1
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Zhu M, Shan Q, Ma L, Dong B, Wang J, Zhang G, Wang M, Zhou J, Cen S, Wang Y. Structure based design and evaluation of benzoheterocycle derivatives as potential dual HIV-1 protease and reverse transcriptase inhibitors. Eur J Med Chem 2023; 246:114981. [PMID: 36481598 DOI: 10.1016/j.ejmech.2022.114981] [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: 06/15/2022] [Revised: 11/19/2022] [Accepted: 11/26/2022] [Indexed: 12/05/2022]
Abstract
The development of dual inhibitors of HIV-1 protease and reverse transcriptase is an attractive strategy for multi-target therapeutic of AIDS, which may be privileged in delaying the occurrence of drug resistance. We herein designed a novel kind of dual inhibitors with benzofuran or indole cores. Biological results showed that a number of inhibitors displayed significant activity against both HIV-1 protease and reverse transcriptase. Among which, inhibitor 10f exhibited a good correlation with an approximate ratio of 1: 2 between the two enzymes. Furthermore, the dual inhibitors illustrated similar potency against both the wild-type virus and drug-resistant mutant. In addition, the molecular dynamic simulation studies verified the dual actions of such inhibitors.
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Affiliation(s)
- Mei Zhu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Qi Shan
- Tianjin Institute of Pharmaceutical Research, Tianjin, 300462, China
| | - Ling Ma
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Biao Dong
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Juxian Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Guoning Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Minghua Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Jinming Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, Jinhua, 321004, China.
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China.
| | - Yucheng Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China.
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2
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Me-Better Drug Design Based on Nevirapine and Mechanism of Molecular Interactions with Y188C Mutant HIV-1 Reverse Transcriptase. Molecules 2022; 27:molecules27217348. [DOI: 10.3390/molecules27217348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 10/14/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2022] Open
Abstract
In this paper, the Y188C mutant HIV-1 reverse transcriptase (Y188CM-RT) target protein was constructed by homology modeling, and new ligands based on nevirapine (NVP) skeleton were designed by means of fragment growth. The binding activity of new ligands to Y188CM-RT was evaluated by structural analysis, ADMET prediction, molecular docking, energy calculation and molecular dynamics. Results show that 10 new ligands had good absorbability, and their binding energies to Y188CM-RT were significantly higher than those of wild-type HIV-1 reverse transcriptase(wt). The binding mode explained that fragment growth contributed to larger ligands, leading to improved suitability at the docking pocket. In the way of fragment growth, the larger side chain with extensive contact at terminal is obviously better than substituted benzene ring. The enhancement of docking activity is mainly due to the new fragments such as alkyl chains and rings with amino groups at NVP terminal, resulting in a large increase in hydrophobic bonding and the new addition of hydrogen bonding or salt bonding. This study is expected to provide reference for the research on non-nucleoside reverse transcriptase inhibitors resistance and AIDS treatment.
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3
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Pashkov EA, Pak AV, Pashkov EP, Bykov AS, Budanova EV, Poddubikov AV, Svitich OA, Zverev VV. [The prospects for the use of drugs based on the phenomenon of RNA interference against HIV infection]. Vopr Virusol 2022; 67:278-289. [PMID: 36097709 DOI: 10.36233/0507-4088-124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 09/11/2022] [Indexed: 06/15/2023]
Abstract
The human immunodeficiency virus (HIV) is currently one of the most pressing global health problems. Since its discovery in 1978, HIV has claimed the lives of more than 35 million people, and the number of people infected today reaches 37 million. In the absence of highly active antiretroviral therapy (HAART), HIV infection is characterized by a steady decrease in the number of CD4+ T-lymphocytes, but its manifestations can affect the central nervous, cardiovascular, digestive, endocrine and genitourinary systems. At the same time, complications induced by representatives of pathogenic and opportunistic microflora, which can lead to the development of bacterial, fungal and viral concomitant infections, are of particular danger. It should be borne in mind that an important problem is the emergence of viruses resistant to standard therapy, as well as the toxicity of the drugs themselves for the body. In the context of this review, of particular interest is the assessment of the prospects for the creation and clinical use of drugs based on small interfering RNAs aimed at suppressing the reproduction of HIV, taking into account the experience of similar studies conducted earlier. RNA interference is a cascade of regulatory reactions in eukaryotic cells, which results in the degradation of foreign messenger RNA. The development of drugs based on the mechanism of RNA interference will overcome the problem of viral resistance. Along with this, this technology makes it possible to quickly respond to outbreaks of new viral diseases.
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Affiliation(s)
- E A Pashkov
- I.M. Sechenov First Moscow State Medical University (Sechenov University); Federal State Budgetary Scientific Institution "I. Mechnikov Research Institute of Vaccines and Sera"
| | - A V Pak
- I.M. Sechenov First Moscow State Medical University (Sechenov University)
| | - E P Pashkov
- I.M. Sechenov First Moscow State Medical University (Sechenov University)
| | - A S Bykov
- I.M. Sechenov First Moscow State Medical University (Sechenov University)
| | - E V Budanova
- I.M. Sechenov First Moscow State Medical University (Sechenov University)
| | - A V Poddubikov
- Federal State Budgetary Scientific Institution "I. Mechnikov Research Institute of Vaccines and Sera"
| | - O A Svitich
- I.M. Sechenov First Moscow State Medical University (Sechenov University); Federal State Budgetary Scientific Institution "I. Mechnikov Research Institute of Vaccines and Sera"
| | - V V Zverev
- I.M. Sechenov First Moscow State Medical University (Sechenov University); Federal State Budgetary Scientific Institution "I. Mechnikov Research Institute of Vaccines and Sera"
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4
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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: 25] [Impact Index Per Article: 12.5] [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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5
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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: 39] [Impact Index Per Article: 13.0] [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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6
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Melo R, Lemos A, Preto AJ, Bueschbell B, Matos-Filipe P, Barreto C, Almeida JG, Silva RDM, Correia JDG, Moreira IS. An Overview of Antiretroviral Agents for Treating HIV Infection in Paediatric Population. Curr Med Chem 2020; 27:760-794. [PMID: 30182840 DOI: 10.2174/0929867325666180904123549] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 07/11/2018] [Accepted: 07/11/2018] [Indexed: 12/19/2022]
Abstract
Paediatric Acquired ImmunoDeficiency Syndrome (AIDS) is a life-threatening and infectious disease in which the Human Immunodeficiency Virus (HIV) is mainly transmitted through Mother-To- Child Transmission (MTCT) during pregnancy, labour and delivery, or breastfeeding. This review provides an overview of the distinct therapeutic alternatives to abolish the systemic viral replication in paediatric HIV-1 infection. Numerous classes of antiretroviral agents have emerged as therapeutic tools for downregulation of different steps in the HIV replication process. These classes encompass Non- Nucleoside Analogue Reverse Transcriptase Inhibitors (NNRTIs), Nucleoside/Nucleotide Analogue Reverse Transcriptase Inhibitors (NRTIs/NtRTIs), INtegrase Inhibitors (INIs), Protease Inhibitors (PIs), and Entry Inhibitors (EIs). Co-administration of certain antiretroviral drugs with Pharmacokinetic Enhancers (PEs) may boost the effectiveness of the primary therapeutic agent. The combination of multiple antiretroviral drug regimens (Highly Active AntiRetroviral Therapy - HAART) is currently the standard therapeutic approach for HIV infection. So far, the use of HAART offers the best opportunity for prolonged and maximal viral suppression, and preservation of the immune system upon HIV infection. Still, the frequent administration of high doses of multiple drugs, their inefficient ability to reach the viral reservoirs in adequate doses, the development of drug resistance, and the lack of patient compliance compromise the complete HIV elimination. The development of nanotechnology-based drug delivery systems may enable targeted delivery of antiretroviral agents to inaccessible viral reservoir sites at therapeutic concentrations. In addition, the application of Computer-Aided Drug Design (CADD) approaches has provided valuable tools for the development of anti-HIV drug candidates with favourable pharmacodynamics and pharmacokinetic properties.
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Affiliation(s)
- Rita Melo
- Centro de Ciencias e Tecnologias Nucleares, Instituto Superior Tecnico, Universidade de Lisboa, CTN, Estrada Nacional 10 (km 139,7), Bobadela LRS 2695-066, Portugal.,CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1ºandar, Universidade de Coimbra, Coimbra 3004-517, Portugal
| | - Agostinho Lemos
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1ºandar, Universidade de Coimbra, Coimbra 3004-517, Portugal.,GIGA Cyclotron Research Centre In Vivo Imaging, University of Liège, Liège 4000, Belgium
| | - António J Preto
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1ºandar, Universidade de Coimbra, Coimbra 3004-517, Portugal
| | - Beatriz Bueschbell
- Pharmaceutical Chemistry I, PharmaCenter, Pharmaceutical Institute, University of Bonn, Bonn, Germany
| | - Pedro Matos-Filipe
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1ºandar, Universidade de Coimbra, Coimbra 3004-517, Portugal
| | - Carlos Barreto
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1ºandar, Universidade de Coimbra, Coimbra 3004-517, Portugal
| | - José G Almeida
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1ºandar, Universidade de Coimbra, Coimbra 3004-517, Portugal
| | - Rúben D M Silva
- Centro de Ciencias e Tecnologias Nucleares, Instituto Superior Tecnico, Universidade de Lisboa, CTN, Estrada Nacional 10 (km 139,7), Bobadela LRS 2695-066, Portugal
| | - João D G Correia
- Centro de Ciencias e Tecnologias Nucleares, Instituto Superior Tecnico, Universidade de Lisboa, CTN, Estrada Nacional 10 (km 139,7), Bobadela LRS 2695-066, Portugal
| | - Irina S Moreira
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1ºandar, Universidade de Coimbra, Coimbra 3004-517, Portugal.,Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht 3584CH, Netherland
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7
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Zhu M, Ma L, Wen J, Dong B, Wang Y, Wang Z, Zhou J, Zhang G, Wang J, Guo Y, Liang C, Cen S, Wang Y. Rational design and Structure-Activity relationship of coumarin derivatives effective on HIV-1 protease and partially on HIV-1 reverse transcriptase. Eur J Med Chem 2019; 186:111900. [PMID: 31771827 DOI: 10.1016/j.ejmech.2019.111900] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 11/18/2019] [Accepted: 11/18/2019] [Indexed: 01/19/2023]
Abstract
Since dual inhibitors may yield lower toxicity and reduce the likelihood of drug resistance, as well as inhibitors of HIV-1 PR and RT constitute the core of chemotherapy for AIDS treatment, we herein designed and synthesized new coumarin derivatives characterized by various linkers that exhibited excellent potency against PR and a weak inhibition of RT. Among which, compounds 6f and 7c inhibited PR with IC50 values of 15.5 and 62.1 nM, respectively, and weakly affected also RT with IC50 values of 241.8 and 188.7 μM, respectively, showing the possibility in the future of developing dual HIV-1 PR/RT inhibitors. Creative stimulation for further research of more potent dual HIV-1 inhibitors was got according to the molecular docking studies.
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Affiliation(s)
- Mei Zhu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Ling Ma
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Jiajia Wen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Biao Dong
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Yujia Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Zhen Wang
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec, Canada
| | - Jinming Zhou
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Guoning Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Juxian Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Ying Guo
- Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Chen Liang
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec, Canada
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China.
| | - Yucheng Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China.
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8
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Wang Y, Wang X, Xiong Y, Kaushik AC, Muhammad J, Khan A, Dai H, Wei DQ. New strategy for identifying potential natural HIV-1 non-nucleoside reverse transcriptase inhibitors against drug-resistance: an in silico study. J Biomol Struct Dyn 2019; 38:3327-3341. [PMID: 31422767 DOI: 10.1080/07391102.2019.1656673] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Non-nucleosides reverse transcriptase inhibitors (NNRTIs), specifically targeting the HIV-1 reverse transcriptase (RT), play a unique role in anti-AIDS agents due to their high antiviral potency, structural diversity, and low toxicity in antiretroviral combination therapies used to treat HIV. However, due to the emergence of new drug-resistant strains, the development of novel NNRTIs with adequate potency, improved resistance profiles and less toxicity is highly required. In this work, a novel virtual screening strategy combined with structure-based drug design was proposed to discover the potential inhibitors against drug-resistant HIV strains. Seven structure-variant RTs, ranging from the wild type to a hypothetical multi-mutant were regarded as target proteins to perform structure-based virtual screening. Totally 23 small molecules with good binding affinity were identified from the Traditional Chinese Medicine database (TCM) as potential NNRTIs candidates. Among these hits, (+)-Hinokinin has confirmed anti-HIV activity, and some hits are structurally identical with anti-HIV compounds. Almost all these hits are consistent with external experimental results. Molecular simulations analysis revealed that top 2 hits (Pallidisetin A and Pallidisetin B) bind stably and in high affinity to HIV-RT, which are ready to be experimental confirmed. These results suggested that the strategy we proposed is feasible, trustworthy and effective. Our finding might be helpful in the identification of novel NNRTIs against drug-resistant, and also provide a new clue for the discovery of HIV drugs in natural products.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yanjing Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China.,Peng Cheng Laboratory, Nanshan District, Shenzhen, Guangdong, China
| | - Xiangeng Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China.,Peng Cheng Laboratory, Nanshan District, Shenzhen, Guangdong, China
| | - Yi Xiong
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Aman Chandra Kaushik
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Junaid Muhammad
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Abbas Khan
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Hao Dai
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
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9
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Torsional flexibility of undecorated catechol diether compound as potent NNRTI targeting HIV-1 reverse transcriptase. J Mol Graph Model 2018; 86:286-297. [PMID: 30445408 DOI: 10.1016/j.jmgm.2018.10.026] [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: 05/16/2018] [Revised: 10/28/2018] [Accepted: 10/29/2018] [Indexed: 11/22/2022]
Abstract
Conformational adaptation of non-nucleoside reverse transcriptase inhibitor (NNRTI) via torsional flexibility is found to be very significant for targeting human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) mutants. Catechol diether derivative including flexible torsions is new potent NNRTI with picomolar activity. Moreover, this derivative also reveals the good solubility, low toxicity and potent inhibition for HIV-1 mutants. In this study, torsional flexibility of an undecorated catechol diether compound in the binding pocket of wild type and mutants (Y181C and K103N/Y181C) HIV-1 RT is investigated by using QM/MM calculations. From the results, the uracil ring is found to exhibit more flexibility in the NNIBP. On the contrary, potential energy surfaces show that high energy is encountered by changing of the corresponding torsion of the cyanovinyl aryl ring indicating the limitation for torsional flexibility. For pointing out the key interaction for the binding, the residual interaction energies are performed by means of QM calculations. Important attractive interactions through hydrogen bonds between the inhibitor and K102, K/N103, V106, and Y188 are observed. The catechol ring is proposed to be modified in order to strengthen interactions with surrounding amino acids. The results may help for the designing of new potent NNRTIs.
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10
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Yang Y, Kang D, Nguyen LA, Smithline ZB, Pannecouque C, Zhan P, Liu X, Steitz TA. Structural basis for potent and broad inhibition of HIV-1 RT by thiophene[3,2- d]pyrimidine non-nucleoside inhibitors. eLife 2018; 7:e36340. [PMID: 30044217 PMCID: PMC6080946 DOI: 10.7554/elife.36340] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 07/18/2018] [Indexed: 12/18/2022] Open
Abstract
Rapid generation of drug-resistant mutations in HIV-1 reverse transcriptase (RT), a prime target for anti-HIV therapy, poses a major impediment to effective anti-HIV treatment. Our previous efforts have led to the development of two novel non-nucleoside reverse transcriptase inhibitors (NNRTIs) with piperidine-substituted thiophene[3,2-d]pyrimidine scaffolds, compounds K-5a2 and 25a, which demonstrate highly potent anti-HIV-1 activities and improved resistance profiles compared with etravirine and rilpivirine, respectively. Here, we have determined the crystal structures of HIV-1 wild-type (WT) RT and seven RT variants bearing prevalent drug-resistant mutations in complex with K-5a2 or 25a at ~2 Å resolution. These high-resolution structures illustrate the molecular details of the extensive hydrophobic interactions and the network of main chain hydrogen bonds formed between the NNRTIs and the RT inhibitor-binding pocket, and provide valuable insights into the favorable structural features that can be employed for designing NNRTIs that are broadly active against drug-resistant HIV-1 variants.
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Affiliation(s)
- Yang Yang
- Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenUnited States
- Howard Hughes Medical InstituteYale UniversityNew HavenUnited States
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical SciencesShandong UniversityJinanChina
| | - Laura A Nguyen
- Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenUnited States
| | - Zachary B Smithline
- Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenUnited States
| | | | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical SciencesShandong UniversityJinanChina
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical SciencesShandong UniversityJinanChina
| | - Thomas A Steitz
- Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenUnited States
- Howard Hughes Medical InstituteYale UniversityNew HavenUnited States
- Department of ChemistryYale UniversityNew HavenUnited States
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11
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Valuev-Elliston VT, Kochetkov SN. Novel HIV-1 Non-nucleoside Reverse Transcriptase Inhibitors: A Combinatorial Approach. BIOCHEMISTRY (MOSCOW) 2018. [PMID: 29523068 DOI: 10.1134/s0006297917130107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Highly active antiretroviral therapy (HAART) is one of the most effective means for fighting against HIV-infection. HAART primarily targets HIV-1 reverse transcriptase (RT), and 14 of 28 compounds approved by the FDA as anti-HIV drugs act on this enzyme. HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs) hold a special place among HIV RT inhibitors owing to their high specificity and unique mode of action. Nonetheless, these drugs show a tendency to decrease their efficacy due to high HIV-1 variability and formation of resistant virus strains tolerant to clinically applied HIV NNRTIs. A combinatorial approach based on varying substituents within various fragments of the parent molecule that results in development of highly potent compounds is one of the approaches aimed at designing novel HIV NNRTIs. Generation of HIV NNRTIs based on pyrimidine derivatives explicitly exemplifies this approach, which is discussed in this review.
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Affiliation(s)
- V T Valuev-Elliston
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.
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12
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Santos LH, Ferreira RS, Caffarena ER. Computational drug design strategies applied to the modelling of human immunodeficiency virus-1 reverse transcriptase inhibitors. Mem Inst Oswaldo Cruz 2016; 110:847-64. [PMID: 26560977 PMCID: PMC4660614 DOI: 10.1590/0074-02760150239] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 09/08/2015] [Indexed: 01/05/2023] Open
Abstract
Reverse transcriptase (RT) is a multifunctional enzyme in the human immunodeficiency
virus (HIV)-1 life cycle and represents a primary target for drug discovery efforts
against HIV-1 infection. Two classes of RT inhibitors, the nucleoside RT inhibitors
(NRTIs) and the nonnucleoside transcriptase inhibitors are prominently used in the
highly active antiretroviral therapy in combination with other anti-HIV drugs.
However, the rapid emergence of drug-resistant viral strains has limited the
successful rate of the anti-HIV agents. Computational methods are a significant part
of the drug design process and indispensable to study drug resistance. In this
review, recent advances in computer-aided drug design for the rational design of new
compounds against HIV-1 RT using methods such as molecular docking, molecular
dynamics, free energy calculations, quantitative structure-activity relationships,
pharmacophore modelling and absorption, distribution, metabolism, excretion and
toxicity prediction are discussed. Successful applications of these methodologies are
also highlighted.
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Affiliation(s)
| | - Rafaela Salgado Ferreira
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
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13
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Zhang Z, Hamatake R, Hong Z. Clinical Utility of Current NNRTIs and Perspectives of New Agents in This Class under Development. ACTA ACUST UNITED AC 2016; 15:121-34. [PMID: 15266894 DOI: 10.1177/095632020401500302] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Highly active antiretroviral therapy (HAART) has significantly reduced the number of deaths caused by AIDS. However, the antiviral efficacy of HAART comprising protease inhibitors (PIs) and nucleoside reverse transcriptase inhibitors (NRTIs) is frequently accompanied by a decrease in patients' quality of life. PI-based therapies often fail due to poor adherence caused by heavy pill burden, complex dosing schedules and undesirable side effects. The current trend is to switch from PI-based to PI-sparing regimens consisting of non-nucleoside reverse transcriptase inhibitors (NNRTIs) and NRTIs. Despite some encouraging results from NNRTI-containing therapies, two major concerns in using the currently available NNRTIs remain: 1) low genetic barrier to the emergence of resistance and 2) cross-resistance due to single mutations that often render the whole class of NNRTIs ineffective. Clearly, new and improved NNRTIs are needed to address these concerns.
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Affiliation(s)
- Zhijun Zhang
- Drug Discovery, Valeant Pharmaceuticals International, Costa Mesa, Calif., USA.
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14
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Abstract
The enzyme reverse transcriptase (RT) was discovered in retroviruses almost 50 years ago. The demonstration that other types of viruses, and what are now called retrotransposons, also replicated using an enzyme that could copy RNA into DNA came a few years later. The intensity of the research in both the process of reverse transcription and the enzyme RT was greatly stimulated by the recognition, in the mid-1980s, that human immunodeficiency virus (HIV) was a retrovirus and by the fact that the first successful anti-HIV drug, azidothymidine (AZT), is a substrate for RT. Although AZT monotherapy is a thing of the past, the most commonly prescribed, and most successful, combination therapies still involve one or both of the two major classes of anti-RT drugs. Although the basic mechanics of reverse transcription were worked out many years ago, and the first high-resolution structures of HIV RT are now more than 20 years old, we still have much to learn, particularly about the roles played by the host and viral factors that make the process of reverse transcription much more efficient in the cell than in the test tube. Moreover, we are only now beginning to understand how various host factors that are part of the innate immunity system interact with the process of reverse transcription to protect the host-cell genome, the host cell, and the whole host, from retroviral infection, and from unwanted retrotransposition.
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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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Bruccoleri A. Positional adaptability in the design of mutation-resistant nonnucleoside HIV-1 reverse transcriptase inhibitors: a supramolecular perspective. AIDS Res Hum Retroviruses 2013; 29:4-12. [PMID: 22938539 DOI: 10.1089/aid.2012.0141] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Drug resistance is a key cause of failed treatment of HIV infection. The efficacy of nonnucleoside reverse transcriptase-inhibiting (NNRTI) drugs is impaired by the rapid emergence of drug-resistant mutations. The literature supports the idea that purposefully designed flexible NNRTIs at an active site may help overcome drug resistance. It is proposed here that the usual "lock and key" model, with respect to NNRTI drug design, be expanded to consider creating "master keys" that would automatically adjust conformations to fit all of the "locks" mutations may make. The present work introduces the novel perspective of designing and creating supramolecular assemblies as potential NNRTIs (instead of the relatively more rigid single-molecule inhibitors). Specifically, flexible self-assembling quinhydrone supramolecular dimers formed from quinonoid monomers (designed to be highly flexible NNRTIs themselves) will be offered as a working example of this new perspective in NNRTI drug design. Quinonoid compounds have demonstrated binding interactions at various sites of the HIV-1 RT enzyme, including the elusive ribonuclease H area. Quinhydrone self-organized dimers have at some point in their molecular architecture a noncovalently interacting donor-acceptor ring pair complex. This complex is at the heart of the increased torsional, rotational, and translational motion this species will experience at a particular active site. Flexible supramolecular assemblies, together with their flexible monomer components, may offer a critical advantage in retaining potency against a wide range of drug-resistant HIV-1 RTs. This new supramolecular perspective may also have broader implications in the general field of antimicrobial drug design.
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Affiliation(s)
- Aldo Bruccoleri
- Faculty of Science (Chemistry), Canadian University College, Lacombe, Alberta, Canada
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Chong P, Sebahar P, Youngman M, Garrido D, Zhang H, Stewart EL, Nolte RT, Wang L, Ferris RG, Edelstein M, Weaver K, Mathis A, Peat A. Rational Design of Potent Non-Nucleoside Inhibitors of HIV-1 Reverse Transcriptase. J Med Chem 2012; 55:10601-9. [DOI: 10.1021/jm301294g] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pek Chong
- GlaxoSmithKline Research & Development, 5 Moore Drive, Research Triangle Park, North Carolina 27709, United States
| | - Paul Sebahar
- GlaxoSmithKline Research & Development, 5 Moore Drive, Research Triangle Park, North Carolina 27709, United States
| | - Michael Youngman
- GlaxoSmithKline Research & Development, 5 Moore Drive, Research Triangle Park, North Carolina 27709, United States
| | - Dulce Garrido
- GlaxoSmithKline Research & Development, 5 Moore Drive, Research Triangle Park, North Carolina 27709, United States
| | - Huichang Zhang
- GlaxoSmithKline Research & Development, 5 Moore Drive, Research Triangle Park, North Carolina 27709, United States
| | - Eugene L. Stewart
- GlaxoSmithKline Research & Development, 5 Moore Drive, Research Triangle Park, North Carolina 27709, United States
| | - Robert T. Nolte
- GlaxoSmithKline Research & Development, 5 Moore Drive, Research Triangle Park, North Carolina 27709, United States
| | - Liping Wang
- GlaxoSmithKline Research & Development, 5 Moore Drive, Research Triangle Park, North Carolina 27709, United States
| | - Robert G. Ferris
- GlaxoSmithKline Research & Development, 5 Moore Drive, Research Triangle Park, North Carolina 27709, United States
| | - Mark Edelstein
- GlaxoSmithKline Research & Development, 5 Moore Drive, Research Triangle Park, North Carolina 27709, United States
| | - Kurt Weaver
- GlaxoSmithKline Research & Development, 5 Moore Drive, Research Triangle Park, North Carolina 27709, United States
| | - Amanda Mathis
- GlaxoSmithKline Research & Development, 5 Moore Drive, Research Triangle Park, North Carolina 27709, United States
| | - Andrew Peat
- GlaxoSmithKline Research & Development, 5 Moore Drive, Research Triangle Park, North Carolina 27709, United States
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de Brito MA, Rodrigues CR, Cirino JJV, Araújo JQ, Honório T, Cabral LM, de Alencastro RB, Castro HC, Albuquerque MG. Residue-ligand interaction energy (ReLIE) on a receptor-dependent 3D-QSAR analysis of S- and NH-DABOs as non-nucleoside reverse transcriptase inhibitors. Molecules 2012; 17:7666-94. [PMID: 22732882 PMCID: PMC6269006 DOI: 10.3390/molecules17077666] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 06/02/2012] [Accepted: 06/05/2012] [Indexed: 11/16/2022] Open
Abstract
A series of 74 dihydroalkoxybenzyloxopyrimidines (DABOs), a class of highly potent non-nucleoside reverse transcriptase inhibitors (NNRTIs), was retrieved from the literature and studied by receptor-dependent (RD) three-dimensional quantitative structure-activity relationship (3D-QSAR) analysis to derive RD-3D-QSAR models. The descriptors in this new method are the steric and electrostatic interaction energies of the protein-ligand complexes (per residue) simulated by molecular dynamics, an approach named Residue-Ligand Interaction Energy (ReLIE). This study was performed using a training set of 59 compounds and the MKC-442/RT complex structure as reference. The ReLIE-3D-QSAR models were constructed and evaluated by genetic algorithm (GA) and partial least squares (PLS). In the best equations, at least one term is related to one of the amino acid residues of the p51 subunit: Asn136, Asn137, Glu138, and Thr139. This fact implies the importance of interchain interaction (p66-p51) in the equations that best describe the structure-activity relationship for this class of compounds. The best equation shows q² = 0.660, SE(cv) = 0.500, r² = 0.930, and SEE = 0.226. The external predictive ability of this best model was evaluated using a test set of 15 compounds. In order to design more potent DABO analogues as anti-HIV/AIDS agents, substituents capable of interactions with residues like Ile94, Lys101, Tyr181, and Tyr188 should be selected. Also, given the importance of the conserved Asn136, this residue could become an attractive target for the design of novel NNRTIs with improved potency and increased ability to avoid the development of drug-resistant viruses.
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Affiliation(s)
- Monique Araújo de Brito
- Laboratory of Computational Medicinal Chemistry (LabQMC), Faculty of Pharmacy, Fluminense Federal University (UFF), Niterói, RJ, 24241-000, Brazil
- Laboratory of Molecular Modeling (LabMMol), Program of Post-Graduation in Chemistry (PPGQu), Institute of Chemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-909, Brazil
- Authors to whom correspondence should be addressed; (M.A.B.); (M.G.A.); Tel.: +55-21-2629-9599 (M.A.B.); +55-21-2562-7132 (M.G.A.)
| | - Carlos Rangel Rodrigues
- Laboratory of Molecular Modeling & QSAR (ModMolQSAR), Faculty of Pharmacy, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-590, Brazil
| | - José Jair Viana Cirino
- Laboratory of Molecular Modeling (LabMMol), Program of Post-Graduation in Chemistry (PPGQu), Institute of Chemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-909, Brazil
| | - Jocley Queiroz Araújo
- Laboratory of Molecular Modeling (LabMMol), Program of Post-Graduation in Chemistry (PPGQu), Institute of Chemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-909, Brazil
| | - Thiago Honório
- Laboratory of Molecular Modeling & QSAR (ModMolQSAR), Faculty of Pharmacy, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-590, Brazil
| | - Lúcio Mendes Cabral
- Laboratory of Molecular Modeling & QSAR (ModMolQSAR), Faculty of Pharmacy, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-590, Brazil
| | - Ricardo Bicca de Alencastro
- Laboratory of Molecular Modeling (LabMMol), Program of Post-Graduation in Chemistry (PPGQu), Institute of Chemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-909, Brazil
| | - Helena Carla Castro
- Laboratory of Antibiotics, Biochemistry, Education and Molecular Modeling (LABiEMol), Institute of Biology, Fluminense Federal University (UFF), Niterói, RJ, 24210-130, Brazil
| | - Magaly Girão Albuquerque
- Laboratory of Molecular Modeling (LabMMol), Program of Post-Graduation in Chemistry (PPGQu), Institute of Chemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-909, Brazil
- Authors to whom correspondence should be addressed; (M.A.B.); (M.G.A.); Tel.: +55-21-2629-9599 (M.A.B.); +55-21-2562-7132 (M.G.A.)
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Pitta E, Geronikaki A, Surmava S, Eleftheriou P, Mehta VP, Van der Eycken EV. Synthesis and HIV-1 RT inhibitory action of novel (4/6-substituted benzo[d]thiazol -2-yl)thiazolidin-4-ones. Divergence from the non-competitive inhibition mechanism. J Enzyme Inhib Med Chem 2012; 28:113-22. [PMID: 22380777 DOI: 10.3109/14756366.2011.636362] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Reverse transcriptase (RT) inhibitors play a major role in the therapy of human immunodeficiency virus type 1 (HIV-1) infection. Although, many compounds are already used as anti-HIV drugs, research on development of novel inhibitors continues, since drug resistant strains appear because of prolonged therapy. In this paper, we present the synthesis and evaluation of HIV-1 RT inhibitory action of eighteen novel (4/6-halogen/MeO/EtO-substituted benzo[d]thiazol-2-yl)thiazolidin-4-ones. The two more active compounds (IC50 : 0.04 µM and 0.25 µM) exhibited better inhibitory action than the reference compound, nevirapine. Docking analysis supports a stable binding of the most active derivative to the allosteric centre of RT. Kinetic analysis of two of the most active compounds indicate an uncompetitive inhibition mode. This is a desired characteristic, since mutations that affect activity of traditional non-competitive NNRTIs may not affect activity of compounds of this series. Interestingly, the less active derivatives (IC50 > 40 µM) exhibit a competitive mode of action.
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Affiliation(s)
- Eleni Pitta
- Department of Medicinal Chemistry, School of Pharmacy, Aristotle University of Thessaloniki, Greece
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20
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Chung S, Miller JT, Johnson BC, Hughes SH, Le Grice SFJ. Mutagenesis of human immunodeficiency virus reverse transcriptase p51 subunit defines residues contributing to vinylogous urea inhibition of ribonuclease H activity. J Biol Chem 2011; 287:4066-75. [PMID: 22105069 DOI: 10.1074/jbc.m111.314781] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The vinylogous urea, NSC727447, was proposed to allosterically inhibit ribonuclease H (RNase H) activity of human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) by interacting with the thumb subdomain of its non-catalytic p51 subunit. Proximity of the p51 thumb to the p66 RNase H domain implied that inhibitor binding altered active site geometry, whereas protein footprinting suggested a contribution from α-helix I residues Cys-280 and Lys-281. To more thoroughly characterize the vinylogous urea binding site, horizontal alanine scanning mutagenesis between p51 residues Lys-275 and Thr-286 (comprising α-helix I and portions of the neighboring αH/αI and αI/αJ connecting loops) was combined with a limited vertical scan of Cys-280. A contribution from Cys-280 was strengthened by our observation that all substitutions at this position rendered selectively mutated, reconstituted p66/p51 heterodimers ∼45-fold less sensitive to inhibition. An ∼19-fold reduced IC(50) for p51 mutant T286A coupled with a 2-8-fold increased IC(50) when intervening residues were substituted supports our original proposal of p51 α-helix I as the vinylogous urea binding site. In contrast to these allosteric inhibitors, mutant enzymes retained equivalent sensitivity to the natural product α-hydroxytropolone inhibitor manicol, which x-ray crystallography has demonstrated functions by chelating divalent metal at the p66 RNase H active site. Finally, reduced DNA strand-transfer activity together with increased vinylogous urea sensitivity of p66/p51 heterodimers containing short p51 C-terminal deletions suggests an additional role for the p51 C terminus in nucleic acid binding that is compromised by inhibitor binding.
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Affiliation(s)
- Suhman Chung
- HIV Drug Resistance Program, National Cancer Institute-Frederick, National Institutes of Health, Frederick, Maryland 21702, USA
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Zhang H, Qin F, Ye W, Li Z, Ma S, Xia Y, Jiang Y, Zhu J, Li Y, Zhang J, Chen HF. Revealing the Drug-Resistant Mechanism for Diarylpyrimidine Analogue Inhibitors of HIV-1 Reverse Transcriptase. Chem Biol Drug Des 2011; 78:427-37. [DOI: 10.1111/j.1747-0285.2011.01163.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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3D-QSAR and docking-based combined in silico study on C-5 methyl substituted 4-arylthio and 4-aryloxy-3-iodopyridin-2-(1H)-one as HIV-1 RT inhibitors. Med Chem Res 2011. [DOI: 10.1007/s00044-011-9720-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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23
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Zhan P, Chen X, Li D, Fang Z, De Clercq E, Liu X. HIV-1 NNRTIs: structural diversity, pharmacophore similarity, and implications for drug design. Med Res Rev 2011; 33 Suppl 1:E1-72. [PMID: 21523792 DOI: 10.1002/med.20241] [Citation(s) in RCA: 152] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nonnucleoside reverse transcriptase inhibitors (NNRTIs) nowadays represent very potent and most promising anti-AIDS agents that specifically target the HIV-1 reverse transcriptase (RT). However, the effectiveness of NNRTI drugs can be hampered by rapid emergence of drug-resistant viruses and severe side effects upon long-term use. Therefore, there is an urgent need to develop novel, highly potent NNRTIs with broad spectrum antiviral activity and improved pharmacokinetic properties, and more efficient strategies that facilitate and shorten the drug discovery process would be extremely beneficial. Fortunately, the structural diversity of NNRTIs provided a wide space for novel lead discovery, and the pharmacophore similarity of NNRTIs gave valuable hints for lead discovery and optimization. More importantly, with the continued efforts in the development of computational tools and increased crystallographic information on RT/NNRTI complexes, structure-based approaches using a combination of traditional medicinal chemistry, structural biology, and computational chemistry are being used increasingly in the design of NNRTIs. First, this review covers two decades of research and development for various NNRTI families based on their chemical scaffolds, and then describes the structural similarity of NNRTIs. We have attempted to assemble a comprehensive overview of the general approaches in NNRTI lead discovery and optimization reported in the literature during the last decade. The successful applications of medicinal chemistry strategies, crystallography, and computational tools for designing novel NNRTIs are highlighted. Future directions for research are also outlined.
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Affiliation(s)
- Peng Zhan
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong, PR China
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24
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Nikolenko GN, Kotelkin AT, Oreshkova SF, Ilyichev AA. Mechanisms of HIV-1 drug resistance to nucleoside and nonnucleoside reverse transcriptase inhibitors. Mol Biol 2011. [DOI: 10.1134/s0026893311010092] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Dupree TB, Keller PA, Griffith R. Investigation into the Extension of the Non-Nucleoside Reverse Transcriptase Binding Pocket. Aust J Chem 2011. [DOI: 10.1071/ch11054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Superimposition of 125 non-nucleoside inhibitors from human immunodeficiency virus reverse transcriptase structures reveals a novel binding space deeper into the enzyme for some of these inhibitors, allowing access to the polymerase active site. This may enable us to design new inhibitors of this enzyme with better mutation resistance profiles. We have analysed this new binding space and have docked our in-house scaffolds into this region, highlighting the possibility of the formation of new hydrogen bonds with residues of the active site.
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Li Z, Zhang H, Li Y, Zhang J, Chen HF. Drug resistant mechanism of diaryltriazine analog inhibitors of HIV-1 reverse transcriptase using molecular dynamics simulation and 3D-QSAR. Chem Biol Drug Des 2010; 77:63-74. [PMID: 21134218 DOI: 10.1111/j.1747-0285.2010.01049.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Diaryltriazine inhibitors have highly potent and effective bioactivities for the wild type of HIV-1 reverse transcription. To design new drug of antimutant HIV-1 reverse transcriptase, the mechanism of drug resistance for four types of mutants was revealed. Molecular dynamics simulations suggest that Lys101, Leu100, Lys103, Tyr181, and Tyr188 are key residues. Different mutants of key residues may have different interaction modes and lead to different drug resistances. Then, CoMFA and CoMSIA methods were employed to construct 3D quantitative structure-activity relationship models. These models were evaluated by test set compounds. These models can be used to make quantitative prediction of their bioactivities for lead compounds before resorting to in vitro and in vivo experimentation.
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Affiliation(s)
- Zeng Li
- College of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, China
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La Regina G, Coluccia A, Silvestri R. Looking for an active conformation of the future HIV type-1 non-nucleoside reverse transcriptase inhibitors. Antivir Chem Chemother 2010; 20:213-37. [PMID: 20710063 DOI: 10.3851/imp1607] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
HIV type-1 (HIV-1) non-nucleoside reverse transcriptase inhibitors (NNRTIs) are key drugs of highly active antiretroviral therapy (HAART) in the clinical management of AIDS/HIV infection. NNRTI-based HAART regimes effectively suppress viral reproduction, are not cytotoxic and show favourable pharmacokinetic properties. First-generation NNRTIs suffer the rapid selection of viral variants, hampering the binding of inhibitors into the reverse transcriptase (RT) non-nucleoside binding site (NNBS). Efforts to improve these first inhibitors led to the discovery of second-generation NNRTIs that proved to be effective against the drug-resistant mutant HIV-1 strains. The success of such agents launched a new season of NNRTI design and synthesis. This paper reviews the characteristics of second-generation NNRTIs, including etravirine, rilpivirine, RDEA-806, UK-453061, BIRL 355 BS, IDX 899, MK-4965 and HBY 097. In particular, the binding modes of these inhibitors into the NNBS of the HIV-1 RT and the most clinically relevant mutant RTs are analysed and discussed.
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Affiliation(s)
- Giuseppe La Regina
- Department of Chimica e Tecnologie del Farmaco, Istituto Pasteur - Fondazione Cenci Bolognetti, Sapienza University, Rome, Italy
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Delviks-Frankenberry KA, Nikolenko GN, Pathak VK. The "Connection" Between HIV Drug Resistance and RNase H. Viruses 2010; 2:1476-1503. [PMID: 21088701 PMCID: PMC2982141 DOI: 10.3390/v2071476] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Revised: 07/20/2010] [Accepted: 07/20/2010] [Indexed: 11/17/2022] Open
Abstract
Currently, nucleoside reverse transcriptase inhibitors (NRTIs) and nonnucleoside reverse transcriptase inhibitors (NNRTIs) are two classes of antiretroviral agents that are approved for treatment of HIV-1 infection. Since both NRTIs and NNRTIs target the polymerase (pol) domain of reverse transcriptase (RT), most genotypic analysis for drug resistance is limited to the first ~300 amino acids of RT. However, recent studies have demonstrated that mutations in the C-terminal domain of RT, specifically the connection subdomain and RNase H domain, can also increase resistance to both NRTIs and NNRTIs. In this review we will present the potential mechanisms by which mutations in the C-terminal domain of RT influence NRTI and NNRTI susceptibility, summarize the prevalence of the mutations in these regions of RT identified to date, and discuss their importance to clinical drug resistance.
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Affiliation(s)
- Krista A. Delviks-Frankenberry
- Viral Mutation Section, HIV Drug Resistance Program, National Cancer Institute at Frederick, Frederick, Maryland 21702, USA; E-Mails: (K.A.D.-F.); (G.N.N.)
| | | | - Vinay K. Pathak
- Viral Mutation Section, HIV Drug Resistance Program, National Cancer Institute at Frederick, Frederick, Maryland 21702, USA; E-Mails: (K.A.D.-F.); (G.N.N.)
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Samuele A, Crespan E, Vitellaro S, Monforte AM, Logoteta P, Chimirri A, Maga G. Slow binding–tight binding interaction between benzimidazol-2-one inhibitors and HIV-1 reverse transcriptase containing the lysine 103 to asparagine mutation. Antiviral Res 2010; 86:268-75. [DOI: 10.1016/j.antiviral.2010.03.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Revised: 03/09/2010] [Accepted: 03/12/2010] [Indexed: 10/19/2022]
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Abstract
HIV-1 Reverse Transcriptase (HIV-1 RT) has been the target of numerous approved anti-AIDS drugs that are key components of Highly Active Anti-Retroviral Therapies (HAART). It remains the target of extensive structural studies that continue unabated for almost twenty years. The crystal structures of wild-type or drug-resistant mutant HIV RTs in the unliganded form or in complex with substrates and/or drugs have offered valuable glimpses into the enzyme’s folding and its interactions with DNA and dNTP substrates, as well as with nucleos(t)ide reverse transcriptase inhibitor (NRTI) and non-nucleoside reverse transcriptase inhibitor (NNRTIs) drugs. These studies have been used to interpret a large body of biochemical results and have paved the way for innovative biochemical experiments designed to elucidate the mechanisms of catalysis and drug inhibition of polymerase and RNase H functions of RT. In turn, the combined use of structural biology and biochemical approaches has led to the discovery of novel mechanisms of drug resistance and has contributed to the design of new drugs with improved potency and ability to suppress multi-drug resistant strains.
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Prajapati DG, Ramajayam R, Yadav MR, Giridhar R. The search for potent, small molecule NNRTIs: A review. Bioorg Med Chem 2009; 17:5744-62. [PMID: 19632850 DOI: 10.1016/j.bmc.2009.06.060] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Revised: 06/22/2009] [Accepted: 06/23/2009] [Indexed: 11/29/2022]
Abstract
AIDS has become the leading pandemic disease, and is the cause of death worldwide. Presently, HAART treatment, a combination of reverse transcriptase (RT) and protease inhibitors is also unsuccessful due to the virus getting resistant to the drugs because of mutational changes. Two types of RT inhibitors exist namely nucleoside reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs). The NNRTIs which bind to an allosteric site on RT are an important arsenal of drugs against HIV-1. The specificity of NNRTIs towards HIV-1 has led to extensive structural and molecular modelling studies of enzyme complexes and chemical synthesis of second and third-generation NNRTIs. The major drawbacks of NNRTIs are generation of resistance and pharmacokinetic problems. By mutational studies of non-nucleoside inhibitor binding pocket (NNIBP) some amino acids which were found to play an important role in proper binding resulted less prone to mutation. In this review we present a chronological history of NNRTI development, also highlighting the need for small molecules belonging to the NNRTI class for the management of AIDS.
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Affiliation(s)
- Dhaval G Prajapati
- Pharmacy Department, Kalabhavan, The M.S. University of Baroda, Vadodara, India
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32
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Crystal structures of HIV-1 nonnucleoside reverse transcriptase inhibitors: N-benzyl-4-methyl-benzimidazoles. J Mol Struct 2009. [DOI: 10.1016/j.molstruc.2009.05.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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33
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Ivetac A, McCammon JA. Elucidating the inhibition mechanism of HIV-1 non-nucleoside reverse transcriptase inhibitors through multicopy molecular dynamics simulations. J Mol Biol 2009; 388:644-58. [PMID: 19324058 DOI: 10.1016/j.jmb.2009.03.037] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Revised: 03/13/2009] [Accepted: 03/16/2009] [Indexed: 10/21/2022]
Abstract
Human immunodeficiency virus-1 reverse transcriptase (RT) inhibition is a major focus of current anti-AIDS drug discovery and development programs, comprising 17 of the 31 Food and Drug Administration-approved compounds. The emergence of the non-nucleoside RT inhibitor (NNRTI) class of compounds provides a highly specific and structurally diverse set of drugs, which act noncompetitively to perturb normal RT function. Despite a relatively rich set of crystallographic data of RT in various states, details of the allosteric modulation of RT dynamics by NNRTIs are lacking. Capturing this inhibitory mechanism could fuel the design of more effective inhibitors at the NNRTI site and also drive the identification of novel allosteric sites. To address this, we have performed multicopy molecular dynamics (MD) simulations of RT in the presence and absence of the NNRTI nevirapine (cumulative total simulation time, 360 ns). By comparing the collective motions of the MD and crystallographic structures, we demonstrate that the chief effect of NNRTIs is to constrain a key rigid-body motion between the "fingers" and "thumb" subdomains of the p66 subunit. We show that the NNRTI binding pocket (NNIBP) is proximal to the hinge points for this essential motion, and NNRTIs therefore act as "molecular wedges," sterically blocking the full range of motion. To explain how this impaired movement might result in the experimentally observed loss of polymerase activity, we show that the motion influences the geometry of key catalytic residues on opposite faces of the NNIBP. From a methodological point of view, our results suggest that the multicopy MD simulation approach is very useful when studying proteins that perform such large conformational changes.
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Affiliation(s)
- Anthony Ivetac
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA 92093-0365, USA.
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34
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Radi M, Maga G, Alongi M, Angeli L, Samuele A, Zanoli S, Bellucci L, Tafi A, Casaluce G, Giorgi G, Armand-Ugon M, Gonzalez E, Esté JA, Baltzinger M, Bec G, Dumas P, Ennifar E, Botta M. Discovery of Chiral Cyclopropyl Dihydro-Alkylthio-Benzyl-Oxopyrimidine (S-DABO) Derivatives as Potent HIV-1 Reverse Transcriptase Inhibitors with High Activity Against Clinically Relevant Mutants. J Med Chem 2009; 52:840-51. [DOI: 10.1021/jm801330n] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marco Radi
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy, Dipartimento di Chimica, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy, Retrovirology Laboratory irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, E-08916 Badalona, Spain, Architecture et Réactivité de l’ARN, UPR 9002 CNRS/Université Louis Pasteur, 15
| | - Giovanni Maga
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy, Dipartimento di Chimica, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy, Retrovirology Laboratory irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, E-08916 Badalona, Spain, Architecture et Réactivité de l’ARN, UPR 9002 CNRS/Université Louis Pasteur, 15
| | - Maddalena Alongi
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy, Dipartimento di Chimica, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy, Retrovirology Laboratory irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, E-08916 Badalona, Spain, Architecture et Réactivité de l’ARN, UPR 9002 CNRS/Université Louis Pasteur, 15
| | - Lucilla Angeli
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy, Dipartimento di Chimica, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy, Retrovirology Laboratory irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, E-08916 Badalona, Spain, Architecture et Réactivité de l’ARN, UPR 9002 CNRS/Université Louis Pasteur, 15
| | - Alberta Samuele
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy, Dipartimento di Chimica, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy, Retrovirology Laboratory irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, E-08916 Badalona, Spain, Architecture et Réactivité de l’ARN, UPR 9002 CNRS/Université Louis Pasteur, 15
| | - Samantha Zanoli
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy, Dipartimento di Chimica, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy, Retrovirology Laboratory irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, E-08916 Badalona, Spain, Architecture et Réactivité de l’ARN, UPR 9002 CNRS/Université Louis Pasteur, 15
| | - Luca Bellucci
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy, Dipartimento di Chimica, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy, Retrovirology Laboratory irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, E-08916 Badalona, Spain, Architecture et Réactivité de l’ARN, UPR 9002 CNRS/Université Louis Pasteur, 15
| | - Andrea Tafi
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy, Dipartimento di Chimica, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy, Retrovirology Laboratory irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, E-08916 Badalona, Spain, Architecture et Réactivité de l’ARN, UPR 9002 CNRS/Université Louis Pasteur, 15
| | - Gianni Casaluce
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy, Dipartimento di Chimica, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy, Retrovirology Laboratory irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, E-08916 Badalona, Spain, Architecture et Réactivité de l’ARN, UPR 9002 CNRS/Université Louis Pasteur, 15
| | - Gianluca Giorgi
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy, Dipartimento di Chimica, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy, Retrovirology Laboratory irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, E-08916 Badalona, Spain, Architecture et Réactivité de l’ARN, UPR 9002 CNRS/Université Louis Pasteur, 15
| | - Mercedes Armand-Ugon
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy, Dipartimento di Chimica, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy, Retrovirology Laboratory irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, E-08916 Badalona, Spain, Architecture et Réactivité de l’ARN, UPR 9002 CNRS/Université Louis Pasteur, 15
| | - Emmanuel Gonzalez
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy, Dipartimento di Chimica, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy, Retrovirology Laboratory irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, E-08916 Badalona, Spain, Architecture et Réactivité de l’ARN, UPR 9002 CNRS/Université Louis Pasteur, 15
| | - José A. Esté
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy, Dipartimento di Chimica, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy, Retrovirology Laboratory irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, E-08916 Badalona, Spain, Architecture et Réactivité de l’ARN, UPR 9002 CNRS/Université Louis Pasteur, 15
| | - Mireille Baltzinger
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy, Dipartimento di Chimica, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy, Retrovirology Laboratory irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, E-08916 Badalona, Spain, Architecture et Réactivité de l’ARN, UPR 9002 CNRS/Université Louis Pasteur, 15
| | - Guillaume Bec
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy, Dipartimento di Chimica, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy, Retrovirology Laboratory irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, E-08916 Badalona, Spain, Architecture et Réactivité de l’ARN, UPR 9002 CNRS/Université Louis Pasteur, 15
| | - Philippe Dumas
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy, Dipartimento di Chimica, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy, Retrovirology Laboratory irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, E-08916 Badalona, Spain, Architecture et Réactivité de l’ARN, UPR 9002 CNRS/Université Louis Pasteur, 15
| | - Eric Ennifar
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy, Dipartimento di Chimica, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy, Retrovirology Laboratory irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, E-08916 Badalona, Spain, Architecture et Réactivité de l’ARN, UPR 9002 CNRS/Université Louis Pasteur, 15
| | - Maurizio Botta
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy, Dipartimento di Chimica, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy, Retrovirology Laboratory irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, E-08916 Badalona, Spain, Architecture et Réactivité de l’ARN, UPR 9002 CNRS/Université Louis Pasteur, 15
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Rossotti R, Rusconi S. Efficacy and resistance of recently developed non-nucleoside reverse transcriptase inhibitors for HIV-1. ACTA ACUST UNITED AC 2009. [DOI: 10.2217/17584310.3.1.63] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Since the introduction of the HAART, non-nucleoside reverse transcriptase inhibitors (NNRTIs) have played an essential role in treating HIV: their strong antiviral potency, good metabolic profile and low pill burden make them an ideal option in the design of an optimized triple drug regimen. Nonetheless, the currently approved NNRTIs (efavirenz and nevirapine) are weighed by peculiar toxicities, while a low genetic barrier and the development of cross-resistance significantly limits their use in cases of suboptimal adherence. Many drugs are in development and they are all designed with the aim to overcome resistance problems. In this review we present data on virological efficacy and resistance profiles of some of the most promising new molecules: some (such as rilpivirine) are close to being marketed, others are in Phase II trials (IDX899 and RDEA806), others again have just completed preclinical studies and are having their first clinical evaluations (RO-5028, UK-453061 and BILR-355 BS); etravirine is already approved by the US FDA, but it is still not licensed in Europe. Other new molecules (Merck MK-4965, GlaxoSmithKline GW678284 and a pyridazinone derivative by Roche), which are currently in early-development phases, are also briefly described.
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Affiliation(s)
- Roberto Rossotti
- Dipartimento di Scienze Cliniche, ‘Luigi Sacco’, Sezione di Malattie Infettive e Immunopatologia, University of Milan, 20157 Milan, Italy
| | - Stefano Rusconi
- Dipartimento di Scienze Cliniche, ‘Luigi Sacco’, Sezione di Malattie Infettive e Immunopatologia, University of Milan, 20157 Milan, Italy
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Sarafianos SG, Marchand B, Das K, Himmel DM, Parniak MA, Hughes SH, Arnold E. Structure and function of HIV-1 reverse transcriptase: molecular mechanisms of polymerization and inhibition. J Mol Biol 2008; 385:693-713. [PMID: 19022262 DOI: 10.1016/j.jmb.2008.10.071] [Citation(s) in RCA: 339] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2008] [Revised: 10/15/2008] [Accepted: 10/15/2008] [Indexed: 11/19/2022]
Abstract
The rapid replication of HIV-1 and the errors made during viral replication cause the virus to evolve rapidly in patients, making the problems of vaccine development and drug therapy particularly challenging. In the absence of an effective vaccine, drugs are the only useful treatment. Anti-HIV drugs work; so far drug therapy has saved more than three million years of life. Unfortunately, HIV-1 develops resistance to all of the available drugs. Although a number of useful anti-HIV drugs have been approved for use in patients, the problems associated with drug toxicity and the development of resistance means that the search for new drugs is an ongoing process. The three viral enzymes, reverse transcriptase (RT), integrase (IN), and protease (PR) are all good drug targets. Two distinct types of RT inhibitors, both of which block the polymerase activity of RT, have been approved to treat HIV-1 infections, nucleoside analogs (NRTIs) and nonnucleosides (NNRTIs), and there are promising leads for compounds that either block the RNase H activity or block the polymerase in other ways. A better understanding of the structure and function(s) of RT and of the mechanism(s) of inhibition can be used to generate better drugs; in particular, drugs that are effective against the current drug-resistant strains of HIV-1.
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Affiliation(s)
- Stefan G Sarafianos
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, Columbia, MO 65211, USA
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37
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D'Cruz OJ, Uckun FM. Novel tight binding PETT, HEPT and DABO-based non-nucleoside inhibitors of HIV-1 reverse transcriptase. J Enzyme Inhib Med Chem 2008; 21:329-50. [PMID: 17059165 DOI: 10.1080/14756360600774413] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Non-nucleoside reverse transcriptase (RT) inhibitors (NNRTIs) are a key component of effective combination antiretroviral therapies for HIV/AIDS. NNRTIs despite their chemical diversity, bind to a common allosteric site of HIV-1 RT, the primary target for anti-AIDS chemotherapy, and noncompetitively inhibit DNA polymerization. NNRTIs currently in clinical use have a low genetic barrier to resistance and therefore, the need for novel NNRTIs active against drug-resistant mutants selected by current therapies is of paramount importance. We describe the chemistry and biological evaluation of highly potent novel phenethylthiazolylthiourea (PETT), 1-[(2-hydroxyethoxy)methyl]-6-(phenylthio)thymine (HEPT) and dihydroalkoxybenzyloxopyrimidine (DABO) derivatives targeting the hydrophobic binding pocket of HIV-1 RT. These NNRTIs were rationally designed by molecular modeling and docking studies using a novel composite binding pocket that predicted how drug-resistant mutations would change the RT binding pocket shape, volume, and chemical make-up and how these changes could affect NNRTI binding. Several ligand derivatization sites were identified for docked NNRTIs that fit the composite binding pocket. The best fit was determined by calculating an inhibition constant (Ludi Ki) of the docked compound for the composite binding pocket. Compounds with a Ludi Ki of <1 microM were identified as the most promising tight binding NNRTIs. These NNRTIs displayed high selective indices with robust anti-HIV-1 activity against the wild-type and drug-resistant isolates carrying multiple RT gene mutations. The high rate of treatment failure due to the emergence of drug resistance mutations makes the discovery of broad-spectrum PETT, HEPT and DABO-based NNRTIs useful as a component of effective combination regimens.
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Affiliation(s)
- Osmond J D'Cruz
- Drug Discovery Program, Parker Hughes Institute, 2657 Patton Road, St. Paul, MN 55113, USA.
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Ren J, Chamberlain PP, Stamp A, Short SA, Weaver KL, Romines KR, Hazen R, Freeman A, Ferris RG, Andrews CW, Boone L, Chan JH, Stammers DK. Structural basis for the improved drug resistance profile of new generation benzophenone non-nucleoside HIV-1 reverse transcriptase inhibitors. J Med Chem 2008; 51:5000-8. [PMID: 18665583 DOI: 10.1021/jm8004493] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Owing to the emergence of resistant virus, next generation non-nucleoside HIV reverse transcriptase inhibitors (NNRTIs) with improved drug resistance profiles have been developed to treat HIV infection. Crystal structures of HIV-1 RT complexed with benzophenones optimized for inhibition of HIV mutants that were resistant to the prototype benzophenone GF128590 indicate factors contributing to the resilience of later compounds in the series (GW4511, GW678248). Meta-substituents on the benzophenone A-ring had the designed effect of inducing better contacts with the conserved W229 while reducing aromatic stacking interactions with the highly mutable Y181 side chain, which unexpectedly adopted a "down" position. Up to four main-chain hydrogen bonds to the inhibitor also appear significant in contributing to resilience. Structures of mutant RTs (K103N, V106A/Y181C) with benzophenones showed only small rearrangements of the NNRTIs relative to wild-type. Hence, adaptation to a mutated NNRTI pocket by inhibitor rearrangement appears less significant for benzophenones than other next-generation NNRTIs.
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Affiliation(s)
- Jingshan Ren
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
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39
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The use of local surface properties for molecular superimposition. J Mol Model 2008; 14:797-805. [DOI: 10.1007/s00894-008-0320-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2008] [Accepted: 04/18/2008] [Indexed: 12/12/2022]
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40
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Srivab P, Hannongbua S. A Study of the Binding Energies of Efavirenz to Wild-Type and K103N/Y181C HIV-1 Reverse Transcriptase Based on the ONIOM Method. ChemMedChem 2008; 3:803-11. [DOI: 10.1002/cmdc.200700181] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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41
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Ren J, Stammers DK. Structural basis for drug resistance mechanisms for non-nucleoside inhibitors of HIV reverse transcriptase. Virus Res 2008; 134:157-70. [PMID: 18313784 DOI: 10.1016/j.virusres.2007.12.018] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2007] [Revised: 12/21/2007] [Accepted: 12/21/2007] [Indexed: 11/25/2022]
Abstract
The selection of drug resistant virus is a significant obstacle to the continued successful treatment of HIV infection. Reverse transcriptase is the target for numerous approved anti-HIV drugs including both nucleoside inhibitor (NRTI) and non-nucleosides (NNRTI). The many available crystal structures of RT reveal that, generally, in relation to their binding sites NRTI resistance mutations are generally more distally positioned, whilst for NNRTIs mutations are clustered. Such clustering implies a direct stereochemical basis for NNRTI resistance mechanisms, which is indeed observed in many cases such as the loss of key ring stacking interactions with inhibitors via mutations at Tyr181 and Tyr188. However, there are also indirect resistance mechanisms observed, e.g. V108I (via perturbation of Tyr188 and Tyr181) and K103N (apo-enzyme stabilisation). The resistance mechanism can be NNRTI-dependent as is the case for K101E where either indirect (nevirapine) or direct effects (efavirenz) apply. Structural studies have contributed to the design of newer generation NNRTIs and identified a number of features which may contribute to their much improved resistance profiles. Such factors include reduced interactions with Tyr181, the presence of inhibitor/main-chain H-bonds and ability to undergo conformational flexing and rearrangement within the mutated drug site.
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Affiliation(s)
- Jingshan Ren
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
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42
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San Juan AA. 3D-QSAR models on clinically relevant K103N mutant HIV-1 reverse transcriptase obtained from two strategic considerations. Bioorg Med Chem Lett 2008; 18:1181-94. [DOI: 10.1016/j.bmcl.2007.11.134] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2007] [Revised: 11/02/2007] [Accepted: 11/30/2007] [Indexed: 10/22/2022]
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43
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Ilina T, Parniak MA. Inhibitors of HIV-1 reverse transcriptase. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2008; 56:121-67. [PMID: 18086411 DOI: 10.1016/s1054-3589(07)56005-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Tatiana Ilina
- Department of Molecular Genetics and Biochemistry, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
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44
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Smith MBK, Rader LH, Franklin AM, Taylor EV, Smith KD, Smith RH, Tirado-Rives J, Jorgensen WL. Energetic effects for observed and unobserved HIV-1 reverse transcriptase mutations of residues L100, V106, and Y181 in the presence of nevirapine and efavirenz. Bioorg Med Chem Lett 2007; 18:969-72. [PMID: 18166457 DOI: 10.1016/j.bmcl.2007.12.033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2007] [Revised: 12/12/2007] [Accepted: 12/14/2007] [Indexed: 10/22/2022]
Abstract
The effect of mutations on amino acid residues L100, V106, and Y181 for unbound HIV-1 reverse transcriptase (RT) and RT bound to nevirapine and efavirenz was investigated using Monte Carlo/free energy perturbation calculations. Using both native and bound crystal structures of RT, mutation of the amino acid residues to both those observed and unobserved in patients was carried out. The results of the calculations revealed that the variant that survives in patients dosed with either nevirapine or efavirenz had a more positive Delta Delta G value than other variants that were not observed in patients. These data suggest that the mutation observed in patients is the most effective (the one that binds the drug most weakly) of all possible codon change mutations.
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45
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Mugnaini C, Alongi M, Togninelli A, Gevariya H, Brizzi A, Manetti F, Bernardini C, Angeli L, Tafi A, Bellucci L, Corelli F, Massa S, Maga G, Samuele A, Facchini M, Clotet-Codina I, Armand-Ugón M, Esté JA, Botta M. Dihydro-alkylthio-benzyl-oxopyrimidines as inhibitors of reverse transcriptase: synthesis and rationalization of the biological data on both wild-type enzyme and relevant clinical mutants. J Med Chem 2007; 50:6580-95. [PMID: 18052319 DOI: 10.1021/jm0708230] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A series of novel S-DABO analogues, characterized by different substitution patterns at positions 2, 5, and 6 of the heterocyclic ring, were synthesized in a straightforward fashion by means of parallel synthesis and evaluated as inhibitors of human immunodeficiency virus type-1 (HIV-1). Most of the compounds proved to be highly active on the wild-type enzyme both in enzymatic and cellular assays, with one of them emerging as the most active reverse transcriptase inhibitor reported so far (EC50wt=25 pM). The general loss of potency displayed by the compounds toward clinically relevant mutant strains was deeply studied through a molecular modeling approach, leading to the evidence that the dynamic of the entrance in the non-nucleoside binding pocket could represent the basis of the inhibitory activity of the molecules.
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Affiliation(s)
- Claudia Mugnaini
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Via Alcide De Gasperi 2, I-53100 Siena, Italy
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46
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Barreiro G, Guimarães CRW, Tubert-Brohman I, Lyons TM, Tirado-Rives J, Jorgensen WL. Search for non-nucleoside inhibitors of HIV-1 reverse transcriptase using chemical similarity, molecular docking, and MM-GB/SA scoring. J Chem Inf Model 2007; 47:2416-28. [PMID: 17949071 PMCID: PMC2564819 DOI: 10.1021/ci700271z] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A virtual screening protocol has been applied to seek non-nucleoside inhibitors of HIV-1 reverse transcriptase (NNRTIs) and its K103N mutant. First, a chemical similarity search on the Maybridge library was performed using known NNRTIs as reference structures. The top-ranked molecules obtained from this procedure plus 26 known NNRTIs were then docked into the binding sites of the wild-type reverse transcriptase (HIV-RT) and its K103N variant (K103N-RT) using Glide 3.5. The top-ranked 100 compounds from the docking for both proteins were post-scored with a procedure using molecular mechanics and continuum solvation (MM-GB/SA). The validity of the virtual screening protocol was supported by (i) testing of the MM-GB/SA procedure, (ii) agreement between predicted and crystallographic binding poses, (iii) recovery of known potent NNRTIs at the top of both rankings, and (iv) identification of top-scoring library compounds that are close in structure to recently reported NNRTI HTS hits. However, purchase and assaying of selected top-scoring compounds from the library failed to yield active anti-HIV agents. Nevertheless, the highest-ranked database compound, S10087, was pursued as containing a potentially viable core. Subsequent synthesis and assaying of S10087 analogues proposed by further computational analysis yielded anti-HIV agents with EC50 values as low as 310 nM. Thus, with the aid of computational tools, it was possible to evolve a false positive into a true active.
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Affiliation(s)
- Gabriela Barreiro
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520−8107
| | | | - Ivan Tubert-Brohman
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520−8107
| | - Theresa M. Lyons
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520−8107
| | - Julian Tirado-Rives
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520−8107
| | - William L. Jorgensen
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520−8107
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47
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Ren J, Nichols CE, Chamberlain PP, Weaver KL, Short SA, Chan JH, Kleim JP, Stammers DK. Relationship of Potency and Resilience to Drug Resistant Mutations for GW420867X Revealed by Crystal Structures of Inhibitor Complexes for Wild-Type, Leu100Ile, Lys101Glu, and Tyr188Cys Mutant HIV-1 Reverse Transcriptases†. J Med Chem 2007; 50:2301-9. [PMID: 17441703 DOI: 10.1021/jm061117m] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The selection of drug resistant viruses is a major problem in efforts to combat HIV and AIDS, hence, new compounds are required. We report crystal structures of wild-type and mutant HIV-1 RT with bound non-nucleoside (NNRTI) GW420867X, aimed at investigating the basis for its high potency and improved drug resistance profile compared to the first-generation drug nevirapine. GW420867X occupies a smaller volume than many NNRTIs, yet accesses key regions of the binding pocket. GW420867X has few contacts with Tyr188, hence, explaining the small effect of mutating this residue on inhibitor-binding potency. In a mutated NNRTI pocket, GW420867X either remains in a similar position compared to wild-type (RT(Leu100Ile) and RT(Tyr188Cys)) or rearranges within the pocket (RT(Lys101Glu)). For RT(Leu100Ile), GW420867X does not shift position, in spite of forming different side-chain contacts. The small bulk of GW420867X allows adaptation to a mutated NNRTI binding site by repositioning or readjustment of side-chain contacts with only small reductions in binding affinity.
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Affiliation(s)
- Jingshan Ren
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, United Kingdom
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Ren J, Nichols CE, Stamp A, Chamberlain PP, Ferris R, Weaver KL, Short SA, Stammers DK. Structural insights into mechanisms of non-nucleoside drug resistance for HIV-1 reverse transcriptases mutated at codons 101 or 138. FEBS J 2006; 273:3850-60. [PMID: 16911530 DOI: 10.1111/j.1742-4658.2006.05392.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Lys101Glu is a drug resistance mutation in reverse transcriptase clinically observed in HIV-1 from infected patients treated with the non-nucleoside inhibitor (NNRTI) drugs nevirapine and efavirenz. In contrast to many NNRTI resistance mutations, Lys101(p66 subunit) is positioned at the surface of the NNRTI pocket where it interacts across the reverse transcriptase (RT) subunit interface with Glu138(p51 subunit). However, nevirapine contacts Lys101 and Glu138 only indirectly, via water molecules, thus the structural basis of drug resistance induced by Lys101Glu is unclear. We have determined crystal structures of RT(Glu138Lys) and RT(Lys101Glu) in complexes with nevirapine to 2.5 A, allowing the determination of water structure within the NNRTI-binding pocket, essential for an understanding of nevirapine binding. Both RT(Glu138Lys) and RT(Lys101Glu) have remarkably similar protein conformations to wild-type RT, except for significant movement of the mutated side-chains away from the NNRTI pocket induced by charge inversion. There are also small shifts in the position of nevirapine for both mutant structures which may influence ring stacking interactions with Tyr181. However, the reduction in hydrogen bonds in the drug-water-side-chain network resulting from the mutated side-chain movement appears to be the most significant contribution to nevirapine resistance for RT(Lys101Glu). The movement of Glu101 away from the NNRTI pocket can also explain the resistance of RT(Lys101Glu) to efavirenz but in this case is due to a loss of side-chain contacts with the drug. RT(Lys101Glu) is thus a distinctive NNRTI resistance mutant in that it can give rise to both direct and indirect mechanisms of drug resistance, which are inhibitor-dependent.
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Affiliation(s)
- Jingshan Ren
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, Henry Wellcome Building for Genomic Medicine, University of Oxford, UK
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49
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Das K, Sarafianos SG, Clark AD, Boyer PL, Hughes SH, Arnold E. Crystal structures of clinically relevant Lys103Asn/Tyr181Cys double mutant HIV-1 reverse transcriptase in complexes with ATP and non-nucleoside inhibitor HBY 097. J Mol Biol 2006; 365:77-89. [PMID: 17056061 DOI: 10.1016/j.jmb.2006.08.097] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2006] [Accepted: 08/22/2006] [Indexed: 11/16/2022]
Abstract
Lys103Asn and Tyr181Cys are the two mutations frequently observed in patients exposed to various non-nucleoside reverse transcriptase inhibitor drugs (NNRTIs). Human immunodeficiency virus (HIV) strains containing both reverse transcriptase (RT) mutations are resistant to all of the approved NNRTI drugs. We have determined crystal structures of Lys103Asn/Tyr181Cys mutant HIV-1 RT with and without a bound non-nucleoside inhibitor (HBY 097, (S)-4-isopropoxycarbonyl-6-methoxy-3-(methylthio-methyl)-3,4-dihydroquinoxalin-2(1H)-thione) at 3.0 A and 2.5 A resolution, respectively. The structure of the double mutant RT/HBY 097 complex shows a rearrangement of the isopropoxycarbonyl group of HBY 097 compared to its binding with wild-type RT. HBY 097 makes a hydrogen bond with the thiol group of Cys181 that helps the drug retain potency against the Tyr181Cys mutation. The structure of the unliganded double mutant HIV-1 RT showed that Lys103Asn mutation facilitates coordination of a sodium ion with Lys101 O, Asn103 N and O(delta1), Tyr188 O(eta), and two water molecules. The formation of the binding pocket requires the removal of the sodium ion. Although the RT alone and the RT/HBY 097 complex were crystallized in the presence of ATP, only the RT has an ATP coordinated with two Mn(2+) at the polymerase active site. The metal coordination mimics a reaction intermediate state in which complete octahedral coordination was observed for both metal ions. Asp186 coordinates at an axial position whereas the carboxylates of Asp110 and Asp185 are in the planes of coordination of both metal ions. The structures provide evidence that NNRTIs restrict the flexibility of the YMDD loop and prevent the catalytic aspartate residues from adopting their metal-binding conformations.
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Affiliation(s)
- Kalyan Das
- Center for Advanced Biotechnology and Medicine, Rutgers University, Department of Chemistry and Chemical Biology, Piscataway, NJ 08854, USA
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50
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Soriano E, Marco-Contelles J, Tomassi C, Nguyen Van Nhien A, Postel D. Computational Analysis of Aza Analogues of [2‘,5‘-Bis-O-(tert-butyldimethylsilyl)-β-d-ribofuranose]-3‘-spiro-5‘ ‘- (4‘ ‘-amino-1‘ ‘,2‘ ‘-oxathiole-2‘ ‘,2‘ ‘-dioxide) (TSAO) as HIV-1 Reverse Transcriptase Inhibitors: Relevance of Conformational Properties on the Inhibitory Activity. J Chem Inf Model 2006; 46:1666-77. [PMID: 16859298 DOI: 10.1021/ci0600410] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have carried out a theoretical analysis of aza analogues of [2',5'-bis-O-(tert-butyldimethylsilyl)-beta-D-ribofuranosyl]-3'-spiro-5"-(4"-amino-1",2"-oxathiole-2",2"-dioxide) by a variety of computational tools, aimed to account for the effect of the endocyclic amino moiety N-2" on the inhibitory activity against HIV-1. Docking studies suggest that compounds substituted at the N-3 and N-2' ' positions present the same binding mode to the [2',5'-bis-O-(tert-butyldimethylsilyl)-beta-D-ribofuranosyl]-3'-spiro-5"-(4"-amino-1",2"-oxathiole-2",2"-dioxide)thymine prototype, where the endocyclic amino group remains mostly exposed to the solvent. A careful conformational analysis performed through different theoretical levels, from molecular mechanics to high-level quantum mechanical calculations, provides a rationalization based on conformational preferences, which appears as strongly determined by the substitution at N-2", and on electrostatic effects from the bulk water.
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Affiliation(s)
- Elena Soriano
- Laboratorio de Resonancia Magnética, Instituto de Investigaciones Biomédicas (CSIC), C/ Arturo Duperier 4, 28029 Madrid, Spain.
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