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Smith SJ, Zhao XZ, Passos DO, Lyumkis D, Burke TR, Hughes SH. Integrase Strand Transfer Inhibitors Are Effective Anti-HIV Drugs. Viruses 2021; 13:v13020205. [PMID: 33572956 PMCID: PMC7912079 DOI: 10.3390/v13020205] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/20/2021] [Accepted: 01/25/2021] [Indexed: 12/12/2022] Open
Abstract
Integrase strand transfer inhibitors (INSTIs) are currently recommended for the first line treatment of human immunodeficiency virus type one (HIV-1) infection. The first-generation INSTIs are effective but can select for resistant viruses. Recent advances have led to several potent second-generation INSTIs that are effective against both wild-type (WT) HIV-1 integrase and many of the first-generation INSTI-resistant mutants. The emergence of resistance to these new second-generation INSTIs has been minimal, which has resulted in alternative treatment strategies for HIV-1 patients. Moreover, because of their high antiviral potencies and, in some cases, their bioavailability profiles, INSTIs will probably have prominent roles in pre-exposure prophylaxis (PrEP). Herein, we review the current state of the clinically relevant INSTIs and discuss the future outlook for this class of antiretrovirals.
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Affiliation(s)
- Steven J. Smith
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA;
| | - Xue Zhi Zhao
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; (X.Z.Z.); (T.R.B.J.)
| | - Dario Oliveira Passos
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; (D.O.P.); (D.L.)
| | - Dmitry Lyumkis
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; (D.O.P.); (D.L.)
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Terrence R. Burke
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; (X.Z.Z.); (T.R.B.J.)
| | - Stephen H. Hughes
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA;
- Correspondence:
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Gupta A, Adami C. Strong Selection Significantly Increases Epistatic Interactions in the Long-Term Evolution of a Protein. PLoS Genet 2016; 12:e1005960. [PMID: 27028897 PMCID: PMC4814079 DOI: 10.1371/journal.pgen.1005960] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 03/06/2016] [Indexed: 11/18/2022] Open
Abstract
Epistatic interactions between residues determine a protein’s adaptability and shape its evolutionary trajectory. When a protein experiences a changed environment, it is under strong selection to find a peak in the new fitness landscape. It has been shown that strong selection increases epistatic interactions as well as the ruggedness of the fitness landscape, but little is known about how the epistatic interactions change under selection in the long-term evolution of a protein. Here we analyze the evolution of epistasis in the protease of the human immunodeficiency virus type 1 (HIV-1) using protease sequences collected for almost a decade from both treated and untreated patients, to understand how epistasis changes and how those changes impact the long-term evolvability of a protein. We use an information-theoretic proxy for epistasis that quantifies the co-variation between sites, and show that positive information is a necessary (but not sufficient) condition that detects epistasis in most cases. We analyze the “fossils” of the evolutionary trajectories of the protein contained in the sequence data, and show that epistasis continues to enrich under strong selection, but not for proteins whose environment is unchanged. The increase in epistasis compensates for the information loss due to sequence variability brought about by treatment, and facilitates adaptation in the increasingly rugged fitness landscape of treatment. While epistasis is thought to enhance evolvability via valley-crossing early-on in adaptation, it can hinder adaptation later when the landscape has turned rugged. However, we find no evidence that the HIV-1 protease has reached its potential for evolution after 9 years of adapting to a drug environment that itself is constantly changing. We suggest that the mechanism of encoding new information into pairwise interactions is central to protein evolution not just in HIV-1 protease, but for any protein adapting to a changing environment. Evolution is often viewed as a process that occurs “mutation by mutation”, suggesting that the effect of each mutation is independent of that of others. However, in reality the effect of a mutation often depends on the context of other mutations, a dependence known as “epistasis”. Even though epistasis can constrain protein evolution, it is actually very common. Such interactions are particularly pervasive in proteins that evolve resistance to a drug via mutations that create defects, and that must be repaired with compensatory mutations. We study how epistasis between protein residues evolves over time in a new and changing environment, and compare these findings to protein evolution in a constant environment. We analyze the sequences of the human immunodeficiency virus type 1 (HIV-1) protease enzyme collected over a period of 9 years from patients treated with anti-viral drugs (as well as from patients that went untreated), and find that epistasis between residues continues to increase as more potent anti-viral drugs enter the market, while epistasis is unchanging in the proteins exposed to a constant environment. Yet, the proteins adapting to the changing landscape do not appear to be constrained by the epistatic interactions and continue to manage to evade new drugs.
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Affiliation(s)
- Aditi Gupta
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, United States of America
| | - Christoph Adami
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, United States of America
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan, United States of America
- * E-mail:
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Hsu M, Keele BF, Aravantinou M, Krawczyk N, Seidor S, Abraham CJ, Zhang S, Rodriguez A, Kizima L, Derby N, Jean-Pierre N, Mizenina O, Gettie A, Grasperge B, Blanchard J, Piatak MJ, Lifson JD, Fernández-Romero JA, Zydowsky TM, Robbiani M. Exposure to MIV-150 from a high-dose intravaginal ring results in limited emergence of drug resistance mutations in SHIV-RT infected rhesus macaques. PLoS One 2014; 9:e89300. [PMID: 24586674 PMCID: PMC3937329 DOI: 10.1371/journal.pone.0089300] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 01/17/2014] [Indexed: 11/19/2022] Open
Abstract
When microbicides used for HIV prevention contain antiretroviral drugs, there is concern for the potential emergence of drug-resistant HIV following use in infected individuals who are either unaware of their HIV infection status or who are aware but still choose to use the microbicide. Resistant virus could ultimately impact their responsiveness to treatment and/or result in subsequent transmission of drug-resistant virus. We tested whether drug resistance mutations (DRMs) would emerge in macaques infected with simian immunodeficiency virus expressing HIV reverse transcriptase (SHIV-RT) after sustained exposure to the potent non-nucleoside reverse transcriptase inhibitor (NNRTI) MIV-150 delivered via an intravaginal ring (IVR). We first treated 4 SHIV-RT-infected animals with daily intramuscular injections of MIV-150 over two 21 day (d) intervals separated by a 7 d drug hiatus. In all 4 animals, NNRTI DRMs (single and combinations) were detected within 14 d and expanded in proportion and diversity with time. Knowing that we could detect in vivo emergence of NNRTI DRMs in response to MIV-150, we then tested whether a high-dose MIV-150 IVR (loaded with >10 times the amount being used in a combination microbicide IVR in development) would select for resistance in 6 infected animals, modeling use of this prevention method by an HIV-infected woman. We previously demonstrated that this MIV-150 IVR provides significant protection against vaginal SHIV-RT challenge. Wearing the MIV-150 IVR for 56 d led to only 2 single DRMs in 2 of 6 animals (430 RT sequences analyzed total, 0.46%) from plasma and lymph nodes despite MIV-150 persisting in the plasma, vaginal fluids, and genital tissues. Only wild type virus sequences were detected in the genital tissues. These findings indicate a low probability for the emergence of DRMs after topical MIV-150 exposure and support the advancement of MIV-150-containing microbicides.
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Affiliation(s)
- Mayla Hsu
- Center for Biomedical Research, Population Council, New York, New York, United States of America
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc. (formerly SAIC-Frederick, Inc.), Frederick National Laboratory, Frederick, Maryland, United States of America
| | - Meropi Aravantinou
- Center for Biomedical Research, Population Council, New York, New York, United States of America
| | - Noa Krawczyk
- Center for Biomedical Research, Population Council, New York, New York, United States of America
| | - Samantha Seidor
- Center for Biomedical Research, Population Council, New York, New York, United States of America
| | - Ciby J. Abraham
- Center for Biomedical Research, Population Council, New York, New York, United States of America
| | - Shimin Zhang
- Center for Biomedical Research, Population Council, New York, New York, United States of America
| | - Aixa Rodriguez
- Center for Biomedical Research, Population Council, New York, New York, United States of America
| | - Larisa Kizima
- Center for Biomedical Research, Population Council, New York, New York, United States of America
| | - Nina Derby
- Center for Biomedical Research, Population Council, New York, New York, United States of America
| | - Ninochka Jean-Pierre
- Center for Biomedical Research, Population Council, New York, New York, United States of America
| | - Olga Mizenina
- Center for Biomedical Research, Population Council, New York, New York, United States of America
| | - Agegnehu Gettie
- Aaron Diamond AIDS Research Center, Rockefeller University, New York, New York, United States of America
| | - Brooke Grasperge
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - James Blanchard
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Michael J. Piatak
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc. (formerly SAIC-Frederick, Inc.), Frederick National Laboratory, Frederick, Maryland, United States of America
| | - Jeffrey D. Lifson
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc. (formerly SAIC-Frederick, Inc.), Frederick National Laboratory, Frederick, Maryland, United States of America
| | - José A. Fernández-Romero
- Center for Biomedical Research, Population Council, New York, New York, United States of America
| | - Thomas M. Zydowsky
- Center for Biomedical Research, Population Council, New York, New York, United States of America
| | - Melissa Robbiani
- Center for Biomedical Research, Population Council, New York, New York, United States of America
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