1
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Liu H, Gao Q, Zhang K, Xu M, Wang H, Wei D. Combining binding pocket mutagenesis and substrate tunnel engineering to improve an (R)-selective transaminase for the efficient synthesis of (R)-3-aminobutanol. Biochem Biophys Res Commun 2024; 731:150383. [PMID: 39024977 DOI: 10.1016/j.bbrc.2024.150383] [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: 03/27/2024] [Revised: 06/28/2024] [Accepted: 07/09/2024] [Indexed: 07/20/2024]
Abstract
(R)-selective transaminases have the potential to act as efficient biocatalysts for the synthesis of important pharmaceutical intermediates. However, their low catalytic efficiency and unfavorable equilibrium limit their industrial application. Seven (R)-selective transaminases were identified using homologous sequence mining. Beginning with the optimal candidate from Mycolicibacterium hippocampi, virtual mutagenesis and substrate tunnel engineering were performed to improve catalytic efficiency. The obtained variant, T282S/Q137E, exhibited 3.68-fold greater catalytic efficiency (kcat/Km) than the wild-type enzyme. Using substrate fed-batch and air sweeping processes, effective conversion of 100 mM 4-hydroxy-2-butanone was achieved with a conversion rate of 93 % and an ee value > 99.9 %. This study provides a basis for mutation of (R)-selective transaminases and offers an efficient biocatalytic process for the asymmetric synthesis of (R)-3-aminobutanol.
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Affiliation(s)
- He Liu
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Qian Gao
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Kaiyue Zhang
- Ludong University Laishan Experimental Middle School, 264000, China
| | - Meng Xu
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Hualei Wang
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
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2
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Liu H, Wang S, Xu M, Zhang K, Gao Q, Wang H, Wei D. Engineering an (R)-selective transaminase for asymmetric synthesis of (R)-3-aminobutanol. Bioorg Chem 2024; 146:107264. [PMID: 38492494 DOI: 10.1016/j.bioorg.2024.107264] [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: 01/20/2024] [Revised: 02/28/2024] [Accepted: 03/06/2024] [Indexed: 03/18/2024]
Abstract
(R)-selective transaminases show promise as catalysts for the asymmetric synthesis of chiral amines, which are building blocks of various small molecule drugs. However, their application is limited by poor substrate acceptance and low catalytic efficiency. Here, a potential (R)-selective transaminase from Fodinicurvata sediminis (FsTA) was identified through a substrate truncating strategy, and used as starting point for enzyme engineering toward catalysis of 4-hydroxy-2-butanone, a substrate that poses challenges in catalysis. Molecular docking and dynamics simulations revealed Y90 as the key residue responsible for poor substrate binding. Starting from the variant (Y90F, mut1) with initial activity, FsTA was systematically modified to improve substrate-binding through active site reshaping and consensus sequence strategy, yielding three variants (H30R, V152K, and Y156F) with improved activity. A quadruple mutation variant H30R/Y90F/V152K/Y156F (mut4) was also found to show a 7.95-fold greater catalytic efficiency (kcat/KM) than the initial variant mut1. Furthermore, mut4 also enhanced the thermostability of enzyme significantly, with the Tm value increasing by 10 °C. This variant also exhibited significantly improved activity toward a series of ketones that are either not accepted or poorly accepted by the wild-type. This study provides a basis for the rational design of an active to creating variants that can accommodate novel substrates.
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Affiliation(s)
- He Liu
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Shixi Wang
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Meng Xu
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Kaiyue Zhang
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Qian Gao
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Hualei Wang
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China.
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
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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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Du S, Hu X, Menéndez-Arias L, Zhan P, Liu X. Target-based drug design strategies to overcome resistance to antiviral agents: opportunities and challenges. Drug Resist Updat 2024; 73:101053. [PMID: 38301487 DOI: 10.1016/j.drup.2024.101053] [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: 10/31/2023] [Revised: 12/22/2023] [Accepted: 01/09/2024] [Indexed: 02/03/2024]
Abstract
Viral infections have a major impact in human health. Ongoing viral transmission and escalating selective pressure have the potential to favor the emergence of vaccine- and antiviral drug-resistant viruses. Target-based approaches for the design of antiviral drugs can play a pivotal role in combating drug-resistant challenges. Drug design computational tools facilitate the discovery of novel drugs. This review provides a comprehensive overview of current drug design strategies employed in the field of antiviral drug resistance, illustrated through the description of a series of successful applications. These strategies include technologies that enhance compound-target affinity while minimizing interactions with mutated binding pockets. Furthermore, emerging approaches such as virtual screening, targeted protein/RNA degradation, and resistance analysis during drug design have been harnessed to curtail the emergence of drug resistance. Additionally, host targeting antiviral drugs offer a promising avenue for circumventing viral mutation. The widespread adoption of these refined drug design strategies will effectively address the prevailing challenge posed by antiviral drug resistance.
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Affiliation(s)
- Shaoqing Du
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Xueping Hu
- Institute of Frontier Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Qingdao 266237, PR China
| | - Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid), Madrid, Spain.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China; China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China; China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
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6
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Sun Q, Biswas A, Lyumkis D, Levy R, Deng N. Elucidating the Molecular Determinants of the Binding Modes of a Third-Generation HIV-1 Integrase Strand Transfer Inhibitor: The Importance of Side Chain and Solvent Reorganization. Viruses 2024; 16:76. [PMID: 38257776 PMCID: PMC11154245 DOI: 10.3390/v16010076] [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: 11/25/2023] [Revised: 12/21/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024] Open
Abstract
The first- and second-generation clinically used HIV-1 integrase (IN) strand transfer inhibitors (INSTIs) are key components of antiretroviral therapy (ART), which work by blocking the integration step in the HIV-1 replication cycle that is catalyzed by a nucleoprotein assembly called an intasome. However, resistance to even the latest clinically used INSTIs is beginning to emerge. Developmental third-generation INSTIs, based on naphthyridine scaffolds, are promising candidates to combat drug-resistant viral variants. Among these novel INSTIs, compound 4f exhibits two distinct conformations when binding with intasomes from HIV-1 and the closely related prototype foamy virus (PFV) despite the high structural similarity of their INSTI binding pockets. The molecular mechanism and the key active site residues responsible for these differing binding modes in closely related intasomes remain elusive. To unravel the molecular determinants governing the two distinct binding modes, we applied a novel molecular dynamics-based free energy method that utilizes alchemical pathways to overcome the sampling challenges associated with transitioning between the two bound conformations of ligand 4f within the crowded environments of the INSTI binding pockets in these intasomes. The calculated conformational free energies successfully recapitulate the experimentally observed binding mode preferences in the two viral intasomes. Analysis of the simulated structures suggests that the observed binding mode preferences are caused by amino acid residue differences in both the front and the central catalytic sub-pocket of the INSTI binding site in HIV-1 and PFV. Additional free energy calculations on mutants of HIV-1 and PFV revealed that while both sub-pockets contribute to binding mode selection, the central sub-pocket plays a more important role. These results highlight the importance of both side chain and solvent reorganization, as well as the conformational entropy in determining the ligand binding mode, and will help inform the development of more effective INSTIs for combatting drug-resistant viral variants.
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Affiliation(s)
- Qinfang Sun
- Center for Biophysics and Computational Biology and Department of Chemistry, Temple University, Philadelphia, PA 19122, USA; (Q.S.); (R.L.)
| | - Avik Biswas
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; (A.B.); (D.L.)
- Department of Physics, University of California San Diego, La Jolla, CA 92093, USA
| | - Dmitry Lyumkis
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; (A.B.); (D.L.)
- Graduate Schools for Biological Sciences, Section of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Ronald Levy
- Center for Biophysics and Computational Biology and Department of Chemistry, Temple University, Philadelphia, PA 19122, USA; (Q.S.); (R.L.)
| | - Nanjie Deng
- Department of Chemistry and Physical Sciences, Pace University, New York, NY 10038, USA
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7
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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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8
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Sun Q, Biswas A, Lyumkis D, Levy R, Deng N. Elucidating the molecular determinants for binding modes of a third-generation HIV-1 integrase strand transfer inhibitor: Importance of side chain and solvent reorganization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.29.569269. [PMID: 38077045 PMCID: PMC10705364 DOI: 10.1101/2023.11.29.569269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
The first and second-generation clinically used HIV-1 integrase (IN) strand transfer inhibitors (INSTIs) are key components of antiretroviral therapy (ART), which work by blocking the integration step in the HIV-1 replication cycle that is catalyzed by a nucleoprotein assembly called an intasome. However, resistance to even the latest clinically used INSTIs is beginning to emerge. Developmental third-generation INSTIs, based on naphthyridine scaffold, are promising candidates to combat drug-resistant viral variants. Among these novel INSTIs, compound 4f exhibits two distinct conformations when binding to intasomes from HIV-1 and the closely related prototype foamy virus (PFV), despite the high structural similarity of their INSTI binding pockets. The molecular mechanism and the key active site residues responsible for these differing binding modes in closely related intasomes remain elusive. To unravel the molecular determinants governing the two distinct binding modes, we employ a novel molecular dynamics-based free energy approach that utilizes alchemical pathways to overcome the sampling challenges associated with transitioning between two ligand conformations within crowded environments along physical pathways. The calculated conformational free energies successfully recapitulate the experimentally observed binding mode preferences in the two viral intasomes. Analysis of the simulated structures suggests that the observed binding mode preferences are caused by amino acid residue differences in both the front and the central catalytic sub-pocket of the INSTI binding site in HIV-1 and PFV. Additional free energy calculations on mutants of HIV-1 and PFV revealed that while both sub-pockets contribute to the binding mode selection, the central sub-pocket plays a more important role. These results highlight the importance of both side chain and solvent reorganization, as well as the conformational entropy in determining the ligand binding mode and will help inform the development of more effective INSTIs for combatting drug-resistant viral variants.
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Affiliation(s)
- Qinfang Sun
- Center for Biophysics and Computational Biology and Department of Chemistry, Temple University, Philadelphia, PA 19122
| | - Avik Biswas
- The Salk Institute for Biological Studies, Laboratory of Genetics, La Jolla, CA 92037
- Department of Physics, University of California San Diego, La Jolla, CA, 92093
| | - Dmitry Lyumkis
- The Salk Institute for Biological Studies, Laboratory of Genetics, La Jolla, CA 92037
- Graduate schools for Biological Sciences, Section of Molecular Biology, University of California, San Diego, La Jolla, CA, 92093
| | - Ronald Levy
- Center for Biophysics and Computational Biology and Department of Chemistry, Temple University, Philadelphia, PA 19122
| | - Nanjie Deng
- Department of Chemistry and Physical Sciences, Pace University, New York, NY10038
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9
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Prévost J, Chen Y, Zhou F, Tolbert WD, Gasser R, Medjahed H, Nayrac M, Nguyen DN, Gottumukkala S, Hessell AJ, Rao VB, Pozharski E, Huang RK, Matthies D, Finzi A, Pazgier M. Structure-function analyses reveal key molecular determinants of HIV-1 CRF01_AE resistance to the entry inhibitor temsavir. Nat Commun 2023; 14:6710. [PMID: 37872202 PMCID: PMC10593844 DOI: 10.1038/s41467-023-42500-2] [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: 05/17/2023] [Accepted: 10/12/2023] [Indexed: 10/25/2023] Open
Abstract
The HIV-1 entry inhibitor temsavir prevents the viral receptor CD4 (cluster of differentiation 4) from interacting with the envelope glycoprotein (Env) and blocks its conformational changes. To do this, temsavir relies on the presence of a residue with small side chain at position 375 in Env and is unable to neutralize viral strains like CRF01_AE carrying His375. Here we investigate the mechanism of temsavir resistance and show that residue 375 is not the sole determinant of resistance. At least six additional residues within the gp120 inner domain layers, including five distant from the drug-binding pocket, contribute to resistance. A detailed structure-function analysis using engineered viruses and soluble trimer variants reveals that the molecular basis of resistance is mediated by crosstalk between His375 and the inner domain layers. Furthermore, our data confirm that temsavir can adjust its binding mode to accommodate changes in Env conformation, a property that likely contributes to its broad antiviral activity.
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Affiliation(s)
- Jérémie Prévost
- Centre de Recherche du CHUM, Montreal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Yaozong Chen
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Fei Zhou
- Unit on Structural Biology, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - William D Tolbert
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Romain Gasser
- Centre de Recherche du CHUM, Montreal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | | | - Manon Nayrac
- Centre de Recherche du CHUM, Montreal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Dung N Nguyen
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Suneetha Gottumukkala
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Ann J Hessell
- Division of Pathobiology and Immunology, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Venigalla B Rao
- Department of Biology, the Catholic University of America, Washington, DC, USA
| | - Edwin Pozharski
- Institute for Bioscience and Biotechnology Research, Rockville, MD, 20850, USA
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Rick K Huang
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, USA
| | - Doreen Matthies
- Unit on Structural Biology, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, QC, Canada.
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada.
| | - Marzena Pazgier
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
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10
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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: 11] [Impact Index Per Article: 11.0] [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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11
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Xu S, Sun L, Liu X, Zhan P. Opportunities and challenges in new HIV therapeutic discovery: what is the next step? Expert Opin Drug Discov 2023; 18:1195-1199. [PMID: 37561085 DOI: 10.1080/17460441.2023.2246872] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 08/08/2023] [Indexed: 08/11/2023]
Affiliation(s)
- Shujing Xu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, PR China
| | - Lin Sun
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, PR China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, PR China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, PR China
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12
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Starosotnikov AM, Bastrakov MA. Recent Developments in the Synthesis of HIV-1 Integrase Strand Transfer Inhibitors Incorporating Pyridine Moiety. Int J Mol Sci 2023; 24:ijms24119314. [PMID: 37298265 DOI: 10.3390/ijms24119314] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Human immunodeficiency virus (HIV) causes one of the most dangerous diseases-acquired immunodeficiency syndrome (AIDS). An estimated about 40 million people are currently living with HIV worldwide, most of whom are already on antiretroviral therapy. This makes the development of effective drugs to combat this virus very relevant. Currently, one of the dynamically developing areas of organic and medicinal chemistry is the synthesis and identification of new compounds capable of inhibiting HIV-1 integrase-one of the HIV enzymes. A significant number of studies on this topic are published annually. Many compounds inhibiting integrase incorporate pyridine core. Therefore, this review is an analysis of the literature on the methods for the synthesis of pyridine-containing HIV-1 integrase inhibitors since 2003 to the present.
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Affiliation(s)
- Alexey M Starosotnikov
- N.D. Zelinsky Institute of Organic Chemistry RAS, Leninsky Prosp. 47, 119991 Moscow, Russia
| | - Maxim A Bastrakov
- N.D. Zelinsky Institute of Organic Chemistry RAS, Leninsky Prosp. 47, 119991 Moscow, Russia
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13
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Xue X, Jiang R, Xie C, Qian G, Shang M, Zhu W, Su Y. Mechanism and kinetic study for the intensification of two‐step synthesis of a dolutegravir intermediate in microreactor. AIChE J 2022. [DOI: 10.1002/aic.17820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Xiao Xue
- Department of Chemical Engineering, School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai China
| | - Rongkun Jiang
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of Chemical Biology, School of Pharmacy East China University of Science and Technology Shanghai China
| | - Chengmin Xie
- Department of Chemical Engineering, School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai China
| | - Guozhi Qian
- Department of Chemical Engineering, School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai China
| | - Minjing Shang
- Department of Chemical Engineering, School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai China
| | - Weiping Zhu
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of Chemical Biology, School of Pharmacy East China University of Science and Technology Shanghai China
| | - Yuanhai Su
- Department of Chemical Engineering, School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai China
- Key Laboratory of Thin Film and Microfabrication (Ministry of Education) Shanghai Jiao Tong University Shanghai China
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14
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Shaqra AM, Zvornicanin SN, Huang QYJ, Lockbaum GJ, Knapp M, Tandeske L, Bakan DT, Flynn J, Bolon DNA, Moquin S, Dovala D, Kurt Yilmaz N, Schiffer CA. Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance. Nat Commun 2022; 13:3556. [PMID: 35729165 PMCID: PMC9211792 DOI: 10.1038/s41467-022-31210-w] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 06/09/2022] [Indexed: 01/01/2023] Open
Abstract
Coronaviruses can evolve and spread rapidly to cause severe disease morbidity and mortality, as exemplified by SARS-CoV-2 variants of the COVID-19 pandemic. Although currently available vaccines remain mostly effective against SARS-CoV-2 variants, additional treatment strategies are needed. Inhibitors that target essential viral enzymes, such as proteases and polymerases, represent key classes of antivirals. However, clinical use of antiviral therapies inevitably leads to emergence of drug resistance. In this study we implemented a strategy to pre-emptively address drug resistance to protease inhibitors targeting the main protease (Mpro) of SARS-CoV-2, an essential enzyme that promotes viral maturation. We solved nine high-resolution cocrystal structures of SARS-CoV-2 Mpro bound to substrate peptides and six structures with cleavage products. These structures enabled us to define the substrate envelope of Mpro, map the critical recognition elements, and identify evolutionarily vulnerable sites that may be susceptible to resistance mutations that would compromise binding of the newly developed Mpro inhibitors. Our results suggest strategies for developing robust inhibitors against SARS-CoV-2 that will retain longer-lasting efficacy against this evolving viral pathogen.
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Affiliation(s)
- Ala M Shaqra
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, US
| | - Sarah N Zvornicanin
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, US
| | - Qiu Yu J Huang
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, US
| | - Gordon J Lockbaum
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, US
| | - Mark Knapp
- Novartis Institutes for Biomedical Research, Emeryville, CA, 94608, USA
| | - Laura Tandeske
- Novartis Institutes for Biomedical Research, Emeryville, CA, 94608, USA
| | - David T Bakan
- Novartis Institutes for Biomedical Research, Emeryville, CA, 94608, USA
| | - Julia Flynn
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, US
| | - Daniel N A Bolon
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, US
| | - Stephanie Moquin
- Novartis Institutes for Biomedical Research, Emeryville, CA, 94608, USA
| | - Dustin Dovala
- Novartis Institutes for Biomedical Research, Emeryville, CA, 94608, USA
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, US.
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, US.
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15
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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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16
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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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17
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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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18
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The KT Jeang Retrovirology prize 2021: Peter Cherepanov. Retrovirology 2021; 18:28. [PMID: 34565404 PMCID: PMC8474919 DOI: 10.1186/s12977-021-00573-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
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19
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Barski MS, Vanzo T, Zhao XZ, Smith SJ, Ballandras-Colas A, Cronin NB, Pye VE, Hughes SH, Burke TR, Cherepanov P, Maertens GN. Structural basis for the inhibition of HTLV-1 integration inferred from cryo-EM deltaretroviral intasome structures. Nat Commun 2021; 12:4996. [PMID: 34404793 PMCID: PMC8370991 DOI: 10.1038/s41467-021-25284-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/20/2021] [Indexed: 02/07/2023] Open
Abstract
Between 10 and 20 million people worldwide are infected with the human T-cell lymphotropic virus type 1 (HTLV-1). Despite causing life-threatening pathologies there is no therapeutic regimen for this deltaretrovirus. Here, we screened a library of integrase strand transfer inhibitor (INSTI) candidates built around several chemical scaffolds to determine their effectiveness in limiting HTLV-1 infection. Naphthyridines with substituents in position 6 emerged as the most potent compounds against HTLV-1, with XZ450 having highest efficacy in vitro. Using single-particle cryo-electron microscopy we visualised XZ450 as well as the clinical HIV-1 INSTIs raltegravir and bictegravir bound to the active site of the deltaretroviral intasome. The structures reveal subtle differences in the coordination environment of the Mg2+ ion pair involved in the interaction with the INSTIs. Our results elucidate the binding of INSTIs to the HTLV-1 intasome and support their use for pre-exposure prophylaxis and possibly future treatment of HTLV-1 infection.
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Affiliation(s)
- Michal S Barski
- Imperial College London, St. Mary's Hospital, Department of Infectious Disease, Section of Virology, Norfolk Place, London, UK
- International Institute of Molecular Mechanisms and Machines, Polish Academy of Sciences, Warsaw, Poland
| | - Teresa Vanzo
- Imperial College London, St. Mary's Hospital, Department of Infectious Disease, Section of Virology, Norfolk Place, London, UK
- Department CIBIO, University of Trento, Povo-Trento, Italy
| | - Xue Zhi Zhao
- Chemical Biology Laboratory, Centre for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Steven J Smith
- Retroviral Replication Laboratory, Centre for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | | | - Nora B Cronin
- LonCEM Facility, The Francis Crick Institute, London, UK
| | - Valerie E Pye
- Chromatin Structure & Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Stephen H Hughes
- Retroviral Replication Laboratory, Centre for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Terrence R Burke
- Chemical Biology Laboratory, Centre for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Peter Cherepanov
- Imperial College London, St. Mary's Hospital, Department of Infectious Disease, Section of Virology, Norfolk Place, London, UK
- Chromatin Structure & Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Goedele N Maertens
- Imperial College London, St. Mary's Hospital, Department of Infectious Disease, Section of Virology, Norfolk Place, London, UK.
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20
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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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21
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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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22
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Matthew AN, Leidner F, Lockbaum GJ, Henes M, Zephyr J, Hou S, Desaboini NR, Timm J, Rusere LN, Ragland DA, Paulsen JL, Prachanronarong K, Soumana DI, Nalivaika EA, Yilmaz NK, Ali A, Schiffer CA. Drug Design Strategies to Avoid Resistance in Direct-Acting Antivirals and Beyond. Chem Rev 2021; 121:3238-3270. [PMID: 33410674 PMCID: PMC8126998 DOI: 10.1021/acs.chemrev.0c00648] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Drug resistance is prevalent across many diseases, rendering therapies ineffective with severe financial and health consequences. Rather than accepting resistance after the fact, proactive strategies need to be incorporated into the drug design and development process to minimize the impact of drug resistance. These strategies can be derived from our experience with viral disease targets where multiple generations of drugs had to be developed to combat resistance and avoid antiviral failure. Significant efforts including experimental and computational structural biology, medicinal chemistry, and machine learning have focused on understanding the mechanisms and structural basis of resistance against direct-acting antiviral (DAA) drugs. Integrated methods show promise for being predictive of resistance and potency. In this review, we give an overview of this research for human immunodeficiency virus type 1, hepatitis C virus, and influenza virus and the lessons learned from resistance mechanisms of DAAs. These lessons translate into rational strategies to avoid resistance in drug design, which can be generalized and applied beyond viral targets. While resistance may not be completely avoidable, rational drug design can and should incorporate strategies at the outset of drug development to decrease the prevalence of drug resistance.
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Affiliation(s)
- Ashley N. Matthew
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
- Virginia Commonwealth University
| | - Florian Leidner
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Gordon J. Lockbaum
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Mina Henes
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Jacqueto Zephyr
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Shurong Hou
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Nages Rao Desaboini
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Jennifer Timm
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
- Rutgers University
| | - Linah N. Rusere
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
- Raybow Pharmaceutical
| | - Debra A. Ragland
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
- University of North Carolina, Chapel Hill
| | - Janet L. Paulsen
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
- Schrodinger, Inc
| | - Kristina Prachanronarong
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
- Icahn School of Medicine at Mount Sinai
| | - Djade I. Soumana
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
- Cytiva
| | - Ellen A. Nalivaika
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Akbar Ali
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
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23
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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: 39] [Impact Index Per Article: 13.0] [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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24
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Vanangamudi M, Nair PC, Engels SEM, Palaniappan S, Namasivayam V. Structural Insights to Human Immunodeficiency Virus (HIV-1) Targets and Their Inhibition. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1322:63-95. [PMID: 34258737 DOI: 10.1007/978-981-16-0267-2_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Human immunodeficiency virus (HIV) is a deadly virus that attacks the body's immune system, subsequently leading to AIDS (acquired immunodeficiency syndrome) and ultimately death. Currently, there is no vaccine or effective cure for this infection; however, antiretrovirals that act at various phases of the virus life cycle have been useful to control the viral load in patients. One of the major problems with antiretroviral therapies involves drug resistance. The three-dimensional structure from crystallography studies are instrumental in understanding the structural basis of drug binding to various targets. This chapter provides key insights into different targets and drugs used in the treatment from a structural perspective. Specifically, an insight into the binding characteristics of drugs at the active and allosteric sites of different targets and the importance of targeting allosteric sites for design of new-generation antiretrovirals to overcome complex and resistant forms of the virus has been reviewed.
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Affiliation(s)
- Murugesan Vanangamudi
- Department of Pharmaceutical Chemistry, Amity Institute of Pharmacy, Amity University Gwalior, Gwalior, Madhya Pradesh, India
| | - Pramod C Nair
- Department of Clinical Pharmacology, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
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25
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Jóźwik IK, Passos DO, Lyumkis D. Structural Biology of HIV Integrase Strand Transfer Inhibitors. Trends Pharmacol Sci 2020; 41:611-626. [PMID: 32624197 PMCID: PMC7429322 DOI: 10.1016/j.tips.2020.06.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/05/2020] [Accepted: 06/08/2020] [Indexed: 12/12/2022]
Abstract
Integrase (IN) strand transfer inhibitors (INSTIs) are recent compounds in the antiretroviral arsenal used against HIV. INSTIs work by blocking retroviral integration; an essential step in the viral lifecycle that is catalyzed by the virally encoded IN protein within a nucleoprotein assembly called an intasome. Recent structures of lentiviral intasomes from simian immunodeficiency virus (SIV) and HIV have clarified the INSTI binding modes within the intasome active sites and helped elucidate an important mechanism of viral resistance. The structures provide an accurate depiction of interactions of intasomes and INSTIs to be leveraged for structure-based drug design. Here, we review these recent structural findings and contrast with earlier studies on prototype foamy virus intasomes. We also present and discuss examples of the latest chemical compounds that show promising inhibitory potential as INSTI candidates.
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Affiliation(s)
- Ilona K Jóźwik
- The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Dario O Passos
- The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Dmitry Lyumkis
- The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA; The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.
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26
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HIV-1 Integrase Inhibitors That Are Active against Drug-Resistant Integrase Mutants. Antimicrob Agents Chemother 2020; 64:AAC.00611-20. [PMID: 32601157 DOI: 10.1128/aac.00611-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/25/2020] [Indexed: 01/01/2023] Open
Abstract
The currently recommended first-line therapy for HIV-1-infected patients is an integrase (IN) strand transfer inhibitor (INSTI), either dolutegravir (DTG) or bictegravir (BIC), in combination with two nucleoside reverse transcriptase inhibitors (NRTIs). Both DTG and BIC potently inhibit most INSTI-resistant IN mutants selected by the INSTIs raltegravir (RAL) and elvitegravir (EVG). BIC has not been reported to select for resistance in treatment-naive patients, and DTG has selected for a small number of resistant viruses in treatment-naive patients. However, some patients who had viruses with substitutions selected by RAL and EVG responded poorly when switched to DTG-based therapies, and there are mutants that cause a considerable decrease in the potencies of DTG and BIC in in vitro assays. The new INSTI cabotegravir (CAB), which is in late-stage clinical trials, has been shown to select for novel resistant mutants in vitro Thus, it is important to develop new and improved INSTIs that are effective against all the known resistant mutants. This led us to test our best inhibitors, in parallel with DTG, BIC, and CAB, in a single-round infection assay against a panel of the new CAB-resistant mutants. Of the INSTIs we tested, BIC and our compound 4d had the broadest efficacy. Both were superior to DTG, as evidenced by the data obtained with the IN mutant T66I/L74M/E138K/S147G/Q148R/S230N, which was selected by CAB using an EVG-resistant lab strain. These results support the preclinical development of compound 4d and provide information that can be used in the design of additional INSTIs that will be effective against a broad spectrum of resistant mutants.
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27
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Du J, Guo J, Kang D, Li Z, Wang G, Wu J, Zhang Z, Fang H, Hou X, Huang Z, Li G, Lu X, Liu X, Ouyang L, Rao L, Zhan P, Zhang X, Zhang Y. New techniques and strategies in drug discovery. CHINESE CHEM LETT 2020. [DOI: 10.1016/j.cclet.2020.03.028] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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28
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Engelman AN, Cherepanov P. Close-up: HIV/SIV intasome structures shed new light on integrase inhibitor binding and viral escape mechanisms. FEBS J 2020; 288:427-433. [PMID: 32506843 DOI: 10.1111/febs.15438] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 05/20/2020] [Accepted: 06/02/2020] [Indexed: 12/16/2022]
Abstract
Integrase strand transfer inhibitors (INSTIs) are important components of drug formulations that are used to treat people living with HIV, and second-generation INSTIs dolutegravir and bictegravir impart high barriers to the development of drug resistance. Reported 10 years ago, X-ray crystal structures of prototype foamy virus (PFV) intasome complexes explained how INSTIs bind integrase to inhibit strand transfer activity and provided initial glimpses into mechanisms of drug resistance. However, comparatively low sequence identity between PFV and HIV-1 integrases limited the depth of information that could be gleaned from the surrogate model system. Recent high-resolution structures of HIV-1 intasomes as well as intasomes from a closely related strain of simian immunodeficiency virus (SIV), which were determined using single-particle cryogenic electron microscopy, have overcome this limitation. The new structures reveal the binding modes of several advanced INSTI compounds to the HIV/SIV integrase active site and critically inform the structural basis of drug resistance. These findings will help guide the continued development of this important class of antiretroviral therapeutics.
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Affiliation(s)
- Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, Francis Crick Institute, London, UK.,Department of Infectious Disease, Imperial College London, St. Mary's Campus, London, UK
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29
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Passos DO, Li M, Jóźwik IK, Zhao XZ, Santos-Martins D, Yang R, Smith SJ, Jeon Y, Forli S, Hughes SH, Burke TR, Craigie R, Lyumkis D. Structural basis for strand-transfer inhibitor binding to HIV intasomes. Science 2020; 367:810-814. [PMID: 32001521 PMCID: PMC7357238 DOI: 10.1126/science.aay8015] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 01/17/2020] [Indexed: 01/21/2023]
Abstract
The HIV intasome is a large nucleoprotein assembly that mediates the integration of a DNA copy of the viral genome into host chromatin. Intasomes are targeted by the latest generation of antiretroviral drugs, integrase strand-transfer inhibitors (INSTIs). Challenges associated with lentiviral intasome biochemistry have hindered high-resolution structural studies of how INSTIs bind to their native drug target. Here, we present high-resolution cryo-electron microscopy structures of HIV intasomes bound to the latest generation of INSTIs. These structures highlight how small changes in the integrase active site can have notable implications for drug binding and design and provide mechanistic insights into why a leading INSTI retains efficacy against a broad spectrum of drug-resistant variants. The data have implications for expanding effective treatments available for HIV-infected individuals.
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Affiliation(s)
- Dario Oliveira Passos
- The Salk Institute for Biological Studies, Laboratory of Genetics, La Jolla, CA 92037, USA
| | - Min Li
- National Institutes of Health, National Institute of Diabetes and Digestive Diseases, Bethesda, MD 20892, USA
| | - Ilona K Jóźwik
- The Salk Institute for Biological Studies, Laboratory of Genetics, La Jolla, CA 92037, USA
| | - Xue Zhi Zhao
- Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Diogo Santos-Martins
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Renbin Yang
- National Institutes of Health, National Institute of Diabetes and Digestive Diseases, Bethesda, MD 20892, USA
| | - Steven J Smith
- Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Youngmin Jeon
- The Salk Institute for Biological Studies, Laboratory of Genetics, La Jolla, CA 92037, USA
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Stephen H Hughes
- Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Terrence R Burke
- Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Robert Craigie
- National Institutes of Health, National Institute of Diabetes and Digestive Diseases, Bethesda, MD 20892, USA
| | - Dmitry Lyumkis
- The Salk Institute for Biological Studies, Laboratory of Genetics, La Jolla, CA 92037, USA.
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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30
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Li M, Chen X, Wang H, Jurado KA, Engelman AN, Craigie R. A Peptide Derived from Lens Epithelium-Derived Growth Factor Stimulates HIV-1 DNA Integration and Facilitates Intasome Structural Studies. J Mol Biol 2020; 432:2055-2066. [PMID: 32061936 PMCID: PMC7350280 DOI: 10.1016/j.jmb.2020.01.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 01/29/2020] [Accepted: 01/30/2020] [Indexed: 01/26/2023]
Abstract
The low solubility and aggregation properties of HIV-1 integrase (IN) are major obstacles for biochemical and structural studies. The lens epithelium-derived growth factor (LEDGF) is a cellular factor that binds IN and tethers preintegration complexes to chromatin before integration. The LEDGF also stimulates HIV-1 IN DNA strand transfer activity and improves its solubility in vitro. We show that these properties are conferred by a short peptide spanning residues 178 to 197 of the LEDGF that encompasses its AT-hook DNA-binding elements. The peptide stimulates HIV-1 IN activity both in trans and in cis. Fusion of the peptide to either the N- or C-terminus of IN results in maximal stimulation of concerted integration activity and greatly improves the solubility of the protein and nucleoprotein complexes of IN with viral DNA ends (intasomes). High-resolution structures of HIV-1 intasomes are required to understand the mechanism of IN strand transfer inhibitors (INSTIs), which are front-line drugs for the treatment of HIV-1, and how the virus can develop resistance to INSTIs. We have previously determined the structure of the HIV-1 strand transfer complex intasome. The improved biophysical properties of intasomes assembled with LEDGF peptide fusion IN have enabled us to determine the structure of the cleaved synaptic complex intasome, which is the direct target of INSTIs.
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Affiliation(s)
- Min Li
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, USA
| | - Xuemin Chen
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, USA
| | - Huaibin Wang
- NIH Multi-Institute Cryo-EM Facility, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kellie A Jurado
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, MA, 02215, USA
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, MA, 02215, USA
| | - Robert Craigie
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, USA.
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31
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Wang L, Sarafianos SG, Wang Z. Cutting into the Substrate Dominance: Pharmacophore and Structure-Based Approaches toward Inhibiting Human Immunodeficiency Virus Reverse Transcriptase-Associated Ribonuclease H. Acc Chem Res 2020; 53:218-230. [PMID: 31880912 DOI: 10.1021/acs.accounts.9b00450] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Human immunodeficiency virus (HIV) reverse transcriptase (RT) contains two distinct functional domains: a DNA polymerase (pol) domain and a ribonuclease H (RNase H) domain, both of which are required for viral genome replication. Over the last 3 decades, RT has been at the forefront of HIV drug discovery efforts with numerous nucleoside reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs) approved by the FDA. However, all these RT inhibitors target only the pol function, and inhibitors of RT-associated RNase H have yet to enter the development pipeline, which in itself manifests both the opportunity and challenges of targeting RNase H: if developed, RT RNase H inhibitors would represent a mechanistically novel class of HIV drugs that can be particularly valuable in treating HIV strains resistant to current drugs. The challenges include (1) the difficulty in selectively targeting RT RNase H over RT pol due to their close interplay both spatially and temporally and over HIV-1 integrase strand transfer (INST) activity because of their active site similarities; (2) to a larger extent, the inability of active site inhibitors to confer significant antiviral effect, presumably due to a steep substrate barrier by which the pre-existing substrate prevents access of small molecules to the active site. As a result, previously reported RT RNase H inhibitors typically lacked target specificity and significant antiviral potency. Achieving meaningful antiviral activity via active site targeting likely entails selective and ultrapotent RNase H inhibition to allow small molecules to cut into the dominance of substrates. Based on a pharmacophore model informed by prior work, we designed and redesigned a few metal-chelating chemotypes, such as 2-hydroxyisoquinolinedione (HID), hydroxypyridonecarboxylic acid (HPCA), 3-hydroxypyrimidine-2,4-dione (HPD), and N-hydroxythienopyrimidine-2,4-dione (HTPD). Analogues of these chemotypes generally exhibited improved potency and selectivity inhibiting RT RNase H over the best previous compounds and further validated the pharmacophore model. Extended structure-activity relationship (SAR) on the HPD inhibitor type by mainly altering the linkage generated a few subtypes showing exceptional potency (single-digit nanomolar) and excellent selectivity over the inhibition of RT pol and INST. In parallel, a structure-based approach also allowed us to design a unique double-winged HPD subtype to potently and selectively inhibit RT RNase H and effectively compete against the RNA/DNA substrate. Significantly, all potent HPD subtypes consistently inhibited HIV-1 in the cell culture, suggesting that carefully designed active site RNase H inhibitors with ultrapotency could partially overcome the barrier to antiviral phenotype. Overall, in addition to identifying our own inhibitor types, our medicinal chemistry efforts demonstrated the value of pharmacophore and structure-based approaches in designing active side-directed RNase H inhibitors and could provide a viable path to validating RNase H as a novel antiviral target.
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Affiliation(s)
- Lei Wang
- State Key Laboratory of Fine Chemicals, Department of Pharmacy, School of Chemical Engineering, Dalian University of Technology, Dalian 116024, China
| | - Stefan G. Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Zhengqiang Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
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32
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Ivashchenko AA, Ivanenkov YA, Koryakova AG, Karapetian RN, Mitkin OD, Aladinskiy VA, Kravchenko DV, Savchuk NP, Ivashchenko AV. Synthesis, biological evaluation and in silico modeling of novel integrase strand transfer inhibitors (INSTIs). Eur J Med Chem 2020; 189:112064. [PMID: 31972393 DOI: 10.1016/j.ejmech.2020.112064] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/10/2020] [Accepted: 01/10/2020] [Indexed: 12/19/2022]
Abstract
Although a relatively wide range of therapeutic options is currently available for the treatment of HIV/AIDS, it is still among the most serious and virulent diseases and is associated with a high mortality rate. Integrase strand transfer inhibitors (INSTIs), e.g., FDA-approved dolutegravir (DTG), bictegravir (BIC) and cabotegravir (CAB), have recently been included in standard highly active antiretroviral therapy (HAART) schemes as one of the five major components responsible for the most beneficial clinical outcome. In this paper, we describe a combinatorial amide synthesis, biological evaluation and in silico modeling of new INSTIs containing heteroaromatic bioisosteric substitution instead of the well-studied halogen-substituted benzyl fragment. With the focus on the mentioned diversity point, a medium-sized library of compounds was selected for synthesis. A biological study revealed that many molecules were highly active INSTIs (EC50 < 10 nM). Two compounds 1{4} and 1{26} demonstrated picomolar antiviral activity that was comparable with CAB and were more active than DTG and BIC. Molecular docking study was performed to evaluate the binding mode of compounds in the active site of HIV-1 IN. In rats, lead compound 1{26} showed two-fold greater bioavailability than CAB and had a similar half-life. Compound 1{26} and its sodium salt were considerably more soluble in water than the parent drugs. Both molecules were very stable in human liver microsomes and plasma, demonstrated high affinity towards plasma proteins and did not show cytochrome (CYP) inhibition. This benefit profile indicates the great potential of these molecules as attractive candidates for subsequent evaluation as oral long-acting drugs and long-acting nanosuspension formulations for intramuscular injection.
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Affiliation(s)
- Andrey A Ivashchenko
- Chemical Diversity Research Institute, Rabochaya St. 2a, Khimki, Moscow Region, 141401, Russia; ChemDiv, 6605 Nancy Ridge Drive, San Diego, CA, 92121, United States
| | - Yan A Ivanenkov
- ChemDiv, 6605 Nancy Ridge Drive, San Diego, CA, 92121, United States; Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Ufa, Russia.
| | - Angela G Koryakova
- Chemical Diversity Research Institute, Rabochaya St. 2a, Khimki, Moscow Region, 141401, Russia
| | - Ruben N Karapetian
- Chemical Diversity Research Institute, Rabochaya St. 2a, Khimki, Moscow Region, 141401, Russia
| | - Oleg D Mitkin
- Chemical Diversity Research Institute, Rabochaya St. 2a, Khimki, Moscow Region, 141401, Russia
| | - Vladimir A Aladinskiy
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Ufa, Russia
| | - Dmitry V Kravchenko
- Chemical Diversity Research Institute, Rabochaya St. 2a, Khimki, Moscow Region, 141401, Russia
| | - Nikolai P Savchuk
- Chemical Diversity Research Institute, Rabochaya St. 2a, Khimki, Moscow Region, 141401, Russia; ChemDiv, 6605 Nancy Ridge Drive, San Diego, CA, 92121, United States; Viriom Inc, 12760 High Bluff Drive, St 370, San Diego, CA, 92130, United States
| | - Alexander V Ivashchenko
- Chemical Diversity Research Institute, Rabochaya St. 2a, Khimki, Moscow Region, 141401, Russia; ChemDiv, 6605 Nancy Ridge Drive, San Diego, CA, 92121, United States; Avisa Pharmaceuticals LLC, 1835 E. Hallandale Beach Blvd, #442, Hallandale Beach, Fl, 33009, United States
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El Khoury L, El Hage K, Piquemal JP, Fermandjian S, Maroun RG, Gresh N, Hobaika Z. Spectrometric and computational studies of the binding of HIV-1 integrase inhibitors to viral DNA extremities. PEERJ PHYSICAL CHEMISTRY 2019. [DOI: 10.7717/peerj-pchem.6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Three integrase strand transfer inhibitors are in intensive clinical use, raltegravir (RAL), elvitegravir (EVG) and dolutegravir (DTG). The onset of integrase resistance mutations limits their therapeutic efficiency. As put forth earlier, the drug affinity for the intasome could be improved by targeting preferentially the retroviral nucleobases, which are little, if at all, mutation-prone. We report experimental results of anisotropy fluorescence titrations of viral DNA by these three drugs. These show the DTG > EVG > RAL ranking of their inhibitory activities of the intasome to correspond to that of their free energies of binding, ∆Gs, to retroviral DNA, and that such a ranking is only governed by the binding enthalpies, ∆H, the entropy undergoing marginal variations. We sought whether this ranking might be reproduced through quantum chemistry (QC) Density Functional Theory calculations of intermolecular interaction energies between simplified models consisting of sole halobenzene ring and the highly conserved retroviral nucleobases G4 and C16. These calculations showed that binding of EVG has a small preference over DTG, while RAL ranked third. This indicates that additional interactions of the diketoacid parts of the drugs with DNA could be necessary to further enable preferential binding of DTG. The corresponding ∆Etotvalues computed with a polarizable molecular mechanics/dynamics procedure, Sum of Interactions Between Fragments Ab initio computed (SIBFA), showed good correlations with this ∆E(QC) ranking. These validations are an important step toward the use of polarizable molecular dynamics simulations on DTG or EVG derivatives in their complexes with the complete intasome, an application now motivated and enabled by the advent of currently developed and improved massively parallel software.
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Affiliation(s)
- Léa El Khoury
- Laboratoire de Chimie Théorique, UMR7616 CNRS, Sorbonne Université, Paris, France
- UR EGP, Centre d’Analyses et de Recherche, Faculté des Sciences, Université Saint-Joseph de Beyrouth, Beirut, Lebanon
- Present address: Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA
| | - Krystel El Hage
- Chemistry and Biology Nucleo(s)tides and Immunology for Therapy (CBNIT), UMR 8601 CNRS, UFR Biomedicale, Paris, France
- Present address: Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, INSERM U829, Université Evry-Val d’Essonne, Evry, France
| | - Jean-Philip Piquemal
- UR EGP, Centre d’Analyses et de Recherche, Faculté des Sciences, Université Saint-Joseph de Beyrouth, Beirut, Lebanon
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
- Institut Universitaire de France, Paris, France
| | - Serge Fermandjian
- Chemistry and Biology Nucleo(s)tides and Immunology for Therapy (CBNIT), UMR 8601 CNRS, UFR Biomedicale, Paris, France
| | - Richard G. Maroun
- UR EGP, Centre d’Analyses et de Recherche, Faculté des Sciences, Université Saint-Joseph de Beyrouth, Beirut, Lebanon
| | - Nohad Gresh
- Laboratoire de Chimie Théorique, UMR7616 CNRS, Sorbonne Université, Paris, France
| | - Zeina Hobaika
- UR EGP, Centre d’Analyses et de Recherche, Faculté des Sciences, Université Saint-Joseph de Beyrouth, Beirut, Lebanon
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Engelman AN. Multifaceted HIV integrase functionalities and therapeutic strategies for their inhibition. J Biol Chem 2019; 294:15137-15157. [PMID: 31467082 DOI: 10.1074/jbc.rev119.006901] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Antiretroviral inhibitors that are used to manage HIV infection/AIDS predominantly target three enzymes required for virus replication: reverse transcriptase, protease, and integrase. Although integrase inhibitors were the last among this group to be approved for treating people living with HIV, they have since risen to the forefront of treatment options. Integrase strand transfer inhibitors (INSTIs) are now recommended components of frontline and drug-switch antiretroviral therapy formulations. Integrase catalyzes two successive magnesium-dependent polynucleotidyl transferase reactions, 3' processing and strand transfer, and INSTIs tightly bind the divalent metal ions and viral DNA end after 3' processing, displacing from the integrase active site the DNA 3'-hydroxyl group that is required for strand transfer activity. Although second-generation INSTIs present higher barriers to the development of viral drug resistance than first-generation compounds, the mechanisms underlying these superior barrier profiles are incompletely understood. A separate class of HIV-1 integrase inhibitors, the allosteric integrase inhibitors (ALLINIs), engage integrase distal from the enzyme active site, namely at the binding site for the cellular cofactor lens epithelium-derived growth factor (LEDGF)/p75 that helps to guide integration into host genes. ALLINIs inhibit HIV-1 replication by inducing integrase hypermultimerization, which precludes integrase binding to genomic RNA and perturbs the morphogenesis of new viral particles. Although not yet approved for human use, ALLINIs provide important probes that can be used to investigate the link between HIV-1 integrase and viral particle morphogenesis. Herein, I review the mechanisms of retroviral integration as well as the promises and challenges of using integrase inhibitors for HIV/AIDS management.
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Affiliation(s)
- Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215 Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115
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35
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Wang X, Chen S, Zhao C, Long L, Wang Y. Preparation of Dolutegravir Intermediate Diastereomer. J Heterocycl Chem 2019. [DOI: 10.1002/jhet.3588] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Xianheng Wang
- Department of Pharmacology and Key Laboratory of Basic Pharmacology of Ministry of EducationZunyi Medical University No. 6 Xue Fu West Road Zunyi 563003 China
| | - Song Chen
- Department of Pharmacology and Key Laboratory of Basic Pharmacology of Ministry of EducationZunyi Medical University No. 6 Xue Fu West Road Zunyi 563003 China
| | - Changkuo Zhao
- Department of Pharmacology and Key Laboratory of Basic Pharmacology of Ministry of EducationZunyi Medical University No. 6 Xue Fu West Road Zunyi 563003 China
| | - Liangye Long
- Department of Pharmacology and Key Laboratory of Basic Pharmacology of Ministry of EducationZunyi Medical University No. 6 Xue Fu West Road Zunyi 563003 China
| | - Yuhe Wang
- Department of PharmacyZunyi Medical University Affiliated Hospital No. 139 Dalian Road Zunyi 563003 China
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36
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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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Tang J, Do HT, Huber AD, Casey MC, Kirby KA, Wilson DJ, Kankanala J, Parniak MA, Sarafianos SG, Wang Z. Pharmacophore-based design of novel 3-hydroxypyrimidine-2,4-dione subtypes as inhibitors of HIV reverse transcriptase-associated RNase H: Tolerance of a nonflexible linker. Eur J Med Chem 2019; 166:390-399. [PMID: 30739822 PMCID: PMC6459026 DOI: 10.1016/j.ejmech.2019.01.081] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/17/2019] [Accepted: 01/30/2019] [Indexed: 11/29/2022]
Abstract
The pharmacophore of active site inhibitors of human immunodeficiency virus (HIV) reverse transcriptase (RT)-associated RNase H typically entails a flexible linker connecting the chelating core and the hydrophobic aromatics. We report herein that novel 3-hydroxypyrimidine-2,4-dione (HPD) subtypes with a nonflexible C-6 carbonyl linkage exhibited potent and selective biochemical inhibitory profiles with strong RNase H inhibition at low nM, weak to moderate integrase strand transfer (INST) inhibition at low μM, and no to marginal RT polymerase (pol) inhibition up to 10 μM. A few analogues also demonstrated significant antiviral activity without cytotoxicity. The overall inhibitory profile is comparable to or better than that of previous HPD subtypes with a flexible C-6 linker, suggesting that the nonflexible carbonyl linker can be tolerated in the design of novel HIV RNase H active site inhibitors.
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Affiliation(s)
- Jing Tang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Ha T Do
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Andrew D Huber
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Christopher S. Bond Life Sciences Center, Columbia, MO, 65211, USA
| | - Mary C Casey
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, Columbia, MO, 65211, USA
| | - Karen A Kirby
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, Columbia, MO, 65211, USA; Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Daniel J Wilson
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Jayakanth Kankanala
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Michael A Parniak
- Department of Microbiology & Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15219, USA
| | - Stefan G Sarafianos
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, Columbia, MO, 65211, USA; Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA; Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Zhengqiang Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA.
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George JM, Kuriakose SS, Dee N, Stoll P, Lalani T, Dewar R, Khan MA, Rehman MT, Grossman Z, Maldarelli F, Pau AK. Rapid Development of High-Level Resistance to Dolutegravir With Emergence of T97A Mutation in 2 Treatment-Experienced Individuals With Baseline Partial Sensitivity to Dolutegravir. Open Forum Infect Dis 2018; 5:ofy221. [PMID: 30568974 PMCID: PMC6172925 DOI: 10.1093/ofid/ofy221] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 08/30/2018] [Indexed: 11/14/2022] Open
Abstract
HIV integrase mutation T97A emerges after suboptimal therapy with integrase strand transfer inhibitors (INSTIs), but the contribution of T97A to dolutegravir resistance remains uncertain. Here we report >10-fold increase in dolutegravir resistance after the single addition of T97A in 2 individuals with prior INSTI resistance receiving dolutegravir salvage therapy.
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Affiliation(s)
- Jomy M George
- Clinical Center, National Institutes of Health, Bethesda, Maryland
| | - Safia S Kuriakose
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland
| | - Nicola Dee
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland
| | - Pam Stoll
- Clinical Center, National Institutes of Health, Bethesda, Maryland
| | - Tahaniyat Lalani
- Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Robin Dewar
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland
| | - Muhammad A Khan
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland
| | - Muhammad T Rehman
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland
| | - Zehava Grossman
- National Cancer Institute, Frederick, Maryland
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Alice K Pau
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
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Smith SJ, Zhao XZ, Burke TR, Hughes SH. HIV-1 Integrase Inhibitors That Are Broadly Effective against Drug-Resistant Mutants. Antimicrob Agents Chemother 2018; 62:e01035-18. [PMID: 29987149 PMCID: PMC6125528 DOI: 10.1128/aac.01035-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 06/29/2018] [Indexed: 01/29/2023] Open
Abstract
Integrase strand transfer inhibitors (INSTIs) have emerged as clinically effective therapeutics that inhibit HIV-1 replication by blocking the strand transfer reaction catalyzed by HIV-1 integrase (IN). Of the three FDA-approved INSTIs, dolutegravir (DTG) is the least apt to select for resistance. However, recent salvage therapy regimens had low response rates with therapies that included DTG, suggesting that DTG resistance can be selected in patients. Using a single-round infection assay, we evaluated a collection of our best inhibitors and DTG against a broad panel of INSTI-resistant mutants. Two of the new compounds, 4c and 4d, had antiviral profiles against the mutants we tested superior to that of DTG. The susceptibility profiles of 4c and 4d suggest that the compounds are candidates for development as INSTIs. Modeling the binding of 4d to HIV-1 IN reinforced the significance of mimicking the DNA substrate in developing compounds that are broadly effective in their abilities to inhibit HIV-1 INs with mutations in the active site.
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Affiliation(s)
- Steven J Smith
- HIV Dynamics and Replication Program, National Cancer Institute-Frederick, National Institutes of Health, Frederick, Maryland, USA
| | - Xue Zhi Zhao
- Chemical Biology Laboratory, National Cancer Institute-Frederick, National Institutes of Health, Frederick, Maryland, USA
| | - Terrence R Burke
- Chemical Biology Laboratory, National Cancer Institute-Frederick, National Institutes of Health, Frederick, Maryland, USA
| | - Stephen H Hughes
- HIV Dynamics and Replication Program, National Cancer Institute-Frederick, National Institutes of Health, Frederick, Maryland, USA
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40
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Smith SJ, Zhao XZ, Burke TR, Hughes SH. Efficacies of Cabotegravir and Bictegravir against drug-resistant HIV-1 integrase mutants. Retrovirology 2018; 15:37. [PMID: 29769116 PMCID: PMC5956922 DOI: 10.1186/s12977-018-0420-7] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/04/2018] [Indexed: 12/17/2022] Open
Abstract
Background Integrase strand transfer inhibitors (INSTIs) are the class of antiretroviral (ARV) drugs most recently approved by the FDA for the treatment of HIV-1 infections. INSTIs block the strand transfer reaction catalyzed by HIV-1 integrase (IN) and have been shown to potently inhibit infection by wild-type HIV-1. Of the three current FDA-approved INSTIs, Dolutegravir (DTG), has been the most effective, in part because treatment does not readily select for resistant mutants. However, recent studies showed that when INSTI-experienced patients are put on a DTG-salvage therapy, they have reduced response rates. Two new INSTIs, Cabotegravir (CAB) and Bictegravir (BIC), are currently in late-stage clinical trials. Results Both CAB and BIC had much broader antiviral profiles than RAL and EVG against the INSTI-resistant single, double, and triple HIV-1 mutants used in this study. BIC was more effective than DTG against several INSTI-resistant mutants. Overall, in terms of their ability to inhibit a broad range of INSTI-resistant IN mutants, BIC was superior to DTG, and DTG was superior to CAB. Modeling the binding of CAB, BIC, and DTG within the active site of IN suggested that the “left side” of the INSTI pharmacophore (the side away from the viral DNA) was important in determining the ability of the compound to inhibit the IN mutants we tested. Conclusions Of the two INSTIs in late stage clinical trials, BIC appears to be better able to inhibit the replication of a broad range of IN mutants. BIC retained potency against several of the INSTI-resistant mutants that caused a decrease in susceptibility to DTG. Electronic supplementary material The online version of this article (10.1186/s12977-018-0420-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Steven J Smith
- HIV Dynamics and Replication Program, National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD, USA
| | - Xue Zhi Zhao
- Chemical Biology Laboratory, National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD, USA
| | - Terrence R Burke
- Chemical Biology Laboratory, National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD, USA
| | - Stephen H Hughes
- HIV Dynamics and Replication Program, National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD, USA.
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41
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A structure-based design approach to advance the allyltyrosine-based series of HIV integrase inhibitors. Tetrahedron 2018. [DOI: 10.1016/j.tet.2017.11.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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