Triumphs of Crystallography in Tackling HIV/AIDS: Drugs by Design

Crystallography has made extraordinary contributions to our understanding of the biology and chemistry of HIV. Judicious applications of structure-based drug design against HIV-1 protease and reverse transcriptase (RT) has led to the discovery of key drugs that are used in combinations to treat HIV infection. Extensive research and development efforts by pharma, academia, and government have made it possible for an HIV-infected person to live a nearly normal life. I will summarize the elegant structures that have been determined of components of HIV, with an emphasis on the enzyme RT, which my laboratory has studied since 1987. HIV-1 RT is responsible for converting the viral 10-kilobase single-stranded RNA genome to double-stranded DNA. This fascinating and essential enzyme is the target of 13 approved anti-AIDS drugs: 8 nucleoside analog RT inhibitors (NRTIs) and 5 non-nucleoside RT inhibitors (NNRTIs). We have determined crystal structures of wild-type and drug-resistant RTs in complexes with nucleic acid and/or inhibitors. We participated in structure-guided discovery and development of two anti-AIDS drugs with exceptional potency against drug-resistant variants. Crystal structures combined with biochemical data help to elucidate intriguing molecular mechanisms by which HIV-1 develops resistance to different anti-AIDS drugs. Recent crystallographic fragment screening has revealed new allosteric inhibitory binding pockets for future drug discovery. I am very grateful to my many co-workers, colleagues, and friends for their contributions, synchrotron resources at CHESS, BNLS, and APS, and generous funding from NIH in support of research on HIV-1 RT.

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Mechanism of Substrate Recognition by Drug-Resistant Human Immunodeficiency Virus Type 1 Protease Variants Revealed by a Novel Structural Intermediate

Journal of Virology ◽

10.1128/jvi.80.7.3607-3616.2006 ◽

2006 ◽

Vol 80 (7) ◽

pp. 3607-3616 ◽

Cited By ~ 41

Author(s):

Moses Prabu-Jeyabalan ◽

Ellen A. Nalivaika ◽

Keith Romano ◽

Celia A. Schiffer

Keyword(s):

Human Immunodeficiency Virus ◽

Crystal Structures ◽

Human Immunodeficiency Virus Type ◽

Virus Type ◽

Structural Model ◽

Substrate Recognition ◽

Drug Resistant ◽

Immunodeficiency Virus ◽

Hiv 1

ABSTRACT Human immunodeficiency virus type 1 (HIV-1) protease processes and cleaves the Gag and Gag-Pol polyproteins, allowing viral maturation, and therefore is an important target for antiviral therapy. Ligand binding occurs when the flaps open, allowing access to the active site. This flexibility in flap geometry makes trapping and crystallizing structural intermediates in substrate binding challenging. In this study, we report two crystal structures of two HIV-1 protease variants bound with their corresponding nucleocapsid-p1 variant. One of the flaps in each of these structures exhibits an unusual “intermediate” conformation. Analysis of the flap-intermediate and flap-closed crystal structures reveals that the intermonomer flap movements may be asynchronous and that the flap which wraps over the P3 to P1 (P3-P1) residues of the substrate might close first. This is consistent with our hypothesis that the P3-P1 region is crucial for substrate recognition. The intermediate conformation is conserved in both the wild-type and drug-resistant variants. The structural differences between the variants are evident only when the flaps are closed. Thus, a plausible structural model for the adaptability of HIV-1 protease to recognize substrates in the presence of drug-resistant mutations has been proposed.

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Relationship of Potency and Resilience to Drug Resistant Mutations for GW420867X Revealed by Crystal Structures of Inhibitor Complexes for Wild-Type, Leu100Ile, Lys101Glu, and Tyr188Cys Mutant HIV-1 Reverse Transcriptases†

Journal of Medicinal Chemistry ◽

10.1021/jm061117m ◽

2007 ◽

Vol 50 (10) ◽

pp. 2301-2309 ◽

Cited By ~ 32

Author(s):

Jingshan Ren ◽

Charles E. Nichols ◽

Philip P. Chamberlain ◽

Kurt L. Weaver ◽

Steven A. Short ◽

...

Keyword(s):

Crystal Structures ◽

Drug Resistant ◽

Wild Type ◽

Reverse Transcriptases ◽

Relationship Of ◽

Hiv 1

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145 Drug-resistant HIV-1 mutants may undergo further mutations in their reverse transcriptase (RT) under continuous pressure of HIV-1-specific RT inhibitors

Antiviral Research ◽

10.1016/0166-3542(94)90268-2 ◽

1994 ◽

Vol 23 ◽

pp. 113

Keyword(s):

Reverse Transcriptase ◽

Drug Resistant ◽

Rt Inhibitors ◽

Hiv 1

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Optimization and Computational Evaluation of a Series of Potential Active Site Inhibitors of the V82F/I84V Drug-resistant Mutant of HIV-1 Protease: an Application of the Relaxed Complex Method of Structure-based Drug Design

Chemical Biology & Drug Design ◽

10.1111/j.1747-0285.2006.00382.x ◽

2006 ◽

Vol 67 (5) ◽

pp. 336-345 ◽

Cited By ~ 17

Author(s):

Alexander L. Perryman ◽

Jung-Hsin Lin ◽

J. Andrew McCammon

Keyword(s):

Drug Design ◽

Active Site ◽

Resistant Mutant ◽

Complex Method ◽

Drug Resistant ◽

Structure Based Drug Design ◽

Computational Evaluation ◽

Drug Resistant Mutant ◽

Hiv 1

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Crystal Structures for HIV-1 Reverse Transcriptase in Complexes with Three Pyridinone Derivatives: A New Class of Non-Nucleoside Inhibitors Effective against a Broad Range of Drug-Resistant Strains

Journal of Medicinal Chemistry ◽

10.1021/jm0500323 ◽

2005 ◽

Vol 48 (24) ◽

pp. 7582-7591 ◽

Cited By ~ 93

Author(s):

Daniel M. Himmel ◽

Kalyan Das ◽

Arthur D. Clark, ◽

Stephen H. Hughes ◽

Abdellah Benjahad ◽

...

Keyword(s):

Reverse Transcriptase ◽

Crystal Structures ◽

Drug Resistant ◽

New Class ◽

Resistant Strains ◽

Drug Resistant Strains ◽

Nucleoside Inhibitors ◽

Hiv 1

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Human Immunodeficiency Virus Mutagenesis during Antiviral Therapy: Impact of Drug-Resistant Reverse Transcriptase and Nucleoside and Nonnucleoside Reverse Transcriptase Inhibitors on Human Immunodeficiency Virus Type 1 Mutation Frequencies

Journal of Virology ◽

10.1128/jvi.79.18.12045-12057.2005 ◽

2005 ◽

Vol 79 (18) ◽

pp. 12045-12057 ◽

Cited By ~ 24

Author(s):

Renxiang Chen ◽

Masaru Yokoyama ◽

Hironori Sato ◽

Cavan Reilly ◽

Louis M. Mansky

Keyword(s):

Human Immunodeficiency Virus ◽

Reverse Transcriptase ◽

Antiviral Drug ◽

Drug Resistant ◽

Resistant Virus ◽

Immunodeficiency Virus ◽

Rt Inhibitors ◽

Hiv 1 ◽

Drug Resistant Virus

ABSTRACT The development of antiviral drug resistance is an important problem in the treatment of human immunodeficiency virus type 1 (HIV-1) infection. Potent antiretroviral therapy is currently used for treatment, and typically consists of at least two reverse transcriptase (RT) inhibitors. We have previously reported that both drugs and drug-resistant RT mutants can increase virus mutation frequencies. To further assess the contributions of nucleoside RT inhibitors (NRTIs), nonnucleoside RT inhibitors (NNRTIs), and drug-resistant RTs to HIV mutagenesis, a new high-throughput assay system was developed. This assay system was designed to specifically detect frameshift mutations in the luciferase gene in a single virus replication cycle. New drug-resistant RTs were identified that significantly altered virus mutation frequencies. Consistent with our previous observations of NRTIs, abacavir, stavudine, and zalcitabine increased HIV-1 mutation frequencies, supporting the general hypothesis that the NRTIs currently used in antiviral drug therapy increase virus mutation frequencies. Interestingly, similar observations were made with NNRTIs. This is the first report to show that NNRTIs can influence virus mutation frequencies. NNRTI combinations, NRTI-NNRTI combinations, and combinations of drug and drug-resistant RTs led to significant changes in the virus mutation frequencies compared to virus replication of drug-resistant virus in the absence of drug or wild-type virus in the presence of drug. This indicates that combinations of RT drugs or drugs and drug-resistant virus created during the evolution of drug resistance can act together to increase HIV-1 mutation frequencies, which would have important implications for drug therapy regimens. Finally, the influence of drug-resistant RT mutants from CRF01_AE viruses on HIV-1 mutation frequencies was analyzed and it was found that only a highly drug resistant RT led to altered virus mutation frequencies. The results further suggest that high-level drug-resistant RT can significantly influence virus mutation frequencies. A structural model that explains the mutation frequency data is discussed.

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140 Effects of combinations of HIV-1 specific RT inhibitors with complementary resistance profiles on the time and type of drug-resistant HIV-1 development

Antiviral Research ◽

10.1016/0166-3542(94)90263-1 ◽

1994 ◽

Vol 23 ◽

pp. 109

Keyword(s):

Drug Resistant ◽

Rt Inhibitors ◽

Hiv 1

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A Rough Set-Based Model of HIV-1 Reverse Transcriptase Resistome

Bioinformatics and Biology Insights ◽

10.4137/bbi.s3382 ◽

2009 ◽

Vol 3 ◽

pp. BBI.S3382 ◽

Cited By ~ 16

Author(s):

Marcin Kierczak ◽

Krzysztof Ginalski ◽

Michał Dramiñski ◽

Jacek Koronacki ◽

Witold Rudnicki ◽

...

Keyword(s):

Drug Resistance ◽

Reverse Transcriptase ◽

Rough Set ◽

Molecular Mechanisms ◽

3D Structure ◽

Feature Selection Method ◽

Resistance Mutations ◽

Monte Carlo Feature Selection ◽

Rt Inhibitors ◽

Hiv 1

Reverse transcriptase (RT) is a viral enzyme crucial for HIV-1 replication. Currently, 12 drugs are targeted against the RT. The low fidelity of the RT-mediated transcription leads to the quick accumulation of drug-resistance mutations. The sequence-resistance relationship remains only partially understood. Using publicly available data collected from over 15 years of HIV proteome research, we have created a general and predictive rule-based model of HIV-1 resistance to eight RT inhibitors. Our rough set-based model considers changes in the physicochemical properties of a mutated sequence as compared to the wild-type strain. Thanks to the application of the Monte Carlo feature selection method, the model takes into account only the properties that significantly contribute to the resistance phenomenon. The obtained results show that drug-resistance is determined in more complex way than believed. We confirmed the importance of many resistance-associated sites, found some sites to be less relevant than formerly postulated and—more importantly—identified several previously neglected sites as potentially relevant. By mapping some of the newly discovered sites on the 3D structure of the RT, we were able to suggest possible molecular-mechanisms of drug-resistance. Importantly, our model has the ability to generalize predictions to the previously unseen cases. The study is an example of how computational biology methods can increase our understanding of the HIV-1 resistome.

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