1
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Huang WJ, Pannecouque C, De Clercq E, Wang S, Chen FE. Structure-based discovery of novel piperidine-biphenyl-DAPY derivatives as non-nucleoside reverse transcriptase inhibitors featuring improved potency, safety, and selectivity: From piperazine-biphenyl-DAPYs to piperidine-biphenyl-DAPYs. Eur J Med Chem 2024; 276:116668. [PMID: 38996652 DOI: 10.1016/j.ejmech.2024.116668] [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: 05/11/2024] [Revised: 07/08/2024] [Accepted: 07/08/2024] [Indexed: 07/14/2024]
Abstract
Starting from our previously reported nonnucleoside reverse transcriptase inhibitor (NNRTI, 3), continuous efforts were made to enhance its potency and safety through a structure-based drug design strategy. This led to the discovery of a series of novel piperidine-biphenyl-diarylpyrimidines (DAPYs). Compound 10p, the most active compound in this series, exhibited an EC50 value of 6 nM against wide-type HIV-1 strain, which was approximately 560-fold more potent than the initial compound 3 (EC50 = 3.36 μM). Furthermore, significant improvements were observed in cytotoxicity and selectivity (CC50 > 202.17 μM, SI > 33144) compared to compound 3 (CC50 = 14.84 μM, SI = 4). Additionally, compound 10p demonstrated increased inhibitory activity against clinically mutant virus strains (EC50 = 7-63 nM). Further toxicity evaluation revealed that compound 10p exhibited minimal CYP enzyme and hERG inhibition. Importantly, single-dose acute toxicity testing did not result in any fatalities or noticeable pathological damage in mice. Therefore, compound 10p can be regarded as a lead candidate for guiding further development of biphenyl-diarylpyrimidine NNRTIs with favorable druggability for HIV therapy.
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Affiliation(s)
- Wen-Juan Huang
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai, 200433, China; Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai, 200433, China
| | | | - Erik De Clercq
- Rega Institute for Medical Research, KU Leuven, Herestraat 49, B-3000, Leuven, Belgium
| | - Shuai Wang
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai, 200433, China; Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai, 200433, China.
| | - Fen-Er Chen
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai, 200433, China; Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai, 200433, China.
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2
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Zhang K, Zhang YJ, Li M, Pannecouque C, De Clercq E, Wang S, Chen FE. Deciphering the enigmas of non-nucleoside reverse transcriptase inhibitors (NNRTIs): A medicinal chemistry expedition towards combating HIV drug resistance. Med Res Rev 2024. [PMID: 39188075 DOI: 10.1002/med.22080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/11/2024] [Accepted: 08/13/2024] [Indexed: 08/28/2024]
Abstract
The pivotal involvement of reverse transcriptase activity in the pathogenesis of the progressive HIV virus has stimulated gradual advancements in drug discovery initiatives spanning three decades. Consequently, nonnucleoside reverse transcriptase inhibitors (NNRTIs) have emerged as a preeminent category of therapeutic agents for HIV management. Academic institutions and pharmaceutical companies have developed numerous NNRTIs, an essential component of antiretroviral therapy. Six NNRTIs have received Food and Drug Administration approval and are widely used in clinical practice, significantly improving the quality of HIV patients. However, the rapid emergence of drug resistance has limited the effectiveness of these medications, underscoring the necessity for perpetual research and development of novel therapeutic alternatives. To supplement the existing literatures on NNRTIs, a comprehensive review has been compiled to synthesize this extensive dataset into a comprehensible format for the medicinal chemistry community. In this review, a thorough investigation and meticulous analysis were conducted on the progressions achieved in NNRTIs within the past 8 years (2016-2023), and the experiences and insights gained in the development of inhibitors with varying chemical structures were also summarized. The provision of a crucial point of reference for the development of wide-ranging anti-HIV medications is anticipated.
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Affiliation(s)
- Kun Zhang
- Department of Chemistry, Engineering Center of Catalysis and Synthesis for Chiral Molecules, Fudan University, Shanghai, China
- Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai, China
- Institute of Pharmaceutical Research and School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Yu-Jie Zhang
- Department of Chemistry, Engineering Center of Catalysis and Synthesis for Chiral Molecules, Fudan University, Shanghai, China
- Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai, China
- Institute of Pharmaceutical Research and School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Min Li
- Institute of Pharmaceutical Research and School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Christophe Pannecouque
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Erik De Clercq
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Shuai Wang
- Department of Chemistry, Engineering Center of Catalysis and Synthesis for Chiral Molecules, Fudan University, Shanghai, China
- Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai, China
| | - Fen-Er Chen
- Department of Chemistry, Engineering Center of Catalysis and Synthesis for Chiral Molecules, Fudan University, Shanghai, China
- Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai, China
- Institute of Pharmaceutical Research and School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
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3
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Phulwale V, Shet H, Gunturu KC, Rout SR, Dandela R, Adhav S, Kapdi AR. Cu(II)/PTABS-Promoted, Chemoselective Amination of HaloPyrimidines. J Org Chem 2024; 89:9243-9254. [PMID: 38878304 DOI: 10.1021/acs.joc.4c00171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
Chemoselective amination is a highly desired synthetic methodology, given its importance as a possible strategy to synthesize various drug molecules and agrochemicals. We, herein, disclose a highly chemoselective Cu(II)-PTABS-promoted amination of pyrimidine structural feature containing different halogen atoms.
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Affiliation(s)
- Vikram Phulwale
- Department of Chemistry, Institute of Chemical Technology, Nathalal Parekh Road, Matunga, Mumbai 400019, India
| | - Harshita Shet
- Department of Chemistry, Institute of Chemical Technology, Nathalal Parekh Road, Matunga, Mumbai 400019, India
| | | | - Smruti Rekha Rout
- Department of Industrial and Engineering Chemistry, Institute of Chemical Technology-Indian Oil Odisha Campus , Samantpuri, Bhubaneswar, Odisha 751013, India
| | - Rambabu Dandela
- Department of Industrial and Engineering Chemistry, Institute of Chemical Technology-Indian Oil Odisha Campus , Samantpuri, Bhubaneswar, Odisha 751013, India
| | - Suyog Adhav
- BASF Chemicals India Pvt. Ltd., Plot No 12, Thane Belapur Road, Navi Mumbai 400705, India
| | - Anant R Kapdi
- Department of Chemistry, Institute of Chemical Technology, Nathalal Parekh Road, Matunga, Mumbai 400019, India
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4
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Aldholmi M, Ahmad R, Shaikh MH, Salem AM, Alqurashi M, Alturki M. Anti-Infective Activity of Momordica charantia Extract with Molecular Docking of Its Triterpenoid Glycosides. Antibiotics (Basel) 2024; 13:544. [PMID: 38927210 PMCID: PMC11200997 DOI: 10.3390/antibiotics13060544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/04/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
Momordica charantia, commonly known as bitter melon, is a fruiting plant that has been used for several diseases including infectious diseases. In this study, we report the antibacterial, antifungal, and antiviral activity of different bitter melon fruit parts originating from India and Saudi Arabia. The in vitro experiments are supported by the molecular docking of karavilosides to verify their role in the bioactivity. The antimicrobial assays revealed activity against Candida albicans, Escherichia coli, and Staphylococcus aureus. The extracts exhibited the potent inhibition of HIV-I reverse transcriptase, with an IC50 of 0.125 mg/mL observed for the pith extract originating from Saudi Arabia and the standard drug doxorubicin. The molecular docking of karavilosides exhibited a significant affinity to reverse transcriptase comparable to Rilpivirine and higher than that of doxorubicin. These outcomes encourage the precious bioactive components of the seed and pith of the Saudi bitter melon fruits to be further studied for isolation and structure elucidation.
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Affiliation(s)
- Mohammed Aldholmi
- Department of Natural Products, College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Rizwan Ahmad
- Department of Natural Products, College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Mohammad Habeeb Shaikh
- Department of Physiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 34224, Saudi Arabia
| | - Ayad Mohammed Salem
- Department of Physiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 34224, Saudi Arabia
| | - Maher Alqurashi
- Department of Microbiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Mansour Alturki
- Department of Pharmaceutical Chemistry, College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
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5
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Duffey M, Shafer RW, Timm J, Burrows JN, Fotouhi N, Cockett M, Leroy D. Combating antimicrobial resistance in malaria, HIV and tuberculosis. Nat Rev Drug Discov 2024; 23:461-479. [PMID: 38750260 DOI: 10.1038/s41573-024-00933-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2024] [Indexed: 06/07/2024]
Abstract
Antimicrobial resistance poses a significant threat to the sustainability of effective treatments against the three most prevalent infectious diseases: malaria, human immunodeficiency virus (HIV) infection and tuberculosis. Therefore, there is an urgent need to develop novel drugs and treatment protocols capable of reducing the emergence of resistance and combating it when it does occur. In this Review, we present an overview of the status and underlying molecular mechanisms of drug resistance in these three diseases. We also discuss current strategies to address resistance during the research and development of next-generation therapies. These strategies vary depending on the infectious agent and the array of resistance mechanisms involved. Furthermore, we explore the potential for cross-fertilization of knowledge and technology among these diseases to create innovative approaches for minimizing drug resistance and advancing the discovery and development of new anti-infective treatments. In conclusion, we advocate for the implementation of well-defined strategies to effectively mitigate and manage resistance in all interventions against infectious diseases.
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Affiliation(s)
- Maëlle Duffey
- Medicines for Malaria Venture (MMV), R&D Department/Drug Discovery, ICC, Geneva, Switzerland
- The Global Antibiotic Research & Development Partnership, Geneva, Switzerland
| | - Robert W Shafer
- Department of Medicine/Infectious Diseases, Stanford University, Palo Alto, CA, USA
| | | | - Jeremy N Burrows
- Medicines for Malaria Venture (MMV), R&D Department/Drug Discovery, ICC, Geneva, Switzerland
| | | | | | - Didier Leroy
- Medicines for Malaria Venture (MMV), R&D Department/Drug Discovery, ICC, Geneva, Switzerland.
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6
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Ahmad G, Sohail M, Bilal M, Rasool N, Qamar MU, Ciurea C, Marceanu LG, Misarca C. N-Heterocycles as Promising Antiviral Agents: A Comprehensive Overview. Molecules 2024; 29:2232. [PMID: 38792094 PMCID: PMC11123935 DOI: 10.3390/molecules29102232] [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: 03/07/2024] [Revised: 04/22/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024] Open
Abstract
Viruses are a real threat to every organism at any stage of life leading to extensive infections and casualties. N-heterocycles can affect the viral life cycle at many points, including viral entrance into host cells, viral genome replication, and the production of novel viral species. Certain N-heterocycles can also stimulate the host's immune system, producing antiviral cytokines and chemokines that can stop the reproduction of viruses. This review focused on recent five- or six-membered synthetic N-heterocyclic molecules showing antiviral activity through SAR analyses. The review will assist in identifying robust scaffolds that might be utilized to create effective antiviral drugs with either no or few side effects.
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Affiliation(s)
- Gulraiz Ahmad
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan; (G.A.); (M.S.)
| | - Maria Sohail
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan; (G.A.); (M.S.)
| | - Muhammad Bilal
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China;
| | - Nasir Rasool
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan; (G.A.); (M.S.)
| | - Muhammad Usman Qamar
- Institute of Microbiology, Faculty of Life Sciences, Government College University, Faisalabad 38000, Pakistan;
- Division of Infectious Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland
- Department of Microbiology and Molecular Medicine, University of Geneva, 1205 Geneva, Switzerland
| | - Codrut Ciurea
- Faculty of Medicine, Transilvania University of Brasov, 500036 Brasov, Romania; (L.G.M.)
| | - Luigi Geo Marceanu
- Faculty of Medicine, Transilvania University of Brasov, 500036 Brasov, Romania; (L.G.M.)
| | - Catalin Misarca
- Faculty of Medicine, Transilvania University of Brasov, 500036 Brasov, Romania; (L.G.M.)
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7
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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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8
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Wang Z. Novel diarylpyrimidine subtypes as HIV-1 nonnucleoside reverse transcriptase inhibitors with improved resistance profile. J Med Virol 2024; 96:e29553. [PMID: 38516803 DOI: 10.1002/jmv.29553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 03/06/2024] [Indexed: 03/23/2024]
Affiliation(s)
- Zhengqiang Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota, USA
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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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Kim MJ, Yu KL, Han R, Lee Y, Oh K, You JC. Identification of a Non-Nucleoside Reverse Transcriptase Inhibitor against Human Immunodeficiency Virus-1. ACS Infect Dis 2023; 9:1582-1592. [PMID: 37415514 DOI: 10.1021/acsinfecdis.3c00166] [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] [Indexed: 07/08/2023]
Abstract
The HIV-1 infection epidemic remains a global health problem. Current antiretroviral treatments are effective in controlling the progression of a severe infection. However, the emergence of drug resistance requires an urgent identification of new treatment regimes. HIV-1 reverse transcriptase (RTs) has been a successful therapeutic target owing to its high specificity and potent antiviral properties; therefore, it has become an essential component of current HIV-1 standard treatments. This study identified a new HIV-1 RTs inhibitor (Compound #8) that is structurally unique and greatly effective against HIV-1 through chemical library screening and a medicinal chemistry program by analyzing the structure-activity relationship (SAR). Further analysis of molecular docking and mechanisms of action demonstrated that Compound #8 is a novel type of HIV-1 non-nucleoside reverse transcriptase inhibitor (NNRTI) with a flexible binding mode. Therefore, it exhibits great therapeutic potential when combined with other existing HIV-1 drugs. Our current studies suggest that Compound #8 is a promising novel scaffold for the development of new HIV-1 treatments.
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Affiliation(s)
- Min-Jung Kim
- Avixgen Inc., 2477 Nambusunhwan-ro, Seocho, Seoul 06725, Republic of Korea
| | - Kyung Lee Yu
- National Research Laboratory of Molecular Virology, Department of Pathology, School of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho, Seoul 06591, Republic of Korea
| | - Ri Han
- College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak, Seoul 06974, Republic of Korea
| | - Yoonji Lee
- College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak, Seoul 06974, Republic of Korea
| | - Kyungsoo Oh
- College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak, Seoul 06974, Republic of Korea
- Center for Metareceptome Research, Graduate School of Pharmaceutical Sciences, Chung-Ang University, 84 Heukseok-ro, Dongjak, Seoul 06974, Republic of Korea
| | - Ji Chang You
- Avixgen Inc., 2477 Nambusunhwan-ro, Seocho, Seoul 06725, Republic of Korea
- National Research Laboratory of Molecular Virology, Department of Pathology, School of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho, Seoul 06591, Republic of Korea
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11
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Lane T, Makarov V, Nelson JAE, Meeker RB, Sanna G, Riabova O, Kazakova E, Monakhova N, Tsedilin A, Urbina F, Jones T, Suchy A, Ekins S. N-Phenyl-1-(phenylsulfonyl)-1 H-1,2,4-triazol-3-amine as a New Class of HIV-1 Non-nucleoside Reverse Transcriptase Inhibitor. J Med Chem 2023; 66:6193-6217. [PMID: 37130343 PMCID: PMC10269403 DOI: 10.1021/acs.jmedchem.2c02055] [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] [Indexed: 05/04/2023]
Abstract
Highly active antiretroviral therapy (HAART) has revolutionized human immunodeficiency virus (HIV) healthcare, turning it from a terminal to a potentially chronic disease, although some patients can develop severe comorbidities. These include neurological complications, such as HIV-associated neurocognitive disorders (HAND), which result in cognitive and/or motor function symptoms. We now describe the discovery, synthesis, and evaluation of a new class of N-phenyl-1-(phenylsulfonyl)-1H-1,2,4-triazol-3-amine HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTI) aimed at avoiding HAND. The most promising molecule, 12126065, exhibited antiviral activity against wild-type HIV-1 in TZM cells (EC50 = 0.24 nM) with low in vitro cytotoxicity (CC50 = 4.8 μM) as well as retained activity against clinically relevant HIV mutants. 12126065 also demonstrated no in vivo acute or subacute toxicity, good in vivo brain penetration, and minimal neurotoxicity in mouse neurons up to 10 μM, with a 50% toxicity concentration (TC50) of >100 μM, well below its EC50.
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Affiliation(s)
- Thomas Lane
- Collaborations Pharmaceuticals Inc., 840 Main Campus Drive, Lab, 3510, Raleigh, NC 27606, USA
| | - Vadim Makarov
- Research Center of Biotechnology RAS, Leninsky Prospekt 33-2, 119071, Moscow 119071, Russia
| | - Julie A. E. Nelson
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Rick B. Meeker
- Department of Neurology, University of North Carolina, NC 27514, USA
| | - Giuseppina Sanna
- Department of Biomedical Science, University of Cagliari, Monserrato, 09042, Italy
| | - Olga Riabova
- Research Center of Biotechnology RAS, Leninsky Prospekt 33-2, 119071, Moscow 119071, Russia
| | - Elena Kazakova
- Research Center of Biotechnology RAS, Leninsky Prospekt 33-2, 119071, Moscow 119071, Russia
| | - Natalia Monakhova
- Research Center of Biotechnology RAS, Leninsky Prospekt 33-2, 119071, Moscow 119071, Russia
| | - Andrey Tsedilin
- Research Center of Biotechnology RAS, Leninsky Prospekt 33-2, 119071, Moscow 119071, Russia
| | - Fabio Urbina
- Collaborations Pharmaceuticals Inc., 840 Main Campus Drive, Lab, 3510, Raleigh, NC 27606, USA
| | - Thane Jones
- Collaborations Pharmaceuticals Inc., 840 Main Campus Drive, Lab, 3510, Raleigh, NC 27606, USA
| | - Ashley Suchy
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Sean Ekins
- Collaborations Pharmaceuticals Inc., 840 Main Campus Drive, Lab, 3510, Raleigh, NC 27606, USA
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12
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Hao QQ, Chen XM, Pannecouque C, De Clercq E, Wang S, Chen FE. Structure-directed linker optimization of novel HEPTs as non-nucleoside inhibitors of HIV-1 reverse transcriptase. Bioorg Chem 2023; 133:106413. [PMID: 36791619 DOI: 10.1016/j.bioorg.2023.106413] [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: 12/17/2022] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 02/11/2023]
Abstract
1-[(2-Hydroxyethoxy)methyl]-6-(phenylthio)thymines (HEPTs) have been previously described as an important class of HIV-1 nonnucleoside reverse transcriptase inhibitors (NNRTIs). In our continuously pursuing HEPT optimization efforts, a series of novel HEPTs, featuring -C(OH)CH2R, -CC, or -CHCH2R linker at the benzylic α-methylene unit, were developed as NNRTIs. Among these new HEPTs, the compound C20 with -CHCH3 group at the benzylic α-methylene unit conferred the highest potency toward WT HIV-1 and selectivity (EC50 = 0.23 μM, SI = 150.20), which was better than the lead compound HEPT (EC50 = 7 μM, SI = 106). Also, C20 was endowed with high efficacy against clinically relevant mutant strains (EC50(L100I) = 1.07 μM; EC50(K103N) = 4.33 μM; EC50(Y181C) = 5.57 μM; EC50(E138K) = 1.06 μM; EC50(F227L+V106A) = 5.45 μM) and wild-type HIV-1 reverse transcriptase (RT) with an IC50 value of 0.55 μM. Molecular docking and molecular dynamics simulations, as well as preliminary structure-activity relationship (SAR) analysis of these new compounds, provided a deeper insight into the key structural features of the interactions between HEPT analogs and HIV-1 RT and laid the foundation for further modification on HEPT scaffold.
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Affiliation(s)
- Qing-Qing Hao
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China; Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai 200433, China; Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Xiao-Mei Chen
- Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | | | - Erik De Clercq
- Rega Institute for Medical Research, KU Leuven, Herestraat 49, B-3000 Leuven, Belgium
| | - Shuai Wang
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China; Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai 200433, China.
| | - Fen-Er Chen
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China; Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai 200433, China; Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China.
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13
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Prener L, Baszczyňski O, Kaiser MM, Dračínský M, Stepan G, Lee YJ, Brumshtein B, Yu H, Jansa P, Lansdon EB, Janeba Z. Design and Synthesis of Novel HIV-1 NNRTIs with Bicyclic Cores and with Improved Physicochemical Properties. J Med Chem 2023; 66:1761-1777. [PMID: 36652602 PMCID: PMC10017027 DOI: 10.1021/acs.jmedchem.2c01574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Indexed: 01/19/2023]
Abstract
Non-nucleoside reverse transcriptase inhibitors (NNRTIs) represent cornerstones of current regimens for treatment of human immunodeficiency virus type 1 (HIV-1) infections. However, NNRTIs usually suffer from low aqueous solubility and the emergence of resistant viral strains. In the present work, novel bicyclic NNRTIs derived from etravirine (ETV) and rilpivirine (RPV), bearing modified purine, tetrahydropteridine, and pyrimidodiazepine cores, were designed and prepared. Compounds 2, 4, and 6 carrying the acrylonitrile moiety displayed single-digit nanomolar activities against the wild-type (WT) virus (EC50 = 2.5, 2.7, and 3.0 nM, respectively), where the low nanomolar activity was retained against HXB2 (EC50 = 2.2-2.8 nM) and the K103N and Y181C mutated strains (fold change, 1.2-6.7×). Most importantly, compound 2 exhibited significantly improved phosphate-buffered saline solubility (10.4 μM) compared to ETV and RPV (≪1 μM). Additionally, the binding modes of compounds 2, 4, and 6 to the reverse transcriptase were studied by X-ray crystallography.
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Affiliation(s)
- Ladislav Prener
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 160 00, Czech Republic
| | - Ondřej Baszczyňski
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 160 00, Czech Republic
- Department
of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, Prague 2 128
43, Czech Republic
| | - Martin M. Kaiser
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 160 00, Czech Republic
| | - Martin Dračínský
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 160 00, Czech Republic
| | - George Stepan
- Gilead
Sciences Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Yu-Jen Lee
- Gilead
Sciences Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Boris Brumshtein
- Gilead
Sciences Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Helen Yu
- Gilead
Sciences Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Petr Jansa
- Gilead
Sciences Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Eric B. Lansdon
- Gilead
Sciences Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Zlatko Janeba
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 160 00, Czech Republic
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14
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Lan S, Neilsen G, Slack RL, Cantara WA, Castaner AE, Lorson ZC, Lulkin N, Zhang H, Lee J, Cilento ME, Tedbury PR, Sarafianos SG. Nirmatrelvir Resistance in SARS-CoV-2 Omicron_BA.1 and WA1 Replicons and Escape Strategies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2022.12.31.522389. [PMID: 36656782 PMCID: PMC9844013 DOI: 10.1101/2022.12.31.522389] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The antiviral component of Paxlovid, nirmatrelvir (NIR), forms a covalent bond with Cys145 of SARS-CoV-2 nsp5. To explore NIR resistance we designed mutations to impair binding of NIR over substrate. Using 12 Omicron (BA.1) and WA.1 SARS-CoV-2 replicons, cell-based complementation and enzymatic assays, we showed that in both strains, E166V imparted high NIR resistance (∼55-fold), with major decrease in WA1 replicon fitness (∼20-fold), but not BA.1 (∼2-fold). WA1 replicon fitness was restored by L50F. These differences may contribute to a potentially lower barrier to resistance in Omicron than WA1. E166V is rare in untreated patients, albeit more prevalent in paxlovid-treated EPIC-HR clinical trial patients. Importantly, NIR-resistant replicons with E166V or E166V/L50F remained susceptible to a) the flexible GC376, and b) PF-00835231, which forms additional interactions. Molecular dynamics simulations show steric clashes between the rigid and bulky NIR t-butyl and β-branched V166 distancing the NIR warhead from its Cys145 target. In contrast, GC376, through "wiggling and jiggling" accommodates V166 and still covalently binds Cys145. PF-00835231 uses its strategically positioned methoxy-indole to form a β-sheet and overcome E166V. Drug design based on strategic flexibility and main chain-targeting may help develop second-generation nsp5-targeting antivirals efficient against NIR-resistant viruses.
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15
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Abstract
The biggest challenge to immune control of HIV infection is the rapid within-host viral evolution, which allows selection of viral variants that escape from T cell and antibody recognition. Thus, it is impossible to clear HIV infection without targeting "immutable" components of the virus. Unlike the adaptive immune system that recognizes cognate epitopes, the CARD8 inflammasome senses the essential enzymatic activity of the HIV-1 protease, which is immutable for the virus. Hence, all subtypes of HIV clinical isolates can be recognized by CARD8. In HIV-infected cells, the viral protease is expressed as a subunit of the viral Gag-Pol polyprotein and remains functionally inactive prior to viral budding. A class of anti-HIV drugs, the non-nucleoside reverse transcriptase inhibitors (NNRTIs), can promote Gag-pol dimerization and subsequent premature intracellular activation of the viral protease. NNRTI treatment triggers CARD8 inflammasome activation, which leads to pyroptosis of HIV-infected CD4+ T cells and macrophages. Targeting the CARD8 inflammasome can be a potent and broadly effective strategy for HIV eradication.
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Affiliation(s)
- Kolin M Clark
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States
| | - Priya Pal
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States
| | - Josh G Kim
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States
| | - Qiankun Wang
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States
| | - Liang Shan
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States; Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO, United States.
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16
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Fordham JM, Piacentini P, Santagostino M. Pd-Catalyzed Ring-Opening/Arylation/Cyclization of 2-Aminothiazole Derivatives Provides Modular Access to Isocytosine Analogues. J Org Chem 2022; 87:12688-12697. [PMID: 36075053 DOI: 10.1021/acs.joc.2c01200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report a Pd-catalyzed ring-opening/arylation/cyclization reaction sequence between 2-aminothiazoles and aryl (pseudo)halides that provides modular access to isocytosine analogues. The scope of the reaction is broad with respect to both coupling partners and a robustness test demonstrated the functional group tolerance of the methodology. Visual kinetic analysis revealed that the product may inhibit catalyst turnover for some substrates.
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Affiliation(s)
- James M Fordham
- Chemical Development Germany, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß 88397, Germany
| | - Paolo Piacentini
- Department of Chemistry, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy
| | - Marco Santagostino
- Chemical Development Germany, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß 88397, Germany
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17
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Shahari MSB, Dolzhenko AV. A closer look at N2,6-substituted 1,3,5-triazine-2,4-diamines: Advances in synthesis and biological activities. Eur J Med Chem 2022; 241:114645. [DOI: 10.1016/j.ejmech.2022.114645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/19/2022] [Accepted: 07/29/2022] [Indexed: 11/03/2022]
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18
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Cryo-EM structures of wild-type and E138K/M184I mutant HIV-1 RT/DNA complexed with inhibitors doravirine and rilpivirine. Proc Natl Acad Sci U S A 2022; 119:e2203660119. [PMID: 35858448 PMCID: PMC9335299 DOI: 10.1073/pnas.2203660119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The enzyme reverse transcriptase (RT) is a key antiviral target, and nonnucleoside RT inhibitors (NNRTIs) are among the frequently used components of antiretroviral therapy for treating HIV-1 infection. The emergence of drug-resistant mutations continues to pose a challenge in HIV treatment. The RT mutations M184I and E138K emerge in patients receiving rilpivirine. We obtained the structural snapshots of rilpivirine, doravirine, and nevirapine inhibited wild-type and M184I/E138K RT/DNA polymerase complexes by cryo-electron microscopy. Key structural changes observed in the rilpivirine- and doravirine-bound structures have implications for understanding NNRTI drug resistance. Additionally, the cryo-EM structure determination strategy outlined in this study can be adapted to aid drug design targeting smaller and flexible proteins. Structures trapping a variety of functional and conformational states of HIV-1 reverse transcriptase (RT) have been determined by X-ray crystallography. These structures have played important roles in explaining the mechanisms of catalysis, inhibition, and drug resistance and in driving drug design. However, structures of several desired complexes of RT could not be obtained even after many crystallization or crystal soaking experiments. The ternary complexes of doravirine and rilpivirine with RT/DNA are such examples. Structural study of HIV-1 RT by single-particle cryo-electron microscopy (cryo-EM) has been challenging due to the enzyme’s relatively smaller size and higher flexibility. We optimized a protocol for rapid structure determination of RT complexes by cryo-EM and determined six structures of wild-type and E138K/M184I mutant RT/DNA in complexes with the nonnucleoside inhibitors rilpivirine, doravirine, and nevirapine. RT/DNA/rilpivirine and RT/DNA/doravirine complexes have structural differences between them and differ from the typical conformation of nonnucleoside RT inhibitor (NNRTI)–bound RT/double-stranded DNA (dsDNA), RT/RNA–DNA, and RT/dsRNA complexes; the primer grip in RT/DNA/doravirine and the YMDD motif in RT/DNA/rilpivirine have large shifts. The DNA primer 3′-end in the doravirine-bound structure is positioned at the active site, but the complex is in a nonproductive state. In the mutant RT/DNA/rilpivirine structure, I184 is stacked with the DNA such that their relative positioning can influence rilpivirine in the pocket. Simultaneously, E138K mutation opens the NNRTI-binding pocket entrance, potentially contributing to a faster rate of rilpivirine dissociation by E138K/M184I mutant RT, as reported by an earlier kinetic study. These structural differences have implications for understanding molecular mechanisms of drug resistance and for drug design.
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19
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Dwivedi R, Wang Y, Kline C, Fischer DK, Ambrose Z. APOBEC3 selects V179I in HIV-1 reverse transcriptase to provide selective advantage for non-nucleoside reverse transcriptase inhibitor-resistant mutants. FRONTIERS IN VIROLOGY 2022; 2. [PMID: 35957953 PMCID: PMC9364801 DOI: 10.3389/fviro.2022.919825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The V179I substitution in human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) is selected in humans or mouse models treated with certain nonnucleoside reverse transcriptase inhibitors (NNRTIs). While it is often observed together with other NNRTI resistance mutations, V179I does not confer drug resistance. To understand how V179I arises during NNRTI treatment, we characterized it in HIV-1 molecular clones with or without the NNRTI resistance mutations Y181C or Y181V. While V179I alone did not confer resistance to any NNRTIs tested, when present with Y181C/V it enhanced drug resistance to some NNRTIs by 3- to 8-fold. In replication competition experiments in the presence of the NNRTI rilpivirine (RPV), V179I modestly enhanced Y181C HIV-1 or Y181V HIV-1 replication compared to viruses without V179I. As V179I arises from a G to A mutation, we evaluated whether it could arise due to host APOBEC3 deaminase activity and be maintained in the presence of a NNRTI to provide a selective advantage for the virus. V179I was detected in some humanized mice treated with RPV and was associated with G to A mutations characteristic of APOBEC3 activity. In RPV selection experiments, the frequency of V179I in HIV-1 was accelerated in CD4+ T cells expressing higher APOBEC3F and APOBEC3G levels. Our results provide evidence that V179I in HIV-1 RT can arise due to APOBEC-mediated G to A hypermutation and can confer a selective advantage to drug-resistant HIV-1 isolates in the presence of some NNRTIs.
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20
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Insights into HIV-1 Reverse Transcriptase (RT) Inhibition and Drug Resistance from Thirty Years of Structural Studies. Viruses 2022; 14:v14051027. [PMID: 35632767 PMCID: PMC9148108 DOI: 10.3390/v14051027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 02/01/2023] Open
Abstract
The enzyme reverse transcriptase (RT) plays a central role in the life cycle of human immunodeficiency virus (HIV), and RT has been an important drug target. Elucidations of the RT structures trapping and detailing the enzyme at various functional and conformational states by X-ray crystallography have been instrumental for understanding RT activities, inhibition, and drug resistance. The structures have contributed to anti-HIV drug development. Currently, two classes of RT inhibitors are in clinical use. These are nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs). However, the error-prone viral replication generates variants that frequently develop resistance to the available drugs, thus warranting a continued effort to seek more effective treatment options. RT also provides multiple additional potential druggable sites. Recently, the use of single-particle cryogenic electron microscopy (cryo-EM) enabled obtaining structures of NNRTI-inhibited HIV-1 RT/dsRNA initiation and RT/dsDNA elongation complexes that were unsuccessful by X-ray crystallography. The cryo-EM platform for the structural study of RT has been established to aid drug design. In this article, we review the roles of structural biology in understanding and targeting HIV RT in the past three decades and the recent structural insights of RT, using cryo-EM.
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21
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Wang Z, Cherukupalli S, Xie M, Wang W, Jiang X, Jia R, Pannecouque C, De Clercq E, Kang D, Zhan P, Liu X. Contemporary Medicinal Chemistry Strategies for the Discovery and Development of Novel HIV-1 Non-nucleoside Reverse Transcriptase Inhibitors. J Med Chem 2022; 65:3729-3757. [PMID: 35175760 DOI: 10.1021/acs.jmedchem.1c01758] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Currently, HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs) are a major component of the highly active anti-retroviral therapy (HAART) regimen. However, the occurrence of drug-resistant strains and adverse reactions after long-term usage have inevitably compromised the clinical application of NNRTIs. Therefore, the development of novel inhibitors with distinct anti-resistance profiles and better pharmacological properties is still an enormous challenge. Herein, we summarize state-of-the-art medicinal chemistry strategies for the discovery of potent NNRTIs, such as structure-based design strategies, contemporary computer-aided drug design, covalent-binding strategies, and the application of multi-target-directed ligands. The strategies described here will facilitate the identification of promising HIV-1 NNRTIs.
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Affiliation(s)
- Zhao Wang
- 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, P.R. China
| | - Srinivasulu Cherukupalli
- 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, P.R. China
| | - Minghui Xie
- 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, P.R. China
| | - Wenbo Wang
- 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, P.R. China
| | - Xiangyi Jiang
- 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, P.R. China
| | - Ruifang Jia
- 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, P.R. China
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Dongwei Kang
- 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, P.R. China.,China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - 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, P.R. China.,China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, P.R. 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, P.R. China.,China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
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22
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Jin X, Piao HR, Pannecouque C, De Clercq E, Zhuang C, Chen FE. Design of the naphthyl-diarylpyrimidines as potent non-nucleoside reverse transcriptase inhibitors (NNRTIs) via structure-based extension into the entrance channel. Eur J Med Chem 2021; 226:113868. [PMID: 34583311 DOI: 10.1016/j.ejmech.2021.113868] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/27/2021] [Accepted: 09/20/2021] [Indexed: 12/12/2022]
Abstract
A series of novel naphthyl-diarylpyrimidine (DAPY) derivatives were designed and synthesized to explore the entrance channel of the non-nucleoside reverse transcriptase inhibitors binding pocket (NNIBP) by incorporating different flexible side chains at the C-6 position. The biological evaluation results showed that all analogues possessed promising HIV-1 inhibitory activity at the nanomolar concentration range. Three compounds (7, 9 and 39) displayed excellent potency against WT HIV-1 strain with EC50 values ranging from 5 to 10 nM and high selectivity indexes (SI = 3504, 30488 and 22846, respectively), which were higher than for nevirapine and comparable to the values for etravirine. The RT inhibition activity, preliminary structure-activity relationship and molecular docking study showed that the side chain at the C-6 position of the DAPYs occupied the entrance channel and significantly influenced anti-HIV activity and selectivity. Additionally, the physicochemical properties were investigated to evaluate the drug-like features, which indicated that introducing various substituents on the pyrimidine ring can improve solubility.
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Affiliation(s)
- Xin Jin
- Key Laboratory of Natural Resources of Changbai Mountain & Functional Molecules, Ministry of Education, Yanbian University College of Pharmacy, Yanbian University, 977 Gongyuan Road, Yanji, Jilin Province, 133002, China
| | - Hu-Ri Piao
- Key Laboratory of Natural Resources of Changbai Mountain & Functional Molecules, Ministry of Education, Yanbian University College of Pharmacy, Yanbian University, 977 Gongyuan Road, Yanji, Jilin Province, 133002, China
| | | | - Erik De Clercq
- Rega Institute for Medical Research, KU Leuven, Herestraat 49, B-3000, Leuven, Belgium
| | - Chunlin Zhuang
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai, 200433, China; Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai, 200433, China.
| | - Fen-Er Chen
- Key Laboratory of Natural Resources of Changbai Mountain & Functional Molecules, Ministry of Education, Yanbian University College of Pharmacy, Yanbian University, 977 Gongyuan Road, Yanji, Jilin Province, 133002, China; Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai, 200433, China; Rega Institute for Medical Research, KU Leuven, Herestraat 49, B-3000, Leuven, Belgium.
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23
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Sluis-Cremer N. Retroviral reverse transcriptase: Structure, function and inhibition. Enzymes 2021; 50:179-194. [PMID: 34861936 DOI: 10.1016/bs.enz.2021.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Reverse transcriptase (RT) is a multifunctional enzyme that has RNA- and DNA-dependent DNA polymerase activity and ribonuclease H (RNase H) activity, and is responsible for the reverse transcription of retroviral single-stranded RNA into double-stranded DNA. The essential role that RT plays in the human immunodeficiency virus (HIV) life cycle is highlighted by the fact that multiple antiviral drugs-which can be classified into two distinct therapeutic classes-are routinely used to treat and/or prevent HIV infection. This book chapter provides detailed insights into the three-dimensional structure of HIV RT, the biochemical mechanisms of DNA polymerization and RNase H activity, and the mechanisms by which nucleoside/nucleotide and nonnucleoside RT inhibitors block reverse transcription.
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Affiliation(s)
- Nicolas Sluis-Cremer
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.
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24
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Patel JJ, Modh RP, Asamdi M, Chikhalia KH. Comparative biological study between quinazolinyl-triazinyl semicarbazide and thiosemicarbazide hybrid derivatives. Mol Divers 2021; 25:2271-2287. [PMID: 32596789 DOI: 10.1007/s11030-020-10117-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 06/17/2020] [Indexed: 11/29/2022]
Abstract
Practical synthesis and biological activities of quinazolinyl-triazinyl semicarbazides (10a-j) and quinazolinyl-triazinyl thiosemicarbazides (11a-j) have been described. The novel semicarbazides and thiosemicarbazides were prepared by condensation of different nucleophiles like isocyanate and isothiocyanate by the displacement of chlorine atoms on the basis of functionality concept on varying conditions. The synthesized quinazolinyl-triazinyl semicarbazide and thiosemicarbazide derivatives were evaluated for their expected antimicrobial activity. All the final synthesized derivatives were characterized by their melting point, mass spectra, 1H NMR and 13C NMR as well as elemental microanalysis. The final analogues were then analyzed for their in vitro antimicrobial activity against bacteria (Gram positive and negative) and fungus using the agar streak dilution method as well as in vitro anti-HIV activity against two types of viral strains, viz. HIV type I (IIIB) and type II (ROD) by using MTT assay method. SAR and HOMO-LUMO studies were also carried out for proving the structural biological activity. Among them, compounds 10e, 10f, 11h and 11j gave best results as their energy gap is very low which makes their activity higher.
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Affiliation(s)
- Janki J Patel
- Department of Chemistry, Veer Narmad South Gujarat University, Surat, 395007, Gujarat, India
| | - Rahul P Modh
- Department of Chemistry, School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Manjoorahmed Asamdi
- Department of Chemistry, School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Kishor H Chikhalia
- Department of Chemistry, Veer Narmad South Gujarat University, Surat, 395007, Gujarat, India.
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25
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Wang X, Wang Y, Li X, Yu Z, Song C, Du Y. Nitrile-containing pharmaceuticals: target, mechanism of action, and their SAR studies. RSC Med Chem 2021; 12:1650-1671. [PMID: 34778767 PMCID: PMC8528211 DOI: 10.1039/d1md00131k] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 06/27/2021] [Indexed: 12/12/2022] Open
Abstract
The nitrile group is an important functional group widely found in both pharmaceutical agents and natural products. More than 30 nitrile-containing pharmaceuticals have been approved by the FDA for the management of a broad range of clinical conditions in the last few decades. Incorporation of a nitrile group into lead compounds has gradually become a promising strategy in rational drug design as it can bring additional benefits including enhanced binding affinity to the target, improved pharmacokinetic profile of parent drugs, and reduced drug resistance. This paper reviews the existing drugs with a nitrile moiety that have been approved or in clinical trials, involving their targets, molecular mechanism of pharmacology and SAR studies, and classifies them into different categories based on their clinical usages.
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Affiliation(s)
- Xi Wang
- School of Pharmaceutical Science and Technology, Tianjin University Tianjin 300072 China
| | - Yuanxun Wang
- National Institution of Biological Sciences, Beijing No. 7 Science Park Road, Zhongguancun Life Science Park Beijing 102206 China
| | - Xuemin Li
- School of Pharmaceutical Science and Technology, Tianjin University Tianjin 300072 China
| | - Zhenyang Yu
- School of Pharmaceutical Science and Technology, Tianjin University Tianjin 300072 China
| | - Chun Song
- State Key Laboratory of Microbial Technology, Shandong University Qingdao City Shandong Province 266237 China
| | - Yunfei Du
- School of Pharmaceutical Science and Technology, Tianjin University Tianjin 300072 China
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26
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Kumar A, Siwach A, Verma P. An overview of the synthetic route to the marketed formulations of pyrimidine: A Review. Mini Rev Med Chem 2021; 22:884-903. [PMID: 34629043 DOI: 10.2174/1389557521666211008153329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 08/05/2021] [Accepted: 08/23/2021] [Indexed: 11/22/2022]
Abstract
Pyrimidine and its derivatives are a very important class of heterocyclic compounds that show interesting applications in the field of medicinal chemistry. Pyrimidine not only plays an important role as an organic reaction intermediate but also has a wide range of interesting biological activities viz. antibacterial, antifungal, anticancer, anti-inflammatory, antiviral, and antiprotozoal activity, etc. Numerous methods are available for the formation of pyrimidine derivatives have been reported in the literature. The advantage of pyrimidine as a starting material for different therapeutically potent derivatives has given momentum to this research. This review aims to report the new work on the synthesis of marketed drugs which consist of pyrimidine moiety.
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Affiliation(s)
- Amit Kumar
- Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, Haryana. India
| | - Ankit Siwach
- Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, Haryana. India
| | - Prabhakar Verma
- Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, Haryana. India
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27
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Zhang T, Zhou Z, Zalloum WA, Wang Z, Fu Z, Cherukupalli S, Feng D, Sun Y, Gao S, De Clercq E, Pannecouque C, Kang D, Zhan P, Liu X. Design, synthesis, and antiviral evaluation of novel piperidine-substituted arylpyrimidines as HIV-1 NNRTIs by exploring the hydrophobic channel of NNIBP. Bioorg Chem 2021; 116:105353. [PMID: 34536931 DOI: 10.1016/j.bioorg.2021.105353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 08/31/2021] [Accepted: 09/07/2021] [Indexed: 11/15/2022]
Abstract
Herein, alkenylpiperidine and alkynylpiperidine moieties were introduced into the left wing of DAPYs (diarylpyrimidines) to explore the new site of the NNIBP (non-nucleoside inhibitor binding pocket) protein-solvent interface region via the structure-based drug design strategy. All the synthesized compounds displayed nanomolar to submicromolar activity against WT (wild-type) HIV-1. Among all, compound FT1 (EC50 = 19 nM) was found to be the most active molecule, which is better than NVP (EC50 = 0.10 μM). In addition, most of the compounds displayed micromolar activity against K103N and E138K mutant strains, while FT1 (EC50(K103N) = 50 nM, EC50(E138K) = 0.19 µM) still has the most effective activity. The molecular dynamics simulation studies revealed that the presence of pyridine moiety of FT1 was essential and played a significant role in its binding with RT (reverse transcriptase).
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Affiliation(s)
- Tao Zhang
- 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
| | - Zhongxia Zhou
- 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
| | - Waleed A Zalloum
- Department of Pharmacy, Faculty of Health Science, American University of Madaba, P.O Box 2882, Amman 11821, Jordan
| | - Zhao Wang
- 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
| | - Zhipeng Fu
- 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
| | - Srinivasulu Cherukupalli
- 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
| | - Da Feng
- 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
| | - Yanying Sun
- 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
| | - Shenghua Gao
- 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
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium.
| | - Dongwei Kang
- 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.
| | - 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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28
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Al-Wahaibi LH, Bysani SRS, Tawfik SS, Abdelbaky MSM, Garcia-Granda S, El-Emam AA, Percino MJ, Thamotharan S. Invariant and Variable Supramolecular Self-Assembly in 6-Substituted Uracil Derivatives: Insights from X-ray Structures and Quantum Chemical Study. CRYSTAL GROWTH & DESIGN 2021. [DOI: 10.1021/acs.cgd.0c01583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lamya H. Al-Wahaibi
- Department of Chemistry, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Sai Ramya Sree Bysani
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, 613 401, India
| | - Samar S. Tawfik
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Mohammed S. M. Abdelbaky
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, Oviedo University-CINN, Oviedo 33006, Spain
| | - Santiago Garcia-Granda
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, Oviedo University-CINN, Oviedo 33006, Spain
| | - Ali A. El-Emam
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - M. Judith Percino
- Unidad de Polímeros y Electrónica Orgánica, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Val3-Ecocampus Valsequillo, Independencia O2 Sur 50, San Pedro Zacachimalpa, Puebla, C.P.72960, México
| | - Subbiah Thamotharan
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, 613 401, India
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29
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Fu Z, Zhang T, Zhou Z, Kang D, Sun L, Gao S, Cherukupalli S, De Clercq E, Pannecouque C, Liu X, Zhan P. Exploiting the hydrophobic channel of the NNIBP: Discovery of novel diarylpyrimidines as HIV-1 NNRTIs against wild-type and K103N mutant viruses. Bioorg Med Chem 2021; 42:116239. [PMID: 34090079 DOI: 10.1016/j.bmc.2021.116239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 05/17/2021] [Accepted: 05/19/2021] [Indexed: 01/19/2023]
Abstract
To further explore the chemical space surrounding the "hydrophobic channel" of the NNRTI binding pocket (NNIBP), a new series of diarylpyrimidines (DAPYs) were designed and synthesized as potent HIV-1 non-nucleoside RT inhibitors (NNRTIs). The target compounds were evaluated for anti-HIV potency in MT-4 cells. Most of the synthesized DAPYs exhibited moderate to excellent activity against the HIV-1 wild-type (WT) strain with EC50 values ranging from 16 nM to 0.722 µM. Interestingly, few compounds displayed remarkable activity in inhibiting K103N mutant virus with EC50 values ranging from 39 nM to 1.708 µM. Notably, FS2 (EC50(IIIB) = 16 nM, EC50(K103N) = 39 nM, SI = 294) was identified as the most significant compound, which was considerably more potent than nevirapine, lamivudine, and comparable to zidovudine. Additionally, the HIV-1 RT inhibition assay confirmed their binding target. Preliminary structure-activity relationships (SARs) and molecular modeling studies were also performed, providing significant suggestions for further optimization.
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Affiliation(s)
- Zhipeng Fu
- 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
| | - Tao Zhang
- 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
| | - Zhongxia Zhou
- 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
| | - Dongwei Kang
- 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
| | - Lin Sun
- 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
| | - Shenghua Gao
- 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
| | - Srinivasulu Cherukupalli
- 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
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium.
| | - 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.
| | - 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.
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30
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Ding L, Pannecouque C, De Clercq E, Zhuang C, Chen FE. Hydrophobic Pocket Occupation Design of Difluoro-Biphenyl-Diarylpyrimidines as Non-Nucleoside HIV-1 Reverse Transcriptase Inhibitors: from N-Alkylation to Methyl Hopping on the Pyrimidine Ring. J Med Chem 2021; 64:5067-5081. [PMID: 33851529 DOI: 10.1021/acs.jmedchem.1c00128] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Considering the nonideal metabolic stability of the difluoro-biphenyl-diarylpyrimidine lead compound 4, a series of novel alkylated difluoro-biphenyl-diarylpyrimidines were designed and synthesized based on their structure. Introducing alkyl or substituted alkyl groups on the linker region to block the potential metabolic sensitive sites generated 22 derivatives. Among them, compound 12a with an N-methyl group displayed excellent anti-HIV-1 activity and selectivity. The methyl group was hopped to the central pyrimidine to occupy the small linker region and maintain the water-mediated hydrogen bond observed in the binding of compound 4 with RT. The resulting compound 16y exhibited an improved anti-HIV-1 activity, much lower cytotoxicity, and nanomolar activity toward multiple mutants. In addition, 16y has a better stability in human liver microsomes than 4. Moreover, no apparent in vivo acute toxicity was observed in 16y-treated female, especially pregnant mice. This series of alkylated compounds with highly potency and safety represent a promising lead template for future discovery.
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Affiliation(s)
- Li Ding
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.,Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China.,Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai 200433, China
| | | | - Erik De Clercq
- Rega Institute for Medical Research, KU Leuven, Herestraat 49, B-3000 Leuven, Belgium
| | - Chunlin Zhuang
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China.,Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai 200433, China
| | - Fen-Er Chen
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.,Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China.,Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai 200433, China.,Institute of Pharmaceutical Science and Technology, Zhejiang University of Technology, 18 Chao Wang Road, 310014 Hangzhou, China
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31
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Ma Y, Frutos-Beltrán E, Kang D, Pannecouque C, De Clercq E, Menéndez-Arias L, Liu X, Zhan P. Medicinal chemistry strategies for discovering antivirals effective against drug-resistant viruses. Chem Soc Rev 2021; 50:4514-4540. [PMID: 33595031 DOI: 10.1039/d0cs01084g] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
During the last forty years we have witnessed impressive advances in the field of antiviral drug discovery culminating with the introduction of therapies able to stop human immunodeficiency virus (HIV) replication, or cure hepatitis C virus infections in people suffering from liver disease. However, there are important viral diseases without effective treatments, and the emergence of drug resistance threatens the efficacy of successful therapies used today. In this review, we discuss strategies to discover antiviral compounds specifically designed to combat drug resistance. Currently, efforts in this field are focused on targeted proteins (e.g. multi-target drug design strategies), but also on drug conformation (either improving drug positioning in the binding pocket or introducing conformational constraints), in the introduction or exploitation of new binding sites, or in strengthening interaction forces through the introduction of multiple hydrogen bonds, covalent binding, halogen bonds, additional van der Waals forces or multivalent binding. Among the new developments, proteolysis targeting chimeras (PROTACs) have emerged as a valid approach taking advantage of intracellular mechanisms involving protein degradation by the ubiquitin-proteasome system. Finally, several molecules targeting host factors (e.g. human dihydroorotate dehydrogenase and DEAD-box polypeptide 3) have been identified as broad-spectrum antiviral compounds. Implementation of herein described medicinal chemistry strategies are expected to contribute to the discovery of new drugs effective against current and future threats due to emerging and re-emerging viral pandemics.
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Affiliation(s)
- Yue Ma
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan, 250012, Shandong Province, P. R. China.
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32
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Zorn KM, Sun S, McConnon CL, Ma K, Chen EK, Foil DH, Lane TR, Liu LJ, El-Sakkary N, Skinner DE, Ekins S, Caffrey CR. A Machine Learning Strategy for Drug Discovery Identifies Anti-Schistosomal Small Molecules. ACS Infect Dis 2021; 7:406-420. [PMID: 33434015 PMCID: PMC7887754 DOI: 10.1021/acsinfecdis.0c00754] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Schistosomiasis is a chronic and
painful disease of poverty caused
by the flatworm parasite Schistosoma. Drug discovery
for antischistosomal compounds predominantly employs in vitro whole organism (phenotypic) screens against two developmental stages
of Schistosoma mansoni, post-infective larvae (somules)
and adults. We generated two rule books and associated scoring systems
to normalize 3898 phenotypic data points to enable machine learning.
The data were used to generate eight Bayesian machine learning models
with the Assay Central software according to parasite’s developmental
stage and experimental time point (≤24, 48, 72, and >72
h).
The models helped predict 56 active and nonactive compounds from commercial
compound libraries for testing. When these were screened against S. mansoni in vitro, the prediction accuracy for active
and inactives was 61% and 56% for somules and adults, respectively;
also, hit rates were 48% and 34%, respectively, far exceeding the
typical 1–2% hit rate for traditional high throughput screens.
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Affiliation(s)
- Kimberley M. Zorn
- Collaborations Pharmaceuticals, 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Shengxi Sun
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093-0021, United States
| | - Cecelia L. McConnon
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093-0021, United States
| | - Kelley Ma
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093-0021, United States
| | - Eric K. Chen
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093-0021, United States
| | - Daniel H. Foil
- Collaborations Pharmaceuticals, 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Thomas R. Lane
- Collaborations Pharmaceuticals, 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Lawrence J. Liu
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093-0021, United States
| | - Nelly El-Sakkary
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093-0021, United States
| | - Danielle E. Skinner
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093-0021, United States
| | - Sean Ekins
- Collaborations Pharmaceuticals, 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Conor R. Caffrey
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093-0021, United States
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33
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Cilento ME, Kirby KA, Sarafianos SG. Avoiding Drug Resistance in HIV Reverse Transcriptase. Chem Rev 2021; 121:3271-3296. [PMID: 33507067 DOI: 10.1021/acs.chemrev.0c00967] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
HIV reverse transcriptase (RT) is an enzyme that plays a major role in the replication cycle of HIV and has been a key target of anti-HIV drug development efforts. Because of the high genetic diversity of the virus, mutations in RT can impart resistance to various RT inhibitors. As the prevalence of drug resistance mutations is on the rise, it is necessary to design strategies that will lead to drugs less susceptible to resistance. Here we provide an in-depth review of HIV reverse transcriptase, current RT inhibitors, novel RT inhibitors, and mechanisms of drug resistance. We also present novel strategies that can be useful to overcome RT's ability to escape therapies through drug resistance. While resistance may not be completely avoidable, designing drugs based on the strategies and principles discussed in this review could decrease the prevalence of drug resistance.
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Affiliation(s)
- Maria E Cilento
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States.,Children's Healthcare of Atlanta, Atlanta, Georgia 30307, United States
| | - Karen A Kirby
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States.,Children's Healthcare of Atlanta, Atlanta, Georgia 30307, United States
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States.,Children's Healthcare of Atlanta, Atlanta, Georgia 30307, United States
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34
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Labh R, Gupta R. Emerging Trends in the Long-Acting Antiretroviral Therapy: Current Status and Therapeutic Challenges. Curr HIV Res 2021; 19:4-13. [PMID: 32838720 DOI: 10.2174/1570162x18666200824104140] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 06/25/2020] [Accepted: 07/17/2020] [Indexed: 11/22/2022]
Abstract
Antiretroviral drug therapy has significantly improved the prognosis and life expectancy of people living with HIV over the years. But this progress comes with an important caveat that antiretroviral regimens generally require adherence to life-long, daily dosing, to keep viral multiplication under check. Non-adherence to such dosing leads to decreased efficacy and increased drug resistance against antiretroviral drugs. Besides, poor drug penetration to certain tissues like CNS and lymph nodes leads to the build-up of viral reservoirs in these sites. To combat some of these challenges and improve patient compliance, long-acting antiretroviral drugs, are a new weapon in the arsenal, in the fight against HIV. Few long-acting preparations have been approved, and several others are in various clinical and preclinical stages of development. However, long-acting formulations also have their share of clinical issues like limited drug distribution, long term adverse drug reactions, drug-drug interactions, and gradual development of drug resistance. Modern technological premises are being tested to mitigate some of these problems. One such promising approach involves nanotechnological methods, which are being used to develop ultra-long acting formulations and drug delivery systems, targeting tissues with residual HIV concentration. Long-Acting Slow Effective Release Antiretroviral Therapy aka LASER ART, also builds on nanotechnology and prodrug modifications to design preparations with tailor-made favorable pharmacokinetics and wider drug distribution. These recent advances are fueling the progression of antiretroviral therapy towards eliminating the disease.
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Affiliation(s)
- Rajpushpa Labh
- Department of Pharmacology, University College of Medical Sciences & GTB Hospital, University of Delhi, New Delhi, India
| | - Rachna Gupta
- Department of Pharmacology, University College of Medical Sciences & GTB Hospital, University of Delhi, New Delhi, India
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35
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Ding L, Zhuang C, Chen F. Druggability modification strategies of the diarylpyrimidine-type non-nucleoside reverse transcriptase inhibitors. Med Res Rev 2021; 41:1255-1290. [PMID: 33497504 DOI: 10.1002/med.21760] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/04/2020] [Accepted: 11/18/2020] [Indexed: 12/20/2022]
Abstract
Drug discovery of human immunodeficiency virus (HIV) is a hot field in medicinal chemistry community for many years. The diarylpyrimidines (DAPYs) are the second-generation non-nucleoside reverse transcriptase inhibitors (NNRTIs) targeting reverse transcriptase, playing a great irreplaceable role in HIV transcriptional therapy. However, fast-growing drug-resistant mutations as nonnegligible challenge are still unpredictably appeared in the clinical practice, leading to deactivate or reduce the existing drugs. In the last 20 years, more and more novel DAPY derivatives have developed with the purpose to counter the mutants. Nevertheless, most of them have dissatisfactory pharmacokinetics (PK) or poor antiviral activity toward resistant mutant strains. In this article, we will analyze the NNRTI derivatives with promising druggability, and summarize a series of druggability modification strategies to improve the antiviral activity, reduce toxicity and improve the PK properties in recent years. The prospects of DAPYs and the directions for future efforts will be discussed.
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Affiliation(s)
- Li Ding
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Engineering Center of Catalysis and Synthesis for Chiral Molecules, Fudan University, Shanghai, China.,Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai, China
| | - Chunlin Zhuang
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Fudan University, Shanghai, China.,Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai, China
| | - Fener Chen
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Engineering Center of Catalysis and Synthesis for Chiral Molecules, Fudan University, Shanghai, China.,Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai, China.,Institute of Pharmaceutical Science and Technology, Zhejiang University of Technology, Hangzhou, China
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36
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The antibiotic sorangicin A inhibits promoter DNA unwinding in a Mycobacterium tuberculosis rifampicin-resistant RNA polymerase. Proc Natl Acad Sci U S A 2020; 117:30423-30432. [PMID: 33199626 PMCID: PMC7720108 DOI: 10.1073/pnas.2013706117] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Rifampicin (Rif) is a first-line therapeutic used to treat the infectious disease tuberculosis (TB), which is caused by the pathogen Mycobacterium tuberculosis (Mtb). The emergence of Rif-resistant (RifR) Mtb presents a need for new antibiotics. Rif targets the enzyme RNA polymerase (RNAP). Sorangicin A (Sor) is an unrelated inhibitor that binds in the Rif-binding pocket of RNAP. Sor inhibits a subset of RifR RNAPs, including the most prevalent clinical RifR RNAP substitution found in Mtb infected patients (S456>L of the β subunit). Here, we present structural and biochemical data demonstrating that Sor inhibits the wild-type Mtb RNAP by a similar mechanism as Rif: by preventing the translocation of very short RNAs. By contrast, Sor inhibits the RifR S456L enzyme at an earlier step, preventing the transition of a partially unwound promoter DNA intermediate to the fully opened DNA and blocking the template-strand DNA from reaching the active site in the RNAP catalytic center. By defining template-strand blocking as a mechanism for inhibition, we provide a mechanistic drug target in RNAP. Our finding that Sor inhibits the wild-type and mutant RNAPs through different mechanisms prompts future considerations for designing antibiotics against resistant targets. Also, we show that Sor has a better pharmacokinetic profile than Rif, making it a suitable starting molecule to design drugs to be used for the treatment of TB patients with comorbidities who require multiple medications.
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37
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vonRanke NL, Ribeiro MMJ, Miceli LA, de Souza NP, Abrahim-Vieira BA, Castro HC, Teixeira VL, Rodrigues CR, Souza AMT. Structure-activity relationship, molecular docking, and molecular dynamic studies of diterpenes from marine natural products with anti-HIV activity. J Biomol Struct Dyn 2020; 40:3185-3195. [PMID: 33183161 DOI: 10.1080/07391102.2020.1845977] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
HIV-1 infection is a global epidemic whose treatment is limited majorly by viral resistance and adverse effects. Natural products from algae have been studied for many years, including antiviral, being an alternative to anti-HIV drug design. Since the isolation of natural products can be a hurdle, molecular modeling is an important tool to study these compounds. Herein, structure-activity relationship, molecular docking, and molecular dynamic studies were performed to direct the studies of ten marine natural products with anti-HIV activity. In the structure-activity relationship, descriptors were identified associating the anti-HIV activity of five diterpenes with possible action on the reverse transcriptase allosteric site. These diterpenes were evaluated by molecular docking, and it was identified that only dolabelladienetriol interacted in the allosteric site. Molecular dynamics suggested that the dolabelladienetriol might interfere with the viral RNA binding to HIV-1 RT by inducing a conformational change of the enzyme. Also, in silico ADMET simulations predicts that the dolabelladienetriol present a high potential to be successfully developed as a drug. Thus, applying in silico approaches was possible to suggest potential anti-HIV compounds derived from marine natural products.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- N L vonRanke
- Laboratory of Molecular Modeling and QSAR (ModMolQSAR), Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - M M J Ribeiro
- Laboratory of Molecular Modeling and QSAR (ModMolQSAR), Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - L A Miceli
- Laboratory of Antibiotics, Biochemistry, Education and Molecular Modeling (LABiEMol), Biology Institute, Federal Fluminense University, Niteroi, Brazil
| | - N P de Souza
- Laboratory of Molecular Modeling and QSAR (ModMolQSAR), Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - B A Abrahim-Vieira
- Laboratory of Molecular Modeling and QSAR (ModMolQSAR), Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - H C Castro
- Laboratory of Antibiotics, Biochemistry, Education and Molecular Modeling (LABiEMol), Biology Institute, Federal Fluminense University, Niteroi, Brazil
| | - V L Teixeira
- Center for Biological Sciences and Health (CCBS), Rectory, Federal University of Rio de Janeiro State, Rio de Janeiro, Brazil
| | - C R Rodrigues
- Laboratory of Molecular Modeling and QSAR (ModMolQSAR), Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - A M T Souza
- Laboratory of Molecular Modeling and QSAR (ModMolQSAR), Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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38
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Yu ZJ, Mosher EP, Bumpus NN. Pharmacogenomics of Antiretroviral Drug Metabolism and Transport. Annu Rev Pharmacol Toxicol 2020; 61:565-585. [PMID: 32960701 DOI: 10.1146/annurev-pharmtox-021320-111248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Antiretroviral therapy has markedly reduced morbidity and mortality for persons living with human immunodeficiency virus (HIV). Individual tailoring of antiretroviral regimens has the potential to further improve the long-term management of HIV through the mitigation of treatment failure and drug-induced toxicities. While the mechanisms underlying anti-HIV drug adverse outcomes are multifactorial, the application of drug-specific pharmacogenomic knowledge is required in order to move toward the personalization of HIV therapy. Thus, detailed understanding of the metabolism and transport of antiretrovirals and the influence of genetics on these pathways is important. To this end, this review provides an up-to-date overview of the metabolism of anti-HIV therapeutics and the impact of genetic variation in drug metabolism and transport on the treatment of HIV. Future perspectives on and current challenges in pursuing personalized HIV treatment are also discussed.
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Affiliation(s)
- Zaikuan J Yu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA;
| | - Eric P Mosher
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA;
| | - Namandjé N Bumpus
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA;
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39
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Kang D, Sun Y, Murugan NA, Feng D, Wei F, Li J, Jiang X, De Clercq E, Pannecouque C, Zhan P, Liu X. Structure-Activity Relationship Exploration of NNIBP Tolerant Region I Leads to Potent HIV-1 NNRTIs. ACS Infect Dis 2020; 6:2225-2234. [PMID: 32619096 DOI: 10.1021/acsinfecdis.0c00327] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Previous efforts in our lab have led to the development of human immunodeficiency virus type 1 (HIV-1) non-nucleoside reverse transcriptase inhibitor (NNRTI) thiophene[3,2-d]pyrimidine compound 1 (K-5a2) with promising activity against wild-type and mutant HIV-1 strains. In this work, a series of novel diarylpyrimidines derivatives carrying a structurally diverse motif at the right wing of the lead K-5a2 was designed and synthesized as potential anti-HIV-1 agents. The results demonstrated that 8a yielded exceptionally potent activity against HIV-1 wild-type (50% effective concentration (EC50) = 3.30 nM) and mutant strain RES056 (EC50 = 22.6 nM) in MT-4 cells; in the reverse transcriptase inhibitory assay, 8a (half maximal inhibitory concentration (IC50) = 0.028 μM) was remarkably superior to that of K-5a2 (IC50 = 0.300 μM) and comparable to that of etravirine (ETR; IC50 = 0.011 μM). Notably, 8a exhibited better druggability than that of K-5a2, including significantly reduced CYP enzymatic inhibitory activity (IC50 > 50 μM), lower human ether-à-go-go related gene (hERG) inhibition (IC50 > 30 μM), and improved metabolic stability (short half-life, T1/2 = 77.5 min) in vitro.
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Affiliation(s)
- Dongwei Kang
- 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
- Suzhou Research Institute, Shandong University, Room 522, Building H of NUSP, No. 388 Ruoshui Road, SIP, 215123 Suzhou, Jiangsu, P.R. China
| | - Yanying Sun
- 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
| | - N. Arul Murugan
- Department of Theoretical Chemistry and Biology, School of Chemistry, Biotechnology and Health,, KTH Royal Institute of Technology, S-106 91 Stockholm, Sweden
| | - Da Feng
- 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
| | - Fenju Wei
- 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
| | - Jing Li
- 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
| | - Xiangyi Jiang
- 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
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - 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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40
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Dey SK, Saini M, Prabhakar P, Kundu S. Dopamine β hydroxylase as a potential drug target to combat hypertension. Expert Opin Investig Drugs 2020; 29:1043-1057. [DOI: 10.1080/13543784.2020.1795830] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Sanjay Kumar Dey
- Department of Biochemistry, University of Delhi South Camp us , New Delhi, India
| | - Manisha Saini
- Department of Biochemistry, University of Delhi South Camp us , New Delhi, India
| | - Pankaj Prabhakar
- Department of Biochemistry, University of Delhi South Camp us , New Delhi, India
| | - Suman Kundu
- Department of Biochemistry, University of Delhi South Camp us , New Delhi, India
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41
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Himmel DM, Arnold E. Non-Nucleoside Reverse Transcriptase Inhibitors Join Forces with Integrase Inhibitors to Combat HIV. Pharmaceuticals (Basel) 2020; 13:ph13060122. [PMID: 32545407 PMCID: PMC7345359 DOI: 10.3390/ph13060122] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/05/2020] [Accepted: 06/05/2020] [Indexed: 12/17/2022] Open
Abstract
In the treatment of acquired immune deficiency syndrome (AIDS), the diarylpyrimidine (DAPY) analogs etravirine (ETR) and rilpivirine (RPV) have been widely effective against human immunodeficiency virus (HIV) variants that are resistant to other non-nucleoside reverse transcriptase inhibitors (NNRTIs). With non-inferior or improved efficacy, better safety profiles, and lower doses or pill burdens than other NNRTIs in the clinic, combination therapies including either of these two drugs have led to higher adherence than other NNRTI-containing treatments. In a separate development, HIV integrase strand transfer inhibitors (INSTIs) have shown efficacy in treating AIDS, including raltegravir (RAL), elvitegravir (EVG), cabotegravir (CAB), bictegravir (BIC), and dolutegravir (DTG). Of these, DTG and BIC perform better against a wide range of resistance mutations than other INSTIs. Nevertheless, drug-resistant combinations of mutations have begun to emerge against all DAPYs and INSTIs, attributable in part to non-adherence. New dual therapies that may promote better adherence combine ETR or RPV with an INSTI and have been safer and non-inferior to more traditional triple-drug treatments. Long-acting dual- and triple-therapies combining ETR or RPV with INSTIs are under study and may further improve adherence. Here, highly resistant emergent mutations and efficacy data on these novel treatments are reviewed. Overall, ETR or RPV, in combination with INSTIs, may be treatments of choice as long-term maintenance therapies that optimize efficacy, adherence, and safety.
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Affiliation(s)
- Daniel M. Himmel
- Himmel Sci Med Com, L.L.C., Bala Cynwyd, PA 19004, USA
- Correspondence: ; Tel.: +1-848-391-5973
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine (CABM), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA;
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42
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Zhuang C, Pannecouque C, De Clercq E, Chen F. Development of non-nucleoside reverse transcriptase inhibitors (NNRTIs): our past twenty years. Acta Pharm Sin B 2020; 10:961-978. [PMID: 32642405 PMCID: PMC7332669 DOI: 10.1016/j.apsb.2019.11.010] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 10/08/2019] [Accepted: 11/08/2019] [Indexed: 11/30/2022] Open
Abstract
Human immunodeficiency virus (HIV) is the primary infectious agent of acquired immunodeficiency syndrome (AIDS), and non-nucleoside reverse transcriptase inhibitors (NNRTIs) are the cornerstone of HIV treatment. In the last 20 years, our medicinal chemistry group has made great strides in developing several distinct novel NNRTIs, including 1-[(2-hydroxyethoxy)methyl]-6-(phenylthio)thymine (HEPT), thio-dihydro-alkoxy-benzyl-oxopyrimidine (S-DABO), diaryltriazine (DATA), diarylpyrimidine (DAPY) analogues, and their hybrid derivatives. Application of integrated modern medicinal strategies, including structure-based drug design, fragment-based optimization, scaffold/fragment hopping, molecular/fragment hybridization, and bioisosterism, led to the development of several highly potent analogues for further evaluations. In this paper, we review the development of NNRTIs in the last two decades using the above optimization strategies, including their structure–activity relationships, molecular modeling, and their binding modes with HIV-1 reverse transcriptase (RT). Future directions and perspectives on the design and associated challenges are also discussed.
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Key Words
- AIDS, acquired immunodeficiency syndrome
- Bioisosterism
- DAPY, diarylpyrimidine
- DAPYs
- DATA, diaryltriazine
- DATAs
- DLV, delavirdine
- DOR, doravirine
- ECD, electronic circular dichroism
- EFV, efavirenz
- ETR, etravirine
- FDA, U.S. Food and Drug Administration
- Fragment-based drug design
- HAART, highly active antiretroviral therapy
- HENT, napthyl-HEPT
- HENTs
- HEPT, 1-[(2-hydroxyethoxy)methyl]-6-(phenylthio)thymine
- HIV, human immunodeficiency virus
- HIV-1
- INSTI, integrase inhibitor
- Molecular hybridization
- NNIBP, NNRTI binding pocket
- NNRTI, non-nucleoside reverse transcriptase inhibitor
- NNRTIs
- NRTI, nucleoside reverse transcriptase inhibitor
- NVP, nevirapine
- PI, protease inhibitor
- PK, pharmacokinetic
- PROTAC, proteolysis targeting chimera
- RPV, rilpivirine
- RT, reverse transcriptase
- S-DABO, thio-dihydro-alkoxy-benzyl-oxopyrimidine
- S-DABOs
- SAR, structure–activity relationship
- SBDD, structure-based drug design
- SFC, supercritical fluid chromatography
- SI, selectivity index
- Structure-based optimization
- UNAIDS, the Joint United Nations Programme on HIV/AIDS
- ee, enantiomeric excess
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Affiliation(s)
- Chunlin Zhuang
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China
- Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai 200433, China
| | | | - Erik De Clercq
- Rega Institute for Medical Research, KU Leuven, Leuven B-3000, Belgium
| | - Fener Chen
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China
- Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai 200433, China
- Institute of Pharmaceutical Science and Technology, Zhejiang University of Technology, Hangzhou 310014, China
- Corresponding author.
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43
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Han S, Sang Y, Wu Y, Tao Y, Pannecouque C, De Clercq E, Zhuang C, Chen FE. Molecular Hybridization-Inspired Optimization of Diarylbenzopyrimidines as HIV-1 Nonnucleoside Reverse Transcriptase Inhibitors with Improved Activity against K103N and E138K Mutants and Pharmacokinetic Profiles. ACS Infect Dis 2020; 6:787-801. [PMID: 31599568 DOI: 10.1021/acsinfecdis.9b00229] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Molecular hybridization is a powerful strategy in drug discovery. A series of novel diarylbenzopyrimidine (DABP) analogues were developed by the hybridization of FDA-approved drugs etravirine (ETR) and efavirenz (EFV) as potential HIV-1 nonnucleoside reverse transcriptase inhibitors (NNRTIs). Substituent modifications resulted in the identification of new DABPs with the combination of the strengths of the two drugs, especially compound 12d, which showed promising activity toward the EFV-resistant K103N mutant. 12d also had a favorable pharmacokinetic (PK) profile with liver microsome clearances of 14.4 μL/min/mg (human) and 33.2 μL/min/mg (rat) and an oral bioavailability of 15.5% in rat. However, its activity against the E138K mutant was still unsatisfactory; E138K is the most prevalent NNRTI resistance-associated mutant in ETR treatment. Further optimizations resulted in a highly potent compound (12z) with no substituents on the phenyl ring and a 2-methyl-6-nitro substitution pattern on the 4-cyanovinyl-2,6-disubstitued phenyl motif. The antiviral activity of this compound was much higher than those of ETR and EFV against the WT, E138K, and K103N variants (EC50 = 3.4, 4.3, and 3.6 nM, respectively), and the cytotoxicity was decreased while the selectivity index (SI) was increased. In particular, this compound exhibited acceptable intrinsic liver microsome stability (human, 34.5 μL/min/mg; rat, 33.2 μL/min/mg) and maintained the good PK profile of its parent compound EFV and showed an oral bioavailability of 16.5% in rat. Molecular docking and structure-activity relationship (SAR) analysis provided further insights into the binding of the DABPs with HIV-1 reverse transcriptase and provided a deeper understanding of the key structural features responsible for their interactions.
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Affiliation(s)
- Sheng Han
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, People’s Republic of China
- Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai 200433, People’s Republic of China
| | - Yali Sang
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, People’s Republic of China
- Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai 200433, People’s Republic of China
| | - Yan Wu
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, People’s Republic of China
- Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai 200433, People’s Republic of China
| | - Yuan Tao
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, People’s Republic of China
- Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai 200433, People’s Republic of China
| | | | - Erik De Clercq
- Rega Institute for Medical Research, KU Leuven, Herestraat 49, B-3000 Leuven, Belgium
| | - Chunlin Zhuang
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, People’s Republic of China
- Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai 200433, People’s Republic of China
| | - Fen-Er Chen
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, People’s Republic of China
- Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai 200433, People’s Republic of China
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Ferreira Pimentel LC, Cunha AC, Boas Hoelz LV, Canzian HF, Leite Firmino Marinho DI, Boechat N, Bastos MM. Phenylamino-pyrimidine (PAP) Privileged Structure: Synthesis and Medicinal Applications. Curr Top Med Chem 2020; 20:227-243. [DOI: 10.2174/1568026620666200124094949] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/17/2019] [Accepted: 12/25/2019] [Indexed: 12/23/2022]
Abstract
The phenylamino-pyrimidine (PAP) nucleus has been demonstrated to be useful for the development of new drugs and is present in a wide variety of antiretroviral agents and tyrosine kinase inhibitors (TKIs). This review aims to evaluate the application of PAP derivatives in drugs and other bioactive compounds. It was concluded that PAP derivatives are still worth exploring, as they may provide highly competitive ATP TKI’s with nano/picomolar activity.
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Affiliation(s)
- Luiz Claudio Ferreira Pimentel
- Fundacao Oswaldo Cruz, Instituto de Tecnologia em Farmacos, Farmanguinhos - Fiocruz, Laboratório de Sintese de Farmacos - LASFAR, Manguinhos, CEP 21041-250, Rio de Janeiro, RJ, Brazil
| | - Anna Claudia Cunha
- Universidade Federal Fluminense, Departamento de Quimica Organica, Campus do Valonguinho, CEP 24020-150, Niteroi, RJ, Brazil
| | - Lucas Villas Boas Hoelz
- Fundacao Oswaldo Cruz, Instituto de Tecnologia em Farmacos, Farmanguinhos - Fiocruz, Laboratório de Sintese de Farmacos - LASFAR, Manguinhos, CEP 21041-250, Rio de Janeiro, RJ, Brazil
| | - Henayle Fernandes Canzian
- Fundacao Oswaldo Cruz, Instituto de Tecnologia em Farmacos, Farmanguinhos - Fiocruz, Laboratório de Sintese de Farmacos - LASFAR, Manguinhos, CEP 21041-250, Rio de Janeiro, RJ, Brazil
| | - Debora Inacio Leite Firmino Marinho
- Fundacao Oswaldo Cruz, Instituto de Tecnologia em Farmacos, Farmanguinhos - Fiocruz, Laboratório de Sintese de Farmacos - LASFAR, Manguinhos, CEP 21041-250, Rio de Janeiro, RJ, Brazil
| | - Nubia Boechat
- Fundacao Oswaldo Cruz, Instituto de Tecnologia em Farmacos, Farmanguinhos - Fiocruz, Laboratório de Sintese de Farmacos - LASFAR, Manguinhos, CEP 21041-250, Rio de Janeiro, RJ, Brazil
| | - Monica Macedo Bastos
- Fundacao Oswaldo Cruz, Instituto de Tecnologia em Farmacos, Farmanguinhos - Fiocruz, Laboratório de Sintese de Farmacos - LASFAR, Manguinhos, CEP 21041-250, Rio de Janeiro, RJ, Brazil
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45
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Han S, Lei Y, Pannecouque C, De Clercq E, Zhuang C, Chen F. Fragment-based discovery of sulfur-containing diarylbenzopyrimidines as novel nonnucleoside reverse transcriptase inhibitors. CHINESE CHEM LETT 2020. [DOI: 10.1016/j.cclet.2019.11.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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46
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Lei Y, Han S, Yang Y, Pannecouque C, De Clercq E, Zhuang C, Chen FE. Design of Biphenyl-Substituted Diarylpyrimidines with a Cyanomethyl Linker as HIV-1 NNRTIs via a Molecular Hybridization Strategy. Molecules 2020; 25:E1050. [PMID: 32111013 PMCID: PMC7179183 DOI: 10.3390/molecules25051050] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/24/2020] [Accepted: 02/25/2020] [Indexed: 02/07/2023] Open
Abstract
The key problems of human immunodeficiency virus (HIV) therapy are the rapid emergence of drug-resistant mutant strains and significant cumulative drug toxicities. Therefore, there is an urgent demand for new anti-HIV agents with low toxicity and broad-spectrum antiviral potency. A series of biphenyl-substituted diarylpyrimidines with a cyanomethyl linker were designed using a molecular hybridization strategy. The cell-based anti-HIV assay showed that most of the compounds exhibited moderate to good activities against wild-type HIV-1 and clinically relevant mutant strains with a more favorable toxicity, and the enzymatic assay showed they had nanomolar activity against reverse transcriptase (RT). Compound 10p exhibited the best activity against wild-type HIV-1 with an EC50 (50% HIV-1 replication inhibitory concentration) value of 0.027 µM, an acceptable CC50 (50% cytotoxic concentration) value of 36.4 µM, and selectivity index of 1361, with moderate activities against the single mutants (EC50: E138K, 0.17 µM; Y181C, 0.87 µM; K103N, 0.9 µM; L100I, 1.21 µM, respectively), and an IC50 value of 0.059 µM against the RT enzyme, which was six-fold higher than nevirapine (NVP). The preliminary structure-activity relationship (SAR) of these new compounds was concluded. The molecular modeling predicted the binding modes of the new compounds with RT, providing molecular insight for further drug design.
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Affiliation(s)
- Yuan Lei
- Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China; (Y.L.); (Y.Y.)
| | - Sheng Han
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China;
- Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai 200433, China
| | - Yang Yang
- Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China; (Y.L.); (Y.Y.)
| | - Christophe Pannecouque
- Rega Institute for Medical Research, KU Leuven, Herestraat 49, B-3000 Leuven, Belgium; (C.P.); (E.D.C.)
| | - Erik De Clercq
- Rega Institute for Medical Research, KU Leuven, Herestraat 49, B-3000 Leuven, Belgium; (C.P.); (E.D.C.)
| | - Chunlin Zhuang
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China;
- Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai 200433, China
| | - Fen-Er Chen
- Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China; (Y.L.); (Y.Y.)
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China;
- Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai 200433, China
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Improving the positional adaptability: structure-based design of biphenyl-substituted diaryltriazines as novel non-nucleoside HIV-1 reverse transcriptase inhibitors. Acta Pharm Sin B 2020; 10:344-357. [PMID: 32082978 PMCID: PMC7016291 DOI: 10.1016/j.apsb.2019.09.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 07/08/2019] [Accepted: 09/20/2019] [Indexed: 02/05/2023] Open
Abstract
In order to improve the positional adaptability of our previously reported naphthyl diaryltriazines (NP-DATAs), synthesis of a series of novel biphenyl-substituted diaryltriazines (BP-DATAs) with a flexible side chain attached at the C-6 position is presented. These compounds exhibited excellent potency against wild-type (WT) HIV-1 with EC50 values ranging from 2.6 to 39 nmol/L and most of them showed low nanomolar anti-viral potency against a panel of HIV-1 mutant strains. Compounds 5j and 6k had the best activity against WT, single and double HIV-1 mutants and reverse transcriptase (RT) enzyme comparable to two reference drugs (EFV and ETR) and our lead compound NP-DATA (1). Molecular modeling disclosed that the side chain at the C-6 position of DATAs occupied the entrance channel of the HIV-1 reverse transcriptase non-nucleoside binding pocket (NNIBP) attributing to the improved activity. The preliminary structure–activity relationship and PK profiles were also discussed.
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Key Words
- AIDS, acquired immunodeficiency syndrome
- BP-DATA, biphenyl-substituted diaryltriazine
- BP-DATAs
- CC50, 50% cytotoxicity concentration
- DAPY, diarylpyrimidine
- DATA, diaryltriazine
- EC50, the concentration causing 50% inhibition of antiviral activity
- EFV, efavirenz
- ETR, etravirine
- HEPT, 1-[(2-hydroxyethoxy)methyl]-6-(phenylthio)thymine
- HIV, human immunodeficiency virus
- HIV-1
- MD, molecular dynamic
- Molecular modeling
- NNIBP, non-nucleoside inhibitor binding pocket
- NNRTI, non-nucleoside reverse transcriptase inhibitor
- NNRTIs
- NP-DATA, naphthyl diaryltriazine
- NP-DATAs
- NVP, nevirapine
- PK, pharmacokinetics
- Positional adaptability
- RMSD, root-mean square deviation
- RPV, rilpivirine
- RT, reverse transcriptase
- SAR, structure–activity relationship
- SI, selectivity index
- TSAO, tert-butyldimethylsilyl-spiroaminooxathioledioxide
- WT, wild-type
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Ayitewala A, Kyeyune F, Ainembabazi P, Nabulime E, Kato CD, Nankya I. Comparison of HIV drug resistance profiles across HIV-1 subtypes A and D for patients receiving a tenofovir-based and zidovudine-based first line regimens in Uganda. AIDS Res Ther 2020; 17:2. [PMID: 32005262 PMCID: PMC6995161 DOI: 10.1186/s12981-020-0258-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 01/21/2020] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Resistance to antiretroviral drugs is a major challenge among Human Immunodeficiency Virus (HIV) positive patients receiving antiretroviral therapy (ART). Mutations that arise as a result of this are diverse across the various drugs, drug classes, drug regimens and subtypes. In Uganda, there is a paucity of information on how these mutations differ among the different drug regimens and the predominant HIV-1 subtypes. The purpose of this study was to determine mutation profile differences between first-line drug regimens: TDF/3TC/EFV and AZT/3TC/EFV and HIV-1 subtypes: A and D in Uganda. The study also investigated the potential usage of rilpivirine, doravirine and etravirine in patients who failed treatment on efavirenz. METHODS A retrospective study was conducted on 182 archived plasma samples obtained from patients who were experiencing virological failure between 2006 and 2017 at five Joint Clinical Research Center (JCRC) sites in Uganda. Sanger sequencing of the Reverse Transcriptase (RT) gene from codons 1-300 was done. Mutation scores were generated using the Stanford University HIV Drug Resistance Database. A Chi-square test was used to determine the association between drug resistance mutations (DRMs) and drug regimens or HIV-1 subtypes. RESULTS The prevalence of DRMs was 84.6% among patients failing a first-line efavirenz (EFV)-based regimen. The most prevalent Nucleoside Reverse Transcriptase Inhibitor (NRTI) mutations were M184V/I (67.3%), K219/Q/E (22.6%) and K65R (21.1%). While K103N (50.8%) and G190A/S/E/G (29.1%) were the most prevalent Non-Nucleoside Reverse Transcriptase Inhibitor (NNTRI) mutations. As expected, discriminatory DRMs such as K65R, L74I, and Y115F were noted in Tenofovir (TDF) containing regimens while the Thymidine Analogue Mutations (TAMs) L210W and T215 mutations were in Zidovudine (AZT)-based regimens. No significant difference (p = 0.336) was found for overall DRMs between HIV-1 subtypes A and D. Among the patients who had resistance to EFV, 37 (23.6%) were susceptible to newer NNRTIs such as Rilpivirine and Etravirine. CONCLUSION Accumulation of DRMs between AZT/3TC/EFV and TDF/3TC/EFV is comparable but individual mutations that confer resistance to particular drugs should be considered at virological failure. Having either HIV-1 subtype A or D is not associated with the acquisition of DRMs, therefore HIV diversity should not determine the choice of treatment. Rilpivirine, etravirine and doravirine had minimal benefits for patients who failed on efavirenz.
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Affiliation(s)
- Alisen Ayitewala
- Center for AIDS Research Laboratories, Joint Clinical Research Center, P.O. Box 10005, Kampala, Uganda. .,School of Biosecurity, Biotechnology and Laboratory Sciences, College of Veterinary Medicine Animal Resources and Biosecurity, Makerere University, P. O. Box 7062, Kampala, Uganda.
| | - Fred Kyeyune
- grid.436163.50000 0004 0648 1108Center for AIDS Research Laboratories, Joint Clinical Research Center, P.O. Box 10005, Kampala, Uganda
| | - Pamela Ainembabazi
- grid.436163.50000 0004 0648 1108Center for AIDS Research Laboratories, Joint Clinical Research Center, P.O. Box 10005, Kampala, Uganda
| | - Eva Nabulime
- grid.436163.50000 0004 0648 1108Center for AIDS Research Laboratories, Joint Clinical Research Center, P.O. Box 10005, Kampala, Uganda
| | - Charles Drago Kato
- grid.11194.3c0000 0004 0620 0548School of Biosecurity, Biotechnology and Laboratory Sciences, College of Veterinary Medicine Animal Resources and Biosecurity, Makerere University, P. O. Box 7062, Kampala, Uganda
| | - Immaculate Nankya
- grid.436163.50000 0004 0648 1108Center for AIDS Research Laboratories, Joint Clinical Research Center, P.O. Box 10005, Kampala, Uganda
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Abstract
Since the approval of nevirapine, the first HIV-1 non-nucleoside reverse transcriptase inhibitor (NNRTI) in 1996, NNRTIs have helped play a critical role in maintaining viral suppression in people living with HIV. The many positive attributes of the class, including potency and long plasma half-life, make them attractive drug discovery targets. Given the availability of multiple once-daily integrase-based treatments for HIV-1 infection, the challenge to develop a new antiretroviral agent that addresses the needs of today's patients is formidable. However, with the increased availability of antiretrovirals for treatment and new pre-exposure prophylaxis guidelines, which should globally expand the use of antiretrovirals in prevention, it will be increasingly important to have access to multiple regimens with options from different classes that are well tolerated and convenient to ensure a sustained impact on the global epidemic. Many attempts to improve upon the NNRTI class have failed to deliver a desirable clinical profile consistent with the current landscape of treatment options. Doravirine is the only NNRTI to successfully advance through phase 3 clinical development and approval in recent years. Learning from the liabilities of approved NNRTIs, as well as past development failures, facilitated a rational approach to the discovery of doravirine by focusing on addressing the known safety/tolerability issues of commonly prescribed NNRTIs, such as central nervous system toxicity with efavirenz and potential cardiotoxicity due to off-target effects on cardiac ion channels with rilpivirine, using structural biology and characterization of resistance in vitro to address resistance liabilities and concentrating on the metabolic profile to limit the potential for drug-drug interactions. These preclinical efforts were critical to the design and selection of doravirine as a novel NNRTI that possessed the desired next-generation profile with the ultimate proof that these attributes translate to patients derived from clinical trials.
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Affiliation(s)
- Carey Hwang
- Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Ming-Tain Lai
- Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Daria Hazuda
- Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
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Collier DA, Monit C, Gupta RK. The Impact of HIV-1 Drug Escape on the Global Treatment Landscape. Cell Host Microbe 2019; 26:48-60. [PMID: 31295424 DOI: 10.1016/j.chom.2019.06.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The rising prevalence of HIV drug resistance (HIVDR) could threaten gains made in combating the HIV epidemic and compromise the 90-90-90 target proposed by United Nations Programme on HIV/AIDS (UNAIDS) to have achieved virological suppression in 90% of all persons receiving antiretroviral therapy (ART) by the year 2020. HIVDR has implications for the persistence of HIV, the selection of current and future ART drug regimens, and strategies of vaccine and cure development. Focusing on drug classes that are in clinical use, this Review critically summarizes what is known about the mechanisms the virus utilizes to escape drug control. Armed with this knowledge, strategies to limit the expansion of HIVDR are proposed.
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Affiliation(s)
- D A Collier
- Division of Infection and Immunity, University College London, London, UK
| | - C Monit
- Division of Infection and Immunity, University College London, London, UK
| | - R K Gupta
- Department of Medicine, University of Cambridge, Cambridge, UK.
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