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Umumararungu T, Nyandwi JB, Katandula J, Twizeyimana E, Claude Tomani J, Gahamanyi N, Ishimwe N, Olawode EO, Habarurema G, Mpenda M, Uyisenga JP, Saeed SI. Current status of the small molecule anti-HIV drugs in the pipeline or recently approved. Bioorg Med Chem 2024; 111:117860. [PMID: 39094527 DOI: 10.1016/j.bmc.2024.117860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 07/24/2024] [Accepted: 07/25/2024] [Indexed: 08/04/2024]
Abstract
Human Immunodeficiency Virus (HIV) is the causative agent of Acquired Immunodeficiency Syndrome (AIDS) with high morbidity and mortality rates. Treatment of AIDS/HIV is being complicated by increasing resistance to currently used antiretroviral (ARV) drugs, mainly in low- and middle-income countries (LMICs) due to drug misuse, poor drug supply and poor treatment monitoring. However, progress has been made in the development of new ARV drugs, targeting different HIV components (Fig. 1). This review aims at presenting and discussing the progress made towards the discovery of new ARVs that are at different stages of clinical trials as of July 2024. For each compound, the mechanism of action, target biomolecule, genes associated with resistance, efficacy and safety, class, and phase of clinical trial are discussed. These compounds include analogues of nucleoside reverse transcriptase inhibitors (NRTIs) - islatravir and censavudine; non-nucleoside reverse transcriptase inhibitors (NNRTIs) - Rilpivirine, elsulfavirine and doravirine; integrase inhibitors namely cabotegravir and dolutegravir and chemokine coreceptors 5 and 2 (CC5/CCR2) antagonists for example cenicriviroc. Also, fostemsavir is being developed as an attachment inhibitor while lenacapavir, VH4004280 and VH4011499 are capsid inhibitors. Others are maturation inhibitors such as GSK-254, GSK3532795, GSK3739937, GSK2838232, and other compounds labelled as miscellaneous (do not belong to the classical groups of anti-HIV drugs or to the newer classes) such as obefazimod and BIT225. There is a considerable progress in the development of new anti-HIV drugs and the effort will continue since HIV infections has no cure or vaccine till now. Efforts are needed to reduce the toxicity of available drugs or discover new drugs with new classes which can delay the development of resistance.
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Affiliation(s)
- Théoneste Umumararungu
- Department of Industrial Pharmacy, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Rwanda.
| | - Jean Baptiste Nyandwi
- Department of Pharmacology and Toxicology, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Rwanda; East African Community Regional Centre of Excellence for Vaccines, Immunization and Health Supply Chain Management, Kigali, Rwanda
| | - Jonathan Katandula
- Department of Pharmacology and Toxicology, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Rwanda
| | - Eric Twizeyimana
- Department of Physiology, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Rwanda
| | - Jean Claude Tomani
- Department of Chemistry, School of Science, College of Science and Technology, University of Rwanda, Rwanda
| | - Noël Gahamanyi
- Department of Biology, School of Science, College of Science and Technology, University of Rwanda, Rwanda
| | - Nestor Ishimwe
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Emmanuel Oladayo Olawode
- Department of Pharmaceutical Sciences, College of Pharmacy, Larkin University, 18301 N Miami Ave #1, Miami, FL 33169, USA
| | - Gratien Habarurema
- Department of Chemistry, School of Science, College of Science and Technology, University of Rwanda, Rwanda
| | - Matabishi Mpenda
- Department of Pharmacology and Toxicology, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Rwanda
| | - Jeanne Primitive Uyisenga
- Department of Biology, School of Science, College of Science and Technology, University of Rwanda, Rwanda
| | - Shamsaldeen Ibrahim Saeed
- Faculty of Veterinary Science, University of Nyala, P.O. Box: 155, Nyala, Sudan; Nanotechnology in Veterinary Medicine (NanoVet) Research Group, Faculty of Veterinary Medicine, University Malaysia Kelantan, Kelantan 16100, Pengkalan Chepa, Malaysia
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Ren P, Li S, Wang S, Zhang X, Bai F. Computer-Aided Prediction of the Interactions of Viral Proteases with Antiviral Drugs: Antiviral Potential of Broad-Spectrum Drugs. Molecules 2023; 29:225. [PMID: 38202808 PMCID: PMC10780089 DOI: 10.3390/molecules29010225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/27/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
Human society is facing the threat of various viruses. Proteases are promising targets for the treatment of viral infections. In this study, we collected and profiled 170 protease sequences from 125 viruses that infect humans. Approximately 73 of them are viral 3-chymotrypsin-like proteases (3CLpro), and 11 are pepsin-like aspartic proteases (PAPs). Their sequences, structures, and substrate characteristics were carefully analyzed to identify their conserved nature for proposing a pan-3CLpro or pan-PAPs inhibitor design strategy. To achieve this, we used computational prediction and modeling methods to predict the binding complex structures for those 73 3CLpro with 4 protease inhibitors of SARS-CoV-2 and 11 protease inhibitors of HCV. Similarly, the complex structures for the 11 viral PAPs with 9 protease inhibitors of HIV were also obtained. The binding affinities between these compounds and proteins were also evaluated to assess their pan-protease inhibition via MM-GBSA. Based on the drugs targeting viral 3CLpro and PAPs, repositioning of the active compounds identified several potential uses for these drug molecules. As a result, Compounds 1-2, modified based on the structures of Ray1216 and Asunaprevir, indicate potential inhibition of DENV protease according to our computational simulation results. These studies offer ideas and insights for future research in the design of broad-spectrum antiviral drugs.
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Affiliation(s)
- Pengxuan Ren
- School of Life Science and Technology, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; (P.R.); (S.L.); (S.W.)
| | - Shiwei Li
- School of Life Science and Technology, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; (P.R.); (S.L.); (S.W.)
| | - Shihang Wang
- School of Life Science and Technology, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; (P.R.); (S.L.); (S.W.)
| | - Xianglei Zhang
- School of Life Science and Technology, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; (P.R.); (S.L.); (S.W.)
| | - Fang Bai
- School of Life Science and Technology, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; (P.R.); (S.L.); (S.W.)
- School of Information Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
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Moranguinho I, Taveira N, Bártolo I. Antiretroviral Treatment of HIV-2 Infection: Available Drugs, Resistance Pathways, and Promising New Compounds. Int J Mol Sci 2023; 24:ijms24065905. [PMID: 36982978 PMCID: PMC10053740 DOI: 10.3390/ijms24065905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/08/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Currently, it is estimated that 1-2 million people worldwide are infected with HIV-2, accounting for 3-5% of the global burden of HIV. The course of HIV-2 infection is longer compared to HIV-1 infection, but without effective antiretroviral therapy (ART), a substantial proportion of infected patients will progress to AIDS and die. Antiretroviral drugs in clinical use were designed for HIV-1 and, unfortunately, some do not work as well, or do not work at all, for HIV-2. This is the case for non-nucleoside reverse transcriptase inhibitors (NNRTIs), the fusion inhibitor enfuvirtide (T-20), most protease inhibitors (PIs), the attachment inhibitor fostemsavir and most broadly neutralizing antibodies. Integrase inhibitors work well against HIV-2 and are included in first-line therapeutic regimens for HIV-2-infected patients. However, rapid emergence of drug resistance and cross-resistance within each drug class dramatically reduces second-line treatment options. New drugs are needed to treat infection with drug-resistant isolates. Here, we review the therapeutic armamentarium available to treat HIV-2-infected patients, as well as promising drugs in development. We also review HIV-2 drug resistance mutations and resistance pathways that develop in HIV-2-infected patients under treatment.
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Affiliation(s)
- Inês Moranguinho
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-019 Lisboa, Portugal
| | - Nuno Taveira
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-019 Lisboa, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciências da Saúde Egas Moniz, 2829-511 Caparica, Portugal
| | - Inês Bártolo
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-019 Lisboa, Portugal
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Bártolo I, Moranguinho I, Gonçalves P, Diniz AR, Borrego P, Martin F, Figueiredo I, Gomes P, Gonçalves F, Alves AJS, Alves N, Caixas U, Pinto IV, Barahona I, Pinho e Melo TMVD, Taveira N. High Instantaneous Inhibitory Potential of Bictegravir and the New Spiro-β-Lactam BSS-730A for HIV-2 Isolates from RAL-Naïve and RAL-Failing Patients. Int J Mol Sci 2022; 23:ijms232214300. [PMID: 36430777 PMCID: PMC9695772 DOI: 10.3390/ijms232214300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 11/19/2022] Open
Abstract
Integrase inhibitors (INIs) are an important class of drugs for treating HIV-2 infection, given the limited number of drugs active against this virus. While the clinical efficacy of raltegravir and dolutegravir is well established, the clinical efficacy of bictegravir for treating HIV-2 infected patients has not been determined. Little information is available regarding the activity of bictegravir against HIV-2 isolates from patients failing raltegravir-based therapy. In this study, we examined the phenotypic and matched genotypic susceptibility of HIV-2 primary isolates from raltegravir-naïve and raltegravir-failing patients to raltegravir, dolutegravir, and bictegravir, and to the new spiro-β-lactam BSS-730A. The instantaneous inhibitory potential (IIP) was calculated to help predict the clinical activity of bictegravir and BSS-730A. Isolates from raltegravir-naïve patients were highly sensitive to all INIs and BSS-730A. Combined integrase mutations E92A and Q148K conferred high-level resistance to raltegravir, and E92Q and T97A conferred resistance to raltegravir and dolutegravir. The antiviral activity of bictegravir and BSS-730A was not affected by these mutations. BSS-730A displayed strong antiviral synergism with raltegravir. Mean IIP values at Cmax were similar for all INIs and were not significantly affected by resistance mutations. IIP values were significantly higher for BSS-730A than for INIs. The high IIP values of bictegravir and BSS-730A for raltegravir-naïve and raltegravir-resistant HIV-2 isolates highlight their potential value for treating HIV-2 infection. Overall, the results are consistent with the high clinical efficacy of raltegravir and dolutegravir for HIV-2 infection and suggest a promising clinical profile for bictegravir and BSS-730A.
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Affiliation(s)
- Inês Bártolo
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-019 Lisboa, Portugal
| | - Inês Moranguinho
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-019 Lisboa, Portugal
| | - Paloma Gonçalves
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-019 Lisboa, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciências da Saúde Egas Moniz, 2829-511 Caparica, Portugal
| | - Ana Rita Diniz
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-019 Lisboa, Portugal
| | - Pedro Borrego
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-019 Lisboa, Portugal
- Centro de Administração e Políticas Públicas (CAPP), Instituto Superior de Ciências Sociais e Políticas (ISCSP), Universidade de Lisboa, 1649-019 Lisboa, Portugal
| | - Francisco Martin
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-019 Lisboa, Portugal
| | - Inês Figueiredo
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-019 Lisboa, Portugal
| | - Perpétua Gomes
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciências da Saúde Egas Moniz, 2829-511 Caparica, Portugal
- Laboratório de Biologia Molecular, LMCBM, SPC, Centro Hospitalar Lisboa Ocidental–HEM, 1649-019 Lisboa, Portugal
| | - Fátima Gonçalves
- Laboratório de Biologia Molecular, LMCBM, SPC, Centro Hospitalar Lisboa Ocidental–HEM, 1649-019 Lisboa, Portugal
| | - Américo J. S. Alves
- Department of Chemistry, Coimbra Chemistry Centre-Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal
| | - Nuno Alves
- Department of Chemistry, Coimbra Chemistry Centre-Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal
| | - Umbelina Caixas
- Serviço de Medicina 1.4, Hospital de S. José, CHLC, EPE, and Faculdade de Ciências Médicas, FCM-Nova, Centro de Estudos de Doenças Crónicas–CEDOC, 1649-019 Lisboa, Portugal
| | - Inês V. Pinto
- Medicina Interna, Hospital de Cascais Dr. José de Almeida, 2755-009 Alcabideche, Portugal
| | - Isabel Barahona
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciências da Saúde Egas Moniz, 2829-511 Caparica, Portugal
| | - Teresa M. V. D. Pinho e Melo
- Department of Chemistry, Coimbra Chemistry Centre-Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal
| | - Nuno Taveira
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-019 Lisboa, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciências da Saúde Egas Moniz, 2829-511 Caparica, Portugal
- Correspondence:
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Yu YX, Wang W, Sun HB, Zhang LL, Wang LF, Yin YY. Decoding drug resistant mechanism of V32I, I50V and I84V mutations of HIV-1 protease on amprenavir binding by using molecular dynamics simulations and MM-GBSA calculations. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2022; 33:805-831. [PMID: 36322686 DOI: 10.1080/1062936x.2022.2140708] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Mutations V32I, I50V and I84V in the HIV-1 protease (PR) induce drug resistance towards drug amprenavir (APV). Multiple short molecular dynamics (MSMD) simulations and molecular mechanics generalized Born surface area (MM-GBSA) method were utilized to investigate drug-resistant mechanism of V32I, I50V and I84V towards APV. Dynamic information arising from MSMD simulations suggest that V32I, I50V and I84V highly affect structural flexibility, motion modes and conformational behaviours of two flaps in the PR. Binding free energies calculated by MM-GBSA method suggest that the decrease in binding enthalpy and the increase in binding entropy induced by mutations V32I, I50V and I84V are responsible for drug resistance of the mutated PRs on APV. The energetic contributions of separate residues on binding of APV to the PR show that V32I, I50V and I84V highly disturb the interactions of two flaps with APV and mostly drive the decrease in binding ability of APV to the PR. Thus, the conformational changes of two flaps in the PR caused by V32I, I50V and I84V play key roles in drug resistance of three mutated PR towards APV. This study can provide useful dynamics information for the design of potent inhibitors relieving drug resistance.
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Affiliation(s)
- Y X Yu
- School of Science, Shandong Jiaotong University, Jinan, China
| | - W Wang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - H B Sun
- School of Science, Shandong Jiaotong University, Jinan, China
| | - L L Zhang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - L F Wang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - Y Y Yin
- School of Science, Shandong Jiaotong University, Jinan, China
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Weber IT, Wang YF, Harrison RW. HIV Protease: Historical Perspective and Current Research. Viruses 2021; 13:v13050839. [PMID: 34066370 PMCID: PMC8148205 DOI: 10.3390/v13050839] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/01/2021] [Accepted: 05/03/2021] [Indexed: 12/15/2022] Open
Abstract
The retroviral protease of human immunodeficiency virus (HIV) is an excellent target for antiviral inhibitors for treating HIV/AIDS. Despite the efficacy of therapy, current efforts to control the disease are undermined by the growing threat posed by drug resistance. This review covers the historical background of studies on the structure and function of HIV protease, the subsequent development of antiviral inhibitors, and recent studies on drug-resistant protease variants. We highlight the important contributions of Dr. Stephen Oroszlan to fundamental knowledge about the function of the HIV protease and other retroviral proteases. These studies, along with those of his colleagues, laid the foundations for the design of clinical inhibitors of HIV protease. The drug-resistant protease variants also provide an excellent model for investigating the molecular mechanisms and evolution of resistance.
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Affiliation(s)
- Irene T. Weber
- Department of Biology, Georgia State University, Atlanta, GA 30302, USA;
- Correspondence:
| | - Yuan-Fang Wang
- Department of Biology, Georgia State University, Atlanta, GA 30302, USA;
| | - Robert W. Harrison
- Department of Computer Science, Georgia State University, Atlanta, GA 30302, USA;
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Tzou PL, Descamps D, Rhee SY, Raugi DN, Charpentier C, Taveira N, Smith RA, Soriano V, de Mendoza C, Holmes SP, Gottlieb GS, Shafer RW. Expanded Spectrum of Antiretroviral-Selected Mutations in Human Immunodeficiency Virus Type 2. J Infect Dis 2021; 221:1962-1972. [PMID: 31965175 DOI: 10.1093/infdis/jiaa026] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 01/17/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND HIV-1 and HIV-2 differ in their antiretroviral (ARV) susceptibilities and drug resistance mutations (DRMs). METHODS We analyzed published HIV-2 pol sequences to identify HIV-2 treatment-selected mutations (TSMs). Mutation prevalences were determined by HIV-2 group and ARV status. Nonpolymorphic mutations were those in <1% of ARV-naive persons. TSMs were those associated with ARV therapy after multiple comparisons adjustment. RESULTS We analyzed protease (PR) sequences from 483 PR inhibitor (PI)-naive and 232 PI-treated persons; RT sequences from 333 nucleoside RT inhibitor (NRTI)-naive and 252 NRTI-treated persons; and integrase (IN) sequences from 236 IN inhibitor (INSTI)-naive and 60 INSTI-treated persons. In PR, 12 nonpolymorphic TSMs occurred in ≥11 persons: V33I, K45R, V47A, I50V, I54M, T56V, V62A, A73G, I82F, I84V, F85L, L90M. In RT, 9 nonpolymorphic TSMs occurred in ≥10 persons: K40R, A62V, K70R, Y115F, Q151M, M184VI, S215Y. In IN, 11 nonpolymorphic TSMs occurred in ≥4 persons: Q91R, E92AQ, T97A, G140S, Y143G, Q148R, A153G, N155H, H156R, R231 5-amino acid insertions. Nine of 32 nonpolymorphic TSMs were previously unreported. CONCLUSIONS This meta-analysis confirmed the ARV association of previously reported HIV-2 DRMs and identified novel TSMs. Genotypic and phenotypic studies of HIV-2 TSMs will improve approaches to predicting HIV-2 ARV susceptibility and treating HIV-2-infected persons.
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Affiliation(s)
- Philip L Tzou
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, USA
| | - Diane Descamps
- Laboratoire de Virologie, Hôpital Bichat-Claude Bernard, APHP.Nord Universite de Paris, France.,INSERM UMR 1137, Paris, France
| | - Soo-Yon Rhee
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, USA
| | - Dana N Raugi
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Charlotte Charpentier
- Laboratoire de Virologie, Hôpital Bichat-Claude Bernard, APHP.Nord Universite de Paris, France.,INSERM UMR 1137, Paris, France
| | - Nuno Taveira
- Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal.,Instituto Universitário Egas Moniz, Monte da Caparica, Portugal
| | - Robert A Smith
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Vicente Soriano
- Health Sciences School and Medical Center, Universidad Internacional de La Rioja, Madrid, Spain
| | - Carmen de Mendoza
- Puerta de Hierro University Hospital and Research Institute, Madrid, Spain
| | - Susan P Holmes
- Department of Statistics, Stanford University, Stanford, California, USA
| | - Geoffrey S Gottlieb
- Department of Medicine, University of Washington, Seattle, Washington, USA.,Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Robert W Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, USA
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Laville P, Petitjean M, Regad L. Structural Impacts of Drug-Resistance Mutations Appearing in HIV-2 Protease. Molecules 2021; 26:molecules26030611. [PMID: 33503916 PMCID: PMC7865771 DOI: 10.3390/molecules26030611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/15/2021] [Accepted: 01/19/2021] [Indexed: 11/16/2022] Open
Abstract
The use of antiretroviral drugs is accompanied by the emergence of HIV-2 resistances. Thus, it is important to elucidate the mechanisms of resistance to antiretroviral drugs. Here, we propose a structural analysis of 31 drug-resistant mutants of HIV-2 protease (PR2) that is an important target against HIV-2 infection. First, we modeled the structures of each mutant. We then located structural shifts putatively induced by mutations. Finally, we compared wild-type and mutant inhibitor-binding pockets and interfaces to explore the impacts of these induced structural deformations on these two regions. Our results showed that one mutation could induce large structural rearrangements in side-chain and backbone atoms of mutated residue, in its vicinity or further. Structural deformations observed in side-chain atoms are frequent and of greater magnitude, that confirms that to fight drug resistance, interactions with backbone atoms should be favored. We showed that these observed structural deformations modify the conformation, volume, and hydrophobicity of the binding pocket and the composition and size of the PR2 interface. These results suggest that resistance mutations could alter ligand binding by modifying pocket properties and PR2 stability by impacting its interface. Our results reinforce the understanding of the effects of mutations that occurred in PR2 and the different mechanisms of PR2 resistance.
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Olotu FA, Agoni C, Soremekun O, Soliman MES. The recent application of 3D-QSAR and docking studies to novel HIV-protease inhibitor drug discovery. Expert Opin Drug Discov 2020; 15:1095-1110. [PMID: 32692273 DOI: 10.1080/17460441.2020.1773428] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
INTRODUCTION Despite the availability of FDA approved inhibitors of HIV protease, numerous efforts are still ongoing to achieve 'near-perfect' drugs devoid of characteristic adverse side effects, toxicities, and mutational resistance. While experimental methods have been plagued with huge consumption of time and resources, there has been an incessant shift towards the use of computational simulations in HIV protease inhibitor drug discovery. AREAS COVERED Herein, the authors review the numerous applications of 3D-QSAR modeling methods over recent years relative to the design of new HIV protease inhibitors from a series of experimentally derived compounds. Also, the augmentative contributions of molecular docking are discussed. EXPERT OPINION Efforts to optimize 3D QSAR and molecular docking for HIV-1 drug discovery are ongoing, which could further incorporate inhibitor motions at the active site using molecular dynamics parameters. Also, highly predictive machine learning algorithms such as random forest, K-means, decision trees, linear regression, hierarchical clustering, and Bayesian classifiers could be employed.
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Affiliation(s)
- Fisayo A Olotu
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus , Durban, 4001, South Africa
| | - Clement Agoni
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus , Durban, 4001, South Africa
| | - Opeyemi Soremekun
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus , Durban, 4001, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus , Durban, 4001, South Africa
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Laville P, Fartek S, Cerisier N, Flatters D, Petitjean M, Regad L. Impacts of drug resistance mutations on the structural asymmetry of the HIV-2 protease. BMC Mol Cell Biol 2020; 21:46. [PMID: 32576133 PMCID: PMC7310402 DOI: 10.1186/s12860-020-00290-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 06/16/2020] [Indexed: 12/13/2022] Open
Abstract
Background Drug resistance is a severe problem in HIV treatment. HIV protease is a common target for the design of new drugs for treating HIV infection. Previous studies have shown that the crystallographic structures of the HIV-2 protease (PR2) in bound and unbound forms exhibit structural asymmetry that is important for ligand recognition and binding. Here, we investigated the effects of resistance mutations on the structural asymmetry of PR2. Due to the lack of structural data on PR2 mutants, the 3D structures of 30 PR2 mutants of interest have been modeled using an in silico protocol. Structural asymmetry analysis was carried out with an in-house structural-alphabet-based approach. Results The systematic comparison of the asymmetry of the wild-type structure and a large number of mutants highlighted crucial residues for PR2 structure and function. In addition, our results revealed structural changes induced by PR2 flexibility or resistance mutations. The analysis of the highlighted structural changes showed that some mutations alter protein stability or inhibitor binding. Conclusions This work consists of a structural analysis of the impact of a large number of PR2 resistant mutants based on modeled structures. It suggests three possible resistance mechanisms of PR2, in which structural changes induced by resistance mutations lead to modifications in the dimerization interface, ligand recognition or inhibitor binding.
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Affiliation(s)
- Pierre Laville
- Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, F-75013, Paris, France
| | - Sandrine Fartek
- Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, F-75013, Paris, France
| | - Natacha Cerisier
- Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, F-75013, Paris, France
| | - Delphine Flatters
- Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, F-75013, Paris, France
| | - Michel Petitjean
- Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, F-75013, Paris, France
| | - Leslie Regad
- Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, F-75013, Paris, France.
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11
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Prosser K, Stokes RW, Cohen SM. Evaluation of 3-Dimensionality in Approved and Experimental Drug Space. ACS Med Chem Lett 2020; 11:1292-1298. [PMID: 32551014 PMCID: PMC7294711 DOI: 10.1021/acsmedchemlett.0c00121] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 05/18/2020] [Indexed: 11/28/2022] Open
Abstract
The 3-dimensional (3D) structure of therapeutics and other bioactive molecules is an important factor in determining the strength and selectivity of their protein-ligand interactions. Previous efforts have considered the strain introduced and tolerated through conformational changes induced upon protein binding. Herein, we present an analysis of 3-dimentionality for energy-minimized structures from the DrugBank and ligands bound to proteins identified in the Protein Data Bank (PDB). This analysis reveals that the majority of molecules found in both the DrugBank and the PDB tend toward linearity and planarity, with few molecules having highly 3D conformations. Decidedly 3D geometries have been historically difficult to achieve, likely due to the synthetic challenge of making 3D organic molecules, and other considerations, such as adherence to the 'rule-of-five'. This has resulted in the dominance of planar and/or linear topologies of the molecules described here. Strategies to address the generally flat nature of these data sets are explored, including the use of 3D organic fragments and inorganic scaffolds as a means of accessing privileged 3D space. This work highlights the potential utility of libraries with greater 3D topological diversity so that the importance of molecular shape to biological behavior can be more fully understood in drug discovery campaigns.
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Affiliation(s)
- Kathleen
E. Prosser
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Ryjul W. Stokes
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Seth M. Cohen
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
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12
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Kovalevsky A, Gerlits O, Beltran K, Weiss KL, Keen DA, Blakeley MP, Louis JM, Weber IT. Proton transfer and drug binding details revealed in neutron diffraction studies of wild-type and drug resistant HIV-1 protease. Methods Enzymol 2020; 634:257-279. [PMID: 32093836 DOI: 10.1016/bs.mie.2019.12.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
HIV-1 protease is an essential therapeutic target for the design and development of antiviral inhibitors to treat AIDS. We used room temperature neutron crystallography to accurately determine hydrogen atom positions in several protease complexes with clinical drugs, amprenavir and darunavir. Hydrogen bonding interactions were carefully mapped to provide an unprecedented picture of drug binding to the protease target. We demonstrate that hydrogen atom positions within the enzyme catalytic site can be altered by introducing drug resistant mutations and by protonating surface residues that trigger proton transfer reactions between the catalytic Asp residues and the hydroxyl group of darunavir. When protein perdeuteration is not feasible, we validate the use of initial H/D exchange with unfolded protein and partial deuteration in pure D2O with hydrogenous glycerol to maximize deuterium incorporation into the protein, with no detrimental effects on the growth of quality crystals suitable for neutron diffraction experiments.
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Affiliation(s)
- Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.
| | - Oksana Gerlits
- Department of Natural Sciences, Tennessee Wesleyan University, Athens, TN, United States
| | - Kaira Beltran
- Department of Natural Sciences, Tennessee Wesleyan University, Athens, TN, United States
| | - Kevin L Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - David A Keen
- ISIS Facility, Rutherford Appleton Laboratory, Harwell Campus, Didcot, United Kingdom
| | | | - John M Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD, United States
| | - Irene T Weber
- Department of Biology, Georgia State University, Atlanta, GA, United States; Department of Chemistry, Georgia State University, Atlanta, GA, United States
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13
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Triki D, Kermarrec M, Visseaux B, Descamps D, Flatters D, Camproux AC, Regad L. Exploration of the effects of sequence variations between HIV-1 and HIV-2 proteases on their three-dimensional structures. J Biomol Struct Dyn 2019; 38:5014-5026. [PMID: 31830870 DOI: 10.1080/07391102.2019.1704877] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
HIV protease inhibitors (PIs) approved by the FDA (US Food and Drug Administration) are a major class of antiretroviral. HIV-2 protease (PR2) is naturally resistant to most of them as PIs were designed for HIV-1 protease (PR1). In this study, we explored the impact of amino-acid substitutions between PR1 and PR2 on the structure of protease (PR) by comparing the structural variability of 13 regions using 24 PR1 and PR2 structures complexed with diverse ligands. Our analyses confirmed structural rigidity of the catalytic region and highlighted the important role of three regions in the conservation of the catalytic region conformation. Surprisingly, we showed that the flap region, corresponding to a flexible region, exhibits similar conformations in PR1 and PR2. Furthermore, we identified regions exhibiting different conformations in PR1 and PR2, which could be explained by the intrinsic flexibility of these regions, by crystal packing, or by PR1 and PR2 substitutions. Some substitutions induce structural changes in the R2 and R4 regions that could have an impact on the properties of PI-binding site and could thus modify PI binding mode. Substitutions involved in structural changes in the elbow region could alter the flexibility of the PR2 flap regions relative to PR1, and thus play a role in the transition from the semi-open form to the closed form, and have an impact on ligand binding. These results improve the understanding of the impact of sequence variations between PR1 and PR2 on the natural resistance of HIV-2 to commercially available PIs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dhoha Triki
- Department of Chemistry, Bioinformatics Research Center, College of Science, North Carolina State University, Raleigh, North Carolina, USA.,Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, Paris, France
| | - Maxime Kermarrec
- Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, Paris, France
| | - Benoît Visseaux
- Université de Paris, IAME, UMR 1137, INSERM, AP-HP, Laboratoire de Virologie, Hôpital Bichat-Claude Bernard, Paris, France
| | - Diane Descamps
- Université de Paris, IAME, UMR 1137, INSERM, AP-HP, Laboratoire de Virologie, Hôpital Bichat-Claude Bernard, Paris, France
| | - Delphine Flatters
- Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, Paris, France
| | | | - Leslie Regad
- Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, Paris, France
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14
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Voshavar C. Protease Inhibitors for the Treatment of HIV/AIDS: Recent Advances and Future Challenges. Curr Top Med Chem 2019; 19:1571-1598. [PMID: 31237209 DOI: 10.2174/1568026619666190619115243] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 05/22/2019] [Accepted: 05/27/2019] [Indexed: 02/07/2023]
Abstract
Acquired Immunodeficiency Syndrome (AIDS) is a chronic disease characterized by multiple life-threatening illnesses caused by a retro-virus, Human Immunodeficiency Virus (HIV). HIV infection slowly destroys the immune system and increases the risk of various other infections and diseases. Although, there is no immediate cure for HIV infection/AIDS, several drugs targeting various cruxes of HIV infection are used to slow down the progress of the disease and to boost the immune system. One of the key therapeutic strategies is Highly Active Antiretroviral Therapy (HAART) or ' AIDS cocktail' in a general sense, which is a customized combination of anti-retroviral drugs designed to combat the HIV infection. Since HAART's inception in 1995, this treatment was found to be effective in improving the life expectancy of HIV patients over two decades. Among various classes of HAART treatment regimen, Protease Inhibitors (PIs) are known to be widely used as a major component and found to be effective in treating HIV infection/AIDS. For the past several years, a variety of protease inhibitors have been reported. This review outlines the drug design strategies of PIs, chemical and pharmacological characteristics of some mechanism-based inhibitors, summarizes the recent developments in small molecule based drug discovery with HIV protease as a drug target. Further discussed are the pharmacology, PI drug resistance on HIV PR, adverse effects of HIV PIs and challenges/impediments in the successful application of HIV PIs as an important class of drugs in HAART regimen for the effective treatment of AIDS.
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Affiliation(s)
- Chandrashekhar Voshavar
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL 32307, United States
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15
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Hattori SI, Hayashi H, Bulut H, Rao KV, Nyalapatla PR, Hasegawa K, Aoki M, Ghosh AK, Mitsuya H. Halogen Bond Interactions of Novel HIV-1 Protease Inhibitors (PI) (GRL-001-15 and GRL-003-15) with the Flap of Protease Are Critical for Their Potent Activity against Wild-Type HIV-1 and Multi-PI-Resistant Variants. Antimicrob Agents Chemother 2019; 63:e02635-18. [PMID: 30962341 PMCID: PMC6535520 DOI: 10.1128/aac.02635-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 04/03/2019] [Indexed: 01/29/2023] Open
Abstract
We generated two novel nonpeptidic HIV-1 protease inhibitors (PIs), GRL-001-15 and GRL-003-15, which contain unique crown-like tetrahydropyranofuran (Crn-THF) and P2'-cyclopropyl-aminobenzothiazole (Cp-Abt) moieties as P2 and P2' ligands, respectively. GRL-001-15 and GRL-003-15 have meta-monofluorophenyl and para-monofluorophenyl at the P1 site, respectively, exert highly potent activity against wild-type HIV-1 with 50% effective concentrations (EC50s) of 57 and 50 pM, respectively, and have favorable cytotoxicity profiles with 50% cytotoxic concentrations (CC50s) of 38 and 11 μM, respectively. The activity of GRL-001-15 against multi-PI-resistant HIV-1 variants was generally greater than that of GRL-003-15. The EC50 of GRL-001-15 against an HIV-1 variant that was highly resistant to multiple PIs, including darunavir (DRV) (HIV-1DRVRP30), was 0.17 nM, and that of GRL-003-15 was 3.3 nM, while DRV was much less active, with an EC50 of 216 nM. The emergence of HIV-1 variants resistant to GRL-001-15 and GRL-003-15 was significantly delayed compared to that of variants resistant to selected PIs, including DRV. Structural analyses of wild-type protease (PRWT) complexed with the novel PIs revealed that GRL-001-15's meta-fluorine atom forms halogen bond interactions (2.9 and 3.0 Å) with Gly49 and Ile50, respectively, of the protease flap region and with Pro81' (2.7 and 3.2 Å), which is located close to the protease active site, and that two fluorine atoms of GRL-142-13 form multiple halogen bond interactions with Gly49, Ile50, Pro81', Ile82', and Arg8'. In contrast, GRL-003-15 forms halogen bond interactions with Pro81' alone, suggesting that the reduced antiviral activity of GRL-003-15 is due to the loss of the interactions with the flap region.
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Affiliation(s)
- Shin-Ichiro Hattori
- Department of Refractory Viral Infections, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Hironori Hayashi
- Department of Refractory Viral Infections, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Haydar Bulut
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Kalapala Venkateswara Rao
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA
- Department of Medicinal Chemistry, Purdue University, West Lafayette, Indiana, USA
| | - Prasanth R Nyalapatla
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA
- Department of Medicinal Chemistry, Purdue University, West Lafayette, Indiana, USA
| | - Kazuya Hasegawa
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, Hyogo, Japan
| | - Manabu Aoki
- Department of Refractory Viral Infections, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Arun K Ghosh
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA
- Department of Medicinal Chemistry, Purdue University, West Lafayette, Indiana, USA
| | - Hiroaki Mitsuya
- Department of Refractory Viral Infections, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
- Department of Clinical Sciences, Kumamoto University Hospital, Kumamoto, Japan
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16
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Structural studies of antiviral inhibitor with HIV-1 protease bearing drug resistant substitutions of V32I, I47V and V82I. Biochem Biophys Res Commun 2019; 514:974-978. [PMID: 31092330 DOI: 10.1016/j.bbrc.2019.05.064] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 05/07/2019] [Indexed: 12/23/2022]
Abstract
HIV-1 protease inhibitors are effective in HIV/AIDS therapy, although drug resistance is a severe problem. This study examines the effects of four investigational inhibitors against HIV-1 protease with drug resistant mutations of V32I, I47V and V82I (PRTri) that model the inhibitor-binding site of HIV-2 protease. These inhibitors contain diverse chemical modifications on the darunavir scaffold and form new interactions with wild type protease, however, the measured inhibition constants for PRTri mutant range from 17 to 40 nM or significantly worse than picomolar values reported for wild type enzyme. The X-ray crystal structure of PRTri mutant in complex with inhibitor 1 at 1.5 Å resolution shows minor changes in interactions with inhibitor compared with the corresponding wild type PR complex. Instead, the basic amine at P2 of inhibitor together with mutation V82I induces two alternate conformations for the side chain of Arg8 with new interactions with inhibitor and Leu10. Hence, inhibition is influenced by small coordinated changes in hydrophobic interactions.
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17
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Mu Y, Kodidela S, Wang Y, Kumar S, Cory TJ. The dawn of precision medicine in HIV: state of the art of pharmacotherapy. Expert Opin Pharmacother 2018; 19:1581-1595. [PMID: 30234392 DOI: 10.1080/14656566.2018.1515916] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Combination antiretroviral therapy (ART) reduces viral load to under the limit of detection, successfully decreasing HIV-related morbidity and mortality. Due to viral mutations, complex drug combinations and different patient response, there is an increasing demand for individualized treatment options for patients. AREAS COVERED This review first summarizes the pharmacokinetic and pharmacodynamic profile of clinical first-line drugs, which serves as guidance for antiretroviral precision medicine. Factors which have influential effects on drug efficacy and thus precision medicine are discussed: patients' pharmacogenetic information, virus mutations, comorbidities, and immune recovery. Furthermore, strategies to improve the application of precision medicine are discussed. EXPERT OPINION Precision medicine for ART requires comprehensive information on the drug, virus, and clinical data from the patients. The clinically available genetic tests are a good starting point. To better apply precision medicine, deeper knowledge of drug concentrations, HIV reservoirs, and efficacy associated genes, such as polymorphisms of drug transporters and metabolizing enzymes, are required. With advanced computer-based prediction systems which integrate more comprehensive information on pharmacokinetics, pharmacodynamics, pharmacogenomics, and the clinically relevant information of the patients, precision medicine will lead to better treatment choices and improved disease outcomes.
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Affiliation(s)
- Ying Mu
- a Department of Clinical Pharmacy and Translational Science , University of Tennessee Health Science Center College of Pharmacy , Memphis , USA
| | - Sunitha Kodidela
- b Department of Pharmaceutical Science , University of Tennessee Health Science Center College of Pharmacy , Memphis , USA
| | - Yujie Wang
- b Department of Pharmaceutical Science , University of Tennessee Health Science Center College of Pharmacy , Memphis , USA
| | - Santosh Kumar
- b Department of Pharmaceutical Science , University of Tennessee Health Science Center College of Pharmacy , Memphis , USA
| | - Theodore J Cory
- a Department of Clinical Pharmacy and Translational Science , University of Tennessee Health Science Center College of Pharmacy , Memphis , USA
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18
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Murphy DJ, Desjardins D, Boyd P, Dereuddre-Bosquet N, Stimmer L, Caldwell A, Le Grand R, Kelly C, van Roey J, Malcolm RK. Impact of ring size and drug loading on the pharmacokinetics of a combination dapivirine-darunavir vaginal ring in cynomolgus macaques. Int J Pharm 2018; 550:300-308. [PMID: 30153490 DOI: 10.1016/j.ijpharm.2018.08.051] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 08/22/2018] [Accepted: 08/24/2018] [Indexed: 01/05/2023]
Abstract
This work investigates the impact of vaginal ring size and drug loading on the in vitro release, safety, ease of fit, and pharmacokinetics in cynomolgus macaques of matrix-type silicone elastomer vaginal rings containing a combination of the non-nucleoside reverse transcriptase inhibitor dapivirine and the protease inhibitor darunavir. Drug-free and drug-loaded vaginal rings having three different geometries were manufactured by reaction injection molding. In vitro drug release was assessed using both a solvent/water mixture and a vaginal fluid simulant. Macaques fitted with drug-free vaginal rings for 28 days were assessed by colposcopy, cytological evaluation of cervico-vaginal lavage and histological evaluation of tissue after ring removal. The 20 × 4.5 mm combination ring, deemed most appropriate for vaginal fit and comfort in the macaques, was evaluated for pharmacokinetics over 28 days. Substantial differences were observed in the in vitro release profiles between the three ring sizes. However, these differences were not manifest in vivo, where measured drug concentrations after 20 × 4.5 mm ring use were not significantly different from those reported previously with a 25 × 6 mm ring. These results suggest that ring placement and fit is an important species-specific study parameter that should be optimised prior to pharmacokinetic testing.
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Affiliation(s)
- Diarmaid J Murphy
- School of Pharmacy, Queen's University Belfast, Belfast BT9 7BL, UK.
| | - Delphine Desjardins
- Université Paris Sud, INSERM, CEA, DRF-Immunology of Viral Infections and Autoimmune Diseases Department (IMVA), U1184, IDMIT Infrastructure, Fontenay-aux-Roses, France.
| | - Peter Boyd
- School of Pharmacy, Queen's University Belfast, Belfast BT9 7BL, UK.
| | - Nathalie Dereuddre-Bosquet
- Université Paris Sud, INSERM, CEA, DRF-Immunology of Viral Infections and Autoimmune Diseases Department (IMVA), U1184, IDMIT Infrastructure, Fontenay-aux-Roses, France.
| | - Lev Stimmer
- Molecular Imaging Research Center, CEA-INSERM US27/U1169, 18 route du Panorama, 92265 Fontenay-aux-Roses, France.
| | - Anna Caldwell
- Mass Spectrometry Facility, King's College London, London SE1 9NH, UK.
| | - Roger Le Grand
- Université Paris Sud, INSERM, CEA, DRF-Immunology of Viral Infections and Autoimmune Diseases Department (IMVA), U1184, IDMIT Infrastructure, Fontenay-aux-Roses, France.
| | - Charles Kelly
- Dental Institute, Guy's Hospital, King's College London, London SE1 9RT, UK.
| | - Jens van Roey
- Janssen GPH, Turnhoutseweg 30, 2340 Beerse, Belgium.
| | - R Karl Malcolm
- School of Pharmacy, Queen's University Belfast, Belfast BT9 7BL, UK.
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19
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Cong Y, Li Y, Jin K, Zhong S, Zhang JZH, Li H, Duan L. Exploring the Reasons for Decrease in Binding Affinity of HIV-2 Against HIV-1 Protease Complex Using Interaction Entropy Under Polarized Force Field. Front Chem 2018; 6:380. [PMID: 30197882 PMCID: PMC6117221 DOI: 10.3389/fchem.2018.00380] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 08/03/2018] [Indexed: 12/28/2022] Open
Abstract
In this study, the differences of binding patterns between two type HIV (HIV-1 and HIV-2) protease and two inhibitors (darunavir and amprenavir) are analyzed and compared using the newly developed interaction entropy (IE) method for the entropy change calculation combined with the polarized force field. The functional role of protonation states in the two HIV-2 complexes is investigated and our study finds that the protonated OD1 atom of Asp25' in B chain is the optimal choice. Those calculated binding free energies obtained from the polarized force field combined with IE method are significantly consistent with the experimental observed. The bridging water W301 is favorable to the binding of HIV-1 complexes; however, it is unfavorable to the HIV-2 complexes in current study. The volume of pocket, B-factor of Cα atoms and the distance of flap tip in HIV-2 complexes are smaller than that of HIV-1 consistently. These changes may cause localized rearrangement of residues lining their surface and finally result in the different binding mode for the two types HIV. Predicated hot-spot residues (Ala28/Ala28', Ile50/Ile50', and Ile84/Ile84') are nearly same in the four systems. However, the contribution to the free energy of Asp30 residue is more favorable in HIV-1 system than in HIV-2 system. Current study, to some extent, reveals the origin for the decrease in binding affinity of inhibitors against HIV-2 compared with HIV-1 and will provides theoretical guidance for future design of potent dual inhibitors targeting two type HIV protease.
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Affiliation(s)
- Yalong Cong
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Yuchen Li
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Kun Jin
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Susu Zhong
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - John Z. H. Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, China
- Department of Chemistry, New York University, New York, NY, United States
| | - Hao Li
- School of Physics and Electronics, Shandong Normal University, Jinan, China
- Department of Science and Technology, Shandong Normal University, Jinan, China
| | - Lili Duan
- School of Physics and Electronics, Shandong Normal University, Jinan, China
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20
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Triki D, Billot T, Visseaux B, Descamps D, Flatters D, Camproux AC, Regad L. Exploration of the effect of sequence variations located inside the binding pocket of HIV-1 and HIV-2 proteases. Sci Rep 2018; 8:5789. [PMID: 29636521 PMCID: PMC5893546 DOI: 10.1038/s41598-018-24124-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 03/26/2018] [Indexed: 01/01/2023] Open
Abstract
HIV-2 protease (PR2) is naturally resistant to most FDA (Food and Drug Administration)-approved HIV-1 protease inhibitors (PIs), a major antiretroviral class. In this study, we compared the PR1 and PR2 binding pockets extracted from structures complexed with 12 ligands. The comparison of PR1 and PR2 pocket properties showed that bound PR2 pockets were more hydrophobic with more oxygen atoms and fewer nitrogen atoms than PR1 pockets. The structural comparison of PR1 and PR2 pockets highlighted structural changes induced by their sequence variations and that were consistent with these property changes. Specifically, substitutions at residues 31, 46, and 82 induced structural changes in their main-chain atoms that could affect PI binding in PR2. In addition, the modelling of PR1 mutant structures containing V32I and L76M substitutions revealed a cooperative mechanism leading to structural deformation of flap-residue 45 that could modify PR2 flexibility. Our results suggest that substitutions in the PR1 and PR2 pockets can modify PI binding and flap flexibility, which could underlie PR2 resistance against PIs. These results provide new insights concerning the structural changes induced by PR1 and PR2 pocket variation changes, improving the understanding of the atomic mechanism of PR2 resistance to PIs.
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Affiliation(s)
- Dhoha Triki
- Molécules thérapeutiques in silico (MTi), INSERM UMR-, S973, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Telli Billot
- Molécules thérapeutiques in silico (MTi), INSERM UMR-, S973, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Benoit Visseaux
- IAME, UMR 1137, INSERM, Laboratoire de Virologie, Hôpital Bichât, AP-HP, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Diane Descamps
- IAME, UMR 1137, INSERM, Laboratoire de Virologie, Hôpital Bichât, AP-HP, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Delphine Flatters
- Molécules thérapeutiques in silico (MTi), INSERM UMR-, S973, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Anne-Claude Camproux
- Molécules thérapeutiques in silico (MTi), INSERM UMR-, S973, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Leslie Regad
- Molécules thérapeutiques in silico (MTi), INSERM UMR-, S973, Paris, France. .,Université Paris Diderot, Sorbonne Paris Cité, Paris, France.
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21
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Sanusi ZK, Govender T, Maguire GEM, Maseko SB, Lin J, Kruger HG, Honarparvar B. An insight to the molecular interactions of the FDA approved HIV PR drugs against L38L↑N↑L PR mutant. J Comput Aided Mol Des 2018; 32:459-471. [PMID: 29397520 DOI: 10.1007/s10822-018-0099-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 01/16/2018] [Indexed: 01/12/2023]
Abstract
The aspartate protease of the human immune deficiency type-1 virus (HIV-1) has become a crucial antiviral target in which many useful antiretroviral inhibitors have been developed. However, it seems the emergence of new HIV-1 PR mutations enhances drug resistance, hence, the available FDA approved drugs show less activity towards the protease. A mutation and insertion designated L38L↑N↑L PR was recently reported from subtype of C-SA HIV-1. An integrated two-layered ONIOM (QM:MM) method was employed in this study to examine the binding affinities of the nine HIV PR inhibitors against this mutant. The computed binding free energies as well as experimental data revealed a reduced inhibitory activity towards the L38L↑N↑L PR in comparison with subtype C-SA HIV-1 PR. This observation suggests that the insertion and mutations significantly affect the binding affinities or characteristics of the HIV PIs and/or parent PR. The same trend for the computational binding free energies was observed for eight of the nine inhibitors with respect to the experimental binding free energies. The outcome of this study shows that ONIOM method can be used as a reliable computational approach to rationalize lead compounds against specific targets. The nature of the intermolecular interactions in terms of the host-guest hydrogen bond interactions is discussed using the atoms in molecules (AIM) analysis. Natural bond orbital analysis was also used to determine the extent of charge transfer between the QM region of the L38L↑N↑L PR enzyme and FDA approved drugs. AIM analysis showed that the interaction between the QM region of the L38L↑N↑L PR and FDA approved drugs are electrostatic dominant, the bond stability computed from the NBO analysis supports the results from the AIM application. Future studies will focus on the improvement of the computational model by considering explicit water molecules in the active pocket. We believe that this approach has the potential to provide information that will aid in the design of much improved HIV-1 PR antiviral drugs.
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Affiliation(s)
- Zainab K Sanusi
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Thavendran Govender
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Glenn E M Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa.,School of Chemistry and Physics, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Sibusiso B Maseko
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Johnson Lin
- School of Life Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Hendrik G Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa.
| | - Bahareh Honarparvar
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa.
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22
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Triki D, Cano Contreras ME, Flatters D, Visseaux B, Descamps D, Camproux AC, Regad L. Analysis of the HIV-2 protease's adaptation to various ligands: characterization of backbone asymmetry using a structural alphabet. Sci Rep 2018; 8:710. [PMID: 29335428 PMCID: PMC5768731 DOI: 10.1038/s41598-017-18941-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 12/18/2017] [Indexed: 12/27/2022] Open
Abstract
The HIV-2 protease (PR2) is a homodimer of 99 residues with asymmetric assembly and binding various ligands. We propose an exhaustive study of the local structural asymmetry between the two monomers of all available PR2 structures complexed with various inhibitors using a structural alphabet approach. On average, PR2 exhibits asymmetry in 31% of its positions-i.e., exhibiting different backbone local conformations in the two monomers. This asymmetry was observed all along its structure, particularly in the elbow and flap regions. We first differentiated structural asymmetry conserved in most PR2 structures from the one specific to some PR2. Then, we explored the origin of the detected asymmetry in PR2. We localized asymmetry that could be induced by PR2's flexibility, allowing transition from the semi-open to closed conformations and the asymmetry potentially induced by ligand binding. This latter could be important for the PR2's adaptation to diverse ligands. Our results highlighted some differences between asymmetry of PR2 bound to darunavir and amprenavir that could explain their differences of affinity. This knowledge is critical for a better description of PR2's recognition and adaptation to various ligands and for a better understanding of the resistance of PR2 to most PR2 inhibitors, a major antiretroviral class.
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Affiliation(s)
- Dhoha Triki
- Molécules thérapeutiques in silico (MTi), INSERM UMR-S973, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Mario Enrique Cano Contreras
- Molécules thérapeutiques in silico (MTi), INSERM UMR-S973, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Delphine Flatters
- Molécules thérapeutiques in silico (MTi), INSERM UMR-S973, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Benoit Visseaux
- IAME, INSERM UMR 1137, Laboratoire de Virologie, Hôpital Bichat, AP-HP, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Diane Descamps
- IAME, INSERM UMR 1137, Laboratoire de Virologie, Hôpital Bichat, AP-HP, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Anne-Claude Camproux
- Molécules thérapeutiques in silico (MTi), INSERM UMR-S973, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Leslie Regad
- Molécules thérapeutiques in silico (MTi), INSERM UMR-S973, Paris, France. .,Université Paris Diderot, Sorbonne Paris Cité, Paris, France.
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23
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Sanusi ZK, Govender T, Maguire GEM, Maseko SB, Lin J, Kruger HG, Honarparvar B. Investigation of the binding free energies of FDA approved drugs against subtype B and C-SA HIV PR: ONIOM approach. J Mol Graph Model 2017; 76:77-85. [PMID: 28711760 DOI: 10.1016/j.jmgm.2017.06.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 06/08/2017] [Accepted: 06/09/2017] [Indexed: 01/15/2023]
Abstract
Human immune virus subtype C is the most widely spread HIV subtype in Sub-Sahara Africa and South Africa. A profound structural insight on finding potential lead compounds is therefore necessary for drug discovery. The focus of this study is to rationalize the nine Food and Drugs Administration (FDA) HIV antiviral drugs complexed to subtype B and C-SA PR using ONIOM approach. To achieve this, an integrated two-layered ONIOM model was used to optimize the geometrics of the FDA approved HIV-1 PR inhibitors for subtype B. In our hybrid ONIOM model, the HIV-1 PR inhibitors as well as the ASP 25/25' catalytic active residues were treated at high level quantum mechanics (QM) theory using B3LYP/6-31G(d), and the remaining HIV PR residues were considered using the AMBER force field. The experimental binding energies of the PR inhibitors were compared to the ONIOM calculated results. The theoretical binding free energies (?Gbind) for subtype B follow a similar trend to the experimental results, with one exemption. The computational model was less suitable for C-SA PR. Analysis of the results provided valuable information about the shortcomings of this approach. Future studies will focus on the improvement of the computational model by considering explicit water molecules in the active pocket. We believe that this approach has the potential to provide much improved binding energies for complex enzyme drug interactions.
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Affiliation(s)
- Z K Sanusi
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
| | - T Govender
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
| | - G E M Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; School of Chemistry and Physics, University of KwaZulu-Natal, 4001 Durban, South Africa
| | - S B Maseko
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
| | - J Lin
- School of Life Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
| | - H G Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa.
| | - B Honarparvar
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa.
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24
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Gerlits O, Keen DA, Blakeley MP, Louis JM, Weber IT, Kovalevsky A. Room Temperature Neutron Crystallography of Drug Resistant HIV-1 Protease Uncovers Limitations of X-ray Structural Analysis at 100 K. J Med Chem 2017; 60:2018-2025. [PMID: 28195728 DOI: 10.1021/acs.jmedchem.6b01767] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
HIV-1 protease inhibitors are crucial for treatment of HIV-1/AIDS, but their effectiveness is thwarted by rapid emergence of drug resistance. To better understand binding of clinical inhibitors to resistant HIV-1 protease, we used room-temperature joint X-ray/neutron (XN) crystallography to obtain an atomic-resolution structure of the protease triple mutant (V32I/I47V/V82I) in complex with amprenavir. The XN structure reveals a D+ ion located midway between the inner Oδ1 oxygen atoms of the catalytic aspartic acid residues. Comparison of the current XN structure with our previous XN structure of the wild-type HIV-1 protease-amprenavir complex suggests that the three mutations do not significantly alter the drug-enzyme interactions. This is in contrast to the observations in previous 100 K X-ray structures of these complexes that indicated loss of interactions by the drug with the triple mutant protease. These findings, thus, uncover limitations of structural analysis of drug binding using X-ray structures obtained at 100 K.
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Affiliation(s)
- Oksana Gerlits
- UT/ORNL Joint Institute of Biological Sciences, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - David A Keen
- ISIS Facility, Rutherford Appleton Laboratory , Harwell Campus, Didcot, OX11 0QX, U.K
| | - Matthew P Blakeley
- Large-Scale Structures Group, Institut Laue Langevin , 71 avenue des Martyrs, 38000 Grenoble, France
| | - John M Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , DHHS, Bethesda, Maryland 20892-0520, United States
| | - Irene T Weber
- Departments of Chemistry and Biology, Georgia State University , Atlanta, Georgia 30302, United States
| | - Andrey Kovalevsky
- Biology and Soft Matter Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
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25
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Navarro J, Curran A. Profile of once-daily darunavir/cobicistat fixed-dose combination for the treatment of HIV/AIDS. HIV AIDS-RESEARCH AND PALLIATIVE CARE 2016; 8:175-182. [PMID: 27843352 PMCID: PMC5098528 DOI: 10.2147/hiv.s56158] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Efficacy is the main objective of antiretroviral treatment and adherence is one of the cornerstones to achieve it. For this reason, treatment simplification is of key importance with regard to antiretroviral regimens. Rezolsta® (darunavir/cobicistat) is the first fixed-dose combination containing a protease inhibitor approved for HIV treatment. This coformulation includes darunavir, a protease inhibitor that has shown its efficacy and safety in naïve and treatment-experienced patients, and cobicistat, the new pharmacokinetic enhancer that is expected to replace ritonavir. Bioequivalence between ritonavir and cobicistat as darunavir boosters has been shown in studies involving healthy volunteers. Furthermore, efficacy and safety of darunavir/cobicistat observed in phase III studies, including naïve and pretreated patients without darunavir-associated resistance mutations, are comparable to historical data of darunavir/ritonavir 800/100 mg once-daily formulation. Adverse events with darunavir/cobicistat are scarce and mild, and basically include skin reactions and gastrointestinal disturbances. Although small increases in plasma creatinine are expected in patients receiving cobicistat due to the inhibition of creatinine transporters in kidney tubules, actual glomerular filtrate rate remains unaltered. Cobicistat does not have an inducer effect on metabolic pathways and shows much more selective inhibition than ritonavir. Therefore, isoenzyms different from CYP3A4 are supposed to be less affected by cobicistat, and thus fewer drug–drug interactions are expected.
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Affiliation(s)
- Jordi Navarro
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Adrian Curran
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
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26
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Hosseini A, Alibés A, Noguera-Julian M, Gil V, Paredes R, Soliva R, Orozco M, Guallar V. Computational Prediction of HIV-1 Resistance to Protease Inhibitors. J Chem Inf Model 2016; 56:915-23. [DOI: 10.1021/acs.jcim.5b00667] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ali Hosseini
- Joint
BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, c/Jordi Girona 29, 08034 Barcelona, Spain
| | - Andreu Alibés
- Joint
BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, c/Jordi Girona 29, 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri i Reixac 8, 08028 Barcelona, Spain
| | - Marc Noguera-Julian
- IrsiCaixa
AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Catalonia, Spain
- Universitat Autònoma de Barcelona, 08193 Bellaterra, Catalonia, Spain
- Universitat de Vic − Universitat Central de Catalunya, 08500 Vic, Catalonia, Spain
| | - Victor Gil
- Joint
BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, c/Jordi Girona 29, 08034 Barcelona, Spain
| | - Roger Paredes
- IrsiCaixa
AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Catalonia, Spain
- Universitat Autònoma de Barcelona, 08193 Bellaterra, Catalonia, Spain
- Universitat de Vic − Universitat Central de Catalunya, 08500 Vic, Catalonia, Spain
| | - Robert Soliva
- Joint
BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, c/Jordi Girona 29, 08034 Barcelona, Spain
| | - Modesto Orozco
- Joint
BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, c/Jordi Girona 29, 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri i Reixac 8, 08028 Barcelona, Spain
- Departament
de Bioquímica, Universitat de Barcelona, Avgda Diagona 647, 08029 Barcelona, Spain
| | - Victor Guallar
- Joint
BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, c/Jordi Girona 29, 08034 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys 23, 08010 Barcelona, Spain
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27
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Chen J. Drug resistance mechanisms of three mutations V32I, I47V and V82I in HIV-1 protease toward inhibitors probed by molecular dynamics simulations and binding free energy predictions. RSC Adv 2016. [DOI: 10.1039/c6ra09201b] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Molecular dynamics simulation and binding free energy calculations were used to probe drug resistance of HIV-1 protease mutations toward inhibitors.
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Affiliation(s)
- Jianzhong Chen
- School of Science
- Shandong Jiaotong University
- Jinan 250357
- China
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28
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Pietrucci F, Vargiu AV, Kranjc A. HIV-1 Protease Dimerization Dynamics Reveals a Transient Druggable Binding Pocket at the Interface. Sci Rep 2015; 5:18555. [PMID: 26692118 PMCID: PMC4686983 DOI: 10.1038/srep18555] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 11/19/2015] [Indexed: 12/30/2022] Open
Abstract
The binding mechanism of HIV-1 protease monomers leading to the catalytically competent dimeric enzyme has been investigated by means of state-of-the-art atomistic simulations. The emerging picture allows a deeper understanding of experimental observations and reveals that water molecules trapped at the interface have an important role in slowing down the kinetics of the association process. Unexpectedly, a cryptic binding pocket is identified at the interface of the complex, corresponding to a partially bound dimer that lacks enzymatic function. The pocket has a transient nature with a lifetime longer than 1 μs, and it displays very favorable druggability features. Docking as well as MM-GBSA free-energy calculations further support the possibility to target the new binding site by means of inhibitors able to prevent the complete dimerization by capturing the inactive conformation. This discovery could open the way to the rational design of a new class of anti-HIV drugs.
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Affiliation(s)
- Fabio Pietrucci
- Sorbonne Universités, UPMC University Paris 6, CNRS - UMR 7590, IMPMC, F-75005 Paris, France
| | | | - Agata Kranjc
- School of Pharmaceutical Sciences, University of Geneva, CH-1211 Geneva, Switzerland
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29
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Mahdi M, Szojka Z, Mótyán JA, Tőzsér J. Inhibition Profiling of Retroviral Protease Inhibitors Using an HIV-2 Modular System. Viruses 2015; 7:6152-62. [PMID: 26633459 PMCID: PMC4690855 DOI: 10.3390/v7122931] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 11/11/2015] [Accepted: 11/13/2015] [Indexed: 12/13/2022] Open
Abstract
Retroviral protease inhibitors (PIs) are fundamental pillars in the treatment of HIV infection and acquired immunodeficiency syndrome (AIDS). Currently used PIs are designed against HIV-1, and their effect on HIV-2 is understudied. Using a modular HIV-2 protease cassette system, inhibition profiling assays were carried out for protease inhibitors both in enzymatic and cell culture assays. Moreover, the treatment-associated resistance mutations (I54M, L90M) were introduced into the modular system, and comparative inhibition assays were performed to determine their effect on the susceptibility of the protease. Our results indicate that darunavir, saquinavir, indinavir and lopinavir were very effective HIV-2 protease inhibitors, while tipranavir, nelfinavir and amprenavir showed a decreased efficacy. I54M, L90M double mutation resulted in a significant reduction in the susceptibility to most of the inhibitors with the exception of tipranavir. To our knowledge, this modular system constitutes a novel approach in the field of HIV-2 protease characterization and susceptibility testing.
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Affiliation(s)
- Mohamed Mahdi
- Laboratory of Retroviral Biochemistry, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4010 Debrecen, Hungary.
| | - Zsófia Szojka
- Laboratory of Retroviral Biochemistry, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4010 Debrecen, Hungary.
| | - János András Mótyán
- Laboratory of Retroviral Biochemistry, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4010 Debrecen, Hungary.
| | - József Tőzsér
- Laboratory of Retroviral Biochemistry, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4010 Debrecen, Hungary.
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30
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Four Amino Acid Changes in HIV-2 Protease Confer Class-Wide Sensitivity to Protease Inhibitors. J Virol 2015; 90:1062-9. [PMID: 26559830 DOI: 10.1128/jvi.01772-15] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 11/02/2015] [Indexed: 12/30/2022] Open
Abstract
UNLABELLED Protease is essential for retroviral replication, and protease inhibitors (PI) are important for treating HIV infection. HIV-2 exhibits intrinsic resistance to most FDA-approved HIV-1 PI, retaining clinically useful susceptibility only to lopinavir, darunavir, and saquinavir. The mechanisms for this resistance are unclear; although HIV-1 and HIV-2 proteases share just 38 to 49% sequence identity, all critical structural features of proteases are conserved. Structural studies have implicated four amino acids in the ligand-binding pocket (positions 32, 47, 76, and 82). We constructed HIV-2ROD9 molecular clones encoding the corresponding wild-type HIV-1 amino acids (I32V, V47I, M76L, and I82V) either individually or together (clone PRΔ4) and compared the phenotypic sensitivities (50% effective concentration [EC50]) of mutant and wild-type viruses to nine FDA-approved PI. Single amino acid replacements I32V, V47I, and M76L increased the susceptibility of HIV-2 to multiple PI, but no single change conferred class-wide sensitivity. In contrast, clone PRΔ4 showed PI susceptibility equivalent to or greater than that of HIV-1 for all PI. We also compared crystallographic structures of wild-type HIV-1 and HIV-2 proteases complexed with amprenavir and darunavir to models of the PRΔ4 enzyme. These models suggest that the amprenavir sensitivity of PRΔ4 is attributable to stabilizing enzyme-inhibitor interactions in the P2 and P2' pockets of the protease dimer. Together, our results show that the combination of four amino acid changes in HIV-2 protease confer a pattern of PI susceptibility comparable to that of HIV-1, providing a structural rationale for intrinsic HIV-2 PI resistance and resolving long-standing questions regarding the determinants of differential PI susceptibility in HIV-1 and HIV-2. IMPORTANCE Proteases are essential for retroviral replication, and HIV-1 and HIV-2 proteases share a great deal of structural similarity. However, only three of nine FDA-approved HIV-1 protease inhibitors (PI) are active against HIV-2. The underlying reasons for intrinsic PI resistance in HIV-2 are not known. We examined the contributions of four amino acids in the ligand-binding pocket of the enzyme that differ between HIV-1 and HIV-2 by constructing HIV-2 clones encoding the corresponding HIV-1 amino acids and testing the PI susceptibilities of the resulting viruses. We found that the HIV-2 clone containing all four changes (PRΔ4) was as susceptible as HIV-1 to all nine PI. We also modeled the PRΔ4 enzyme structure and compared it to existing crystallographic structures of HIV-1 and HIV-2 proteases complexed with amprenavir and darunavir. Our findings demonstrate that four positions in the ligand-binding cleft of protease are the primary cause of HIV-2 PI resistance.
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31
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Lv Z, Chu Y, Wang Y. HIV protease inhibitors: a review of molecular selectivity and toxicity. HIV AIDS-RESEARCH AND PALLIATIVE CARE 2015; 7:95-104. [PMID: 25897264 PMCID: PMC4396582 DOI: 10.2147/hiv.s79956] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Highly active antiretroviral therapy (HAART) is recognized as the most effective treatment method for AIDS, and protease inhibitors play a very important role in HAART. However, poor bioavailability and unbearable toxicity are their common disadvantages. Thus, the development of safer and potentially promising protease inhibitors is eagerly needed. In this review, we introduced the chemical characteristics and associated side effects of HIV protease inhibitors, as well as the possible off-target mechanisms causing the side effects. From the chemical structures of HIV protease inhibitors and their possible off-target molecules, we could obtain hints for optimizing the molecular selectivity of the inhibitors, to provide help in the design of new compounds with enhanced bioavailability and reduced side effects.
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Affiliation(s)
- Zhengtong Lv
- Department of Immunology, School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, Hunan, People's Republic of China
| | - Yuan Chu
- Department of Immunology, School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, Hunan, People's Republic of China
| | - Yong Wang
- Department of Immunology, School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, Hunan, People's Republic of China
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32
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Chen J, Liang Z, Wang W, Yi C, Zhang S, Zhang Q. Revealing origin of decrease in potency of darunavir and amprenavir against HIV-2 relative to HIV-1 protease by molecular dynamics simulations. Sci Rep 2014; 4:6872. [PMID: 25362963 PMCID: PMC4217091 DOI: 10.1038/srep06872] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 10/13/2014] [Indexed: 12/30/2022] Open
Abstract
Clinical inhibitors Darunavir (DRV) and Amprenavir (APV) are less effective on HIV-2 protease (PR2) than on HIV-1 protease (PR1). To identify molecular basis associated with the lower inhibition, molecular dynamics (MD) simulations and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) calculations were performed to investigate the effectiveness of the PR1 inhibitors DRV and APV against PR1/PR2. The rank of predicted binding free energies agrees with the experimental determined one. Moreover, our results show that two inhibitors bind less strongly to PR2 than to PR1, again in agreement with the experimental findings. The decrease in binding free energies for PR2 relative to PR1 is found to arise from the reduction of the van der Waals interactions induced by the structural adjustment of the triple mutant V32I, I47V and V82I. This result is further supported by the difference between the van der Waals interactions of inhibitors with each residue in PR2 and in PR1. The results from the principle component analysis suggest that inhibitor binding tends to make the flaps of PR2 close and the one of PR1 open. We expect that this study can theoretically provide significant guidance and dynamics information for the design of potent dual inhibitors targeting PR1/PR2.
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Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Zhiqiang Liang
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Wei Wang
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Changhong Yi
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Shaolong Zhang
- College of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Qinggang Zhang
- College of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
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33
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Zhang Y, Chang YCE, Louis JM, Wang YF, Harrison RW, Weber IT. Structures of darunavir-resistant HIV-1 protease mutant reveal atypical binding of darunavir to wide open flaps. ACS Chem Biol 2014; 9:1351-8. [PMID: 24738918 PMCID: PMC4076034 DOI: 10.1021/cb4008875] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
The molecular basis for high resistance
to clinical inhibitors
of HIV-1 protease (PR) was examined for the variant designated PRP51 that was selected for resistance to darunavir (DRV). High
resolution crystal structures of PRP51 with the active
site D25N mutation revealed a ligand-free form and an inhibitor-bound
form showing a unique binding site and orientation for DRV. This inactivating
mutation is known to increase the dimer dissociation constant and
decrease DRV affinity of PR. The PRP51-D25N dimers
were in the open conformation with widely separated flaps, as reported
for other highly resistant variants. PRP51-D25N dimer
bound two DRV molecules and showed larger separation of 8.7 Å
between the closest atoms of the two flaps compared with 4.4 Å
for the ligand-free structure of this mutant. The ligand-free structure,
however, lacked van der Waals contacts between Ile50 and Pro81′
from the other subunit in the dimer, unlike the majority of PR structures.
DRV is bound inside the active site cavity; however, the inhibitor
is oriented almost perpendicular to its typical position and exhibits
only 2 direct hydrogen bond and two water-mediated interactions with
atoms of PRP51-D25N compared with 11 hydrogen bond
interactions seen for DRV bound in the typical position in wild-type
enzyme. The atypical location of DRV may provide opportunities for
design of novel inhibitors targeting the open conformation of PR drug-resistant
mutants.
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Affiliation(s)
| | | | - John M. Louis
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland 20892-0520, United States
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34
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Menéndez-Arias L, Alvarez M. Antiretroviral therapy and drug resistance in human immunodeficiency virus type 2 infection. Antiviral Res 2013; 102:70-86. [PMID: 24345729 DOI: 10.1016/j.antiviral.2013.12.001] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 12/02/2013] [Accepted: 12/06/2013] [Indexed: 12/19/2022]
Abstract
One to two million people worldwide are infected with the human immunodeficiency virus type 2 (HIV-2), with highest prevalences in West African countries, but also present in Western Europe, Asia and North America. Compared to HIV-1, HIV-2 infection undergoes a longer asymptomatic phase and progresses to AIDS more slowly. In addition, HIV-2 shows lower transmission rates, probably due to its lower viremia in infected individuals. There is limited experience in the treatment of HIV-2 infection and several antiretroviral drugs used to fight HIV-1 are not effective against HIV-2. Effective drugs against HIV-2 include nucleoside analogue reverse transcriptase (RT) inhibitors (e.g. zidovudine, tenofovir, lamivudine, emtricitabine, abacavir, stavudine and didanosine), protease inhibitors (saquinavir, lopinavir and darunavir), and integrase inhibitors (raltegravir, elvitegravir and dolutegravir). Maraviroc, a CCR5 antagonist blocking coreceptor binding during HIV entry, is active in vitro against CCR5-tropic HIV-2 but more studies are needed to validate its use in therapeutic treatments against HIV-2 infection. HIV-2 strains are naturally resistant to a few antiretroviral drugs developed to suppress HIV-1 propagation such as nonnucleoside RT inhibitors, several protease inhibitors and the fusion inhibitor enfuvirtide. Resistance selection in HIV-2 appears to be faster than in HIV-1. In this scenario, the development of novel drugs specific for HIV-2 is an important priority. In this review, we discuss current anti-HIV-2 therapies and mutational pathways leading to drug resistance.
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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.
| | - Mar Alvarez
- 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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35
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Agniswamy J, Shen CH, Wang YF, Ghosh AK, Rao KV, Xu CX, Sayer JM, Louis JM, Weber IT. Extreme multidrug resistant HIV-1 protease with 20 mutations is resistant to novel protease inhibitors with P1'-pyrrolidinone or P2-tris-tetrahydrofuran. J Med Chem 2013; 56:4017-27. [PMID: 23590295 DOI: 10.1021/jm400231v] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Extreme drug resistant mutant of HIV-1 protease (PR) bearing 20 mutations (PR20) has been studied with the clinical inhibitor amprenavir (1) and two potent antiviral investigational inhibitors GRL-02031 (2) and GRL-0519 (3). Clinical inhibitors are >1000-fold less active on PR20 than on wild-type enzyme, which is consistent with dissociation constants (KL) from isothermal titration calorimetry of 40 nM for 3, 178 nM for amprenavir, and 960 nM for 2. High resolution crystal structures of PR20-inhibitor complexes revealed altered interactions compared with the corresponding wild-type PR complexes in agreement with relative inhibition. Amprenavir lacks interactions due to PR20 mutations in the S2/S2' subsites relative to PR. Inhibitors 2 and 3 lose interactions with Arg8' in PR20 relative to the wild-type enzyme because Arg8' shifts to interact with mutated L10F side chain. Overall, inhibitor 3 compares favorably with darunavir in affinity for PR20 and shows promise for further development.
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Affiliation(s)
- Johnson Agniswamy
- Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, Georgia 30303, USA
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36
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Agniswamy J, Shen CH, Aniana A, Sayer JM, Louis JM, Weber IT. HIV-1 protease with 20 mutations exhibits extreme resistance to clinical inhibitors through coordinated structural rearrangements. Biochemistry 2012; 51:2819-28. [PMID: 22404139 PMCID: PMC3328860 DOI: 10.1021/bi2018317] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The escape mutant of HIV-1 protease (PR) containing 20 mutations (PR20) undergoes efficient polyprotein processing even in the presence of clinical protease inhibitors (PIs). PR20 shows >3 orders of magnitude decreased affinity for PIs darunavir (DRV) and saquinavir (SQV) relative to PR. Crystal structures of PR20 crystallized with yttrium, substrate analogue p2-NC, DRV, and SQV reveal three distinct conformations of the flexible flaps and diminished interactions with inhibitors through the combination of multiple mutations. PR20 with yttrium at the active site exhibits widely separated flaps lacking the usual intersubunit contacts seen in other inhibitor-free dimers. Mutations of residues 35-37 in the hinge loop eliminate interactions and perturb the flap conformation. Crystals of PR20/p2-NC contain one uninhibited dimer with one very open flap and one closed flap and a second inhibitor-bound dimer in the closed form showing six fewer hydrogen bonds with the substrate analogue relative to wild-type PR. PR20 complexes with PIs exhibit expanded S2/S2' pockets and fewer PI interactions arising from coordinated effects of mutations throughout the structure, in agreement with the strikingly reduced affinity. In particular, insertion of the large aromatic side chains of L10F and L33F alters intersubunit interactions and widens the PI binding site through a network of hydrophobic contacts. The two very open conformations of PR20 as well as the expanded binding site of the inhibitor-bound closed form suggest possible approaches for modifying inhibitors to target extreme drug-resistant HIV.
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Affiliation(s)
- Johnson Agniswamy
- Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, Georgia 30303, United States
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