101
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Zhao QY, Yuan ZL, Shi M. Highly Diastereo- and Enantioselective Vinylogous Mannich Reactions of Fluorinated Aldimines with Siloxyfurans. Adv Synth Catal 2011. [DOI: 10.1002/adsc.201000843] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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102
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La Regina G, Coluccia A, Brancale A, Piscitelli F, Gatti V, Maga G, Samuele A, Pannecouque C, Schols D, Balzarini J, Novellino E, Silvestri R. Indolylarylsulfones as HIV-1 non-nucleoside reverse transcriptase inhibitors: new cyclic substituents at indole-2-carboxamide. J Med Chem 2011; 54:1587-98. [PMID: 21366296 DOI: 10.1021/jm101614j] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
New indolylarylsulfone derivatives bearing cyclic substituents at indole-2-carboxamide linked through a methylene/ethylene spacer were potent inhibitors of the WT HIV-1 replication in CEM and PBMC cells with inhibitory concentrations in the low nanomolar range. Against the mutant L100I and K103N RT HIV-1 strains in MT-4 cells, compounds 20, 24-26, 36, and 40 showed antiviral potency superior to that of NVP and EFV. Against these mutant strains, derivatives 20, 24-26, and 40 were equipotent to ETV. Molecular docking experiments on this novel series of IAS analogues have also suggested that the H-bond interaction between the nitrogen atom in the carboxamide chain of IAS and Glu138:B is important in the binding of these compounds. These results are in accordance with the experimental data obtained on the WT and on the mutant HIV-1 strains tested.
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Affiliation(s)
- Giuseppe La Regina
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro 5, I-00185 Roma, Italy
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103
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Alcaro S, Alteri C, Artese A, Ceccherini-Silberstein F, Costa G, Ortuso F, Parrotta L, Perno CF, Svicher V. Molecular and structural aspects of clinically relevant mutations related to the approved non-nucleoside inhibitors of HIV-1 reverse transcriptase. Drug Resist Updat 2011; 14:141-9. [PMID: 21295512 DOI: 10.1016/j.drup.2011.01.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 01/07/2011] [Accepted: 01/07/2011] [Indexed: 10/18/2022]
Abstract
In recent years relevant progress has been made in the treatment of HIV-1 with a consequent decrease in mortality. The availability of potent antiretroviral drugs and the ability of viral load assays that accurately evaluate the true level of viral replication, have led to a better understanding of pathogenesis of the disease and how to obtain improved therapeutic profiles. The highly active antiretroviral therapy (HAART), based on a combination of three or more antiretroviral drugs, has radically changed the clinical outcome of HIV. In particular, reverse transcriptase non-nucleoside inhibitors (NNRTIs) play an essential role in most protocols and are often used in first line treatment. The high specificity of these inhibitors towards HIV-1 has increased the number of structural and molecular modeling studies of enzyme complexes and that have led to chemical syntheses of more selective second and third-generation NNRTIs. However, a considerable percentage of new HIV-1 infections are caused by the emergence of drug-resistant mutant viruses that complicate treatment strategies. In this review we discuss relevant clinical and structural aspects for the management of antiretroviral drug resistance, with detailed explanations of mechanisms and mutation patterns useful to better understand the relation between drug resistance and therapy failure.
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Affiliation(s)
- Stefano Alcaro
- Laboratorio di Chimica Farmaceutica Computazionale, Dipartimento di Scienze Farmacobiologiche Università"Magna Græcia" di Catanzaro, Campus Universitario, Italy
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104
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Weitman M, Lerman K, Nudelman A, Major DT, Hizi A, Herschhorn A. Structure–activity relationship studies of 1-(4-chloro-2,5-dimethoxyphenyl)-3-(3-propoxypropyl)thiourea, a non-nucleoside reverse transcriptase inhibitor of human immunodeficiency virus type-1. Eur J Med Chem 2011; 46:447-67. [DOI: 10.1016/j.ejmech.2010.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Revised: 11/01/2010] [Accepted: 11/02/2010] [Indexed: 01/17/2023]
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105
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Boonsri P, Kuno M, Hannongbua S. Key interactions of the mutant HIV-1 reverse transcriptase/efavirenz: an evidence obtained from ONIOM method. MEDCHEMCOMM 2011. [DOI: 10.1039/c1md00162k] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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106
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Alexandre FR, Amador A, Bot S, Caillet C, Convard T, Jakubik J, Musiu C, Poddesu B, Vargiu L, Liuzzi M, Roland A, Seifer M, Standring D, Storer R, Dousson CB. Synthesis and biological evaluation of aryl-phospho-indole as novel HIV-1 non-nucleoside reverse transcriptase inhibitors. J Med Chem 2010; 54:392-5. [PMID: 21142105 DOI: 10.1021/jm101142k] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A novel series of 3-aryl-phospho-indole (API) non-nucleoside reverse transcriptase inhibitors of HIV-1 was developed. Chemical variation in the phosphorus linker led to the discovery of 3-phenyl-methyl-phosphinate-2-carboxamide 14, which possessed excellent potency against wild-type HIV-1 as well as viruses bearing K103N and Y181C single mutants in the reverse transcriptase gene. Chiral separation of the enantiomers showed that only R enantiomer retained the activity. The pharmacokinetic, solubility, and metabolic properties of 14 were assessed.
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107
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Ribone SR, Quevedo MA, Madrid M, Briñón MC. Rational Approaches for the Design of Effective Human Immunodeficiency Virus Type 1 Nonnucleoside Reverse Transcriptase Inhibitors. J Chem Inf Model 2010; 51:130-8. [DOI: 10.1021/ci1001636] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sergio R. Ribone
- Departamento de Farmacia, Facultad de Ciencias Químicas, Ciudad Universitaria, Universidad Nacional de Córdoba, X5000HUA, Córdoba, Argentina, and Pittsburgh Supercomputing Center, Pittsburgh, Pennsylvania 15213, United States
| | - Mario A. Quevedo
- Departamento de Farmacia, Facultad de Ciencias Químicas, Ciudad Universitaria, Universidad Nacional de Córdoba, X5000HUA, Córdoba, Argentina, and Pittsburgh Supercomputing Center, Pittsburgh, Pennsylvania 15213, United States
| | - Marcela Madrid
- Departamento de Farmacia, Facultad de Ciencias Químicas, Ciudad Universitaria, Universidad Nacional de Córdoba, X5000HUA, Córdoba, Argentina, and Pittsburgh Supercomputing Center, Pittsburgh, Pennsylvania 15213, United States
| | - Margarita C. Briñón
- Departamento de Farmacia, Facultad de Ciencias Químicas, Ciudad Universitaria, Universidad Nacional de Córdoba, X5000HUA, Córdoba, Argentina, and Pittsburgh Supercomputing Center, Pittsburgh, Pennsylvania 15213, United States
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108
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Xiao H, Huang Y, Qing FL. Highly diastereoselective synthesis of α-trifluoromethylated α-propargylamines by acetylide addition to chiral CF3-substituted N-tert-butanesulfinyl ketimines. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.tetasy.2010.11.028] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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109
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Braz VA, Barkley MD, Jockusch RA, Wintrode PL. Efavirenz binding site in HIV-1 reverse transcriptase monomers. Biochemistry 2010; 49:10565-73. [PMID: 21090588 DOI: 10.1021/bi101480z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Efavirenz (EFV) is a potent nonnucleoside reverse transcriptase inhibitor (NNRTI) used in the treatment of AIDS. NNRTIs bind in a hydrophobic pocket located in the p66 subunit of reverse transcriptase (RT), which is not present in crystal structures of RT without an inhibitor. Recent studies showed that monomeric forms of the p66 and p51 subunits bind efavirenz with micromolar affinity. The effect of efavirenz on the solution conformations of p66 and p51 monomers was studied by hydrogen-deuterium exchange mass spectrometry (HXMS) and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). HXMS data reveal that five peptides, four of which contain efavirenz contact residues seen in the crystal structure of the RT-EFV complex, exhibit a reduced level of exchange in monomer-EFV complexes. Moreover, peptide 232-246 undergoes slow cooperative unfolding-refolding in the bound monomers, but at a rate much slower than that observed in the p66 subunit of the RT heterodimer [Seckler, J. M., Howard, K. J., Barkley, M. D., and Wintrode, P. L. (2009) Biochemistry 48, 7646-7655]. These results suggest that the efavirenz binding site on p66 and p51 monomers is similar to the NNRTI binding pocket in the p66 subunit of RT. Nanoelectrospray ionization FT-ICR mass spectra indicate that the intact monomers each have (at least) two different conformations. In the presence of efavirenz, the mass spectra change significantly and suggest that p51 adopts a single, more compact conformation, whereas p66 undergoes facile, electrospray-induced cleavage. The population shift is consistent with a selected-fit binding mechanism.
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Affiliation(s)
- Valerie A Braz
- Department of Chemistry, Case Western Reserve University,10900 Euclid Avenue, Cleveland, Ohio 44106, United States
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110
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Lersivirine, a nonnucleoside reverse transcriptase inhibitor with activity against drug-resistant human immunodeficiency virus type 1. Antimicrob Agents Chemother 2010; 54:4451-63. [PMID: 20660667 DOI: 10.1128/aac.01455-09] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The nonnucleoside reverse transcriptase inhibitors (NNRTIs) are key components of highly active antiretroviral therapy (HAART) for the treatment of human immunodeficiency virus type 1 (HIV-1). A major problem with the first approved NNRTIs was the emergence of mutations in the HIV-1 reverse transcriptase (RT), in particular K103N and Y181C, which led to resistance to the entire class. We adopted an iterative strategy to synthesize and test small molecule inhibitors from a chemical series of pyrazoles against wild-type (wt) RT and the most prevalent NNRTI-resistant mutants. The emerging candidate, lersivirine (UK-453,061), binds the RT enzyme in a novel way (resulting in a unique resistance profile), inhibits over 60% of viruses bearing key RT mutations, with 50% effective concentrations (EC(50)s) within 10-fold of those for wt viruses, and has excellent selectivity against a range of human targets. Altogether lersivirine is a highly potent and selective NNRTI, with excellent efficacy against NNRTI-resistant viruses.
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111
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Decha P, Intharathep P, Udommaneethanakit T, Sompornpisut P, Hannongbua S, Wolschann P, Parasuk V. Theoretical studies on the molecular basis of HIV-1RT/NNRTIs interactions. J Enzyme Inhib Med Chem 2010; 26:29-36. [DOI: 10.3109/14756360903563393] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Panita Decha
- Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
- Computational Chemistry Research Unit, Department of Chemistry, Faculty of Science, Thaksin University, Phatthalung 93110, Thailand
| | - Pathumwadee Intharathep
- Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Thanyarat Udommaneethanakit
- Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Pornthep Sompornpisut
- Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Supot Hannongbua
- Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Peter Wolschann
- Institute of Theoretical Chemistry, University of Vienna, Waehringer Strasse 17, Vienna 1090, Austria
| | - Vudhichai Parasuk
- Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
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112
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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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113
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Chen W, Li W, Ling X, Wang X, Liu J. Study on the interaction between HIV reverse transcriptase and its non-nucleoside inhibitor nevirapine by capillary electrophoresis. J Chromatogr B Analyt Technol Biomed Life Sci 2010; 878:1714-7. [PMID: 20457546 DOI: 10.1016/j.jchromb.2010.04.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Revised: 04/08/2010] [Accepted: 04/09/2010] [Indexed: 11/26/2022]
Abstract
The HIV reverse transcriptase (RT) is an important antiviral target for the chemotherapy of AIDS because of its key role in virus replication. Nevirapine is a first generation of non-nucleoside reverse transcriptase inhibitors (NNRTIs), which is usually used for the therapy of AIDS. In this study, a high-performance analytical method based on capillary electrophoresis (CE) to investigate interactions between HIV RT and nevirapine was developed. Samples containing HIV RT and nevirapine at various ratios were incubated at 37 degrees C for 45 min and then separated by CE with Tris-acetate buffer at pH 7.3 containing 0.15% SDS. Both qualitative and quantitative characterizations of the binding were determined by CE for the first time. The binding constants of the interactions between HIV RT and nevirapine were calculated as (3.25+/-0.16)x10(4) and (1.25+/-0.07)x10(2) M(-1) by Scatchard analysis. HIV RT and nevirapine have two binding sites. The presented methodology should be generally applicable to study the interactions between HIV RT and nevirapine quantitatively and qualitatively.
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Affiliation(s)
- Wenjing Chen
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
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114
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Cruz-Monteagudo M, PhamThe H, Cordeiro MNDS, Borges F. Prioritizing Hits with Appropriate Trade-Offs Between HIV-1 Reverse Transcriptase Inhibitory Efficacy and MT4 Blood Cells Toxicity Through Desirability-Based Multiobjective Optimization and Ranking. Mol Inform 2010; 29:303-21. [PMID: 27463058 DOI: 10.1002/minf.200900047] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2009] [Accepted: 02/19/2010] [Indexed: 11/07/2022]
Abstract
Nonnucleoside reverse transcriptase (RT) inhibitors (NNRTIs) constitute a promising therapeutic option for AIDS. However, the emergence of virus-NNRTIs resistance was found to be a major problem in the field. Toward that goal, a "knock-out" strategy stands out between the several options to circumvent the problem. However the high drug or drug-drug concentrations often used generate additional safety concerns. The need for approaches able to early integrate drug- or lead-likeness, toxicity and bioavailability criteria in the drug discovery phase is an emergent issue. Given that, we propose a combined strategy based on desirability-based multiobjective optimization (MOOP) and ranking for the prioritization of HIV-1 NNRTIs hits with appropriate trade-offs between inhibitory efficacy over the HIV-1 RT and toxic effects over MT4 blood cells. Through the MOOP process, the theoretical levels of the predictive variables required to reach a desirable RT inhibitor candidate with the best possible compromise between efficacy and safety were found. This information is used as a pattern to rank the library of compounds according to a similarity-based structural criterion, providing a ranking quality of 64 %/71 %/73 % in training/validation/test set. A comparative study between the sequential, parallel and multiobjective virtual screening revealed that the multiobjective approach can outperform the other approaches. These results suggest that the identification of NNRTIs hits with appropriate trade-offs between potency and safety, rather than fully optimized hits solely based on potency, can facilitate the hit to lead transition and increase the likelihood of the candidate to evolve into a successful antiretroviral drug.
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Affiliation(s)
- Maykel Cruz-Monteagudo
- Department of Chemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal. , .,Department of Organic Chemistry, Faculty of Pharmacy, University of Porto, 4150-047 Porto, Portugal. , .,Applied Chemistry Research Center (CEQA), Faculty of Chemistry and Pharmacy, Central University of "Las Villas", Santa Clara, 54830, Cuba. , .,Molecular Simulation and Drug Design Group, Chemical Bioactive Center (CBQ), Central University of "Las Villas", Santa Clara, 54830, Cuba. ,
| | - Hai PhamThe
- Molecular Simulation and Drug Design Group, Chemical Bioactive Center (CBQ), Central University of "Las Villas", Santa Clara, 54830, Cuba
| | - M Natalia D S Cordeiro
- REQUIMTE, Department of Chemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal.
| | - Fernanda Borges
- Department of Chemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
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115
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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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116
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Abram ME, Sarafianos SG, Parniak MA. The mutation T477A in HIV-1 reverse transcriptase (RT) restores normal proteolytic processing of RT in virus with Gag-Pol mutated in the p51-RNH cleavage site. Retrovirology 2010; 7:6. [PMID: 20122159 PMCID: PMC2831009 DOI: 10.1186/1742-4690-7-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2009] [Accepted: 02/01/2010] [Indexed: 12/04/2022] Open
Abstract
Background The p51 subunit of the HIV-1 reverse transcriptase (RT) p66/p51 heterodimer arises from proteolytic cleavage of the RT p66 subunit C-terminal ribonuclease H (RNH) domain during virus maturation. Our previous work showed that mutations in the RT p51↓RNH cleavage site resulted in virus with defects in proteolytic processing of RT and significantly attenuated infectivity. In some cases, virus fitness was restored after repeated passage of mutant viruses, due to reversion of the mutated sequences to wild-type. However, in one case, the recovered virus retained the mutated p51↓RNH cleavage site but also developed an additional mutation, T477A, distal to the cleavage site. In this study we have characterized in detail the impact of the T477A mutation on intravirion processing of RT. Results While the T477A mutation arose during serial passage only with the F440V mutant background, introduction of this substitution into a variety of RT p51↓RNH cleavage site lethal mutant backgrounds was able to restore substantial infectivity and normal RT processing to these mutants. T477A had no phenotypic effect on wild-type HIV-1. We also evaluated the impact of T477A on the kinetics of intravirion Gag-Pol polyprotein processing of p51↓RNH cleavage site mutants using the protease inhibitor ritonavir. Early processing intermediates accumulated in p51↓RNH cleavage site mutant viruses, whereas introduction of T477A promoted the completion of processing and formation of the fully processed RT p66/p51 heterodimer. Conclusions This work highlights the extraordinary plasticity of HIV-1 in adapting to seemingly lethal mutations that prevent RT heterodimer formation during virion polyprotein maturation. The ability of T477A to restore RT heterodimer formation and thus intravirion stability of the enzyme may arise from increased conformation flexibility in the RT p51↓RNH cleavage site region, due to loss of a hydrogen bond associated with the normal threonine residue, thereby enabling proteolytic cleavage near the normal RT p51↓RNH cleavage site.
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Affiliation(s)
- Michael E Abram
- University of Pittsburgh School of Medicine, Department of Microbiology and Molecular Genetics, Pittsburgh, PA 15219, USA
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117
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Braz VA, Holladay LA, Barkley MD. Efavirenz binding to HIV-1 reverse transcriptase monomers and dimers. Biochemistry 2010; 49:601-10. [PMID: 20039714 PMCID: PMC2896556 DOI: 10.1021/bi901579y] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Efavirenz (EFV) is a nonnucleoside reverse transcriptase inhibitor (NNRTI) of HIV-1 reverse transcriptase (RT) used for the treatment of AIDS. RT is a heterodimer composed of p66 and p51 subunits; p51 is produced from p66 by C-terminal truncation by HIV protease. The monomers can form p66/p66 and p51/p51 homodimers as well as the p66/p51 heterodimer. Dimerization and efavirenz binding are coupled processes. In the crystal structure of the p66/p51-EFV complex, the drug is bound to the p66 subunit. The binding of efavirenz to wild-type and dimerization-defective RT proteins was studied by equilibrium dialysis, tryptophan fluorescence, and native gel electrophoresis. A 1:1 binding stoichiometry was determined for both monomers and homodimers. Equilibrium dissociation constants are approximately 2.5 microM for both p66- and p51-EFV complexes, 250 nM for the p66/p66-EFV complex, and 7 nM for the p51/p51-EFV complex. An equilibrium dissociation constant of 92 nM for the p66/p51-EFV complex was calculated from the thermodynamic linkage between dimerization and inhibitor binding. Binding and unbinding kinetics monitored by fluorescence were slow. Progress curve analyses revealed a one-step, direct binding mechanism with association rate constants k(1) of approximately 13.5 M(-1) s(-1) for monomers and heterodimer and dissociation rate constants k(-1) of approximately 9 x 10(-5) s(-1) for monomers. A conformational selection mechanism is proposed to account for the slow association rate. These results show that efavirenz is a slow, tight-binding inhibitor capable of binding all forms of RT and suggest that the NNRTI binding site in monomers and dimers is similar.
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Affiliation(s)
| | | | - Mary D. Barkley
- To whom correspondence should be addressed. Telephone: (216) 368-0602. Fax: (216) 368-0604.
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118
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Monforte AM, Logoteta P, De Luca L, Iraci N, Ferro S, Maga G, De Clercq E, Pannecouque C, Chimirri A. Novel 1,3-dihydro-benzimidazol-2-ones and their analogues as potent non-nucleoside HIV-1 reverse transcriptase inhibitors. Bioorg Med Chem 2010; 18:1702-10. [PMID: 20097079 DOI: 10.1016/j.bmc.2009.12.059] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2009] [Revised: 12/18/2009] [Accepted: 12/23/2009] [Indexed: 10/20/2022]
Abstract
A series of novel benzimidazolones and their analogues, characterized by the presence of one or more methyl groups or other bioisosteric moieties at different positions of the phenyl ring at N-1, were synthesized and evaluated as inhibitors of human immunodeficiency virus type-1 (HIV-1). Most of the new compounds proved to be highly effective in inhibiting both HIV-1 replication in MT4 cells with minimal cytotoxicity and RT enzyme at nanomolar concentrations. Some derivatives were also tested against RTs containing single amino acid mutations responsible for resistance to non-nucleoside reverse transcriptase inhibitors (NNRTIs). The different potencies displayed by the new compounds were studied using molecular modeling.
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Affiliation(s)
- Anna-Maria Monforte
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, 98168 Messina, Italy.
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119
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Non-nucleoside reverse transcriptase inhibitors (NNRTIs), their discovery, development, and use in the treatment of HIV-1 infection: A review of the last 20 years (1989–2009). Antiviral Res 2010; 85:75-90. [DOI: 10.1016/j.antiviral.2009.09.008] [Citation(s) in RCA: 288] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Revised: 09/08/2009] [Accepted: 09/12/2009] [Indexed: 11/20/2022]
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120
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Sakuma R, Sakuma T, Ohmine S, Silverman RH, Ikeda Y. Xenotropic murine leukemia virus-related virus is susceptible to AZT. Virology 2009; 397:1-6. [PMID: 19959199 DOI: 10.1016/j.virol.2009.11.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Revised: 10/20/2009] [Accepted: 11/06/2009] [Indexed: 10/20/2022]
Abstract
The xenotropic murine leukemia virus-related virus (XMRV) is a human retrovirus, recently isolated from tissues of prostate cancer patients with impaired RNase L activity. In this study, we evaluated 10 licensed anti-HIV-1 compounds for their activity against XMRV, including protease inhibitors (PI), nucleoside reverse transcriptase (RT) inhibitors (NRTI), non-nucleoside RT inhibitors (NNRTI) and an integrase inhibitor. No PI affected XMRV production; even high concentrations of Ritonavir failed to inhibit the maturation of XMRV Gag polyproteins. Among the NRTI, NNRTI and integrase inhibitors used in this study, only AZT blocked XMRV infection and replication through inhibition of viral reverse transcription. This sensitivity of XMRV to AZT may be explained by the modest homology in the motif D sequences of HIV-1 and XMRV reverse transcriptases. If XMRV becomes established as an etiological agent for prostate cancer or other diseases, AZT may be useful for preventing or treating XMRV infections in humans.
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Affiliation(s)
- Ryuta Sakuma
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55906, USA
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Carta A, Pricl S, Piras S, Fermeglia M, La Colla P, Loddo R. Activity and molecular modeling of a new small molecule active against NNRTI-resistant HIV-1 mutants. Eur J Med Chem 2009; 44:5117-22. [DOI: 10.1016/j.ejmech.2009.08.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Revised: 08/18/2009] [Accepted: 08/20/2009] [Indexed: 11/17/2022]
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122
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Loksha YM, Pedersen EB, Loddo R, La Colla P. Synthesis and anti-HIV-1 activity of 1-substiuted 6-(3-cyanobenzoyl) and [(3-cyanophenyl)fluoromethyl]-5-ethyl-uracils. Arch Pharm (Weinheim) 2009; 342:501-6. [PMID: 19637180 DOI: 10.1002/ardp.200900058] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
1-Substiuted 6-(3-cyanobenzoyl) and [(3-cyanophenyl)fluoromethyl]-5-ethyl-uracils were synthesized and evaluated in cell-based assays against HIV-1 wild-type and its clinically relevant non-nucleoside reverse transcriptase inhibitor (NNRTI)-resistant mutants. Some of the synthesized compounds showed activity against HIV-1 wild-type in the same range as Emivirine (MKC-442). 3-{[3-(Allyloxymethyl)-5-ethyl-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl]fluoromethyl}-benzonitrile 11b showed moderate activity against the Y181C HIV-1 mutant strain.
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Affiliation(s)
- Yasser M Loksha
- Nucleic Acid Centre, Department of Physics and Chemistry, University of Southern Denmark, Odense M, Denmark
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123
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Factors associated with virological response to etravirine in nonnucleoside reverse transcriptase inhibitor-experienced HIV-1-infected patients. Antimicrob Agents Chemother 2009; 54:72-7. [PMID: 19901096 DOI: 10.1128/aac.01051-09] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To identify factors associated with virological response (VR) to an etravirine (ETR)-based regimen, 243 patients previously treated with nonnucleoside reverse transcriptase inhibitors (NNRTIs) were studied. The impact of baseline HIV-1 RNA, CD4 cell count, past NNRTIs used, 57 NNRTI resistance mutations, genotypic sensitivity score (GSS) for nucleoside reverse transcriptase inhibitors (NRTIs) and protease inhibitors (PIs), and the number of new drugs used with ETR for the first time on the VR to an ETR regimen were investigated. Among the 243 patients, the median baseline HIV-1 RNA level was 4.4 log(10) copies/ml (interquartile range [IQR], 3.7 to 4.9) and the median CD4 count was 175 cells/mm(3) (IQR, 69 to 312). Patients had been previously exposed to a median of 6 NRTIs, 1, NNRTI, and 5 PIs. Overall, 82% of patients achieved a VR at month 2, as defined by a decrease of at least 1.5 log(10) copies/ml and/or HIV-1 RNA level of <50 copies/ml. No difference in VR was observed between patients receiving or not a boosted PI in combination with ETR. Factors independently associated with a better VR to ETR were the number of drugs (among enfuvirtide, darunavir, or raltegravir) used for the first time in combination with ETR and the presence of the K103N mutation at baseline. Mutations Y181V and E138A were independently associated with poor VR, whereas no effect of the Y181C on VR was observed. In conclusion, ETR was associated with high response rates in NNRTI-experienced patients in combination with other active drugs regardless of the therapeutic class used.
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124
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Menéndez-Arias L. Molecular basis of human immunodeficiency virus drug resistance: an update. Antiviral Res 2009; 85:210-31. [PMID: 19616029 DOI: 10.1016/j.antiviral.2009.07.006] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2009] [Revised: 06/26/2009] [Accepted: 07/03/2009] [Indexed: 11/25/2022]
Abstract
Antiretroviral therapy has led to a significant decrease in human immunodeficiency virus (HIV)-related mortality. Approved antiretroviral drugs target different steps of the viral life cycle including viral entry (coreceptor antagonists and fusion inhibitors), reverse transcription (nucleoside and non-nucleoside inhibitors of the viral reverse transcriptase), integration (integrase inhibitors) and viral maturation (protease inhibitors). Despite the success of combination therapies, the emergence of drug resistance is still a major factor contributing to therapy failure. Viral resistance is caused by mutations in the HIV genome coding for structural changes in the target proteins that can affect the binding or activity of the antiretroviral drugs. This review provides an overview of the molecular mechanisms involved in the acquisition of resistance to currently used and promising investigational drugs, emphasizing the structural role of drug resistance mutations. The optimization of current antiretroviral drug regimens and the development of new drugs are still challenging issues in HIV chemotherapy. This article forms part of a special issue of Antiviral Research marking the 25th anniversary of antiretroviral drug discovery and development, Vol 85, issue 1, 2010.
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Affiliation(s)
- Luis Menéndez-Arias
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid), c/Nicolás Cabrera 1, Campus de Cantoblanco, 28049 Madrid, Spain.
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Nichols SE, Domaoal RA, Thakur VV, Tirado-Rives J, Anderson KS, Jorgensen WL. Discovery of wild-type and Y181C mutant non-nucleoside HIV-1 reverse transcriptase inhibitors using virtual screening with multiple protein structures. J Chem Inf Model 2009; 49:1272-9. [PMID: 19374380 DOI: 10.1021/ci900068k] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To discover non-nucleoside inhibitors of HIV-1 reverse transcriptase (NNRTIs) that are effective against both wild-type (WT) virus and variants that encode the clinically troublesome Tyr181Cys (Y181C) RT mutation, virtual screening by docking was carried out using three RT structures and more than 2 million commercially available compounds. Two of the structures are for WT-virus with different conformations of Tyr181, while the third structure incorporates the Y181C modification. Eventually nine compounds were purchased and assayed. Three of the compounds show low-micromolar antiviral activity toward either or both the wild-type and Y181C HIV-1 strains. The study illustrates a viable protocol to seek anti-HIV agents with enhanced resistance profiles.
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Affiliation(s)
- Sara E Nichols
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06511, USA
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126
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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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127
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Piscitelli F, Coluccia A, Brancale A, La Regina G, Sansone A, Giordano C, Balzarini J, Maga G, Zanoli S, Samuele A, Cirilli R, La Torre F, Lavecchia A, Novellino E, Silvestri R. Indolylarylsulfones bearing natural and unnatural amino acids. Discovery of potent inhibitors of HIV-1 non-nucleoside wild type and resistant mutant strains reverse transcriptase and coxsackie B4 virus. J Med Chem 2009; 52:1922-34. [PMID: 19281225 DOI: 10.1021/jm801470b] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
New potent indolylarylsulfone (IAS) HIV-1 NNRTIs were obtained by coupling natural and unnatural amino acids to the 2-carboxamide and introducing different electron-withdrawing substituents at position 4 and 5 of the indole nucleus. The new IASs inhibited the HIV-1 replication in human T-lymphocyte (CEM) cells at low/subnanomolar concentration and were weakly cytostatic. Against the mutant L100I, K103N, and Y181C RT HIV-1 strains in CEM cells, sulfones 3, 4, 19, 27, and 31 were comparable to EFV. The new IASs were inhibitors to Coxsackie B4 virus at low micromolar (2-9 microM) concentrations. Superimposition of PLANTS docked conformations of IASs 19 and 9 revealed different hydrophobic interactions of the 3,5-dimethylphenyl group, for which a staking interaction with Tyr181 aromatic side chain was observed. The binding mode of 19 was not affected by the L100I mutation and was consistent with the interactions reported for the WT strain.
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Affiliation(s)
- Francesco Piscitelli
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza Universita di Roma, Roma, Italy
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128
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Xu B, Sun Y, Guo Y, Cao Y, Yu T. Synthesis and biological evaluation of N4-(hetero)arylsulfonylquinoxalinones as HIV-1 reverse transcriptase inhibitors. Bioorg Med Chem 2009; 17:2767-74. [DOI: 10.1016/j.bmc.2009.02.039] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2008] [Revised: 02/17/2009] [Accepted: 02/19/2009] [Indexed: 10/21/2022]
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129
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Jones LH, Allan G, Barba O, Burt C, Corbau R, Dupont T, Knöchel T, Irving S, Middleton DS, Mowbray CE, Perros M, Ringrose H, Swain NA, Webster R, Westby M, Phillips C. Novel Indazole Non-Nucleoside Reverse Transcriptase Inhibitors Using Molecular Hybridization Based on Crystallographic Overlays. J Med Chem 2009; 52:1219-23. [DOI: 10.1021/jm801322h] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lyn H. Jones
- Discovery Chemistry, Discovery Biology, Pharmacokinetics, Dynamics, and Metabolism, Structural Biology, Molecular Informatics and Structure-Based Design, Sandwich Laboratories, Pfizer Global Research and Development, Ramsgate Road, Sandwich, Kent CT13 9NJ, United Kingdom
| | - Gill Allan
- Discovery Chemistry, Discovery Biology, Pharmacokinetics, Dynamics, and Metabolism, Structural Biology, Molecular Informatics and Structure-Based Design, Sandwich Laboratories, Pfizer Global Research and Development, Ramsgate Road, Sandwich, Kent CT13 9NJ, United Kingdom
| | - Oscar Barba
- Discovery Chemistry, Discovery Biology, Pharmacokinetics, Dynamics, and Metabolism, Structural Biology, Molecular Informatics and Structure-Based Design, Sandwich Laboratories, Pfizer Global Research and Development, Ramsgate Road, Sandwich, Kent CT13 9NJ, United Kingdom
| | - Catherine Burt
- Discovery Chemistry, Discovery Biology, Pharmacokinetics, Dynamics, and Metabolism, Structural Biology, Molecular Informatics and Structure-Based Design, Sandwich Laboratories, Pfizer Global Research and Development, Ramsgate Road, Sandwich, Kent CT13 9NJ, United Kingdom
| | - Romuald Corbau
- Discovery Chemistry, Discovery Biology, Pharmacokinetics, Dynamics, and Metabolism, Structural Biology, Molecular Informatics and Structure-Based Design, Sandwich Laboratories, Pfizer Global Research and Development, Ramsgate Road, Sandwich, Kent CT13 9NJ, United Kingdom
| | - Thomas Dupont
- Discovery Chemistry, Discovery Biology, Pharmacokinetics, Dynamics, and Metabolism, Structural Biology, Molecular Informatics and Structure-Based Design, Sandwich Laboratories, Pfizer Global Research and Development, Ramsgate Road, Sandwich, Kent CT13 9NJ, United Kingdom
| | - Thorsten Knöchel
- Discovery Chemistry, Discovery Biology, Pharmacokinetics, Dynamics, and Metabolism, Structural Biology, Molecular Informatics and Structure-Based Design, Sandwich Laboratories, Pfizer Global Research and Development, Ramsgate Road, Sandwich, Kent CT13 9NJ, United Kingdom
| | - Steve Irving
- Discovery Chemistry, Discovery Biology, Pharmacokinetics, Dynamics, and Metabolism, Structural Biology, Molecular Informatics and Structure-Based Design, Sandwich Laboratories, Pfizer Global Research and Development, Ramsgate Road, Sandwich, Kent CT13 9NJ, United Kingdom
| | - Donald S. Middleton
- Discovery Chemistry, Discovery Biology, Pharmacokinetics, Dynamics, and Metabolism, Structural Biology, Molecular Informatics and Structure-Based Design, Sandwich Laboratories, Pfizer Global Research and Development, Ramsgate Road, Sandwich, Kent CT13 9NJ, United Kingdom
| | - Charles E. Mowbray
- Discovery Chemistry, Discovery Biology, Pharmacokinetics, Dynamics, and Metabolism, Structural Biology, Molecular Informatics and Structure-Based Design, Sandwich Laboratories, Pfizer Global Research and Development, Ramsgate Road, Sandwich, Kent CT13 9NJ, United Kingdom
| | - Manos Perros
- Discovery Chemistry, Discovery Biology, Pharmacokinetics, Dynamics, and Metabolism, Structural Biology, Molecular Informatics and Structure-Based Design, Sandwich Laboratories, Pfizer Global Research and Development, Ramsgate Road, Sandwich, Kent CT13 9NJ, United Kingdom
| | - Heather Ringrose
- Discovery Chemistry, Discovery Biology, Pharmacokinetics, Dynamics, and Metabolism, Structural Biology, Molecular Informatics and Structure-Based Design, Sandwich Laboratories, Pfizer Global Research and Development, Ramsgate Road, Sandwich, Kent CT13 9NJ, United Kingdom
| | - Nigel A. Swain
- Discovery Chemistry, Discovery Biology, Pharmacokinetics, Dynamics, and Metabolism, Structural Biology, Molecular Informatics and Structure-Based Design, Sandwich Laboratories, Pfizer Global Research and Development, Ramsgate Road, Sandwich, Kent CT13 9NJ, United Kingdom
| | - Robert Webster
- Discovery Chemistry, Discovery Biology, Pharmacokinetics, Dynamics, and Metabolism, Structural Biology, Molecular Informatics and Structure-Based Design, Sandwich Laboratories, Pfizer Global Research and Development, Ramsgate Road, Sandwich, Kent CT13 9NJ, United Kingdom
| | - Mike Westby
- Discovery Chemistry, Discovery Biology, Pharmacokinetics, Dynamics, and Metabolism, Structural Biology, Molecular Informatics and Structure-Based Design, Sandwich Laboratories, Pfizer Global Research and Development, Ramsgate Road, Sandwich, Kent CT13 9NJ, United Kingdom
| | - Chris Phillips
- Discovery Chemistry, Discovery Biology, Pharmacokinetics, Dynamics, and Metabolism, Structural Biology, Molecular Informatics and Structure-Based Design, Sandwich Laboratories, Pfizer Global Research and Development, Ramsgate Road, Sandwich, Kent CT13 9NJ, United Kingdom
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130
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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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131
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Shibata N, Mizuta S, Kawai H. Recent advances in enantioselective trifluoromethylation reactions. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.tetasy.2008.11.011] [Citation(s) in RCA: 320] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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132
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Sweeney ZK, Harris SF, Arora N, Javanbakht H, Li Y, Fretland J, Davidson JP, Billedeau JR, Gleason SK, Hirschfeld D, Kennedy-Smith JJ, Mirzadegan T, Roetz R, Smith M, Sperry S, Suh JM, Wu J, Tsing S, Villaseñor AG, Paul A, Su G, Heilek G, Hang JQ, Zhou AS, Jernelius JA, Zhang FJ, Klumpp K. Design of Annulated Pyrazoles as Inhibitors of HIV-1 Reverse Transcriptase. J Med Chem 2008; 51:7449-58. [DOI: 10.1021/jm800527x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zachary K. Sweeney
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Seth F. Harris
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Nidhi Arora
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Hassan Javanbakht
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Yu Li
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Jennifer Fretland
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - James P. Davidson
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - J. Roland Billedeau
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Shelley K. Gleason
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Donald Hirschfeld
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Joshua J. Kennedy-Smith
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Taraneh Mirzadegan
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Ralf Roetz
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Mark Smith
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Sarah Sperry
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Judy M. Suh
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Jeffrey Wu
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Stan Tsing
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Armando G. Villaseñor
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Amber Paul
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Guoping Su
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Gabrielle Heilek
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Julie Q. Hang
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Amy S. Zhou
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Jesper A. Jernelius
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Fang-Jie Zhang
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
| | - Klaus Klumpp
- Departments of Medicinal Chemistry, Discovery Sciences and Technologies, Viral Disease Biology, Viral Disease Biochemistry, Non-Clinical Safety, and Chemical Synthesis, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304
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Abstract
OBJECTIVE To clarify the role of novel mutations selected by treatment with efavirenz or nevirapine, and investigate the influence of HIV-1 subtype on nonnucleoside reverse transcriptase inhibitor (nNRTI) resistance pathways. DESIGN By finding direct dependencies between treatment-selected mutations, the involvement of these mutations as minor or major resistance mutations against efavirenz, nevirapine, or coadministrated nucleoside analogue reverse transcriptase inhibitors (NRTIs) is hypothesized. In addition, direct dependencies were investigated between treatment-selected mutations and polymorphisms, some of which are linked with subtype, and between NRTI and nNRTI resistance pathways. METHODS Sequences from a large collaborative database of various subtypes were jointly analyzed to detect mutations selected by treatment. Using Bayesian network learning, direct dependencies were investigated between treatment-selected mutations, NRTI and nNRTI treatment history, and known NRTI resistance mutations. RESULTS Several novel minor resistance mutations were found: 28K and 196R (for resistance against efavirenz), 101H and 138Q (nevirapine), and 31L (lamivudine). Robust interactions between NRTI mutations (65R, 74V, 75I/M, and 184V) and nNRTI resistance mutations (100I, 181C, 190E and 230L) may affect resistance development to particular treatment combinations. For example, an interaction between 65R and 181C predicts that the nevirapine and tenofovir and lamivudine/emtricitabine combination should be more prone to failure than efavirenz and tenofovir and lamivudine/emtricitabine. CONCLUSION Bayesian networks were helpful in untangling the selection of mutations by NRTI versus nNRTI treatment, and in discovering interactions between resistance mutations within and between these two classes of inhibitors.
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134
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Herschhorn A, Hizi A. Virtual screening, identification, and biochemical characterization of novel inhibitors of the reverse transcriptase of human immunodeficiency virus type-1. J Med Chem 2008; 51:5702-13. [PMID: 18800765 DOI: 10.1021/jm800473d] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The reverse transcriptase (RT) of human immunodeficiency virus type-1 (HIV-1) is a leading target in current antiretroviral therapy. Unfortunately, drug-resistant RT mutants evolve under the pressure of these drugs, and therefore, new anti-RT inhibitors are constantly required for HIV-1/AIDS treatment. We virtually screened a large chemical library of compounds against two crystal structures of HIV-1 RT to identify novel inhibitors. Top-scoring compounds were tested experimentally; 71 inhibited the RT-associated DNA polymerase, while several also inhibited HIV-1 pseudovirus infection in a cell-based assay. A combination of substituents from two structurally related inhibitors in a single molecule improved the inhibition efficacy. This compound strongly suppressed the RT-associated activity also protecting human lymphocytes from HIV-1 infection. RT inhibition by this compound was reversible and noncompetitive. This molecule and another structurally unrelated potent compound inhibited a known drug-resistant mutant of HIV-1 RT and affected moderately the HIV-2 RT-associated DNA polymerase. These inhibitors may serve as promising anti-HIV lead compounds.
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Affiliation(s)
- Alon Herschhorn
- Department of Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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135
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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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136
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Loksha YM, Globisch D, Pedersen EB, La Colla P, Collu G, Loddo R. Synthesis and anti-HIV-1 evaluation of 1,5-disubstituted pyrimidine-2,4-diones. J Heterocycl Chem 2008. [DOI: 10.1002/jhet.5570450434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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137
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Binding Modes of Two Novel Non-Nucleoside Reverse Transcriptase Inhibitors, YM-215389 and YM-228855, to HIV Type-1 Reverse Transcriptase. ACTA ACUST UNITED AC 2008; 19:133-41. [DOI: 10.1177/095632020801900304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Background: YM-215389 and YM-228855 are thiazolidenebenzenesulfonamide (TBS) derivatives and novel non-nucleoside reverse transcriptase inhibitors (NNRTIs) that inhibit not only wild-type, but also the K103N- and Y181C-substituted reverse transcriptase (RT) of HIV type-1 (HIV-1). Methods: To characterize the binding modes of the TBS derivatives in detail, the anti-HIV-1 activities of YM-215389 and YM-228855 against various NNRTI-resistant clones were examined. Docking studies with HIV-1 RT were also performed. Results: YM-215389, which effectively inhibits various NNRTI-resistant clones, interacted with L100, K103, V106 and Y318 through the benzene ring and with E138, V179, Y181, Y188 and W229 through the thiazole ring. A single amino acid substitution confers only moderate resistance to YM-215389; indeed, four amino acid substitutions (V106L, V108I, E138K and L214F) were necessary for high- level resistance. Although the activity of YM-228855, a derivative of YM-215389 that has two bulky and rigid cyano-moieties on the benzene ring, was 10x more potent against HIV-1 than YM-215389, its anti-HIV-1 activity was readily reduced with single substitutions as with Y181I and K103N. Conclusions: These results provide structural information for optimizing the TBS derivatives in an attempt to construct ideal NNRTIs that maintain anti-HIV-1 activity to various HIV-1 variants.
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138
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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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139
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Nervall M, Hanspers P, Carlsson J, Boukharta L, Aqvist J. Predicting binding modes from free energy calculations. J Med Chem 2008; 51:2657-67. [PMID: 18410080 DOI: 10.1021/jm701218j] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To produce reliable predictions of bioactive conformations is a major challenge in the field of structure-based inhibitor design and is a requirement for accurate binding free energy predictions with structure-based methods. A series of HIV-1 reverse transcriptase inhibitors was cross-docked using a non-native crystal structure that resulted in two distinct clusters of possible conformations. One of these clusters was compatible with an existing crystal structure, whereas the other displayed a flipped heterocyclic group. Binding free energies, using the non-native crystal structure, calculated from several scoring functions, were similar for the two clusters, and no conclusion about the binding mode could be drawn from these results. The two clusters could be separated through rescoring with the linear interaction method (LIE) in combination with molecular dynamics simulations, which leads to a binding mode prediction in line with experimental crystallographic data. Further, the LIE model produces the best correlation between experimental and calculated binding free energies among the tested scoring methods.
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Affiliation(s)
- Martin Nervall
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
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140
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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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141
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Chen XY, Qiu XL, Qing FL. Asymmetric synthesis of trifluoromethylated propargylamines via 1,2-additions of trifluoromethylacetylide to N-tert-butanesulfinyl imines. Tetrahedron 2008. [DOI: 10.1016/j.tet.2008.01.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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142
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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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143
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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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144
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Nagao H, Kawano Y, Mukaiyama T. Enantioselective Trifluoromethylation of Ketones with (Trifluoromethyl)trimethylsilane Catalyzed by Chiral Quaternary Ammonium Phenoxides. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2007. [DOI: 10.1246/bcsj.80.2406] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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145
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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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146
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Xia Q, Radzio J, Anderson KS, Sluis-Cremer N. Probing nonnucleoside inhibitor-induced active-site distortion in HIV-1 reverse transcriptase by transient kinetic analyses. Protein Sci 2007; 16:1728-37. [PMID: 17656585 PMCID: PMC2203366 DOI: 10.1110/ps.072829007] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Nonnucleoside reverse transcriptase inhibitors (NNRTI) are a group of structurally diverse compounds that bind to a single site in HIV-1 reverse transcriptase (RT), termed the NNRTI-binding pocket (NNRTI-BP). NNRTI binding to RT induces conformational changes in the enzyme that affect key elements of the polymerase active site and also the association between the two protein subunits. To determine which conformational changes contribute to the mechanism of inhibition of HIV-1 reverse transcription, we used transient kinetic analyses to probe the catalytic events that occur directly at the enzyme's polymerase active site when the NNRTI-BP was occupied by nevirapine, efavirenz, or delavirdine. Our results demonstrate that all NNRTI-RT-template/primer (NNRTI-RT-T/P) complexes displayed a metal-dependent increase in dNTP binding affinity (K(d) ) and a metal-independent decrease in the maximum rate of dNTP incorporation (k (pol)). The magnitude of the decrease in k (pol) was dependent on the NNRTI used in the assay: Efavirenz caused the largest decrease followed by delavirdine and then nevirapine. Analyses that were designed to probe direct effects on phosphodiester bond formation suggested that the NNRTI mediate their effects on the chemistry step of the DNA polymerization reaction via an indirect manner. Because each of the NNRTI analyzed in this study exerted largely similar phenotypic effects on single nucleotide addition reactions, whereas each of them are known to exert differential effects on RT dimerization, we conclude that the NNRTI effects on subunit association do not directly contribute to the kinetic mechanism of inhibition of DNA polymerization.
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Affiliation(s)
- Qing Xia
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
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147
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Famulok M, Hartig JS, Mayer G. Functional aptamers and aptazymes in biotechnology, diagnostics, and therapy. Chem Rev 2007; 107:3715-43. [PMID: 17715981 DOI: 10.1021/cr0306743] [Citation(s) in RCA: 673] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Michael Famulok
- LIMES Institute, Program Unit Chemical Biology and Medicinal Chemistry, c/o Kekulé-Institut für Organische Chemie und Biochemie, Gerhard Domagk-Strasse 1, 53121 Bonn, Germany.
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148
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Garner J, Deadman J, Rhodes D, Griffith R, Keller PA. A new methodology for the simulation of flexible protein–ligand interactions. J Mol Graph Model 2007; 26:187-97. [PMID: 17229583 DOI: 10.1016/j.jmgm.2006.11.004] [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: 07/07/2006] [Revised: 10/16/2006] [Accepted: 11/15/2006] [Indexed: 10/23/2022]
Abstract
A methodology has been developed for the simulation of induced fit between a ligand and its target protein. It utilizes constrained molecular dynamics where atoms determined to be immobile from difference distance matrix studies are fixed. Application of this methodology to HIV-1 reverse transcriptase (RT) as the example target protein has demonstrated its robustness. Short simulation times are sufficient to achieve good refinement of docking poses resulting from exchange of structurally dissimilar inhibitors between crystal structures.
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Affiliation(s)
- James Garner
- Department of Chemistry, University of Wollongong, Wollongong, NSW 2522, Australia
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149
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Design, synthesis, and biological evaluation of new 3-hydroxy-2-oxo-3-trifluoromethylindole as potential HIV-1 reverse transcriptase inhibitors. Med Chem Res 2007. [DOI: 10.1007/s00044-007-9004-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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150
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Nagao H, Yamane Y, Mukaiyama T. Asymmetric Trifluoromethylation of Ketones with (Trifluoromethyl)trimethylsilane Catalyzed by Chiral Quaternary Ammonium Phenoxides. CHEM LETT 2007. [DOI: 10.1246/cl.2007.666] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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