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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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2
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Chapala VL, Paidikondala K, M GP, Katari NK, Kerru N, Jonnalagadda SB. A New Method for Preparation of Rilpivirine Intermediate. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2021.1933105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Vijaya Lakshmi Chapala
- Department of Chemistry, School of Science, GITAM Deemed to be University, Hyderabad, India
| | - Kalyani Paidikondala
- Department of Chemistry, School of Science, GITAM Deemed to be University, Hyderabad, India
| | - Giri Prasad M
- Department of Chemistry, School of Science, GITAM Deemed to be University, Hyderabad, India
| | - Naresh Kumar Katari
- Department of Chemistry, School of Science, GITAM Deemed to be University, Hyderabad, India
- School of Chemistry & Physics, College of Agriculture, Engineering & Science, Westville Campus, University of KwaZulu-Natal, Durban, South Africa
| | - Nagaraju Kerru
- Department of Chemistry. GITAM School of Sciences, GITAM Deemed to be University, Bengaluru, India
| | - Sreekantha B. Jonnalagadda
- School of Chemistry & Physics, College of Agriculture, Engineering & Science, Westville Campus, University of KwaZulu-Natal, Durban, South Africa
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3
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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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4
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Small Conformational Changes Underlie Evolution of Resistance to NNRTI in HIV Reverse Transcriptase. Biophys J 2020; 118:2489-2501. [PMID: 32348721 DOI: 10.1016/j.bpj.2020.04.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 02/12/2020] [Accepted: 04/06/2020] [Indexed: 11/23/2022] Open
Abstract
Despite achieving considerable success in reducing the number of fatalities due to acquired immunodeficiency syndrome, emergence of resistance against the reverse transcriptase (RT) inhibitor drugs remains one of the biggest challenges of the human immunodeficiency virus antiretroviral therapy (ART). Non-nucleoside reverse transcriptase inhibitors (NNRTIs) form a large class of drugs and a crucial component of ART. In NNRTIs, even a single resistance mutation is known to make the drugs completely ineffective. Additionally, several inhibitor-bound RTs with single resistance mutations do not exhibit any significant variations in their three-dimensional structures compared with the inhibitor-bound RT but completely nullify their inhibitory functions. This makes understanding the structural mechanism of these resistance mutations crucial for drug development. Here, we study several single resistance mutations in the allosteric inhibitor (nevirapine)-bound RT to analyze the mechanism of small structural changes leading to these large functional effects. In this study, we have shown that in absence of significant conformational variations in the inhibitor-bound wild-type RT and RT with single resistance mutations, the protein contact network analysis of their static structures, along with molecular dynamics simulations, can be a useful approach to understand the functional effect of small local conformational variations. The simple network analysis exposes the localized contact changes that lead to global rearrangement in the communication pattern within RT. Furthermore, these conformational changes have implications on the overall dynamics of RT. Using various measures, we show that a single resistance mutation can change the network structure and dynamics of RT to behave more like unbound RT, even in the presence of the inhibitor. This combined coarse-grained contact network and molecular dynamics approach promises to be a useful tool to analyze structure-function studies of proteins that show large functional changes with negligible variations in their overall conformation.
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5
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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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6
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Sang Y, Pannecouque C, De Clercq E, Zhuang C, Chen F. Pharmacophore-fusing design of pyrimidine sulfonylacetanilides as potent non-nucleoside inhibitors of HIV-1 reverse transcriptase. Bioorg Chem 2020; 96:103595. [PMID: 32006797 DOI: 10.1016/j.bioorg.2020.103595] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 01/14/2020] [Accepted: 01/18/2020] [Indexed: 11/28/2022]
Abstract
Twenty-seven derivatives (40-66) were generated by pharmacophore fusing of sulfonylacetanilide-diarylpyrimidine (1) with rilpivirine or biphenyl-diarylpyrimidines. They displayed up to single-digit nanomolar activity against wild-type (WT) virus and various drug-resistant mutant strains in HIV-1-infected MT-4 cells, thereby targeting the reverse transcriptase (RT) enzyme. Compound 51 displayed exceptionally potent activity against WT virus (EC50 = 6 nM) and several mutant strains (L100I, EC50 = 8 nM, K103N, EC50 = 6 nM, Y181C, EC50 = 26 nM, Y188L, EC50 = 122 nM, E138K, EC50 = 26 nM). The structure-activity relationships of the newly obtained pyrimidine sulfonylacetanilides were also elucidated. Molecular docking analysis explained the activity and provided a structural insight for follow-up research.
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Affiliation(s)
- 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
| | | | - 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.
| | - Fener 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; Institute of Pharmaceutical Science and Technology, Zhejiang University of Technology, 18 Chao Wang Road, 310014 Hangzhou, People's Republic of China.
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7
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Follow on-based optimization of the biphenyl-DAPYs as HIV-1 nonnucleoside reverse transcriptase inhibitors against the wild-type and mutant strains. Bioorg Chem 2019; 89:102974. [DOI: 10.1016/j.bioorg.2019.102974] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/16/2019] [Accepted: 05/04/2019] [Indexed: 11/24/2022]
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8
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Namasivayam V, Vanangamudi M, Kramer VG, Kurup S, Zhan P, Liu X, Kongsted J, Byrareddy SN. The Journey of HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs) from Lab to Clinic. J Med Chem 2018; 62:4851-4883. [PMID: 30516990 DOI: 10.1021/acs.jmedchem.8b00843] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Human immunodeficiency virus (HIV) infection is now pandemic. Targeting HIV-1 reverse transcriptase (HIV-1 RT) has been considered as one of the most successful targets for the development of anti-HIV treatment. Among the HIV-1 RT inhibitors, non-nucleoside reverse transcriptase inhibitors (NNRTIs) have gained a definitive place due to their unique antiviral potency, high specificity, and low toxicity in antiretroviral combination therapies used to treat HIV. Until now, >50 structurally diverse classes of compounds have been reported as NNRTIs. Among them, six NNRTIs were approved for HIV-1 treatment, namely, nevirapine (NVP), delavirdine (DLV), efavirenz (EFV), etravirine (ETR), rilpivirine (RPV), and doravirine (DOR). In this perspective, we focus on the six NNRTIs and lessons learned from their journey through development to clinical studies. It demonstrates the obligatory need of understanding the physicochemical and biological principles (lead optimization), resistance mutations, synthesis, and clinical requirements for drugs.
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Affiliation(s)
- Vigneshwaran Namasivayam
- Pharmaceutical Institute, Pharmaceutical Chemistry II , University of Bonn , 53121 Bonn , Germany
| | - Murugesan Vanangamudi
- Department of Medicinal and Pharmaceutical Chemistry , Sree Vidyanikethan College of Pharmacy , Tirupathi , Andhra Pradesh 517102 , India
| | | | - Sonali Kurup
- College of Pharmacy , Roosevelt University , Schaumburg , Illinois 60173 , United States
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , Jinan 250012 , P.R. China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , Jinan 250012 , P.R. China
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy , University of Southern Denmark , DK-5230 , Odense M , Denmark
| | - Siddappa N Byrareddy
- Department of Pharmacology and Experimental Neuroscience , University of Nebraska Medical Center , Omaha 68198-5880 , United States
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9
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Battini L, Bollini M. Challenges and approaches in the discovery of human immunodeficiency virus type‐1 non‐nucleoside reverse transcriptase inhibitors. Med Res Rev 2018; 39:1235-1273. [DOI: 10.1002/med.21544] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/04/2018] [Accepted: 10/04/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Leandro Battini
- Laboratorio de Química Medicinal, Centro de Investigaciones en Bionanociencias (CIBION), CONICETCiudad de Buenos Aires Argentina
| | - Mariela Bollini
- Laboratorio de Química Medicinal, Centro de Investigaciones en Bionanociencias (CIBION), CONICETCiudad de Buenos Aires Argentina
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10
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Costa G, Rocca R, Corona A, Grandi N, Moraca F, Romeo I, Talarico C, Gagliardi MG, Ambrosio FA, Ortuso F, Alcaro S, Distinto S, Maccioni E, Tramontano E, Artese A. Novel natural non-nucleoside inhibitors of HIV-1 reverse transcriptase identified by shape- and structure-based virtual screening techniques. Eur J Med Chem 2018; 161:1-10. [PMID: 30342421 DOI: 10.1016/j.ejmech.2018.10.029] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 10/10/2018] [Accepted: 10/11/2018] [Indexed: 10/28/2022]
Abstract
In this work we report a parallel application of both docking- and shape-based virtual screening (VS) methods, followed by Molecular Dynamics simulations (MDs), for discovering new compounds able to inhibit the human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) RNA-dependent DNA polymerase activity. Specifically, we screened more than 143000 natural compounds commercially available in the ZINC database against the best five RT crystallographic models, taking into account the five approved NNRTIs as query compounds. As a result, 20 hit molecules were selected and tested on biochemical assays for the inhibition of the RNA dependent DNA polymerase RT function and, among them, an indoline pyrrolidine (hit1), an indonyl piperazine (hit2) and an indolyl indolinone (hit3) derivatives were identified as novel non-nucleoside RT inhibitors in the low micromolar range.
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Affiliation(s)
- Giosuè Costa
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Roberta Rocca
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Angela Corona
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cittadella Universitaria di Monserrato, SS554, 09042, Monserrato, Cagliari, Italy
| | - Nicole Grandi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cittadella Universitaria di Monserrato, SS554, 09042, Monserrato, Cagliari, Italy
| | - Federica Moraca
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy; Department of Chemical Sciences, University of Napoli Federico II, Via Cinthia 4, I-80126, Napoli, Italy.
| | - Isabella Romeo
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Carmine Talarico
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Maria Giovanna Gagliardi
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Francesca Alessandra Ambrosio
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Francesco Ortuso
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Simona Distinto
- Dipartimento di Scienze della Vita e dell'Ambiente, Università degli Studi di Cagliari, Via Ospedale 72, 09124, Cagliari, Italy
| | - Elias Maccioni
- Dipartimento di Scienze della Vita e dell'Ambiente, Università degli Studi di Cagliari, Via Ospedale 72, 09124, Cagliari, Italy
| | - Enzo Tramontano
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cittadella Universitaria di Monserrato, SS554, 09042, Monserrato, Cagliari, Italy
| | - Anna Artese
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
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11
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Bielenica A, Sanna G, Madeddu S, Struga M, Jóźwiak M, Kozioł AE, Sawczenko A, Materek IB, Serra A, Giliberti G. New thiourea and 1,3-thiazolidin-4-one derivatives effective on the HIV-1 virus. Chem Biol Drug Des 2017; 90:883-891. [PMID: 28434186 DOI: 10.1111/cbdd.13009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 04/12/2017] [Accepted: 04/14/2017] [Indexed: 12/24/2022]
Abstract
Thiourea derivatives have been reported to possess many biological activities, among them antiviral and antitumoral properties. As part of our continuing effort to develop new active compounds, we report the synthesis and the evaluation of new fifteen thiourea derivatives with 1,3-benzothiazole-2-yl moiety, among them a group of biologically active (1-7) also underwent cyclization to 1,3-thiazolidin-4-ones. Molecular structure of four compounds (4, 13, 15 and 3a) was determined by an X-ray crystallography. We here report the evaluation of their cytotoxicity against human leukaemia/lymphoma- and solid tumour-derived cell lines and of their antiviral activity against HIV-1 and representatives of ssRNA and dsDNA viruses. Derivative 5 showed an interesting activity against HIV-1 wild type and against variants carrying clinically relevant mutations. A colorimetric enzyme immunoassay clarified its mode of action as a non-nucleoside inhibitor of the reverse transcriptase.
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Affiliation(s)
- Anna Bielenica
- Chair and Department of Biochemistry, Medical University of Warsaw, Warszawa, Poland
| | - Giuseppina Sanna
- Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria, Monserrato, Cagliari, Italy
| | - Silvia Madeddu
- Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria, Monserrato, Cagliari, Italy
| | - Marta Struga
- Department of Biochemistry and Pharmacogenomics, Faculty of Pharmacy, Medical University of Warsaw, Warsaw, Poland.,Laboratory of Centre for Preclinical Research, Medical University of Warsaw, Warsaw, Poland
| | - Michał Jóźwiak
- Laboratory of Centre for Preclinical Research, Medical University of Warsaw, Warsaw, Poland.,Department of Biochemistry, Second Faculty of Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Anna E Kozioł
- Faculty of Chemistry, Maria Curie-Sklodowska University, Lublin, Poland
| | | | - Ilona B Materek
- Faculty of Chemistry, Maria Curie-Sklodowska University, Lublin, Poland
| | - Alessandra Serra
- Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria, Monserrato, Cagliari, Italy
| | - Gabriele Giliberti
- Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria, Monserrato, Cagliari, Italy
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12
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Pagano N, Teriete P, Mattmann ME, Yang L, Snyder BA, Cai Z, Heil ML, Cosford NDP. An integrated chemical biology approach reveals the mechanism of action of HIV replication inhibitors. Bioorg Med Chem 2017; 25:6248-6265. [PMID: 28442262 DOI: 10.1016/j.bmc.2017.03.061] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 03/25/2017] [Accepted: 03/29/2017] [Indexed: 10/19/2022]
Abstract
Continuous flow (microfluidic) chemistry was employed to prepare a small focused library of dihydropyrimidinone (DHPM) derivatives. Compounds in this class have been reported to exhibit activity against the human immunodeficiency virus (HIV), but their molecular target had not been identified. We tested the initial set of DHPMs in phenotypic assays providing a hit (1i) that inhibited the replication of the human immunodeficiency virus HIV in cells. Flow chemistry-driven optimization of 1i led to the identification of HIV replication inhibitors such as 1l with cellular potency comparable with the clinical drug nevirapine (NVP). Mechanism of action (MOA) studies using cellular and biochemical assays coupled with 3D fingerprinting and in silico modeling demonstrated that these drug-like probe compounds exert their effects by inhibiting the viral reverse transcriptase polymerase (RT). This led to the design and synthesis of the novel DHPM 1at that inhibits the replication of drug resistant strains of HIV. Our work demonstrates that combining flow chemistry-driven analogue refinement with phenotypic assays, in silico modeling and MOA studies is a highly effective strategy for hit-to-lead optimization applicable to the discovery of future therapeutic agents.
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Affiliation(s)
- Nicholas Pagano
- Cancer Metabolism & Signaling Networks Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Rd., La Jolla, CA 92037, United States
| | - Peter Teriete
- Cancer Metabolism & Signaling Networks Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Rd., La Jolla, CA 92037, United States
| | - Margrith E Mattmann
- Cancer Metabolism & Signaling Networks Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Rd., La Jolla, CA 92037, United States
| | - Li Yang
- Cancer Metabolism & Signaling Networks Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Rd., La Jolla, CA 92037, United States
| | - Beth A Snyder
- Southern Research Institute, Drug Development Division, 431 Aviation Way, Frederick, MD 21701, United States
| | - Zhaohui Cai
- Southern Research Institute, Drug Development Division, 431 Aviation Way, Frederick, MD 21701, United States
| | - Marintha L Heil
- Southern Research Institute, Drug Development Division, 431 Aviation Way, Frederick, MD 21701, United States
| | - Nicholas D P Cosford
- Cancer Metabolism & Signaling Networks Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Rd., La Jolla, CA 92037, United States.
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Sonar VP, Corona A, Distinto S, Maccioni E, Meleddu R, Fois B, Floris C, Malpure NV, Alcaro S, Tramontano E, Cottiglia F. Natural product-inspired esters and amides of ferulic and caffeic acid as dual inhibitors of HIV-1 reverse transcriptase. Eur J Med Chem 2017; 130:248-260. [PMID: 28254698 DOI: 10.1016/j.ejmech.2017.02.054] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 02/20/2017] [Accepted: 02/21/2017] [Indexed: 11/24/2022]
Abstract
Using an HIV-1 Reverse Transcriptase (RT)-associated RNase H inhibition assay as lead, bioguided fractionation of the dichloromethane extract of the Ocimum sanctum leaves led to the isolation of five triterpenes (1-5) along with three 3-methoxy-4-hydroxy phenyl derivatives (6-8). The structure of this isolates were determined by 1D and 2D NMR experiments as well as ESI-MS. Tetradecyl ferulate (8) showed an interesting RNase H IC50 value of 12.4 μM and due to the synthetic accessibility of this secondary metabolite, a structure-activity relationship study was carried out. A series of esters and amides of ferulic and caffeic acids were synthesized and, among all, the most active was N-oleylcaffeamide displaying a strong inhibitory activity towards both RT-associated functions, ribonuclease H and DNA polymerase. Molecular modeling studies together with Yonetani-Theorell analysis, demonstrated that N-oleylcaffeamide is able to bind both two allosteric site located one close to the NNRTI binding pocket and the other close to RNase H catalytic site.
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Affiliation(s)
- Vijay P Sonar
- Department of Life and Environmental Sciences, Drug Sciences Section, University of Cagliari, via Ospedale 72, 09124 Cagliari, Italy
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella di Monserrato SS554, 09042, Monserrato, Cagliari, Italy
| | - Simona Distinto
- Department of Life and Environmental Sciences, Drug Sciences Section, University of Cagliari, via Ospedale 72, 09124 Cagliari, Italy
| | - Elias Maccioni
- Department of Life and Environmental Sciences, Drug Sciences Section, University of Cagliari, via Ospedale 72, 09124 Cagliari, Italy
| | - Rita Meleddu
- Department of Life and Environmental Sciences, Drug Sciences Section, University of Cagliari, via Ospedale 72, 09124 Cagliari, Italy
| | - Benedetta Fois
- Department of Life and Environmental Sciences, Drug Sciences Section, University of Cagliari, via Ospedale 72, 09124 Cagliari, Italy
| | - Costantino Floris
- Dipartimento di Scienze Chimiche, University of Cagliari, Cittadella di Monserrato, 09042, Monserrato, Cagliari, Italy
| | - Nilesh V Malpure
- Department of Botany, S. S. G. M. College, IN-423601 Kopargaon, District Ahmednagar, MS, India
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università"Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, 88100 Catanzaro, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella di Monserrato SS554, 09042, Monserrato, Cagliari, Italy
| | - Filippo Cottiglia
- Department of Life and Environmental Sciences, Drug Sciences Section, University of Cagliari, via Ospedale 72, 09124 Cagliari, Italy.
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Meleddu R, Distinto S, Corona A, Tramontano E, Bianco G, Melis C, Cottiglia F, Maccioni E. Isatin thiazoline hybrids as dual inhibitors of HIV-1 reverse transcriptase. J Enzyme Inhib Med Chem 2016; 32:130-136. [PMID: 27766892 PMCID: PMC6010014 DOI: 10.1080/14756366.2016.1238366] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
A series of 3-3-{2-[2-3-methyl-4-phenyl-2,3-dihydro-1,3-thiazol-2-ylidene]hydrazin-1-ylidene-2,3-dihydro-1H-indol-2-one derivatives has been designed and synthesized to study their activity on both HIV-1 (Human Immunodeficiency Virus type 1) RT (Reverse Transcriptase) associated functions. These derivatives are analogs of previously reported series whose biological activity and mode of action have been investigated. In this work we investigated the influence of the introduction of a methyl group in the position 3 of the dihydrothiazole ring and of a chlorine atom in the position 5 of the isatin nucleus. The new synthesized compounds are active towards both DNA polymerase and ribonuclease H in the µM range. The nature of the aromatic group in the position 4 of the thiazole was relevant in determining the biological activity.
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Affiliation(s)
- Rita Meleddu
- a Department of Life and Environmental Sciences , University of Cagliari , Cagliari , Italy
| | - Simona Distinto
- a Department of Life and Environmental Sciences , University of Cagliari , Cagliari , Italy
| | - Angela Corona
- b Department of Life and Environmental Sciences , University of Cagliari, Cittadella Universitaria di Monserrato , Cagliari , Italy
| | - Enzo Tramontano
- b Department of Life and Environmental Sciences , University of Cagliari, Cittadella Universitaria di Monserrato , Cagliari , Italy
| | - Giulia Bianco
- a Department of Life and Environmental Sciences , University of Cagliari , Cagliari , Italy
| | - Claudia Melis
- a Department of Life and Environmental Sciences , University of Cagliari , Cagliari , Italy
| | - Filippo Cottiglia
- a Department of Life and Environmental Sciences , University of Cagliari , Cagliari , Italy
| | - Elias Maccioni
- a Department of Life and Environmental Sciences , University of Cagliari , Cagliari , Italy
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Structural Maturation of HIV-1 Reverse Transcriptase-A Metamorphic Solution to Genomic Instability. Viruses 2016; 8:v8100260. [PMID: 27690082 PMCID: PMC5086598 DOI: 10.3390/v8100260] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/12/2016] [Indexed: 12/13/2022] Open
Abstract
Human immunodeficiency virus 1 (HIV-1) reverse transcriptase (RT)—a critical enzyme of the viral life cycle—undergoes a complex maturation process, required so that a pair of p66 precursor proteins can develop conformationally along different pathways, one evolving to form active polymerase and ribonuclease H (RH) domains, while the second forms a non-functional polymerase and a proteolyzed RH domain. These parallel maturation pathways rely on the structural ambiguity of a metamorphic polymerase domain, for which the sequence–structure relationship is not unique. Recent nuclear magnetic resonance (NMR) studies utilizing selective labeling techniques, and structural characterization of the p66 monomer precursor have provided important insights into the details of this maturation pathway, revealing many aspects of the three major steps involved: (1) domain rearrangement; (2) dimerization; and (3) subunit-selective RH domain proteolysis. This review summarizes the major structural changes that occur during the maturation process. We also highlight how mutations, often viewed within the context of the mature RT heterodimer, can exert a major influence on maturation and dimerization. It is further suggested that several steps in the RT maturation pathway may provide attractive targets for drug development.
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Dousson C, Alexandre FR, Amador A, Bonaric S, Bot S, Caillet C, Convard T, da Costa D, Lioure MP, Roland A, Rosinovsky E, Maldonado S, Parsy C, Trochet C, Storer R, Stewart A, Wang J, Mayes BA, Musiu C, Poddesu B, Vargiu L, Liuzzi M, Moussa A, Jakubik J, Hubbard L, Seifer M, Standring D. Discovery of the Aryl-phospho-indole IDX899, a Highly Potent Anti-HIV Non-nucleoside Reverse Transcriptase Inhibitor. J Med Chem 2016; 59:1891-8. [PMID: 26804933 DOI: 10.1021/acs.jmedchem.5b01430] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Here, we describe the design, synthesis, biological evaluation, and identification of a clinical candidate non-nucleoside reverse transcriptase inhibitors (NNRTIs) with a novel aryl-phospho-indole (APhI) scaffold. NNRTIs are recommended components of highly active antiretroviral therapy (HAART) for the treatment of HIV-1. Since a major problem associated with NNRTI treatment is the emergence of drug resistant virus, this work focused on optimization of the APhI against clinically relevant HIV-1 Y181C and K103N mutants and the Y181C/K103N double mutant. Optimization of the phosphinate aryl substituent led to the discovery of the 3-Me,5-acrylonitrile-phenyl analogue RP-13s (IDX899) having an EC50 of 11 nM against the Y181C/K103N double mutant.
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Affiliation(s)
- Cyril Dousson
- IDENIX, an MSD Company , 1682 rue de la Valsière, Cap Gamma, BP 50001, 34189 Cedex 4 Montpellier, France
| | - François-René Alexandre
- IDENIX, an MSD Company , 1682 rue de la Valsière, Cap Gamma, BP 50001, 34189 Cedex 4 Montpellier, France
| | - Agnès Amador
- IDENIX, an MSD Company , 1682 rue de la Valsière, Cap Gamma, BP 50001, 34189 Cedex 4 Montpellier, France
| | - Séverine Bonaric
- IDENIX, an MSD Company , 1682 rue de la Valsière, Cap Gamma, BP 50001, 34189 Cedex 4 Montpellier, France
| | - Stéphanie Bot
- IDENIX, an MSD Company , 1682 rue de la Valsière, Cap Gamma, BP 50001, 34189 Cedex 4 Montpellier, France
| | - Catherine Caillet
- IDENIX, an MSD Company , 1682 rue de la Valsière, Cap Gamma, BP 50001, 34189 Cedex 4 Montpellier, France
| | - Thierry Convard
- IDENIX, an MSD Company , 1682 rue de la Valsière, Cap Gamma, BP 50001, 34189 Cedex 4 Montpellier, France
| | - Daniel da Costa
- IDENIX, an MSD Company , 1682 rue de la Valsière, Cap Gamma, BP 50001, 34189 Cedex 4 Montpellier, France
| | - Marie-Pierre Lioure
- IDENIX, an MSD Company , 1682 rue de la Valsière, Cap Gamma, BP 50001, 34189 Cedex 4 Montpellier, France
| | - Arlène Roland
- IDENIX, an MSD Company , 1682 rue de la Valsière, Cap Gamma, BP 50001, 34189 Cedex 4 Montpellier, France
| | - Elodie Rosinovsky
- IDENIX, an MSD Company , 1682 rue de la Valsière, Cap Gamma, BP 50001, 34189 Cedex 4 Montpellier, France
| | - Sébastien Maldonado
- IDENIX, an MSD Company , 1682 rue de la Valsière, Cap Gamma, BP 50001, 34189 Cedex 4 Montpellier, France
| | - Christophe Parsy
- IDENIX, an MSD Company , 1682 rue de la Valsière, Cap Gamma, BP 50001, 34189 Cedex 4 Montpellier, France
| | - Christophe Trochet
- IDENIX, an MSD Company , 1682 rue de la Valsière, Cap Gamma, BP 50001, 34189 Cedex 4 Montpellier, France
| | - Richard Storer
- IDENIX, an MSD Company , 1682 rue de la Valsière, Cap Gamma, BP 50001, 34189 Cedex 4 Montpellier, France
| | - Alistair Stewart
- IDENIX , 320 Bent Street, 4th Floor, Cambridge, Massachusetts 02139, United States
| | - Jingyang Wang
- IDENIX , 320 Bent Street, 4th Floor, Cambridge, Massachusetts 02139, United States
| | - Benjamin A Mayes
- IDENIX , 320 Bent Street, 4th Floor, Cambridge, Massachusetts 02139, United States
| | - Chiara Musiu
- IDENIX , 320 Bent Street, 4th Floor, Cambridge, Massachusetts 02139, United States
| | - Barbara Poddesu
- IDENIX , 320 Bent Street, 4th Floor, Cambridge, Massachusetts 02139, United States
| | - Luana Vargiu
- IDENIX , 320 Bent Street, 4th Floor, Cambridge, Massachusetts 02139, United States
| | - Michel Liuzzi
- IDENIX , 320 Bent Street, 4th Floor, Cambridge, Massachusetts 02139, United States
| | - Adel Moussa
- IDENIX , 320 Bent Street, 4th Floor, Cambridge, Massachusetts 02139, United States
| | - Jocelyn Jakubik
- IDENIX , 320 Bent Street, 4th Floor, Cambridge, Massachusetts 02139, United States
| | - Luke Hubbard
- IDENIX , 320 Bent Street, 4th Floor, Cambridge, Massachusetts 02139, United States
| | - Maria Seifer
- IDENIX , 320 Bent Street, 4th Floor, Cambridge, Massachusetts 02139, United States
| | - David Standring
- IDENIX , 320 Bent Street, 4th Floor, Cambridge, Massachusetts 02139, United States
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17
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Ribonuclease H/DNA Polymerase HIV-1 Reverse Transcriptase Dual Inhibitor: Mechanistic Studies on the Allosteric Mode of Action of Isatin-Based Compound RMNC6. PLoS One 2016; 11:e0147225. [PMID: 26800261 PMCID: PMC4723341 DOI: 10.1371/journal.pone.0147225] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 12/30/2015] [Indexed: 12/11/2022] Open
Abstract
The DNA polymerase and ribonuclease H (RNase H) activities of human immunodeficiency virus type 1 (HIV-1) are needed for the replication of the viral genome and are validated drug targets. However, there are no approved drugs inhibiting RNase H and the efficiency of DNA polymerase inhibitors can be diminished by the presence of drug resistance mutations. In this context, drugs inhibiting both activities could represent a significant advance towards better anti-HIV therapies. We report on the mechanisms of allosteric inhibition of a newly synthesized isatin-based compound designated as RMNC6 that showed IC50 values of 1.4 and 9.8 μM on HIV-1 RT-associated RNase H and polymerase activities, respectively. Blind docking studies predict that RMNC6 could bind two different pockets in the RT: one in the DNA polymerase domain (partially overlapping the non-nucleoside RT inhibitor [NNRTI] binding pocket), and a second one close to the RNase H active site. Enzymatic studies showed that RMNC6 interferes with efavirenz (an approved NNRTI) in its binding to the RT polymerase domain, although NNRTI resistance-associated mutations such as K103N, Y181C and Y188L had a minor impact on RT susceptibility to RMNC6. In addition, despite being naturally resistant to NNRTIs, the polymerase activity of HIV-1 group O RT was efficiently inhibited by RMNC6. The compound was also an inhibitor of the RNase H activity of wild-type HIV-1 group O RT, although we observed a 6.5-fold increase in the IC50 in comparison with the prototypic HIV-1 group M subtype B enzyme. Mutagenesis studies showed that RT RNase H domain residues Asn474 and Tyr501, and in a lesser extent Ala502 and Ala508, are critical for RMNC6 inhibition of the endonuclease activity of the RT, without affecting its DNA polymerization activity. Our results show that RMNC6 acts as a dual inhibitor with allosteric sites in the DNA polymerase and the RNase H domains of HIV-1 RT.
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18
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Stanton RA, Nettles JH, Schinazi RF. Ligand similarity guided receptor selection enhances docking accuracy and recall for non-nucleoside HIV reverse transcriptase inhibitors. J Mol Model 2015; 21:282. [PMID: 26450349 DOI: 10.1007/s00894-015-2826-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 09/22/2015] [Indexed: 11/27/2022]
Abstract
Non-nucleoside reverse transcriptase inhibitors (NNRTI) are allosteric inhibitors of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT), a viral polymerase essential to infection. Despite the availability of >150 NNRTI-bound RT crystal structures, rational design of new NNRTI remains challenging because of the variability of their induced fit, hydrophobic binding patterns. Docking NNRTI yields inconsistent results that vary markedly depending on the receptor structure used, as only 27% of the >20k cross-docking calculations we performed using known NNRTI were accurate. In order to determine if a hospitable receptor for docking could be selected a priori, we evaluated more than 40 chemical descriptors for their ability to pre-select a best receptor for NNRTI cross-docking. The receptor selection was based on similarity scores between the bound- and target-ligands generated by each descriptor. The top descriptors were able to double the probability of cross-docking accuracy over random receptor selection. Additionally, recall of known NNRTI from a large library of similar decoys was increased using the same approach. The results demonstrate the utility of pre-selecting receptors when docking into difficult targets. Graphical Abstract Cross-docking accuracy increases when using chemical descriptors to determine the NNRTI with maximum similarity to the new compound and then docking into its respective receptor.
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Affiliation(s)
- Richard A Stanton
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - James H Nettles
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Raymond F Schinazi
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
- Veterans Affairs Medical Center, Atlanta, GA, 30033, USA.
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19
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Wan ZY, Yao J, Mao TQ, Wang XL, Wang HF, Chen WX, Yin H, Chen FE, De Clercq E, Daelemans D, Pannecouque C. Pyrimidine sulfonylacetanilides with improved potency against key mutant viruses of HIV-1 by specific targeting of a highly conserved residue. Eur J Med Chem 2015; 102:215-22. [DOI: 10.1016/j.ejmech.2015.08.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Revised: 07/21/2015] [Accepted: 08/02/2015] [Indexed: 10/23/2022]
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Double Variational Binding--(SMILES) Conformational Analysis by Docking Mechanisms for Anti-HIV Pyrimidine Ligands. Int J Mol Sci 2015; 16:19553-601. [PMID: 26295229 PMCID: PMC4581313 DOI: 10.3390/ijms160819553] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 07/30/2015] [Accepted: 08/11/2015] [Indexed: 12/11/2022] Open
Abstract
Variational quantitative binding–conformational analysis for a series of anti-HIV pyrimidine-based ligands is advanced at the individual molecular level. This was achieved by employing ligand-receptor docking algorithms for each molecule in the 1,3-disubstituted uracil derivative series that was studied. Such computational algorithms were employed for analyzing both genuine molecular cases and their simplified molecular input line entry system (SMILES) transformations, which were created via the controlled breaking of chemical bonds, so as to generate the longest SMILES molecular chain (LoSMoC) and Branching SMILES (BraS) conformations. The study identified the most active anti-HIV molecules, and analyzed their special and relevant bonding fragments (chemical alerts), and the recorded energetic and geometric docking results (i.e., binding and affinity energies, and the surface area and volume of bonding, respectively). Clear computational evidence was also produced concerning the ligand-receptor pocket binding efficacies of the LoSMoc and BraS conformation types, thus confirming their earlier presence (as suggested by variational quantitative structure-activity relationship, variational-QSAR) as active intermediates for the molecule-to-cell transduction process.
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21
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Discovery of piperidin-4-yl-aminopyrimidine derivatives as potent non-nucleoside HIV-1 reverse transcriptase inhibitors. Eur J Med Chem 2015; 97:1-9. [DOI: 10.1016/j.ejmech.2015.04.050] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 04/23/2015] [Accepted: 04/24/2015] [Indexed: 11/18/2022]
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22
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Meleddu R, Cannas V, Distinto S, Sarais G, Del Vecchio C, Esposito F, Bianco G, Corona A, Cottiglia F, Alcaro S, Parolin C, Artese A, Scalise D, Fresta M, Arridu A, Ortuso F, Maccioni E, Tramontano E. Design, synthesis, and biological evaluation of 1,3-diarylpropenones as dual inhibitors of HIV-1 reverse transcriptase. ChemMedChem 2014; 9:1869-79. [PMID: 24850787 DOI: 10.1002/cmdc.201402015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Indexed: 12/12/2022]
Abstract
A small library of 1,3-diarylpropenones was designed and synthesized as dual inhibitors of both HIV-1 reverse transcriptase (RT) DNA polymerase (DP) and ribonuclease H (RNase H) associated functions. Compounds were assayed on these enzyme activities, which highlighted dual inhibition properties in the low-micromolar range. Interestingly, mutations in the non-nucleoside RT inhibitor binding pocket strongly affected RNase H inhibition by the propenone derivatives without decreasing their capacity to inhibit DP activity, which suggests long-range RT structural effects. Biochemical and computational studies indicated that the propenone derivatives bind two different interdependent allosteric pockets.
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Affiliation(s)
- Rita Meleddu
- Department of Life and Environmental Sciences, University of Cagliari, Via Ospedale 72, 09124 Cagliari (Italy)
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Seckler JM, Leioatts N, Miao H, Grossfield A. The interplay of structure and dynamics: insights from a survey of HIV-1 reverse transcriptase crystal structures. Proteins 2013; 81:1792-801. [PMID: 23720322 DOI: 10.1002/prot.24325] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 04/12/2013] [Accepted: 04/19/2013] [Indexed: 11/07/2022]
Abstract
HIV-1 reverse transcriptase (RT) is a critical drug target for HIV treatment, and understanding the exact mechanisms of its function and inhibition would significantly accelerate the development of new anti-HIV drugs. It is well known that structure plays a critical role in protein function, but for RT, structural information has proven to be insufficient-despite enormous effort-to explain the mechanism of inhibition and drug resistance of non-nucleoside RT inhibitors. We hypothesize that the missing link is dynamics, information about the motions of the system. However, many of the techniques that give the best information about dynamics, such as solution nuclear magnetic resonance and molecular dynamics simulations, cannot be easily applied to a protein as large as RT. As an alternative, we combine elastic network modeling with simultaneous hierarchical clustering of structural and dynamic data. We present an extensive survey of the dynamics of RT bound to a variety of ligands and with a number of mutations, revealing a novel mechanism for drug resistance to non-nucleoside RT inhibitors. Hydrophobic core mutations restore active-state motion to multiple functionally significant regions of HIV-1 RT. This model arises out of a combination of structural and dynamic information, rather than exclusively from one or the other.
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Affiliation(s)
- James M Seckler
- Department of Biostatistics and Computational Biology, University of Rochester, Rochester, New York
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24
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Menéndez-Arias L. Molecular basis of human immunodeficiency virus type 1 drug resistance: overview and recent developments. Antiviral Res 2013; 98:93-120. [PMID: 23403210 DOI: 10.1016/j.antiviral.2013.01.007] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 01/26/2013] [Accepted: 01/29/2013] [Indexed: 12/15/2022]
Abstract
The introduction of potent combination therapies in the mid-90s had a tremendous effect on AIDS mortality. However, drug resistance has been a major factor contributing to antiretroviral therapy failure. Currently, there are 26 drugs approved for treating human immunodeficiency virus (HIV) infections, although some of them are no longer prescribed. Most of the available antiretroviral drugs target HIV genome replication (i.e. reverse transcriptase inhibitors) and viral maturation (i.e. viral protease inhibitors). Other drugs in clinical use include a viral coreceptor antagonist (maraviroc), a fusion inhibitor (enfuvirtide) and two viral integrase inhibitors (raltegravir and elvitegravir). Elvitegravir and the nonnucleoside reverse transcriptase inhibitor rilpivirine have been the most recent additions to the antiretroviral drug armamentarium. An overview of the molecular mechanisms involved in antiretroviral drug resistance and the role of drug resistance-associated mutations was previously presented (Menéndez-Arias, L., 2010. Molecular basis of human immunodeficiency virus drug resistance: an update. Antiviral Res. 85, 210-231). This article provides now an updated review that covers currently approved drugs, new experimental agents (e.g. neutralizing antibodies) and selected drugs in preclinical or early clinical development (e.g. experimental integrase inhibitors). Special attention is dedicated to recent research on resistance to reverse transcriptase and integrase inhibitors. In addition, recently discovered interactions between HIV and host proteins and novel strategies to block HIV assembly or viral entry emerge as promising alternatives for the development of effective antiretroviral treatments.
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Affiliation(s)
- Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa"-Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid, c/ Nicolás Cabrera 1, Campus de Cantoblanco, 28049 Madrid, Spain.
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Extensive mutagenesis of the conserved box E motif in duck hepatitis B virus P protein reveals multiple functions in replication and a common structure with the primer grip in HIV-1 reverse transcriptase. J Virol 2012; 86:6394-407. [PMID: 22514339 DOI: 10.1128/jvi.00011-12] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Hepadnaviruses, including the pathogenic hepatitis B virus (HBV), replicate their small DNA genomes through protein-primed reverse transcription, mediated by the terminal protein (TP) domain in their P proteins and an RNA stem-loop, ε, on the pregenomic RNA (pgRNA). No direct structural data are available for P proteins, but their reverse transcriptase (RT) domains contain motifs that are conserved in all RTs (box A to box G), implying a similar architecture; however, experimental support for this notion is limited. Exploiting assays available for duck HBV (DHBV) but not the HBV P protein, we assessed the functional consequences of numerous mutations in box E, which forms the DNA primer grip in human immunodeficiency virus type 1 (HIV-1) RT. This substructure coordinates primer 3'-end positioning and RT subdomain movements during the polymerization cycle and is a prime target for nonnucleosidic RT inhibitors (NNRTIs) of HIV-1 RT. Box E was indeed critical for DHBV replication, with the mutations affecting the folding, ε RNA interactions, and polymerase activity of the P protein in a position- and amino acid side chain-dependent fashion similar to that of HIV-1 RT. Structural similarity to HIV-1 RT was underlined by molecular modeling and was confirmed by the replication activity of chimeric P proteins carrying box E, or even box C to box E, from HIV-1 RT. Hence, box E in the DHBV P protein and likely the HBV P protein forms a primer grip-like structure that may provide a new target for anti-HBV NNRTIs.
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Mishra S, Tandon P, Ayala AP. Study on the structure and vibrational spectra of efavirenz conformers using DFT: comparison to experimental data. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 88:116-123. [PMID: 22206896 DOI: 10.1016/j.saa.2011.12.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 12/04/2011] [Indexed: 05/31/2023]
Abstract
Efavirenz, (S)-6-chloro-4-(cyclopropylethynyl)-1,4-dihydro-4-(trifluoromethyl)-2H-3,1-benzoxazin-2-one, is an anti HIV agent belonging to the class of the non-nucleoside inhibitors of the HIV-1 virus reverse transcriptase. A systematic quantum chemical study of the possible conformations, their relative stabilities and vibrational spectra of efavirenz has been reported. Structural and spectral characteristics of efavirenz have been studied by vibrational spectroscopy and quantum chemical methods. Density functional theory (DFT) calculations for potential energy curve, optimized geometries and vibrational spectra have been carried out using 6-311++G(d,p) basis sets and B3LYP functionals. Based on these results, we have discussed the correlation between the vibrational modes and the crystalline structure of the most stable form of efavirenz. A complete analysis of the experimental infrared and Raman spectra has been reported on the basis of wavenumber of the vibrational bands and potential energy distribution. The infrared and the Raman spectra of the molecule based on DFT calculations show reasonable agreement with the experimental results. The calculated HOMO and LUMO energies shows that charge transfer occur within the molecule.
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Affiliation(s)
- Soni Mishra
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, India
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Li D, Zhan P, De Clercq E, Liu X. Strategies for the design of HIV-1 non-nucleoside reverse transcriptase inhibitors: lessons from the development of seven representative paradigms. J Med Chem 2012; 55:3595-613. [PMID: 22268494 DOI: 10.1021/jm200990c] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Dongyue Li
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University, 44, West Culture Road, 250012, Jinan, Shandong, P. R. China
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Minkara MS, Davis PH, Radhakrishnan ML. Multiple drugs and multiple targets: An analysis of the electrostatic determinants of binding between non-nucleoside HIV-1 reverse transcriptase inhibitors and variants of HIV-1 RT. Proteins 2011; 80:573-90. [DOI: 10.1002/prot.23221] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Revised: 09/13/2011] [Accepted: 10/06/2011] [Indexed: 11/09/2022]
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García-Sosa AT, Sild S, Takkis K, Maran U. Combined Approach Using Ligand Efficiency, Cross-Docking, and Antitarget Hits for Wild-Type and Drug-Resistant Y181C HIV-1 Reverse Transcriptase. J Chem Inf Model 2011; 51:2595-611. [DOI: 10.1021/ci200203h] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
| | - Sulev Sild
- Institute of Chemistry, University of Tartu, Ravila 14a, Tartu 50411, Estonia
| | - Kalev Takkis
- Institute of Chemistry, University of Tartu, Ravila 14a, Tartu 50411, Estonia
| | - Uko Maran
- Institute of Chemistry, University of Tartu, Ravila 14a, Tartu 50411, Estonia
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De Clercq E. From TIBO to Rilpivirine: The Chronicle of the Discovery of the Ideal Nonnucleoside Reverse Transcriptase Inhibitor. ANTIVIRAL DRUG STRATEGIES 2011. [DOI: 10.1002/9783527635955.ch15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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31
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Das K, Bauman JD, Rim AS, Dharia C, Clark AD, Camarasa MJ, Balzarini J, Arnold E. Crystal structure of tert-butyldimethylsilyl-spiroaminooxathioledioxide-thymine (TSAO-T) in complex with HIV-1 reverse transcriptase (RT) redefines the elastic limits of the non-nucleoside inhibitor-binding pocket. J Med Chem 2011; 54:2727-37. [PMID: 21446702 PMCID: PMC3361896 DOI: 10.1021/jm101536x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
tert-Butyldimethylsilyl-spiroaminooxathioledioxide (TSAO) compounds have an embedded thymidine-analogue backbone; however, TSAO compounds invoke non-nucleoside RT inhibitor (NNRTI) resistance mutations. Our crystal structure of RT:7 (TSAO-T) complex shows that 7 binds inside the NNRTI-binding pocket, assuming a "dragon" shape, and interacts extensively with almost all the pocket residues. The structure also explains the structure-activity relationships and resistance data for TSAO compounds. The binding of 7 causes hyper-expansion of the pocket and significant rearrangement of RT subdomains. This nonoptimal complex formation is apparently responsible (1) for the lower stability of a RT (p66/p51) dimer and (2) for the lower potency of 7 despite of its extensive interactions with RT. However, the HIV-1 RT:7 structure reveals novel design features such as (1) interactions with the conserved Tyr183 from the YMDD-motif and (2) a possible way for an NNRTI to reach the polymerase active site that may be exploited in designing new NNRTIs.
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Affiliation(s)
- Kalyan Das
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Joseph D. Bauman
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Angela S. Rim
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Chhaya Dharia
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Arthur D. Clark
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - María-José Camarasa
- Instituto de Química Médica (C.S.I.C.). Juan de la Cierva 3, 28006 Madrid, Spain
| | - Jan Balzarini
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
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Brandt P, Geitmann M, Danielson UH. Deconstruction of non-nucleoside reverse transcriptase inhibitors of human immunodeficiency virus type 1 for exploration of the optimization landscape of fragments. J Med Chem 2011; 54:709-18. [PMID: 21207958 DOI: 10.1021/jm101052g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
This study has taken a closer look at the theoretical basis for protein-fragment interactions. The approach involved the deconstruction of 3 non-nucleoside inhibitors of HIV-1 reverse transcriptase and investigation of the interaction between 21 substructures and the enzyme. It focused on the concept of ligand efficiency and showed that ligand independent free energy fees (ΔG(ind)) are crucial for the understanding of the binding affinities of fragments. A value of 7.0 kcal mol(-1) for the ΔG(ind) term is shown to be a lower limit for the NNRTI binding pocket of HIV-1 RT. The addition of the ΔG(ind) term to the dissociation free energy in the calculation of a corrected ligand efficiency, in combination with the lack of an efficient ligand binding hot spot in the NNIBP, fully explains the existence of nonbinding NNRTI substructures. By applying the concept to a larger set of ligands, we could define a binding site profile that indicates the absence of an efficient fragment binding hot spot but an efficient binding of full-sized NNRTIs. The analysis explains some of the challenges in identifying fragments against flexible targets involving conformational changes and how fragments may be prioritized.
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van Westen GJP, Wegner JK, Bender A, Ijzerman AP, van Vlijmen HWT. Mining protein dynamics from sets of crystal structures using "consensus structures". Protein Sci 2010; 19:742-52. [PMID: 20120021 DOI: 10.1002/pro.350] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In this work, we describe two novel approaches to utilize the dynamic structure information implicitly contained in large crystal structure data sets. The first approach visualizes both consistent as well as variable ligand-induced changes in ligand-bound compared with apo protein crystal structures. For this purpose, information was mined from B-factors and ligand-induced residue displacements in multiple crystal structures, minimizing experimental error and noise. With this approach, the mechanism of action of non-nucleoside reverse transcriptase inhibitors (NNRTIs) as an inseparable combination of distortion of protein dynamics and conformational changes of HIV-1 reverse transcriptase was corroborated (a combination of the previously proposed "molecular arthritis" and "distorted site" mechanisms). The second approach presented here uses "consensus structures" to map common binding features that are present in a set of structures of NNRTI-bound HIV-1 reverse transcriptase. Consensus structures are based on different levels of structural overlap of multiple crystal structures and are used to analyze protein-ligand interactions. The structures are shown to yield information about conserved hydrogen bonding interactions as well as binding-pocket flexibility, shape, and volume. From the consensus structures, a common wild type NNRTI binding pocket emerges. Furthermore, we were able to identify a conserved backbone hydrogen bond acceptor at P236 and a novel hydrophobic subpocket, which are not yet utilized by current drugs. Our methods introduced here reinterpret the atom information and make use of the data variability by using multiple structures, complementing classical 3D structural information of single structures.
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Affiliation(s)
- Gerard J P van Westen
- Division of Medicinal Chemistry, Leiden/Amsterdam Center for Drug Research, Einsteinweg 55, 2333 CC Leiden, Netherlands
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