment and act by inhibiting the essential HIV protein integrase from inserting the viral DNA genome into the host cell’s chromatin. Three drugs of this class are currently approved for use in HIV-positive individuals: raltegravir (RAL), elvitegravir (EVG), and dolutegravir (DTG), while cabotegravir (CAB) and bictegravir (BIC) are currently in clinical trials. RAL and EVG have been successful in clinical settings but have relatively low genetic barriers to resistance. Furthermore, they share a high degree of cross-resistance, which necessitated the development of so-called second-generation drugs of this class (DTG, CAB, and BIC) that could retain activity against these resistant variants. In vitro selection experiments have been instrumental to the clinical development of INSTIs, however they cannot completely recapitulate the situation in an HIV-positive individual. This review summarizes and compares all the currently available information as it pertains to both in vitro and in vivo selections with all five INSTIs, and the measured fold-changes in resistance of resistant variants in in vitro assays. While the selection of resistance substitutions in response to RAL and EVG bears high similarity in patients as compared to laboratory studies, there is less concurrence regarding the “second-generation” drugs of this class. This highlights the unpredictability of HIV resistance to these inhibitors, which is of concern as CAB and BIC proceed in their clinical development.
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Laskey SB, Siliciano RF. Quantitative evaluation of the antiretroviral efficacy of dolutegravir. JCI Insight 2016; 1:e90033. [PMID: 27882352 DOI: 10.1172/jci.insight.90033] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The second-generation HIV-1 integrase strand transfer inhibitor (InSTI) dolutegravir (DTG) has had a major impact on the treatment of HIV-1 infection. Here we describe important but previously undetermined pharmacodynamic parameters for DTG. We show that the dose-response curve slope, which indicates cooperativity and is a major determinant of antiviral activity, is higher for DTG than for first-generation InSTIs. This steepness does not reflect inhibition of multiple steps in the HIV-1 life cycle, as is the case for allosteric integrase inhibitors and HIV-1 protease inhibitors. We also show that degree of independence, a metric of interaction favorability between antiretroviral drugs, is high for DTG and nucleoside reverse transcriptase inhibitors. Finally, we demonstrate poor selective advantage for HIV-1 bearing InSTI resistance mutations. Selective advantage, which incorporates both the magnitude of resistance conferred by a mutation and its fitness cost, explains the high genetic barrier to DTG resistance. Together, these parameters provide an explanation for the remarkable clinical success of DTG.
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Affiliation(s)
- Sarah B Laskey
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Howard Hughes Medical Institute, Baltimore, Maryland, USA
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Corona A, di Leva FS, Rigogliuso G, Pescatori L, Madia VN, Subra F, Delelis O, Esposito F, Cadeddu M, Costi R, Cosconati S, Novellino E, di Santo R, Tramontano E. New insights into the interaction between pyrrolyl diketoacids and HIV-1 integrase active site and comparison with RNase H. Antiviral Res 2016; 134:236-243. [PMID: 27659398 DOI: 10.1016/j.antiviral.2016.09.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/16/2016] [Accepted: 09/19/2016] [Indexed: 12/18/2022]
Abstract
HIV-1 integrase (IN) inhibitors are one of the most recent innovations in the treatment of HIV infection. The selection of drug resistance viral strains is however a still open issue requiring constant efforts to identify new anti-HIV-1 drugs. Pyrrolyl diketo acid (DKA) derivatives inhibit HIV-1 replication by interacting with the Mg2+ cofactors within the HIV-1 IN active site or within the HIV-1 reverse-transcriptase associated ribonuclease H (RNase H) active site. While the interaction mode of pyrrolyl DKAs with the RNase H active site has been recently reported and substantiated by mutagenesis experiments, their interaction within the IN active site still lacks a detailed understanding. In this study, we investigated the binding mode of four pyrrolyl DKAs to the HIV-1 IN active site by molecular modeling coupled with site-directed mutagenesis studies showing that the DKA pyrrolyl scaffold primarily interacts with the IN amino residues P145, Q146 and Q148. Importantly, the tested DKAs demonstrated good effectiveness against HIV-1 Raltegravir resistant Y143A and N155H INs, thus showing an interaction pattern with relevant differences if compared with the first generation IN inhibitors. These data provide precious insights for the design of new HIV inhibitors active on clinically selected Raltegravir resistant variants. Furthermore, this study provides new structural information to modulate IN and RNase H inhibitory activities for development of dual-acting anti-HIV agents.
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Affiliation(s)
- Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria SS554, 09042, Monserrato, Italy
| | - Francesco Saverio di Leva
- Department of Pharmacy, University of Naples "Federico II", Via Domenico Montesano, 49 80131, Naples, Italy
| | - Giuseppe Rigogliuso
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria SS554, 09042, Monserrato, Italy; LBPA, ENS Cachan, CNRS, 61 Avenue du président Wilson, 94235, Cachan Cedex, France
| | - Luca Pescatori
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, Piazzale Aldo Moro 5, 00185, Roma, Italy
| | - Valentina Noemi Madia
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, Piazzale Aldo Moro 5, 00185, Roma, Italy
| | - Frederic Subra
- LBPA, ENS Cachan, CNRS, 61 Avenue du président Wilson, 94235, Cachan Cedex, France
| | - Olivier Delelis
- LBPA, ENS Cachan, CNRS, 61 Avenue du président Wilson, 94235, Cachan Cedex, France
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria SS554, 09042, Monserrato, Italy
| | - Marta Cadeddu
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria SS554, 09042, Monserrato, Italy
| | - Roberta Costi
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, Piazzale Aldo Moro 5, 00185, Roma, Italy
| | - Sandro Cosconati
- DiSTABiF, Seconda Università di Napoli, Via Vivaldi, 43, 81100, Caserta, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples "Federico II", Via Domenico Montesano, 49 80131, Naples, Italy
| | - Roberto di Santo
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, Piazzale Aldo Moro 5, 00185, Roma, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria SS554, 09042, Monserrato, Italy.
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Dolutegravir-Selected HIV-1 Containing the N155H and R263K Resistance Substitutions Does Not Acquire Additional Compensatory Mutations under Drug Pressure That Lead to Higher-Level Resistance and Increased Replicative Capacity. J Virol 2015; 89:10482-8. [PMID: 26246578 DOI: 10.1128/jvi.01725-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 07/31/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED We have previously shown that the addition of the raltegravir/elvitegavir (RAL/EVG) primary resistance mutation N155H to the R263K dolutegravir (DTG) resistance mutation partially compensated for the fitness cost imposed by R263K while also slightly increasing DTG resistance in vitro (K. Anstett, T. Mesplede, M. Oliveira, V. Cutillas, and M. A. Wainberg, J Virol 89:4681-4684, 2015, doi:10.1128/JVI.03485-14). Since many patients failing RAL/EVG are given DTG as part of rescue therapy, and given that the N155H substitution often is found in combination with other compensatory resistance mutations in such individuals, we investigated the effects of multiple such substitutions within integrase (IN) on each of integrase function, HIV-1 infectivity, and levels of drug resistance. To this end, each of the L74M, E92Q, T97A, E157Q, and G163R substitutions were introduced into NL4.3 subtype B HIV-1 vectors harboring N155H and R263K in tandem [termed NL4.3IN(N155H/R263K)]. Relevant recombinant integrase enzymes also were expressed, and purified and biochemical assays of strand transfer efficiency as well as viral infectivity and drug resistance studies were performed. We found that the addition of T97A, E157Q, or G163R somewhat improved the affinity of INN155H/R263K for its target DNA substrate, while the presence of L74M or E92Q had a negative effect on this process. However, viral infectivity was significantly decreased from that of NL4.3IN(N155H/R263K) after the addition of each tertiary mutation, and no increases in levels of DTG resistance were observed. This work shows that the compensatory mutations that evolve after N155H under continued DTG or RAL/EVG pressure in patients are unable to improve either enzyme efficiency or viral infectivity in an N155H/R263K background. IMPORTANCE In contrast to other drugs, dolutegravir has not selected for resistance in HIV-positive individuals when used in first-line therapy. We had previously shown that HIV containing the primary raltegravir/elvitegravir resistance substitution N155H could select for R263K under dolutegravir pressure and that this virus was fit and displayed low-level resistance to dolutegravir (Anstett et al., J Virol 89: 4681-4684). Therefore, the current study aimed to uncover whether accessory mutations that appear after N155H in response to raltegravir/elvitegravir were compatible with N155H and R263K. We found, however, that the addition of a third mutation negatively impacted both the enzyme and the virus in terms of activity and infectivity without large shifts in integrase inhibitor resistance. Thus, it is unlikely that these substitutions would be selected under dolutegravir pressure. These data support the hypothesis that primary resistance against DTG cannot evolve through RAL/EVG resistance pathways and that the selection of R263K leads HIV into an evolutionary dead-end.
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