Codon optimization and improved delivery/immunization regimen enhance the immune response against wild-type and drug-resistant HIV-1 reverse transcriptase, preserving its Th2-polarity

ABSTRACT Indolyl aryl sulfone (IAS) nonnucleoside inhibitors have been shown to potently inhibit the growth of wild-type and drug-resistant human immunodeficiency virus type 1 (HIV-1), but their exact mechanism of action has not been elucidated yet. Here, we describe the mechanism of inhibition of HIV-1 reverse transcriptase (RT) by selected IAS derivatives. Our results showed that, depending on the substitutions introduced in the IAS common pharmacophore, these compounds can be made selective for different enzyme-substrate complexes. Moreover, we showed that the molecular basis for this selectivity was a different association rate of the drug to a particular enzymatic form along the reaction pathway. By comparing the activities of the different compounds against wild-type RT and the nonnucleoside reverse transcriptase inhibitor-resistant mutant Lys103Asn, it was possible to hypothesize, on the basis of their mechanism of action, a rationale for the design of drugs which could overcome the steric barrier imposed by the Lys103Asn mutation.

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Roles of Conformational and Positional Adaptability in Structure-Based Design of TMC125-R165335 (Etravirine) and Related Non-nucleoside Reverse Transcriptase Inhibitors That Are Highly Potent and Effective against Wild-Type and Drug-Resistant HIV-1 Variants

Journal of Medicinal Chemistry ◽

10.1021/jm030558s ◽

2004 ◽

Vol 47 (10) ◽

pp. 2550-2560 ◽

Cited By ~ 360

Author(s):

Kalyan Das ◽

Arthur D. Clark, ◽

Paul J. Lewi ◽

Jan Heeres ◽

Marc R. de Jonge ◽

...

Keyword(s):

Reverse Transcriptase ◽

Drug Resistant ◽

Wild Type ◽

Reverse Transcriptase Inhibitors ◽

Nucleoside Reverse Transcriptase Inhibitors ◽

Hiv 1

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Potent cross-reactive immune response against the wild-type and drug-resistant forms of HIV reverse transcriptase after the chimeric gene immunization

Vaccine ◽

10.1016/j.vaccine.2009.10.098 ◽

2010 ◽

Vol 28 (8) ◽

pp. 1975-1986 ◽

Cited By ~ 9

Author(s):

Elizaveta Starodubova ◽

Andreas Boberg ◽

Alexander Ivanov ◽

Oleg Latyshev ◽

Natalia Petrakova ◽

...

Keyword(s):

Immune Response ◽

Reverse Transcriptase ◽

Chimeric Gene ◽

Drug Resistant ◽

Wild Type ◽

Hiv Reverse Transcriptase ◽

Gene Immunization

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Individual Contributions of Mutant Protease and Reverse Transcriptase to Viral Infectivity, Replication, and Protein Maturation of Antiretroviral Drug-Resistant Human Immunodeficiency Virus Type 1

Journal of Virology ◽

10.1128/jvi.75.7.3291-3300.2001 ◽

2001 ◽

Vol 75 (7) ◽

pp. 3291-3300 ◽

Cited By ~ 57

Author(s):

Gabriela Bleiber ◽

Miguel Munoz ◽

Angela Ciuffi ◽

Pascal Meylan ◽

Amalio Telenti

Keyword(s):

Human Immunodeficiency Virus ◽

Reverse Transcriptase ◽

Drug Resistant ◽

Wild Type ◽

Protein Maturation ◽

Antiretroviral Drug ◽

Immunodeficiency Virus ◽

Individual Contributions ◽

Hiv 1

ABSTRACT Human immunodeficiency virus type 1 (HIV-1) variants resistant to protease (PR) and reverse transcriptase (RT) inhibitors may display impaired infectivity and replication capacity. The individual contributions of mutated HIV-1 PR and RT to infectivity, replication, RT activity, and protein maturation (herein referred to as “fitness”) in recombinant viruses were investigated by separately cloning PR, RT, and PR-RT cassettes from drug-resistant mutant viral isolates into the wild-type NL4-3 background. Both mutant PR and RT contributed to measurable deficits in fitness of viral constructs. In peripheral blood mononuclear cells, replication rates (means ± standard deviations) of RT recombinants were 72.5% ± 27.3% and replication rates of PR recombinants were 60.5% ± 33.6% of the rates of NL4-3. PR mutant deficits were enhanced in CEM T cells, with relative replication rates of PR recombinants decreasing to 15.8% ± 23.5% of NL4-3 replication rates. Cloning of the cognate RT improved fitness of some PR mutant clones. For a multidrug-resistant virus transmitted through sexual contact, RT constructs displayed a marked infectivity and replication deficit and diminished packaging of Pol proteins (RT content in virions diminished by 56.3% ± 10.7%, and integrase content diminished by 23.3% ± 18.4%), a novel mechanism for a decreased-fitness phenotype. Despite the identified impairment of recombinant clones, fitness of two of the three drug-resistant isolates was comparable to that of wild-type, susceptible viruses, suggestive of extensive compensation by genomic regions away from PR and RT. Only limited reversion of mutated positions to wild-type amino acids was observed for the native isolates over 100 viral replication cycles in the absence of drug selective pressure. These data underscore the complex relationship between PR and RT adaptive changes and viral evolution in antiretroviral drug-resistant HIV-1.

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Combined Approach Using Ligand Efficiency, Cross-Docking, and Antitarget Hits for Wild-Type and Drug-Resistant Y181C HIV-1 Reverse Transcriptase

Journal of Chemical Information and Modeling ◽

10.1021/ci200203h ◽

2011 ◽

Vol 51 (10) ◽

pp. 2595-2611 ◽

Cited By ~ 22

Author(s):

Alfonso T. García-Sosa ◽

Sulev Sild ◽

Kalev Takkis ◽

Uko Maran

Keyword(s):

Reverse Transcriptase ◽

Drug Resistant ◽

Combined Approach ◽

Wild Type ◽

Ligand Efficiency ◽

Cross Docking ◽

Hiv 1

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Competitive Fitness of Nevirapine-Resistant Human Immunodeficiency Virus Type 1 Mutants

Journal of Virology ◽

10.1128/jvi.78.2.603-611.2004 ◽

2004 ◽

Vol 78 (2) ◽

pp. 603-611 ◽

Cited By ~ 69

Author(s):

Jennifer A. Collins ◽

M. Gregory Thompson ◽

Elijah Paintsil ◽

Melisa Ricketts ◽

Joanna Gedzior ◽

...

Keyword(s):

Human Immunodeficiency Virus ◽

Reverse Transcriptase ◽

Drug Resistant ◽

Wild Type ◽

Competitive Fitness ◽

Immunodeficiency Virus ◽

Resistant Mutants ◽

Nevirapine Resistance ◽

Hiv 1

ABSTRACT Determining the fitness of drug-resistant human immunodeficiency virus type 1 (HIV-1) strains is necessary for the development of population-based studies of resistance patterns. For this purpose, we have developed a reproducible, systematic assay to determine the competitive fitness of HIV-1 drug-resistant mutants. To demonstrate the applicability of this assay, we tested the fitness of the five most common nevirapine-resistant mutants (103N, 106A, 181C, 188C, and 190A), with mutations in HIV-1 reverse transcriptase (RT), singly and in combination (for a total of 31 variants) in a defined HIV-1 background. For these experiments, the 27 RT variants that produced viable virus were cocultured with wild-type virus without nevirapine. The ratios of the viral species were determined over time by utilization of a quantitative real-time RT-PCR-based assay. These experiments revealed that all of the viable variants were less fit than the wild type and demonstrated that the order of relative fitness of the single mutants tested was as follows: 103N > 181C > 190A > 188C > 106A. This order correlated with the commonality of these mutants as a result of nevirapine monotherapy. These investigations also revealed that, on average, the double mutants were less fit than the single mutants and the triple mutants were less fit than the double mutants. However, the fitness of the single and double mutants was often not predictive of the fitness of the derivative triple mutants, suggesting the presence of complex interactions between the closely aligned residues that confer nevirapine resistance. This complexity was also evident from the observation that all three of the replication-competent quadruple mutants were fitter than most of the triple mutants, and in some cases, even the double mutants. Our data suggest that, in many cases, viral fitness is the determining factor in the evolution of nevirapine-resistant mutants in vivo, that interactions between the residues that confer nevirapine resistance are complex, and that these interactions substantially affect reverse transcriptase structure and/or function.

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Benzophenone derivatives of pyrimidines as effective non-nucleoside inhibitors of wild-type and drug-resistant HIV-1 reverse transcriptase

Doklady Biochemistry and Biophysics ◽

10.1134/s160767291206004x ◽

2012 ◽

Vol 447 (1) ◽

pp. 280-281 ◽

Cited By ~ 1

Author(s):

M. M. Prokofjeva ◽

V. T. Valuev-Elliston ◽

A. V. Ivanov ◽

S. N. Kochetkov ◽

M. S. Novikov ◽

...

Keyword(s):

Reverse Transcriptase ◽

Drug Resistant ◽

Wild Type ◽

Nucleoside Inhibitors ◽

Derivatives Of ◽

Hiv 1

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Identification of a Novel Scaffold for Allosteric Inhibition of Wild Type and Drug Resistant HIV-1 Reverse Transcriptase by Fragment Library Screening

Journal of Medicinal Chemistry ◽

10.1021/jm1010513 ◽

2011 ◽

Vol 54 (3) ◽

pp. 699-708 ◽

Cited By ~ 33

Author(s):

Matthis Geitmann ◽

Malin Elinder ◽

Christian Seeger ◽

Peter Brandt ◽

Iwan J. P. de Esch ◽

...

Keyword(s):

Reverse Transcriptase ◽

Library Screening ◽

Drug Resistant ◽

Wild Type ◽

Allosteric Inhibition ◽

Fragment Library ◽

Novel Scaffold ◽

Hiv 1

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Application of Molecular Docking for the Development of Improved HIV-1 Reverse Transcriptase Inhibitors

Current Computer - Aided Drug Design ◽

10.2174/1573409916666200628103359 ◽

2020 ◽

Vol 16 ◽

Author(s):

Arash Soltani ◽

Seyed Isaac Hashemy ◽

Farnaz Zahedi Avval ◽

Houshang Rafatpanah ◽

Seyed Abdolrahim Rezaee ◽

...

Keyword(s):

Reverse Transcriptase ◽

Binding Capacity ◽

Binding Pocket ◽

Ligand Docking ◽

Binding Modes ◽

Wild Type ◽

Parent Molecule ◽

Discovery Studio ◽

Approved Drugs ◽

Hiv 1

Introoduction: Inhibition of the reverse transcriptase (RT) enzyme of human immunodeficiency virus (HIV) by low molecular weight inhibitors is still an active area of research. Here, protein-ligand interactions and possible binding modes of novel compounds with the HIV-1 RT binding pocket (the wild-type as well as Y181C and K103N mutants) were obtained and discussed. Methods: A molecular fragment-based approach using FDA-approved drugs were followed to design novel chemical derivatives using delavirdine, efavirenz, etravirine and rilpivirine as the scaffolds. The drug-likeliness of the derivatives was evaluated using Swiss-ADME. Then the parent molecule and derivatives were docked into the binding pocket of related crystal structures (PDB ID: 4G1Q, 1IKW, 1KLM and 3MEC). Genetic Optimization for Ligand Docking (GOLD) Suite 5.2.2 software was used for docking and the results analyzed in the Discovery Studio Visualizer 4. A derivative was chosen for further analysis, if it passed drug-likeliness and the docked energy was more favorable than that of its parent molecule. Out of the fifty-seven derivatives, forty-eight failed in druglikeness screening by Swiss-ADME or in docking stage. Results: The final results showed that the selected compounds had higher predicted binding affinities than their parent scaffolds in both wild-type and the mutants. Binding energy improvement was higher for the structures designed based on second-generation NNRTIs (etravirine and rilpivirine) than the first-generation NNRTIs (delavirdine and efavirenz). For example, while the docked energy for rilpivirine was -51 KJ/mol, it was improved for its derivatives RPV01 and RPV15 up to -58.3 and -54.5 KJ/mol, respectively. Conclusion: In this study, we have identified and proposed some novel molecules with improved binding capacity for HIV RT using fragment-based approach.

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