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Nyame P, Togami A, Yoshida T, Masunaga T, Begum MM, Terasawa H, Monde N, Tahara Y, Tanaka R, Tanaka Y, Appiah-Kubi J, Amesimeku WAO, Hossain MJ, Otsuka M, Yoshimura K, Ikeda T, Sawa T, Satou Y, Fujita M, Maeda Y, Tateishi H, Monde K. A heterocyclic compound inhibits viral release by inducing cell surface BST2/Tetherin/CD317/HM1.24. J Biol Chem 2024; 300:107701. [PMID: 39173946 PMCID: PMC11419809 DOI: 10.1016/j.jbc.2024.107701] [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: 05/31/2024] [Revised: 08/01/2024] [Accepted: 08/14/2024] [Indexed: 08/24/2024] Open
Abstract
The introduction of combined antiretroviral therapy (cART) has greatly improved the quality of life of human immunodeficiency virus type 1 (HIV-1)-infected individuals. Nonetheless, the ever-present desire to seek out a full remedy for HIV-1 infections makes the discovery of novel antiviral medication compelling. Owing to this, a new late-stage inhibitor, Lenacapavir/Sunlenca, an HIV multi-phase suppressor, was clinically authorized in 2022. Besides unveiling cutting-edge antivirals inhibiting late-stage proteins or processes, newer therapeutics targeting host restriction factors hold promise for the curative care of HIV-1 infections. Notwithstanding, bone marrow stromal antigen 2 (BST2)/Tetherin/CD317/HM1.24, which entraps progeny virions is an appealing HIV-1 therapeutic candidate. In this study, a novel drug screening system was established, using the Jurkat/Vpr-HiBiT T cells, to identify drugs that could obstruct HIV-1 release; the candidate compounds were selected from the Ono Pharmaceutical compound library. Jurkat T cells expressing Vpr-HiBiT were infected with NL4-3, and the amount of virus release was quantified indirectly by the amount of Vpr-HiBiT incorporated into the progeny virions. Subsequently, the candidate compounds that suppressed viral release were used to synthesize the heterocyclic compound, HT-7, which reduces HIV-1 release with less cellular toxicity. Notably, HT-7 increased cell surface BST2 coupled with HIV-1 release reduction in Jurkat cells but not Jurkat/KO-BST2 cells. Seemingly, HT-7 impeded simian immunodeficiency virus (SIV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) release. Concisely, these results suggest that the reduction in viral release, following HT-7 treatment, resulted from the modulation of cell surface expression of BST2 by HT-7.
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Affiliation(s)
- Perpetual Nyame
- Department of Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Akihiro Togami
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Tomofumi Yoshida
- Department of Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Takuya Masunaga
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Mst Monira Begum
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Hiromi Terasawa
- Department of Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Nami Monde
- Department of Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Yurika Tahara
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Reiko Tanaka
- Laboratory of Hemato-Immunology, Graduate School of Health Sciences, University of the Ryukyus, Okinawa, Japan
| | - Yuetsu Tanaka
- Laboratory of Hemato-Immunology, Graduate School of Health Sciences, University of the Ryukyus, Okinawa, Japan
| | - Joyce Appiah-Kubi
- Department of Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | | | - Md Jakir Hossain
- Department of Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Masami Otsuka
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan; Department of Drug Discovery, Science Farm Ltd, Kumamoto, Japan
| | - Kazuhisa Yoshimura
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Tomohiro Sawa
- Department of Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Yorifumi Satou
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Mikako Fujita
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Yosuke Maeda
- Department of Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan; Department of Nursing, Kibi International University, Takahashi, Japan
| | - Hiroshi Tateishi
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan; Research & Development, Hirata Corporation, Kumamoto, Japan.
| | - Kazuaki Monde
- Department of Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan; Collaboration Unit for Infection, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.
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Lang S, Fletcher DA, Petit AP, Luise N, Fyfe P, Zuccotto F, Porter D, Hope A, Bellany F, Kerr C, Mackenzie CJ, Wyatt PG, Gray DW. Application of an NMR/Crystallography Fragment Screening Platform for the Assessment and Rapid Discovery of New HIV-CA Binding Fragments. ChemMedChem 2024; 19:e202400025. [PMID: 38581280 DOI: 10.1002/cmdc.202400025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/05/2024] [Accepted: 04/05/2024] [Indexed: 04/08/2024]
Abstract
Identification and assessment of novel targets is essential to combat drug resistance in the treatment of HIV/AIDS. HIV Capsid (HIV-CA), the protein playing a major role in both the early and late stages of the viral life cycle, has emerged as an important target. We have applied an NMR fragment screening platform and identified molecules that bind to the N-terminal domain (NTD) of HIV-CA at a site close to the interface with the C-terminal domain (CTD). Using X-ray crystallography, we have been able to obtain crystal structures to identify the binding mode of these compounds. This allowed for rapid progression of the initial, weak binding, fragment starting points to compounds 37 and 38, which have 19F-pKi values of 5.3 and 5.4 respectively.
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Affiliation(s)
- Stuart Lang
- Cresset Discovery, New Cambridge House, Bassingbourn Road, Litlington, Cambridgeshire, SG80SSS
| | - Daniel A Fletcher
- BioAscent Discovery Ltd, Bo'Ness Road, Newhouse, Lanarkshire, ML1 5UH
| | | | - Nicola Luise
- Alira Health, Av. De Josep Tarradellas, 123, 7th Floor, 08029, Barcelona, Spain
| | - Paul Fyfe
- Drug Discovery Unit, University of Dundee, Dow Street, Dundee, DD1 5EH
| | - Fabio Zuccotto
- Vertex Pharmaceuticals (Europe) Ltd, 86-88, Jubilee Avenue, Milton Park, Abingdon, Oxfordshire, OX14 4RW
| | - David Porter
- Evotec (UK) Ltd, Dorothy Crowfoot Hodgkin Campus, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ
| | - Anthony Hope
- Drug Discovery Unit, University of Dundee, Dow Street, Dundee, DD1 5EH
| | - Fiona Bellany
- Drug Discovery Unit, University of Dundee, Dow Street, Dundee, DD1 5EH
| | - Catrina Kerr
- Drug Discovery Unit, University of Dundee, Dow Street, Dundee, DD1 5EH
| | | | - Paul G Wyatt
- Sitala Bio Ltd, Unit D6, Grain House Mill Court, Great Shelford, Cambridge, CB22 5LD
| | - David W Gray
- Drug Discovery Unit, University of Dundee, Dow Street, Dundee, DD1 5EH
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3
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Li Y, Wu M, Fu Y, Xue J, Yuan F, Qu T, Rissanou AN, Wang Y, Li X, Hu H. Therapeutic stapled peptides: Efficacy and molecular targets. Pharmacol Res 2024; 203:107137. [PMID: 38522761 DOI: 10.1016/j.phrs.2024.107137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/06/2024] [Accepted: 03/06/2024] [Indexed: 03/26/2024]
Abstract
Peptide stapling, by employing a stable, preformed alpha-helical conformation, results in the production of peptides with improved membrane permeability and enhanced proteolytic stability, compared to the original peptides, and provides an effective solution to accelerate the rapid development of peptide drugs. Various reviews present peptide stapling chemistries, anchoring residues and one- or two-component cyclization, however, therapeutic stapled peptides have not been systematically summarized, especially focusing on various disease-related targets. This review highlights the latest advances in therapeutic peptide drug development facilitated by the application of stapling technology, including different stapling techniques, synthetic accessibility, applicability to biological targets, potential for solving biological problems, as well as the current status of development. Stapled peptides as therapeutic drug candidates have been classified and analysed mainly by receptor- and ligand-based stapled peptide design against various diseases, including cancer, infectious diseases, inflammation, and diabetes. This review is expected to provide a comprehensive reference for the rational design of stapled peptides for different diseases and targets to facilitate the development of therapeutic peptides with enhanced pharmacokinetic and biological properties.
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Affiliation(s)
- Yulei Li
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China.
| | - Minghao Wu
- School of Medicine, Shanghai University, 99 Shangda Road, Shanghai 200444, China
| | - Yinxue Fu
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China
| | - Jingwen Xue
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China
| | - Fei Yuan
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China
| | - Tianci Qu
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China
| | - Anastassia N Rissanou
- Theoretical & Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, Athens 11635, Greece
| | - Yilin Wang
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, 131 Dong'an Road, Shanghai 200032, China
| | - Xiang Li
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, China.
| | - Honggang Hu
- School of Medicine, Shanghai University, 99 Shangda Road, Shanghai 200444, China.
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Sever B, Otsuka M, Fujita M, Ciftci H. A Review of FDA-Approved Anti-HIV-1 Drugs, Anti-Gag Compounds, and Potential Strategies for HIV-1 Eradication. Int J Mol Sci 2024; 25:3659. [PMID: 38612471 PMCID: PMC11012182 DOI: 10.3390/ijms25073659] [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: 01/11/2024] [Revised: 03/22/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024] Open
Abstract
Acquired immunodeficiency syndrome (AIDS) is an enormous global health threat stemming from human immunodeficiency virus (HIV-1) infection. Up to now, the tremendous advances in combination antiretroviral therapy (cART) have shifted HIV-1 infection from a fatal illness into a manageable chronic disorder. However, the presence of latent reservoirs, the multifaceted nature of HIV-1, drug resistance, severe off-target effects, poor adherence, and high cost restrict the efficacy of current cART targeting the distinct stages of the virus life cycle. Therefore, there is an unmet need for the discovery of new therapeutics that not only bypass the limitations of the current therapy but also protect the body's health at the same time. The main goal for complete HIV-1 eradication is purging latently infected cells from patients' bodies. A potential strategy called "lock-in and apoptosis" targets the budding phase of the life cycle of the virus and leads to susceptibility to apoptosis of HIV-1 infected cells for the elimination of HIV-1 reservoirs and, ultimately, for complete eradication. The current work intends to present the main advantages and disadvantages of United States Food and Drug Administration (FDA)-approved anti-HIV-1 drugs as well as plausible strategies for the design and development of more anti-HIV-1 compounds with better potency, favorable pharmacokinetic profiles, and improved safety issues.
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Affiliation(s)
- Belgin Sever
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskisehir 26470, Türkiye;
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan;
| | - Masami Otsuka
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan;
- Department of Drug Discovery, Science Farm Ltd., Kumamoto 862-0976, Japan
| | - Mikako Fujita
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan;
| | - Halilibrahim Ciftci
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan;
- Department of Drug Discovery, Science Farm Ltd., Kumamoto 862-0976, Japan
- Department of Bioengineering Sciences, Izmir Katip Celebi University, Izmir 35620, Türkiye
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5
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Zhang DW, Xu XS, Zhou R, Fu Z. Modulation of HIV-1 capsid multimerization by sennoside A and sennoside B via interaction with the NTD/CTD interface in capsid hexamer. Front Microbiol 2023; 14:1270258. [PMID: 37817748 PMCID: PMC10561090 DOI: 10.3389/fmicb.2023.1270258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/11/2023] [Indexed: 10/12/2023] Open
Abstract
Small molecules that bind to the pocket targeted by a peptide, termed capsid assembly inhibitor (CAI), have shown antiviral effects with unique mechanisms of action. We report the discovery of two natural compounds, sennoside A (SA) and sennoside B (SB), derived from medicinal plants that bind to this pocket in the C-terminal domain of capsid (CA CTD). Both SA and SB were identified via a drug-screening campaign that utilized a time-resolved fluorescence resonance energy transfer assay. They inhibited the HIV-1 CA CTD/CAI interaction at sub-micromolar concentrations of 0.18 μM and 0.08 μM, respectively. Mutation of key residues (including Tyr 169, Leu 211, Asn 183, and Glu 187) in the CA CTD decreased their binding affinity to the CA monomer, from 1.35-fold to 4.17-fold. Furthermore, both compounds induced CA assembly in vitro and bound directly to the CA hexamer, suggesting that they interact with CA beyond the CA CTD. Molecular docking showed that both compounds were bound to the N-terminal domain (NTD)/CTD interface between adjacent protomers within the CA hexamer. SA established a hydrogen-bonding network with residues N57, V59, Q63, K70, and N74 of CA1-NTD and Q179 of CA2-CTD. SB formed hydrogen bonds with the N53, N70, and N74 residues of CA1-NTD, and the A177and Q179 residues of CA2-CTD. Both compounds, acting as glue, can bring αH4 in the NTD and αH9 in the CTD of the NTD/CTD interface close to each other. Collectively, our research indicates that SA and SB, which enhance CA assembly, could serve as novel chemical tools to identify agents that modulate HIV-1 CA assembly. These natural compounds may potentially lead to the development of new antiviral therapies with unique mechanisms of action.
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Affiliation(s)
- Da-Wei Zhang
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Xiao-Shuang Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Rui Zhou
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhiguo Fu
- Department of Orthopedics, Changzhou Hospital of Traditional Chinese Medicine, Changzhou, China
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Zhao S, Zhang X, da Silva-Júnior EF, Zhan P, Liu X. Computer-aided drug design in seeking viral capsid modulators. Drug Discov Today 2023; 28:103581. [PMID: 37030533 DOI: 10.1016/j.drudis.2023.103581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/16/2023] [Accepted: 03/30/2023] [Indexed: 04/09/2023]
Abstract
Approved or licensed antiviral drugs have limited applications because of their drug resistance and severe adverse effects. By contrast, by stabilizing or destroying the viral capsid, compounds known as capsid modulators prevent viral replication by acting on new targets and, therefore, overcoming the problem of clinical drug resistance. For example. computer-aided drug design (CADD) methods, using strategies based on structures of biological targets (structure-based drug design; SBDD), such as docking, molecular dynamics (MD) simulations, and virtual screening (VS), have provided opportunities for fast and effective development of viral capsid modulators. In this review, we summarize the application of CADD in the discovery, optimization, and mechanism prediction of capsid-targeting small molecules, providing new insights into antiviral drug discovery modalities. Teaser: Computer-aided drug design will accelerate the development of viral capsid regulators, which brings new hope for the treatment of refractory viral diseases.
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Affiliation(s)
- Shujie Zhao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Xujie Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Edeildo Ferreira da Silva-Júnior
- Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, 57072-970 Maceió, Alagoas, Brazil.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
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Zhang DW, Xie L, Xu XS, Li Y, Xu X. A Broad-Spectrum Antiviral Molecule, Protoporphyrin IX, Acts as a Moderator of HIV-1 Capsid Assembly by Targeting the Capsid Hexamer. Microbiol Spectr 2023; 11:e0266322. [PMID: 36475726 PMCID: PMC9927277 DOI: 10.1128/spectrum.02663-22] [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] [Indexed: 12/12/2022] Open
Abstract
The capsid protein (CA), an essential component of human immunodeficiency virus type 1 (HIV-1), represents an appealing target for antivirals. Small molecules targeting the CAI-binding cavity in the C-terminal domain of HIV-1 CA (CA CTD) confer potent antiviral activities. In this study, we report that a small molecule, protoporphyrin IX (PPIX), targets the HIV-1 CA by binding to this pocket. PPIX was identified via in vitro drug screening, using a homogeneous and time-resolved fluorescence-based assay. CA multimerization and a biolayer interferometry (BLI) assay showed that PPIX promoted CA multimerization and bound directly to CA. The binding model of PPIX to CA CTD revealed that PPIX forms hydrogen bonds with the L211and E212 residues in the CA CTD. Moreover, the BLI assay demonstrated that this compound preferentially binds to the CA hexamer versus the monomer. The superposition of the CAI CTD-PPIX complex and the hexameric CA structure suggests that PPIX binds to the interface formed by the NTD and the CTD between adjacent protomers in the CA hexamer via the T72 and E212 residues, serving as a glue to enhance the multimerization of CA. Taken together, our studies demonstrate that PPIX, a hexamer-targeted CA assembly enhancer, should be a new chemical probe for the discovery of modulators of the HIV-1 capsid assembly. IMPORTANCE CA and its assembled viral core play essential roles in distinct steps during HIV-1 replication, including reverse transcription, integration, nuclear entry, virus assembly, and maturation through CA-CA or CA-host factor interactions. These functions of CA are fundamental for HIV-1 pathogenesis, making it an appealing target for antiviral therapy. In the present study, we identified protoporphyrin IX (PPIX) as a candidate CA modulator that can promote CA assembly and prefers binding the CA hexamer versus the monomer. PPIX, like a glue, bound at the interfaces between CA subunits to accelerate CA multimerization. Therefore, PPIX could be used as a new lead for a CA modulator, and it holds potential research applications.
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Affiliation(s)
- Da-Wei Zhang
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Liangxu Xie
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Xiao-Shuang Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Yimin Li
- College of Pharmacy and Key Laboratory for Research and Development of “Qin Medicine” of Shaanxi Administration of Chinese Medicine, Shaanxi University of Chinese Medicine, Xixian New District, China
| | - Xiaojun Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
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Ndashimye E, Reyes PS, Arts EJ. New antiretroviral inhibitors and HIV-1 drug resistance: more focus on 90% HIV-1 isolates? FEMS Microbiol Rev 2023; 47:fuac040. [PMID: 36130204 PMCID: PMC9841967 DOI: 10.1093/femsre/fuac040] [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: 07/25/2022] [Revised: 09/13/2022] [Accepted: 09/18/2022] [Indexed: 01/21/2023] Open
Abstract
Combined HIV antiretroviral therapy (cART) has been effective except if drug resistance emerges. As cART has been rolled out in low-income countries, drug resistance has emerged at higher rates than observed in high income countries due to factors including initial use of these less tolerated cART regimens, intermittent disruptions in drug supply, and insufficient treatment monitoring. These socioeconomic factors impacting drug resistance are compounded by viral mechanistic differences by divergent HIV-1 non-B subtypes compared to HIV-1 subtype B that largely infects the high-income countries (just 10% of 37 million infected). This review compares the inhibition and resistance of diverse HIV-1 subtypes and strains to the various approved drugs as well as novel inhibitors in clinical trials. Initial sequence variations and differences in replicative fitness between HIV-1 subtypes pushes strains through different fitness landscapes to escape from drug selective pressure. The discussions here provide insight to patient care givers and policy makers on how best to use currently approved ART options and reduce the emergence of drug resistance in ∼33 million individuals infected with HIV-1 subtype A, C, D, G, and recombinants forms. Unfortunately, over 98% of the literature on cART resistance relates to HIV-1 subtype B.
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Affiliation(s)
- Emmanuel Ndashimye
- Department of Microbiology and Immunology, Western University Schulich School of Medicine & Dentistry, Western University, N6A 3K7, London, Ontario, Canada
- Joint Clinical Research Centre, -Center for AIDS Research Laboratories, 256, Kampala, Uganda
| | - Paul S Reyes
- Department of Microbiology and Immunology, Western University Schulich School of Medicine & Dentistry, Western University, N6A 3K7, London, Ontario, Canada
| | - Eric J Arts
- Department of Microbiology and Immunology, Western University Schulich School of Medicine & Dentistry, Western University, N6A 3K7, London, Ontario, Canada
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Ding D, Xu S, Zhang X, Jiang X, Cocklin S, Dick A, Zhan P, Liu X. The discovery and design of novel HIV-1 capsid modulators and future perspectives. Expert Opin Drug Discov 2023; 18:5-12. [PMID: 36480372 DOI: 10.1080/17460441.2023.2157401] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Although combination antiretroviral therapy (cART) has achieved significant success in treating HIV, the emergence of multidrug-resistant viruses and cumulative medication toxicity make it necessary to find new classes of antiretroviral agents with novel mechanisms of action. With high sequence conservation, the HIV-1 capsid (CA) protein has attracted attention as a prospective therapeutic target due to its crucial structural and regulatory functions in the HIV-1 replication cycle. AREA COVERED Herein, the authors provide a cutting-edge overview of current advances in the design and discovery of CA modulators, PF74, GS-6207 and their derivativeswhich targets a therapeutically attractive NTD-CTD interprotomer pocket within the hexameric configuration of HIV-1 CA. The discovery and development of these compounds, and derivatives thereof, have provided valuable information for the design of second-generation CA-targeting antivirals. EXPERT OPINION Despite some successes in designing and discovering HIV-1 CA modulators, more studies are required to decipher which chemical groups confer specific desirable properties. The future of CA-modulating compounds may lie in covalent inhibition and the creation of proteolysis-targeting chimeras (PROTACs). Moreover, biological interrogation of the process of CA uncoating, virus-host interactions, and studies on the lattice-binding restriction factors may improve our knowledge of HIV-1 CA and support the design of new antiviral agents.
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Affiliation(s)
- Dang Ding
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, PR China
| | - Shujing Xu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, PR China
| | - Xujie Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, PR China
| | - Xiangyi Jiang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, PR China
| | - Simon Cocklin
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Alexej Dick
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, PR China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, PR China
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Moonmuang S, Maniratanachote R, Chetprayoon P, Sornsuwan K, Thongkum W, Chupradit K, Tayapiwatana C. Specific Interaction of DARPin with HIV-1 CA NTD Disturbs the Distribution of Gag, RNA Packaging, and Tetraspanin Remodelling in the Membrane. Viruses 2022; 14:v14040824. [PMID: 35458554 PMCID: PMC9025900 DOI: 10.3390/v14040824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 11/22/2022] Open
Abstract
A designed repeat scaffold protein (AnkGAG1D4) recognizing the human immunodeficiency virus-1 (HIV-1) capsid (CA) was formerly established with antiviral assembly. Here, we investigated the molecular mechanism of AnkGAG1D4 function during the late stages of the HIV-1 replication cycle. By applying stimulated emission-depletion (STED) microscopy, Gag polymerisation was interrupted at the plasma membrane. Disturbance of Gag polymerisation triggered Gag accumulation inside producer cells and trapping of the CD81 tetraspanin on the plasma membrane. Moreover, reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) experiments were performed to validate the packaging efficiency of RNAs. Our results advocated that AnkGAG1D4 interfered with the Gag precursor protein from selecting HIV-1 and cellular RNAs for encapsidation into viral particles. These findings convey additional information on the antiviral activity of AnkGAG1D4 at late stages of the HIV-1 life cycle, which is potential for an alternative anti-HIV molecule.
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Affiliation(s)
- Sutpirat Moonmuang
- Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (S.M.); (K.S.); (W.T.); (K.C.)
- Department of Medical Technology, Division of Clinical Immunology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Rawiwan Maniratanachote
- Toxicology and Bio Evaluation Service Center (TBES), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand; (R.M.); (P.C.)
| | - Paninee Chetprayoon
- Toxicology and Bio Evaluation Service Center (TBES), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand; (R.M.); (P.C.)
| | - Kanokporn Sornsuwan
- Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (S.M.); (K.S.); (W.T.); (K.C.)
| | - Weeraya Thongkum
- Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (S.M.); (K.S.); (W.T.); (K.C.)
- Center of Innovative Immunodiagnostic Development, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Koollawat Chupradit
- Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (S.M.); (K.S.); (W.T.); (K.C.)
- Siriraj Center for Regenerative Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Chatchai Tayapiwatana
- Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (S.M.); (K.S.); (W.T.); (K.C.)
- Department of Medical Technology, Division of Clinical Immunology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
- Center of Innovative Immunodiagnostic Development, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
- Correspondence:
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11
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Domínguez-Zotes S, Valbuena A, Mateu MG. Antiviral compounds modulate elasticity, strength and material fatigue of a virus capsid framework. Biophys J 2022; 121:919-931. [PMID: 35151634 PMCID: PMC8943814 DOI: 10.1016/j.bpj.2022.02.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/18/2022] [Accepted: 02/09/2022] [Indexed: 11/30/2022] Open
Abstract
This study investigates whether the biochemical and antiviral effects of organic compounds that bind different sites in the mature human immunodeficiency virus capsid may be related to the modulation of different mechanical properties of the protein lattice from which the capsid is built. Mechanical force was used as a probe to quantify, in atomic force microscopy experiments at physiological pH and ionic strength, ligand-mediated changes in capsid lattice elasticity, breathing, strength against local dislocation by mechanical stress, and resistance to material fatigue. The results indicate that the effects of the tested compounds on assembly or biochemical stability can be linked, from a physics-based perspective, to their interference with the mechanical behavior of the viral capsid framework. The antivirals CAP-1 and CAI-55 increased the intrinsic elasticity and breathing of the capsid protein lattice and may entropically decrease the probability of the capsid protein to assemble into a functionally competent conformation. Antiviral PF74 increased the resistance of the capsid protein lattice to disruption by mechanical stress and material fatigue and may enthalpically strengthen the basal capsid lattice against breakage and disintegration. This study provides proof of concept that the interrogation of the mechanical properties of the nanostructured protein material that makes a virus capsid may provide fundamental insights into the biophysical action of capsid-binding antiviral agents. The implications for drug design by specifically targeting the biomechanics of viruses are discussed.
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Affiliation(s)
- Santos Domínguez-Zotes
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
| | - Alejandro Valbuena
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain.
| | - Mauricio G Mateu
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain.
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12
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Tzotzos S. Stapled peptides as potential inhibitors of SARS‐CoV‐2 binding to the hACE2 receptor. J Pept Sci 2022; 28:e3409. [PMID: 35165970 PMCID: PMC9111031 DOI: 10.1002/psc.3409] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 02/10/2022] [Accepted: 02/10/2022] [Indexed: 12/03/2022]
Abstract
Stapled peptides are synthetic peptidomimetics of bioactive sites in folded proteins which carry chemical links, introduced during peptide synthesis, designed to retain the secondary structure in the native protein molecule. Stapled peptides have been investigated as potential modulators of protein–protein interactions for over two decades. The potential use of stapled peptides as inhibitors of viral entry, and therefore as antiviral therapeutics, has been established for several important viruses causing disease in humans, such as the human immunodeficiency virus type 1 (HIV‐1), respiratory syncytial virus (RSV), and Middle East Respiratory Syndrome (MERS) coronavirus. Several independent research initiatives have investigated the inhibitory effect of stapled peptides on binding of the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), the causative agent of COVID‐19, to its receptor, angiotensin‐converting‐enzyme 2 (ACE2). These stapled peptides, which mimic Helix 1 of the human ACE2 receptor, have demonstrated mixed ability to prevent infection with SARS‐CoV‐2 in cell‐based studies.
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13
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Selyutina A, Hu P, Miller S, Simons LM, Yu HJ, Hultquist JF, Lee K, KewalRamani VN, Diaz-Griffero F. GS-CA1 and lenacapavir stabilize the HIV-1 core and modulate the core interaction with cellular factors. iScience 2022; 25:103593. [PMID: 35005542 PMCID: PMC8718827 DOI: 10.1016/j.isci.2021.103593] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/11/2021] [Accepted: 12/07/2021] [Indexed: 12/02/2022] Open
Abstract
The HIV-1 capsid is the target for the antiviral drugs GS-CA1 and Lenacapavir (GS-6207). We investigated the mechanism by which GS-CA1 and GS-6207 inhibit HIV-1 infection. HIV-1 inhibition by GS-CA1 did not require CPSF6 in CD4+ T cells. Contrary to PF74 that accelerates uncoating of HIV-1, GS-CA1 and GS-6207 stabilized the core. GS-CA1, unlike PF74, allowed the core to enter the nucleus, which agrees with the fact that GS-CA1 inhibits infection after reverse transcription. Unlike PF74, GS-CA1 did not disaggregate preformed CPSF6 complexes in nuclear speckles, suggesting that PF74 and GS-CA1 have different mechanisms of action. GS-CA1 stabilized the HIV-1 core, possibly by inducing a conformational shift in the core; in agreement, HIV-1 cores bearing N74D regained their ability to bind CPSF6 in the presence of GS-CA1. We showed that GS-CA1 binds to the HIV-1 core, changes its conformation, stabilizes the core, and thereby prevents viral uncoating and infection. GS-CA1 and Lenacapavir (GS-6207) stabilizes the HIV-1 core during infection GS-CA1/GS-6207 inhibit the interaction of the HIV-1 core with host factors GS-CA1/GS-6207 do not disaggregate preformed CPSF6 complexes in nuclear speckles GS-CA1/GS-6207 affects the dynamic surface of the HIV-1 core
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Affiliation(s)
- Anastasia Selyutina
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1301 Morris Park - Price Center 501, Bronx, NY 10461, USA
| | - Pan Hu
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1301 Morris Park - Price Center 501, Bronx, NY 10461, USA
| | - Sorin Miller
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Lacy M Simons
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Hyun Jae Yu
- Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory, Frederick, MD 21702, USA
| | - Judd F Hultquist
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - KyeongEun Lee
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Vineet N KewalRamani
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Felipe Diaz-Griffero
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1301 Morris Park - Price Center 501, Bronx, NY 10461, USA
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14
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Targeting the Virus Capsid as a Tool to Fight RNA Viruses. Viruses 2022; 14:v14020174. [PMID: 35215767 PMCID: PMC8879806 DOI: 10.3390/v14020174] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/14/2022] [Accepted: 01/16/2022] [Indexed: 12/10/2022] Open
Abstract
Several strategies have been developed to fight viral infections, not only in humans but also in animals and plants. Some of them are based on the development of efficient vaccines, to target the virus by developed antibodies, others focus on finding antiviral compounds with activities that inhibit selected virus replication steps. Currently, there is an increasing number of antiviral drugs on the market; however, some have unpleasant side effects, are toxic to cells, or the viruses quickly develop resistance to them. As the current situation shows, the combination of multiple antiviral strategies or the combination of the use of various compounds within one strategy is very important. The most desirable are combinations of drugs that inhibit different steps in the virus life cycle. This is an important issue especially for RNA viruses, which replicate their genomes using error-prone RNA polymerases and rapidly develop mutants resistant to applied antiviral compounds. Here, we focus on compounds targeting viral structural capsid proteins, thereby inhibiting virus assembly or disassembly, virus binding to cellular receptors, or acting by inhibiting other virus replication mechanisms. This review is an update of existing papers on a similar topic, by focusing on the most recent advances in the rapidly evolving research of compounds targeting capsid proteins of RNA viruses.
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15
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Islam MS, Junod SL, Zhang S, Buuh ZY, Guan Y, Zhao M, Kaneria KH, Kafley P, Cohen C, Maloney R, Lyu Z, Voelz VA, Yang W, Wang RE. Unprotected peptide macrocyclization and stapling via a fluorine-thiol displacement reaction. Nat Commun 2022; 13:350. [PMID: 35039490 PMCID: PMC8763920 DOI: 10.1038/s41467-022-27995-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/19/2021] [Indexed: 12/31/2022] Open
Abstract
We report the discovery of a facile peptide macrocyclization and stapling strategy based on a fluorine thiol displacement reaction (FTDR), which renders a class of peptide analogues with enhanced stability, affinity, cellular uptake, and inhibition of cancer cells. This approach enabled selective modification of the orthogonal fluoroacetamide side chains in unprotected peptides in the presence of intrinsic cysteines. The identified benzenedimethanethiol linker greatly promoted the alpha helicity of a variety of peptide substrates, as corroborated by molecular dynamics simulations. The cellular uptake of benzenedimethanethiol stapled peptides appeared to be universally enhanced compared to the classic ring-closing metathesis (RCM) stapled peptides. Pilot mechanism studies suggested that the uptake of FTDR-stapled peptides may involve multiple endocytosis pathways in a distinct pattern in comparison to peptides stapled by RCM. Consistent with the improved cell permeability, the FTDR-stapled lead Axin and p53 peptide analogues demonstrated enhanced inhibition of cancer cells over the RCM-stapled analogues and the unstapled peptides. Strategies capable of stapling unprotected peptides in a straightforward, chemoselective, and clean manner, as well as promoting cellular uptake are of great interest. Here the authors report a peptide macrocyclization and stapling strategy which satisfies those criteria, based on a fluorine thiol displacement reaction.
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Affiliation(s)
- Md Shafiqul Islam
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Samuel L Junod
- Department of Biology, Temple University, 1900 N. 12th Street, Philadelphia, PA, 19122, USA
| | - Si Zhang
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Zakey Yusuf Buuh
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Yifu Guan
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Mi Zhao
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Kishan H Kaneria
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Parmila Kafley
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Carson Cohen
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Robert Maloney
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Zhigang Lyu
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Vincent A Voelz
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Weidong Yang
- Department of Biology, Temple University, 1900 N. 12th Street, Philadelphia, PA, 19122, USA
| | - Rongsheng E Wang
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA.
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16
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McFadden WM, Snyder AA, Kirby KA, Tedbury PR, Raj M, Wang Z, Sarafianos SG. Rotten to the core: antivirals targeting the HIV-1 capsid core. Retrovirology 2021; 18:41. [PMID: 34937567 PMCID: PMC8693499 DOI: 10.1186/s12977-021-00583-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/09/2021] [Indexed: 12/20/2022] Open
Abstract
The capsid core of HIV-1 is a large macromolecular assembly that surrounds the viral genome and is an essential component of the infectious virus. In addition to its multiple roles throughout the viral life cycle, the capsid interacts with multiple host factors. Owing to its indispensable nature, the HIV-1 capsid has been the target of numerous antiretrovirals, though most capsid-targeting molecules have not had clinical success until recently. Lenacapavir, a long-acting drug that targets the HIV-1 capsid, is currently undergoing phase 2/3 clinical trials, making it the most successful capsid inhibitor to-date. In this review, we detail the role of the HIV-1 capsid protein in the virus life cycle, categorize antiviral compounds based on their targeting of five sites within the HIV-1 capsid, and discuss their molecular interactions and mechanisms of action. The diverse range of inhibition mechanisms provides insight into possible new strategies for designing novel HIV-1 drugs and furthers our understanding of HIV-1 biology. ![]()
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Affiliation(s)
- William M McFadden
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Alexa A Snyder
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Karen A Kirby
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA.,Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Philip R Tedbury
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA.,Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Monika Raj
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Zhengqiang Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA. .,Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA.
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17
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Fullerene Derivatives Prevent Packaging of Viral Genomic RNA into HIV-1 Particles by Binding Nucleocapsid Protein. Viruses 2021; 13:v13122451. [PMID: 34960720 PMCID: PMC8705927 DOI: 10.3390/v13122451] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 02/02/2023] Open
Abstract
Fullerene derivatives with hydrophilic substituents have been shown to exhibit a range of biological activities, including antiviral ones. For a long time, the anti-HIV activity of fullerene derivatives was believed to be due to their binding into the hydrophobic pocket of HIV-1 protease, thereby blocking its activity. Recent work, however, brought new evidence of a novel, protease-independent mechanism of fullerene derivatives' action. We studied in more detail the mechanism of the anti-HIV-1 activity of N,N-dimethyl[70]fulleropyrrolidinium iodide fullerene derivatives. By using a combination of in vitro and cell-based approaches, we showed that these C70 derivatives inhibited neither HIV-1 protease nor HIV-1 maturation. Instead, our data indicate effects of fullerene C70 derivatives on viral genomic RNA packaging and HIV-1 cDNA synthesis during reverse transcription-without impairing reverse transcriptase activity though. Molecularly, this could be explained by a strong binding affinity of these fullerene derivatives to HIV-1 nucleocapsid domain, preventing its proper interaction with viral genomic RNA, thereby blocking reverse transcription and HIV-1 infectivity. Moreover, the fullerene derivatives' oxidative activity and fluorescence quenching, which could be one of the reasons for the inconsistency among reported anti-HIV-1 mechanisms, are discussed herein.
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18
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Sandow JJ, Tan IK, Huang AS, Masaldan S, Bernardini JP, Wardak AZ, Birkinshaw RW, Ninnis RL, Liu Z, Dalseno D, Lio D, Infusini G, Czabotar PE, Webb AI, Dewson G. Dynamic reconfiguration of pro-apoptotic BAK on membranes. EMBO J 2021; 40:e107237. [PMID: 34523147 DOI: 10.15252/embj.2020107237] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 08/02/2021] [Accepted: 08/06/2021] [Indexed: 12/16/2022] Open
Abstract
BAK and BAX, the effectors of intrinsic apoptosis, each undergo major reconfiguration to an activated conformer that self-associates to damage mitochondria and cause cell death. However, the dynamic structural mechanisms of this reconfiguration in the presence of a membrane have yet to be fully elucidated. To explore the metamorphosis of membrane-bound BAK, we employed hydrogen-deuterium exchange mass spectrometry (HDX-MS). The HDX-MS profile of BAK on liposomes comprising mitochondrial lipids was consistent with known solution structures of inactive BAK. Following activation, HDX-MS resolved major reconfigurations in BAK. Mutagenesis guided by our HDX-MS profiling revealed that the BCL-2 homology (BH) 4 domain maintains the inactive conformation of BAK, and disrupting this domain is sufficient for constitutive BAK activation. Moreover, the entire N-terminal region preceding the BAK oligomerisation domains became disordered post-activation and remained disordered in the activated oligomer. Removal of the disordered N-terminus did not impair, but rather slightly potentiated, BAK-mediated membrane permeabilisation of liposomes and mitochondria. Together, our HDX-MS analyses reveal new insights into the dynamic nature of BAK activation on a membrane, which may provide new opportunities for therapeutic targeting.
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Affiliation(s)
- Jarrod J Sandow
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
| | - Iris Kl Tan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
| | - Alan S Huang
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
| | - Shashank Masaldan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
| | - Jonathan P Bernardini
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
| | - Ahmad Z Wardak
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia
| | - Richard W Birkinshaw
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
| | - Robert L Ninnis
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
| | - Ziyan Liu
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
| | - Destiny Dalseno
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
| | - Daisy Lio
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia
| | - Giuseppi Infusini
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
| | - Peter E Czabotar
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
| | - Andrew I Webb
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
| | - Grant Dewson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
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19
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Design, synthesis, and antiviral activity of phenylalanine derivatives as HIV-1 capsid inhibitors. Bioorg Med Chem 2021; 48:116414. [PMID: 34562701 DOI: 10.1016/j.bmc.2021.116414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 09/07/2021] [Accepted: 09/09/2021] [Indexed: 11/23/2022]
Abstract
The HIV-1 Capsid (CA) is considered as a promising target for the development of potent antiviral drugs, due to its multiple roles during the viral life cycle. Herein, we report the design, synthesis, and antiviral activity evaluation of series of novel phenylalanine derivatives as HIV-1 CA protein inhibitors. Among them, 4-methoxy-N-methylaniline substituted phenylalanine (II-13c) and indolin-5-amine substituted phenylalanine (V-25i) displayed exceptional anti-HIV-1 activity with the EC50 value of 5.14 and 2.57 μM respectively, which is slightly weaker than that of lead compound PF-74 (EC50 = 0.42 μM). Besides, surface plasmon resonance (SPR) binding assay demonstrated II-13c and V-25i prefer to combine with CA hexamer rather than monomer, which is similar to PF-74. Subsequently, molecular dynamics simulation (MD) revealed potential interactions between representative compounds with HIV-1 CA hexamer. Overall, this work laid a solid foundation for further structural optimization to discover novel promising HIV-1 CA inhibitors.
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20
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Alfadhli A, Romanaggi C, Barklis RL, Merutka I, Bates TA, Tafesse FG, Barklis E. Capsid-specific nanobody effects on HIV-1 assembly and infectivity. Virology 2021; 562:19-28. [PMID: 34246112 DOI: 10.1016/j.virol.2021.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/01/2021] [Accepted: 07/01/2021] [Indexed: 11/15/2022]
Abstract
The capsid (CA) domain of the HIV-1 precursor Gag (PrGag) protein plays multiple roles in HIV-1 replication, and is central to the assembly of immature virions, and mature virus cores. CA proteins themselves are composed of N-terminal domains (NTDs) and C-terminal domains (CTDs). We have investigated the interactions of CA with anti-CA nanobodies, which derive from the antigen recognition regions of camelid heavy chain-only antibodies. The one CA NTD-specific and two CTD-specific nanobodies we analyzed proved sensitive and specific HIV-1 CA detection reagents in immunoassays. When co-expressed with HIV-1 Gag proteins in cells, the NTD-specific nanobody was efficiently assembled into virions and did not perturb virus assembly. In contrast, the two CTD-specific nanobodies reduced PrGag processing, virus release and HIV-1 infectivity. Our results demonstrate the feasibility of Gag-targeted nanobody inhibition of HIV-1.
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Affiliation(s)
- Ayna Alfadhli
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239-3098, USA
| | - CeAnn Romanaggi
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239-3098, USA
| | - Robin Lid Barklis
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239-3098, USA
| | - Ilaria Merutka
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239-3098, USA
| | - Timothy A Bates
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239-3098, USA
| | - Fikadu G Tafesse
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239-3098, USA.
| | - Eric Barklis
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239-3098, USA.
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21
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AlBurtamani N, Paul A, Fassati A. The Role of Capsid in the Early Steps of HIV-1 Infection: New Insights into the Core of the Matter. Viruses 2021; 13:v13061161. [PMID: 34204384 PMCID: PMC8234406 DOI: 10.3390/v13061161] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/10/2021] [Accepted: 06/14/2021] [Indexed: 01/27/2023] Open
Abstract
In recent years, major advances in research and experimental approaches have significantly increased our knowledge on the role of the HIV-1 capsid in the virus life cycle, from reverse transcription to integration and gene expression. This makes the capsid protein a good pharmacological target to inhibit HIV-1 replication. This review covers our current understanding of the role of the viral capsid in the HIV-1 life cycle and its interaction with different host factors that enable reverse transcription, trafficking towards the nucleus, nuclear import and integration into host chromosomes. It also describes different promising small molecules, some of them in clinical trials, as potential targets for HIV-1 therapy.
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Sokullu E, Gauthier MS, Coulombe B. Discovery of Antivirals Using Phage Display. Viruses 2021; 13:v13061120. [PMID: 34200959 PMCID: PMC8230593 DOI: 10.3390/v13061120] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/05/2021] [Accepted: 06/07/2021] [Indexed: 02/06/2023] Open
Abstract
The latest coronavirus disease outbreak, COVID-19, has brought attention to viral infections which have posed serious health threats to humankind throughout history. The rapid global spread of COVID-19 is attributed to the increased human mobility of today's world, yet the threat of viral infections to global public health is expected to increase continuously in part due to increasing human-animal interface. Development of antiviral agents is crucial to combat both existing and novel viral infections. Recently, there is a growing interest in peptide/protein-based drug molecules. Antibodies are becoming especially predominant in the drug market. Indeed, in a remarkably short period, four antibody therapeutics were authorized for emergency use in COVID-19 treatment in the US, Russia, and India as of November 2020. Phage display has been one of the most widely used screening methods for peptide/antibody drug discovery. Several phage display-derived biologics are already in the market, and the expiration of intellectual property rights of phage-display antibody discovery platforms suggests an increment in antibody drugs in the near future. This review summarizes the most common phage display libraries used in antiviral discovery, highlights the approaches employed to enhance the antiviral potency of selected peptides/antibody fragments, and finally provides a discussion about the present status of the developed antivirals in clinic.
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Affiliation(s)
- Esen Sokullu
- Department of Translational Proteomics, Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada;
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Correspondence: (E.S.); (B.C.)
| | - Marie-Soleil Gauthier
- Department of Translational Proteomics, Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada;
| | - Benoit Coulombe
- Department of Translational Proteomics, Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada;
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Correspondence: (E.S.); (B.C.)
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Long M, Cantrelle FX, Robert X, Boll E, Sierra N, Gouet P, Hanoulle X, Alvarez GI, Guillon C. Identification of a Potential Inhibitor of the FIV p24 Capsid Protein and Characterization of Its Binding Site. Biochemistry 2021; 60:1896-1908. [PMID: 34096272 DOI: 10.1021/acs.biochem.1c00228] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Feline immunodeficiency virus (FIV) is a veterinary infective agent for which there is currently no efficient drug available. Drugs targeting the lentivirus capsid are currently under development for the treatment of human immunodeficiency virus 1 (HIV-1). Here we describe a lead compound that interacts with the FIV capsid. This compound, 696, modulates the in vitro assembly of and stabilizes the assembled capsid protein. To decipher the mechanism of binding of this compound to the protein, we performed the first nuclear magnetic resonance (NMR) assignment of the FIV p24 capsid protein. Experimental NMR chemical shift perturbations (CSPs) observed after the addition of 696 enabled the characterization of a specific binding site for 696 on p24. This site was further analyzed by molecular modeling of the protein:compound interaction, demonstrating a strong similarity with the binding sites of existing drugs targeting the HIV-1 capsid protein. Taken together, we characterized a promising capsid-interacting compound with a low cost of synthesis, for which derivatives could lead to the development of efficient treatments for FIV infection. More generally, our strategy combining the NMR assignment of FIV p24 with NMR CSPs and molecular modeling will be useful for the analysis of future compounds targeting p24 in the quest to identify an efficient treatment for FIV.
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Affiliation(s)
- Mathieu Long
- UMR 5086, Molecular Microbiology and Structural Biochemistry, CNRS/Université Lyon 1, 69367 Lyon, France
| | - François-Xavier Cantrelle
- CNRS, ERL9002, Integrative Structural Biology, F-59000 Lille, France.,Univ. Lille, INSERM, CHU Lille University Hospital, Institut Pasteur de Lille, UMR1167-RID-AGE-Risk factors and molecular determinants of aging-related, F-59000 Lille, France
| | - Xavier Robert
- UMR 5086, Molecular Microbiology and Structural Biochemistry, CNRS/Université Lyon 1, 69367 Lyon, France
| | - Emmanuelle Boll
- CNRS, ERL9002, Integrative Structural Biology, F-59000 Lille, France.,Univ. Lille, INSERM, CHU Lille University Hospital, Institut Pasteur de Lille, UMR1167-RID-AGE-Risk factors and molecular determinants of aging-related, F-59000 Lille, France
| | - Natalia Sierra
- Laboratorio de Moléculas Bioactivas, CENUR Litoral Norte, Universidad de la República, 60000 Paysandú, Uruguay
| | - Patrice Gouet
- UMR 5086, Molecular Microbiology and Structural Biochemistry, CNRS/Université Lyon 1, 69367 Lyon, France
| | - Xavier Hanoulle
- CNRS, ERL9002, Integrative Structural Biology, F-59000 Lille, France.,Univ. Lille, INSERM, CHU Lille University Hospital, Institut Pasteur de Lille, UMR1167-RID-AGE-Risk factors and molecular determinants of aging-related, F-59000 Lille, France
| | - Guzmán I Alvarez
- Laboratorio de Moléculas Bioactivas, CENUR Litoral Norte, Universidad de la República, 60000 Paysandú, Uruguay
| | - Christophe Guillon
- UMR 5086, Molecular Microbiology and Structural Biochemistry, CNRS/Université Lyon 1, 69367 Lyon, France
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24
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Sun L, Zhang X, Xu S, Huang T, Song S, Cherukupalli S, Zhan P, Liu X. An insight on medicinal aspects of novel HIV-1 capsid protein inhibitors. Eur J Med Chem 2021; 217:113380. [PMID: 33751981 DOI: 10.1016/j.ejmech.2021.113380] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/05/2021] [Accepted: 03/07/2021] [Indexed: 12/11/2022]
Abstract
A capsid is the protein shell of a virus, encircling its genetic material. The HIV capsid is erected from a single protein, known as capsid protein. The capsid of HIV-1 significantly involved in many processes of the virus life cycle, which makes it as a novel target for the new inhibitors. Recently many novel HIV-1 inhibitors binding to capsid proteins have been reported successfully. Most of these inhibitors can inhibit or accelerate the disassembly or assembly of the capsid, and some of them can inhibit reverse transcription. Unfortunately, none of them are currently approved by U.S. FDA. However, GS-6207, an inhibitor binds to the NTD-CTD interface with potent antiviral activity and the long metabolic cycle, is expected to be the first approved drug targeting HIV-1 capsid. Herein, we provide a concise report focusing on the recent prospective of HIV-1 capsid inhibitors in medicinal chemistry in order to enlighten drug design.
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Affiliation(s)
- Lin Sun
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Xujie Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Shujing Xu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Tianguang Huang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Shu Song
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Srinivasulu Cherukupalli
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China; China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong, Province, 44 West Culture Road, 250012, Jinan, Shandong, PR China.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China; China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong, Province, 44 West Culture Road, 250012, Jinan, Shandong, PR China.
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Wilbourne M, Zhang P. Visualizing HIV-1 Capsid and Its Interactions with Antivirals and Host Factors. Viruses 2021; 13:246. [PMID: 33557422 PMCID: PMC7914784 DOI: 10.3390/v13020246] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 01/31/2021] [Accepted: 02/01/2021] [Indexed: 02/03/2023] Open
Abstract
Understanding of the construction and function of the HIV capsid has advanced considerably in the last decade. This is due in large part to the development of more sophisticated structural techniques, particularly cryo-electron microscopy (cryoEM) and cryo-electron tomography (cryoET). The capsid is known to be a pleomorphic fullerene cone comprised of capsid protein monomers arranged into 200-250 hexamers and 12 pentamers. The latter of these induce high curvature necessary to close the cone at both ends. CryoEM/cryoET, NMR, and X-ray crystallography have collectively described these interactions to atomic or near-atomic resolutions. Further, these techniques have helped to clarify the role the HIV capsid plays in several parts of the viral life cycle, from reverse transcription to nuclear entry and integration into the host chromosome. This includes visualizing the capsid bound to host factors. Multiple proteins have been shown to interact with the capsid. Cyclophilin A, nucleoporins, and CPSF6 promote viral infectivity, while MxB and Trim5α diminish the viral infectivity. Finally, structural insights into the intra- and intermolecular interactions that govern capsid function have enabled development of small molecules, peptides, and truncated proteins to disrupt or stabilize the capsid to inhibit HIV replication. The most promising of these, GS6207, is now in clinical trial.
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Affiliation(s)
| | - Peijun Zhang
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
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Structure, Function, and Interactions of the HIV-1 Capsid Protein. Life (Basel) 2021; 11:life11020100. [PMID: 33572761 PMCID: PMC7910843 DOI: 10.3390/life11020100] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/25/2021] [Accepted: 01/27/2021] [Indexed: 11/30/2022] Open
Abstract
The capsid (CA) protein of the human immunodeficiency virus type 1 (HIV-1) is an essential structural component of a virion and facilitates many crucial life cycle steps through interactions with host cell factors. Capsid shields the reverse transcription complex from restriction factors while it enables trafficking to the nucleus by hijacking various adaptor proteins, such as FEZ1 and BICD2. In addition, the capsid facilitates the import and localization of the viral complex in the nucleus through interaction with NUP153, NUP358, TNPO3, and CPSF-6. In the later stages of the HIV-1 life cycle, CA plays an essential role in the maturation step as a constituent of the Gag polyprotein. In the final phase of maturation, Gag is cleaved, and CA is released, allowing for the assembly of CA into a fullerene cone, known as the capsid core. The fullerene cone consists of ~250 CA hexamers and 12 CA pentamers and encloses the viral genome and other essential viral proteins for the next round of infection. As research continues to elucidate the role of CA in the HIV-1 life cycle and the importance of the capsid protein becomes more apparent, CA displays potential as a therapeutic target for the development of HIV-1 inhibitors.
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Identification of an Antiretroviral Small Molecule That Appears To Be a Host-Targeting Inhibitor of HIV-1 Assembly. J Virol 2021; 95:JVI.00883-20. [PMID: 33148797 PMCID: PMC7925099 DOI: 10.1128/jvi.00883-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 10/25/2020] [Indexed: 12/16/2022] Open
Abstract
Given the projected increase in multidrug-resistant HIV-1, there is an urgent need for development of antiretrovirals that act on virus life cycle stages not targeted by drugs currently in use. Host-targeting compounds are of particular interest because they can offer a high barrier to resistance. Here, we report identification of two related small molecules that inhibit HIV-1 late events, a part of the HIV-1 life cycle for which potent and specific inhibitors are lacking. This chemotype was discovered using cell-free protein synthesis and assembly systems that recapitulate intracellular host-catalyzed viral capsid assembly pathways. These compounds inhibit replication of HIV-1 in human T cell lines and peripheral blood mononuclear cells, and are effective against a primary isolate. They reduce virus production, likely by inhibiting a posttranslational step in HIV-1 Gag assembly. Notably, the compound colocalizes with HIV-1 Gag in situ; however, unexpectedly, selection experiments failed to identify compound-specific resistance mutations in gag or pol, even though known resistance mutations developed upon parallel nelfinavir selection. Thus, we hypothesized that instead of binding to Gag directly, these compounds localize to assembly intermediates, the intracellular multiprotein complexes containing Gag and host factors that form during immature HIV-1 capsid assembly. Indeed, imaging of infected cells shows compound colocalized with two host enzymes found in assembly intermediates, ABCE1 and DDX6, but not two host proteins found in other complexes. While the exact target and mechanism of action of this chemotype remain to be determined, our findings suggest that these compounds represent first-in-class, host-targeting inhibitors of intracellular events in HIV-1 assembly.IMPORTANCE The success of antiretroviral treatment for HIV-1 is at risk of being undermined by the growing problem of drug resistance. Thus, there is a need to identify antiretrovirals that act on viral life cycle stages not targeted by drugs in use, such as the events of HIV-1 Gag assembly. To address this gap, we developed a compound screen that recapitulates the intracellular events of HIV-1 assembly, including virus-host interactions that promote assembly. This effort led to the identification of a new chemotype that inhibits HIV-1 replication at nanomolar concentrations, likely by acting on assembly. This compound colocalized with Gag and two host enzymes that facilitate capsid assembly. However, resistance selection did not result in compound-specific mutations in gag, suggesting that the chemotype does not directly target Gag. We hypothesize that this chemotype represents a first-in-class inhibitor of virus production that acts by targeting a virus-host complex important for HIV-1 Gag assembly.
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Zhou XR, Liu Y, Huang Z, Yao Q, He F, Gao Y. Gag Protein Oriented Supramolecular Nets as Potential HIV Traps. Bioconjug Chem 2021; 32:106-110. [PMID: 33405891 DOI: 10.1021/acs.bioconjchem.0c00706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
For HIV/AIDS treatment, the cocktail therapy which uses a combination of anti-retroviral drugs remains the most widely accepted practice. However, the potential drug toxicity, patient tolerability, and emerging drug resistance have limited its long-term efficiency. Here, we design a HIV Gag protein-targeting redox supramolecular assembly (ROSA) system for potential HIV inhibition. An assembling precursor was constructed through conjugation of an oxidation-activatable fluorogenic compound BQA with a selected tetrapeptide GGFF. Since BQA shares a similar structure with the known Gag inhibitor, the precursor could bind to HIV Gag protein with moderate affinity. Moreover, after oxidation, the corresponding nanofibers could bind to Gag protein and trap HIV to realize virus control, thus providing a potential anti-HIV strategy.
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Affiliation(s)
- Xi-Rui Zhou
- Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing 100029, China
| | - Ye Liu
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming 650031, China
| | - Zhentao Huang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory of Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Qingxin Yao
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory of Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Fangfei He
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory of Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Yuan Gao
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory of Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China
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Capsid Lattice Destabilization Leads to Premature Loss of the Viral Genome and Integrase Enzyme during HIV-1 Infection. J Virol 2020; 95:JVI.00984-20. [PMID: 33115869 DOI: 10.1128/jvi.00984-20] [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] [Received: 05/19/2020] [Accepted: 10/24/2020] [Indexed: 01/28/2023] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) capsid (CA) protein forms a conical lattice around the viral ribonucleoprotein complex (vRNP) consisting of a dimeric viral genome and associated proteins, together constituting the viral core. Upon entry into target cells, the viral core undergoes a process termed uncoating, during which CA molecules are shed from the lattice. Although the timing and degree of uncoating are important for reverse transcription and integration, the molecular basis of this phenomenon remains unclear. Using complementary approaches, we assessed the impact of core destabilization on the intrinsic stability of the CA lattice in vitro and fates of viral core components in infected cells. We found that substitutions in CA can impact the intrinsic stability of the CA lattice in vitro in the absence of vRNPs, which mirrored findings from an assessment of CA stability in virions. Altering CA stability tended to increase the propensity to form morphologically aberrant particles, in which the vRNPs were mislocalized between the CA lattice and the viral lipid envelope. Importantly, destabilization of the CA lattice led to premature dissociation of CA from vRNPs in target cells, which was accompanied by proteasomal-independent losses of the viral genome and integrase enzyme. Overall, our studies show that the CA lattice protects the vRNP from untimely degradation in target cells and provide the mechanistic basis of how CA stability influences reverse transcription.IMPORTANCE The human immunodeficiency virus type 1 (HIV-1) capsid (CA) protein forms a conical lattice around the viral RNA genome and the associated viral enzymes and proteins, together constituting the viral core. Upon infection of a new cell, viral cores are released into the cytoplasm where they undergo a process termed "uncoating," i.e., shedding of CA molecules from the conical lattice. Although proper and timely uncoating has been shown to be important for reverse transcription, the molecular mechanisms that link these two events remain poorly understood. In this study, we show that destabilization of the CA lattice leads to premature dissociation of CA from viral cores, which exposes the viral genome and the integrase enzyme for degradation in target cells. Thus, our studies demonstrate that the CA lattice protects the viral ribonucleoprotein complexes from untimely degradation in target cells and provide the first causal link between how CA stability affects reverse transcription.
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Kleinpeter AB, Freed EO. HIV-1 Maturation: Lessons Learned from Inhibitors. Viruses 2020; 12:E940. [PMID: 32858867 PMCID: PMC7552077 DOI: 10.3390/v12090940] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/19/2020] [Accepted: 08/20/2020] [Indexed: 02/06/2023] Open
Abstract
Since the emergence of HIV and AIDS in the early 1980s, the development of safe and effective therapies has accompanied a massive increase in our understanding of the fundamental processes that drive HIV biology. As basic HIV research has informed the development of novel therapies, HIV inhibitors have been used as probes for investigating basic mechanisms of HIV-1 replication, transmission, and pathogenesis. This positive feedback cycle has led to the development of highly effective combination antiretroviral therapy (cART), which has helped stall the progression to AIDS, prolong lives, and reduce transmission of the virus. However, to combat the growing rates of virologic failure and toxicity associated with long-term therapy, it is important to diversify our repertoire of HIV-1 treatments by identifying compounds that block additional steps not targeted by current drugs. Most of the available therapeutics disrupt early events in the replication cycle, with the exception of the protease (PR) inhibitors, which act at the virus maturation step. HIV-1 maturation consists of a series of biochemical changes that facilitate the conversion of an immature, noninfectious particle to a mature infectious virion. These changes include proteolytic processing of the Gag polyprotein by the viral protease (PR), structural rearrangement of the capsid (CA) protein, and assembly of individual CA monomers into hexamers and pentamers that ultimately form the capsid. Here, we review the development and therapeutic potential of maturation inhibitors (MIs), an experimental class of anti-HIV-1 compounds with mechanisms of action distinct from those of the PR inhibitors. We emphasize the key insights into HIV-1 biology and structure that the study of MIs has provided. We will focus on three distinct groups of inhibitors that block HIV-1 maturation: (1) compounds that block the processing of the CA-spacer peptide 1 (SP1) cleavage intermediate, the original class of compounds to which the term MI was applied; (2) CA-binding inhibitors that disrupt capsid condensation; and (3) allosteric integrase inhibitors (ALLINIs) that block the packaging of the viral RNA genome into the condensing capsid during maturation. Although these three classes of compounds have distinct structures and mechanisms of action, they share the ability to block the formation of the condensed conical capsid, thereby blocking particle infectivity.
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Affiliation(s)
| | - Eric O. Freed
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA;
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Medicinal chemistry strategies of targeting HIV-1 capsid protein for antiviral treatment. Future Med Chem 2020; 12:1281-1284. [PMID: 32483985 DOI: 10.4155/fmc-2020-0084] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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32
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Sun L, Dick A, Meuser ME, Huang T, Zalloum WA, Chen CH, Cherukupalli S, Xu S, Ding X, Gao P, Kang D, De Clercq E, Pannecouque C, Cocklin S, Lee KH, Liu X, Zhan P. Design, Synthesis, and Mechanism Study of Benzenesulfonamide-Containing Phenylalanine Derivatives as Novel HIV-1 Capsid Inhibitors with Improved Antiviral Activities. J Med Chem 2020; 63:4790-4810. [PMID: 32298111 DOI: 10.1021/acs.jmedchem.0c00015] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The HIV-1 CA protein has gained remarkable attention as a promising therapeutic target for the development of new antivirals, due to its pivotal roles in HIV-1 replication (structural and regulatory). Herein, we report the design and synthesis of three series of benzenesulfonamide-containing phenylalanine derivatives obtained by further structural modifications of PF-74 to aid in the discovery of more potent and drug-like HIV-1 CA inhibitors. Structure-activity relationship studies of these compounds led to the identification of new phenylalanine derivatives with a piperazinone moiety, represented by compound 11l, which exhibited anti-HIV-1NL4-3 activity 5.78-fold better than PF-74. Interestingly, 11l also showed anti-HIV-2ROD activity (EC50 = 31 nM), with almost 120 times increased potency over PF-74. However, due to the higher significance of HIV-1 as compared to HIV-2 for the human population, this manuscript focuses on the mechanism of action of our compounds in the context of HIV-1. SPR studies on representative compounds confirmed CA as the binding target. The action stage determination assay demonstrated that these inhibitors exhibited antiviral activities with a dual-stage inhibition profile. The early-stage inhibitory activity of compound 11l was 6.25 times more potent as compared to PF-74 but appeared to work via the accelerating capsid core assembly rather than stabilization. However, the mechanism by which they exert their antiviral activity in the late stage appears to be the same as PF-74 with less infectious HIV-1 virions produced in their presence, as judged p24 content studies. MD simulations provided the key rationale for the promising antiviral potency of 11l. Additionally, 11l exhibited a modest increase in HLM and human plasma metabolic stabilities as compared to PF-74, as well as a moderately improved pharmacokinetic profile, favorable oral bioavailability, and no acute toxicity. These studies provide insights and serve as a starting point for subsequent medicinal chemistry efforts in optimizing these promising HIV inhibitors.
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Affiliation(s)
- Lin Sun
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Ji'nan, Shandong 250012, People's Republic of China
| | - Alexej Dick
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Megan E Meuser
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Tianguang Huang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Ji'nan, Shandong 250012, People's Republic of China
| | - Waleed A Zalloum
- Department of Pharmacy, Faculty of Health Science, American University of Madaba, P.O Box 2882, Amman 11821, Jordan
| | - Chin-Ho Chen
- Duke University Medical Center, Surgical Oncology Research Facility, Box 2926, Durham, North Carolina 27710, United States
| | - Srinivasulu Cherukupalli
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Ji'nan, Shandong 250012, People's Republic of China
| | - Shujing Xu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Ji'nan, Shandong 250012, People's Republic of China
| | - Xiao Ding
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Ji'nan, Shandong 250012, People's Republic of China
| | - Ping Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Ji'nan, Shandong 250012, People's Republic of China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Ji'nan, Shandong 250012, People's Republic of China
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000, Leuven, Belgium
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000, Leuven, Belgium
| | - Simon Cocklin
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Kuo-Hsiung Lee
- Natural Products Research Laboratories, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Ji'nan, Shandong 250012, People's Republic of China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Ji'nan, Shandong 250012, People's Republic of China
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PF74 and Its Novel Derivatives Stabilize Hexameric Lattice of HIV-1 Mature-Like Particles. Molecules 2020; 25:molecules25081895. [PMID: 32325987 PMCID: PMC7221806 DOI: 10.3390/molecules25081895] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/09/2020] [Accepted: 04/15/2020] [Indexed: 01/23/2023] Open
Abstract
A major structural retroviral protein, capsid protein (CA), is able to oligomerize into two different hexameric lattices, which makes this protein a key component for both the early and late stages of HIV-1 replication. During the late stage, the CA protein, as part of the Gag polyprotein precursor, facilitates protein–protein interactions that lead to the assembly of immature particles. Following protease activation and Gag polyprotein processing, CA also drives the assembly of the mature viral core. In the early stage of infection, the role of the CA protein is distinct. It controls the disassembly of the mature CA hexameric lattice i.e., uncoating, which is critical for the reverse transcription of the single-stranded RNA genome into double stranded DNA. These properties make CA a very attractive target for small molecule functioning as inhibitors of HIV-1 particle assembly and/or disassembly. Of these, inhibitors containing the PF74 scaffold have been extensively studied. In this study, we reported a series of modifications of the PF74 molecule and its characterization through a combination of biochemical and structural approaches. Our data supported the hypothesis that PF74 stabilizes the mature HIV-1 CA hexameric lattice. We identified derivatives with a higher in vitro stabilization activity in comparison to the original PF74 molecule.
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Dick A, Cocklin S. Recent Advances in HIV-1 Gag Inhibitor Design and Development. Molecules 2020; 25:molecules25071687. [PMID: 32272714 PMCID: PMC7181048 DOI: 10.3390/molecules25071687] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/31/2020] [Accepted: 04/05/2020] [Indexed: 02/06/2023] Open
Abstract
Acquired Immune Deficiency Syndrome (AIDS) treatment with combination antiretroviral therapy (cART) has improved the life quality of many patients since its implementation. However, resistance mutations and the accumulation of severe side effects associated with cART remain enormous challenges that need to be addressed with the continual design and redesign of anti-HIV drugs. In this review, we focus on the importance of the HIV-1 Gag polyprotein as the master coordinator of HIV-1 assembly and maturation and as an emerging drug target. Due to its multiple roles in the HIV-1 life cycle, the individual Gag domains are attractive but also challenging targets for inhibitor design. However, recent encouraging developments in targeting the Gag domains such as the capsid protein with highly potent and potentially long-acting inhibitors, as well as the exploration and successful targeting of challenging HIV-1 proteins such as the matrix protein, have demonstrated the therapeutic viability of this important protein. Such Gag-directed inhibitors have great potential for combating the AIDS pandemic and to be useful tools to dissect HIV-1 biology.
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35
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Zhang DW, Luo RH, Xu L, Yang LM, Xu XS, Zheng YT, Luo H. Natural-product-library-based screening for discovery of capsid C-terminal domain targeted HIV-1 inhibitors. Int J Antimicrob Agents 2020; 55:105926. [PMID: 32092396 DOI: 10.1016/j.ijantimicag.2020.105926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 02/10/2020] [Accepted: 02/14/2020] [Indexed: 01/31/2023]
Abstract
Antiretroviral therapy (ART) can effectively suppress replication of human immunodeficiency virus type 1 (HIV-1) and limit disease progression. However, ART is unable to eradicate the virus, and the requirement for lifelong treatment may have side effects and may lead to the development of resistance. New approaches to prevent and treat HIV-1 infection should therefore be developed. HIV-1 capsid (CA) protein is an unexploited but attractive target for antiviral drug development. The hydrophobic cavity of the C-terminal domain of CA (CA CTD) has been validated as a potential target for antiviral drugs. Binding of compounds to this conserved non-polar groove in CA CTD allosterically disrupts the CA assembly. This study screened 2080 natural products to identify potential antiviral agents for further development to combat HIV-1 infection. From the primary screen at a fixed concentration of 50 µM, 16 compounds were found to be effective against this target. Six compounds observed in the primary screen were confirmed in dose-response experiments, and were tested against HIV-1-induced cytopathic effects. Two compounds were found to inhibit HIV-1 replication, and the most active compound - rubranol - inhibited viral replication at a moderate micromolar concentration (EC50 = 15.85 μM). The binding modes of rubranol and hirsutanonol to CA CTD were analysed by molecular docking, providing insight for the design of drugs targeting HIV-1 CA. This study reports, for the first time, identification of natural products that showed potential as anti-HIV-1 agents by targeting the conserved hydrophobic cavity of HIV-1 CA CTD.
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Affiliation(s)
- Da-Wei Zhang
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Rong-Hua Luo
- Key Laboratory of Bioactive Peptides of Yunnan Province/Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, the National Kunming High Level Biosafety Research Center for Nonhuman Primates, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Liu-Meng Yang
- Key Laboratory of Bioactive Peptides of Yunnan Province/Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, the National Kunming High Level Biosafety Research Center for Nonhuman Primates, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xiao-Shuang Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Yong-Tang Zheng
- Key Laboratory of Bioactive Peptides of Yunnan Province/Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, the National Kunming High Level Biosafety Research Center for Nonhuman Primates, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
| | - Heng Luo
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, Guizhou, China.
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36
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Maeda K, Das D, Kobayakawa T, Tamamura H, Takeuchi H. Discovery and Development of Anti-HIV Therapeutic Agents: Progress Towards Improved HIV Medication. Curr Top Med Chem 2019; 19:1621-1649. [PMID: 31424371 PMCID: PMC7132033 DOI: 10.2174/1568026619666190712204603] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/14/2019] [Accepted: 06/21/2019] [Indexed: 01/09/2023]
Abstract
The history of the human immunodeficiency virus (HIV)/AIDS therapy, which spans over 30 years, is one of the most dramatic stories of science and medicine leading to the treatment of a disease. Since the advent of the first AIDS drug, AZT or zidovudine, a number of agents acting on different drug targets, such as HIV enzymes (e.g. reverse transcriptase, protease, and integrase) and host cell factors critical for HIV infection (e.g. CD4 and CCR5), have been added to our armamentarium to combat HIV/AIDS. In this review article, we first discuss the history of the development of anti-HIV drugs, during which several problems such as drug-induced side effects and the emergence of drug-resistant viruses became apparent and had to be overcome. Nowadays, the success of Combination Antiretroviral Therapy (cART), combined with recently-developed powerful but nonetheless less toxic drugs has transformed HIV/AIDS from an inevitably fatal disease into a manageable chronic infection. However, even with such potent cART, it is impossible to eradicate HIV because none of the currently available HIV drugs are effective in eliminating occult “dormant” HIV cell reservoirs. A number of novel unique treatment approaches that should drastically improve the quality of life (QOL) of patients or might actually be able to eliminate HIV altogether have also been discussed later in the review.
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Affiliation(s)
- Kenji Maeda
- National Center for Global Health and Medicine (NCGM) Research Institute, Tokyo 162-8655, Japan
| | - Debananda Das
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health (NCI/NIH), Bethesda, MD, United States
| | - Takuya Kobayakawa
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Tokyo 101-0062, Japan
| | - Hirokazu Tamamura
- Department of Molecular Virology, Tokyo Medical and Dental University (TMDU), Tokyo 113-8519, Japan
| | - Hiroaki Takeuchi
- Department of Molecular Virology, Tokyo Medical and Dental University (TMDU), Tokyo 113-8519, Japan
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37
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McArthur C, Gallazzi F, Quinn TP, Singh K. HIV Capsid Inhibitors Beyond PF74. Diseases 2019; 7:diseases7040056. [PMID: 31671622 PMCID: PMC6956309 DOI: 10.3390/diseases7040056] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/21/2019] [Accepted: 10/27/2019] [Indexed: 01/13/2023] Open
Abstract
Human immunodeficiency virus (HIV) capsid plays important roles at multiple stages of viral replication. At the initial stages, controlled uncoating (disassembly) of the capsid ensures efficient reverse transcription of the single-stranded RNA genome, into the double-stranded DNA. Whereas at later stages, a proper assembly of capsid ensures the formation of a mature infectious virus particle. Hence, the inhibition of capsid assembly and/or disassembly has been recognized as a potential therapeutic strategy, and several capsid inhibitors have been reported. Of these, PF-3450074 (PF74) has been extensively studied. Recently reported GS-CA inhibitors (GS-CA1 and GS-6207), have shown a strong potential and appear to contain a PF74 scaffold. The location of resistance mutations and the results of structural studies further suggest that GS-CA compounds and PF74 share the same binding pocket, which is located between capsid monomers. Additionally, phenylalanine derivatives containing the PF74 scaffold show slightly enhanced capsid inhibiting activity. A comparison of capsid structures in complex with host factors and PF74, reveals the presence of common chemical entities at topologically equivalent positions. Here we present the status of capsid inhibitors that contain PF74 scaffolds and propose that the PF74 scaffold may be used to develop strong and safe capsid inhibitors.
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Affiliation(s)
- Carole McArthur
- Department of Oral and Craniofacial Sciences, School of Dentistry, University of Missouri, Kansas, MO 64108, USA.
- Kansas City School of Medicine, University of Missouri, Kansas, MO 64108, USA.
- Department of Pathology, Truman Medical Center, Kansas, MO, 64108, USA.
| | - Fabio Gallazzi
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
- Department of Chemistry, University of Missouri, Columbia, MO 65211, USA.
| | - Thomas P Quinn
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.
| | - Kamal Singh
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65211, USA.
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, 14186 Stockholm, Sweden.
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38
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Pak AJ, Grime JMA, Yu A, Voth GA. Off-Pathway Assembly: A Broad-Spectrum Mechanism of Action for Drugs That Undermine Controlled HIV-1 Viral Capsid Formation. J Am Chem Soc 2019; 141:10214-10224. [PMID: 31244184 PMCID: PMC6739737 DOI: 10.1021/jacs.9b01413] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Indexed: 12/21/2022]
Abstract
The early and late stages of human immunodeficiency virus (HIV) replication are orchestrated by the capsid (CA) protein, which self-assembles into a conical protein shell during viral maturation. Small molecule drugs known as capsid inhibitors (CIs) impede the highly regulated activity of CA. Intriguingly, a few CIs, such as PF-3450074 (PF74) and GS-CA1, exhibit effects at multiple stages of the viral lifecycle at effective concentrations in the pM to nM regimes, while the majority of CIs target a single stage of the viral lifecycle and are effective at nM to μM concentrations. In this work, we use coarse-grained molecular dynamics simulations to elucidate the molecular mechanisms that enable CIs to have such curious broad-spectrum activity. Our quantitatively analyzed findings show that CIs can have a profound impact on the hierarchical self-assembly of CA by perturbing populations of small CA oligomers. The self-assembly process is accelerated by the emergence of alternative assembly pathways that favor the rapid incorporation of CA pentamers, and leads to increased structural pleomorphism in mature capsids. Two relevant phenotypes are observed: (1) eccentric capsid formation that may fail to encase the viral genome and (2) rapid disassembly of the capsid, which express at late and early stages of infection, respectively. Finally, our study emphasizes the importance of adopting a dynamical perspective on inhibitory mechanisms and provides a basis for the design of future therapeutics that are effective at low stoichiometric ratios of drug to protein.
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Affiliation(s)
- Alexander J. Pak
- Department of Chemistry, Institute for Biophysical Dynamics,
and James Franck Institute, The University
of Chicago, Chicago, Illinois 60637, United States
| | - John M. A. Grime
- Department of Chemistry, Institute for Biophysical Dynamics,
and James Franck Institute, The University
of Chicago, Chicago, Illinois 60637, United States
| | - Alvin Yu
- Department of Chemistry, Institute for Biophysical Dynamics,
and James Franck Institute, The University
of Chicago, Chicago, Illinois 60637, United States
| | - Gregory A. Voth
- Department of Chemistry, Institute for Biophysical Dynamics,
and James Franck Institute, The University
of Chicago, Chicago, Illinois 60637, United States
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39
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Zhang DW, Luo RH, Xu L, Yang LM, Xu XS, Bedwell GJ, Engelman AN, Zheng YT, Chang S. A HTRF based competitive binding assay for screening specific inhibitors of HIV-1 capsid assembly targeting the C-Terminal domain of capsid. Antiviral Res 2019; 169:104544. [PMID: 31254557 DOI: 10.1016/j.antiviral.2019.104544] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 06/13/2019] [Accepted: 06/20/2019] [Indexed: 02/02/2023]
Abstract
Due to its multifaceted essential roles in virus replication and extreme genetic fragility, the human immunodeficiency virus type 1 (HIV-1) capsid (CA) protein is a valued therapeutic target. However, CA is as yet unexploited clinically, as there are no antiviral agents that target it currently on the market. To facilitate the identification of potential HIV-1 CA inhibitors, we established a homogeneous time-resolved fluorescence (HTRF) assay to screen for small molecules that target a biologically active and specific binding pocket in the C-terminal domain of HIV-1 CA (CA CTD). The assay, which is based on competition of small molecules for the binding of a known CA inhibitor (CAI) to the CA CTD, exhibited a signal-to-background ratio (S/B) > 10 and a Z' value > 0.9. In a pilot screen of three kinase inhibitor libraries containing 464 compounds, we identified one compound, TX-1918, as a low micromolecular inhibitor of the HIV-1 CA CTD-CAI interaction (IC50 = 3.81 μM) that also inhibited viral replication at moderate micromolar concentration (EC50 = 15.16 μM) and inhibited CA assembly in vitro. Based on the structure of TX-1918, an additional compound with an antiviral EC50 of 6.57 μM and cellular cytotoxicity CC50 of 102.55 μM was obtained from a compound similarity search. Thus, the HTRF-based assay has properties that are suitable for screening large compound libraries to identify novel anti-HIV-1 inhibitors targeting the CA CTD.
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Affiliation(s)
- Da-Wei Zhang
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, 213001, China; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Rong-Hua Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, The National Kunming High Level Biosafety Research Center for Nonhuman Primate, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, 213001, China
| | - Liu-Meng Yang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, The National Kunming High Level Biosafety Research Center for Nonhuman Primate, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Xiao-Shuang Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, 213001, China
| | - Gregory J Bedwell
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, The National Kunming High Level Biosafety Research Center for Nonhuman Primate, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.
| | - Shan Chang
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, 213001, China.
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40
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Singh K, Gallazzi F, Hill KJ, Burke DH, Lange MJ, Quinn TP, Neogi U, Sönnerborg A. GS-CA Compounds: First-In-Class HIV-1 Capsid Inhibitors Covering Multiple Grounds. Front Microbiol 2019; 10:1227. [PMID: 31312185 PMCID: PMC6613529 DOI: 10.3389/fmicb.2019.01227] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 05/16/2019] [Indexed: 01/09/2023] Open
Abstract
Recently reported HIV-1 capsid (CA) inhibitors GS-CA1 and GS-6207 (an analog of GS-CA1) are first-in-class compounds with long-acting potential. Reportedly, both compounds have greater potency than currently approved anti-HIV drugs. Due to the limited access to experimental data and the compounds themselves, a detailed mechanism of their inhibition is yet to be delineated. Using crystal structures of capsid-hexamers bound to well-studied capsid inhibitor PF74 and molecular modeling, we predict that GS-CA compounds bind in the pocket that is shared by previously reported CA inhibitors and host factors. Additionally, comparative modeling suggests that GS-CA compounds have unique structural features contributing to interactions with capsid. To test their proposed binding mode, we also report the design of a cyclic peptide combining structural units from GS-CA compounds, host factors, and previously reported capsid inhibitors. This peptide (Pep-1) binds CA-hexamer with a docking score comparable to GS-CA compounds. Affinity determination by MicroScale thermophoresis (MST) assays showed that CA binds Pep-1 with a ~7-fold better affinity than well-studied capsid inhibitor PF74, suggesting that it can be developed as a possible CA inhibitor.
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Affiliation(s)
- Kamal Singh
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, United States.,Bond Life Sciences Center, University of Missouri, Columbia, MO, United States.,Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Fabio Gallazzi
- Bond Life Sciences Center, University of Missouri, Columbia, MO, United States.,Department of Chemistry, University of Missouri, Columbia, MO, United States
| | - Kyle J Hill
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, United States.,Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Donald H Burke
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, United States.,Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Margaret J Lange
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, United States.,Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Thomas P Quinn
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden.,Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden
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41
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Novikova M, Zhang Y, Freed EO, Peng K. Multiple Roles of HIV-1 Capsid during the Virus Replication Cycle. Virol Sin 2019; 34:119-134. [PMID: 31028522 PMCID: PMC6513821 DOI: 10.1007/s12250-019-00095-3] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 01/16/2019] [Indexed: 11/29/2022] Open
Abstract
Human immunodeficiency virus-1 capsid (HIV-1 CA) is involved in different stages of the viral replication cycle. During virion assembly, CA drives the formation of the hexameric lattice in immature viral particles, while in mature virions CA monomers assemble in cone-shaped cores surrounding the viral RNA genome and associated proteins. In addition to its functions in late stages of the viral replication cycle, CA plays key roles in a number of processes during early phases of HIV-1 infection including trafficking, uncoating, recognition by host cellular proteins and nuclear import of the viral pre-integration complex. As a result of efficient cooperation of CA with other viral and cellular proteins, integration of the viral genetic material into the host genome, which is an essential step for productive viral infection, successfully occurs. In this review, we will summarize available data on CA functions in HIV-1 replication, describing in detail its roles in late and early phases of the viral replication cycle.
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Affiliation(s)
- Mariia Novikova
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Yulan Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Eric O Freed
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
| | - Ke Peng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
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42
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Abstract
PURPOSE OF REVIEW To summarize recent advances in the discovery of chemical inhibitors targeting the HIV capsid and research on their mechanisms of action. RECENT FINDINGS HIV infection is critically dependent on functions of the viral capsid. Numerous studies have reported the identification of a variety of compounds that bind to the capsid protein; some of these inhibit reverse transcription and nuclear entry, steps required for infection. Other capsid-targeting compounds appear to act by perturbing capsid assembly, resulting in noninfectious progeny virions. Inhibitors may bind to several different positions on the capsid protein, including sites in both protein domains. However, the antiviral activity of many reported capsid-targeting inhibitors has not been definitively linked to capsid binding. Until recently, the low-to-moderate potency of reported capsid-targeting inhibitors has precluded their further clinical development. In 2017, GS-CA1, a highly potent capsid inhibitor, was described that holds promise for clinical development. SUMMARY Small molecules that bind to the viral capsid protein can be potent inhibitors of HIV infection. Capsid-targeting drugs are predicted to exhibit high barriers to viral resistance, and ongoing work in this area is contributing to an understanding of the molecular biology of HIV uncoating and maturation.
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43
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New targets for HIV drug discovery. Drug Discov Today 2019; 24:1139-1147. [PMID: 30885676 DOI: 10.1016/j.drudis.2019.03.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/23/2019] [Accepted: 03/11/2019] [Indexed: 02/07/2023]
Abstract
Recent estimates suggest close to one million people per year die globally owing to HIV-related illnesses. Therefore, there is still a need to identify new targets to develop future treatments. Many of the more recently identified targets are host-related and these might be more difficult for the virus to develop drug resistance to. In addition, there are virus-related targets (capsid and RNAse H) that have yet to be exploited clinically. Several of the newer targets also address virulence factors, virus latency or target persistence. The targets highlighted in this review could represent the next generation of viable candidates for drug discovery projects as well as continue the search for a cure for this disease.
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44
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Zhou Q, Zhang J, Huang R, Huang S, Wu Y, Huang L, He J, Xie J. An affinity peptide exerts antiviral activity by strongly binding nervous necrosis virus to block viral entry. FISH & SHELLFISH IMMUNOLOGY 2019; 86:465-473. [PMID: 30521966 DOI: 10.1016/j.fsi.2018.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 11/25/2018] [Accepted: 12/01/2018] [Indexed: 06/09/2023]
Abstract
Nervous necrosis virus (NNV) causes viral nervous necrosis (VNN), a disease that leads to almost 100% mortality among larvae and juvenile fish, severely affecting the aquaculture industry. VNN vaccines based on inactivated viruses or virus-like particles (VLPs) are unsuitable for fish fry with immature adaptive immune systems. Here, we applied an anti-NNV strategy based on affinity peptides (AFPs). Three phage display peptide libraries were screened against RBS, the VLP of orange-spotted grouper nervous necrosis virus (OGNNV). From the positive clones, a dodecapeptide with the highest binding capacity (BC) to RBS was selected. This AFP agglutinated or disrupted virion particles, inhibiting RBS entry into sea bass (SB) cells. To enhance BC and solubility, we amended the AFP sequence as "LHWDFQSWVPLL" and named as 12C. One to three copies of 12C in tandem were prokaryotically expressed with a maltose binding protein (MBP) linked by a flexible peptide. Of the recombinant proteins expressed, MBP-triple-12C (MBP-T12C) exhibited the highest BC, efficiently blocked RBS entry, and strongly inhibited OGNNV infection at viral entry. Moreover, MBP-T12C bound the VLPs of all NNV serotypes, displaying broad-spectrum anti-NNV ability, and recognized only OGNNV and mud crab virus, demonstrating binding specificity. Therefore, these anti-NNV AFPs specifically bound NNV, aggregating or disrupting the viral particles, to reduce the contact probability between the virus and cell surface, subsequently inhibiting viral infection. Our results not only provided a candidate of anti-NNV AFP, but a framework for the development of antiviral AFP.
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Affiliation(s)
- Qiong Zhou
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory of Improved Variety Reproduction in Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jing Zhang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory of Improved Variety Reproduction in Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Runqing Huang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory of Improved Variety Reproduction in Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Siyou Huang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory of Improved Variety Reproduction in Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yujia Wu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory of Improved Variety Reproduction in Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Lijie Huang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory of Improved Variety Reproduction in Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jianguo He
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory of Improved Variety Reproduction in Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China; School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Junfeng Xie
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory of Improved Variety Reproduction in Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
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45
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Abstract
The capsid protein is a promising target for the development of therapeutic anti-virus agents.
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Affiliation(s)
- Ding-Yi Fu
- State Key Laboratory of Supramolecular Structure and Materials
- Institute of Theoretical Chemistry
- Jilin University
- Changchun
- China
| | - Ya-Rong Xue
- State Key Laboratory of Supramolecular Structure and Materials
- Institute of Theoretical Chemistry
- Jilin University
- Changchun
- China
| | - Xianghui Yu
- National Engineering Laboratory for AIDS Vaccine
- School of Life Sciences
- Jilin University
- Changchun
- China
| | - Yuqing Wu
- State Key Laboratory of Supramolecular Structure and Materials
- Institute of Theoretical Chemistry
- Jilin University
- Changchun
- China
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46
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Broad-Spectrum Antiviral Activity of an Ankyrin Repeat Protein on Viral Assembly against Chimeric NL4-3 Viruses Carrying Gag/PR Derived from Circulating Strains among Northern Thai Patients. Viruses 2018; 10:v10110625. [PMID: 30428529 PMCID: PMC6265948 DOI: 10.3390/v10110625] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/08/2018] [Accepted: 11/09/2018] [Indexed: 01/06/2023] Open
Abstract
Certain proteins have demonstrated proficient human immunodeficiency virus (HIV-1) life cycle disturbance. Recently, the ankyrin repeat protein targeting the HIV-1 capsid, AnkGAG1D4, showed a negative effect on the viral assembly of the HIV-1NL4-3 laboratory strain. To extend its potential for future clinical application, the activity of AnkGAG1D4 in the inhibition of other HIV-1 circulating strains was evaluated. Chimeric NL4-3 viruses carrying patient-derived Gag/PR-coding regions were generated from 131 antiretroviral drug-naïve HIV-1 infected individuals in northern Thailand during 2001–2012. SupT1, a stable T-cell line expressing AnkGAG1D4 and ankyrin non-binding control (AnkA32D3), were challenged with these chimeric viruses. The p24CA sequences were analysed and classified using the K-means clustering method. Among all the classes of virus classified using the p24CA sequences, SupT1/AnkGAG1D4 demonstrated significantly lower levels of p24CA than SupT1/AnkA32D3, which was found to correlate with the syncytia formation. This result suggests that AnkGAG1D4 can significantly interfere with the chimeric viruses derived from patients with different sequences of the p24CA domain. It supports the possibility of ankyrin-based therapy as a broad alternative therapeutic molecule for HIV-1 gene therapy in the future.
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47
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Lopes RS, Queiroz MAF, Gomes STM, Vallinoto ACR, Goulart LR, Ishak R. Phage display: an important tool in the discovery of peptides with anti-HIV activity. Biotechnol Adv 2018; 36:1847-1854. [PMID: 30012540 DOI: 10.1016/j.biotechadv.2018.07.003] [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: 02/20/2018] [Revised: 06/14/2018] [Accepted: 07/12/2018] [Indexed: 10/28/2022]
Abstract
Human immunodeficiency virus (HIV) remains a worldwide health problem despite huge investments and research breakthroughs, and no single drug is effective in killing the virus yet. Among new strategies to control HIV infection, the phage display (PD) technology has become a promising tool in the discovery of peptides that can be used as new drugs, or also as possible vaccine candidates. This review discusses basic aspects of PD and its use to advance two main objectives related to combating HIV-1 infection: the identification of peptides that inhibit virus replication and the identification of peptides that induce the production of neutralizing antibodies. We will cover the different approaches used for mapping and selection of mimotopes, and discuss the promising results of these biologicals as antiviral agents.
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Affiliation(s)
- Ronaldo Souza Lopes
- Biological Sciences Institute, Federal University of Para (Instituto de Ciências Biológicas/Universidade Feral do Pará - ICB/UFPA), Rua Augusto Corrêa, 1 - Guamá, Belém, PA 66075-110, Brazil.
| | - Maria Alice Freitas Queiroz
- Biological Sciences Institute, Federal University of Para (Instituto de Ciências Biológicas/Universidade Feral do Pará - ICB/UFPA), Rua Augusto Corrêa, 1 - Guamá, Belém, PA 66075-110, Brazil
| | - Samara Tatielle Monteiro Gomes
- Biological Sciences Institute, Federal University of Para (Instituto de Ciências Biológicas/Universidade Feral do Pará - ICB/UFPA), Rua Augusto Corrêa, 1 - Guamá, Belém, PA 66075-110, Brazil
| | - Antonio Carlos Rosário Vallinoto
- Biological Sciences Institute, Federal University of Para (Instituto de Ciências Biológicas/Universidade Feral do Pará - ICB/UFPA), Rua Augusto Corrêa, 1 - Guamá, Belém, PA 66075-110, Brazil.
| | - Luiz Ricardo Goulart
- Institute of Biotechnology, Federal University of Uberlândia (Universidade Federal de Uberlândia - UFU), Laboratory of Nanobiotechnology, Av. Amazonas s/n, Bloco 2E, Sala 248 - Campus Umuarama, Uberlândia, MG, CEP 38400-902, Brazil.
| | - Ricardo Ishak
- Biological Sciences Institute, Federal University of Para (Instituto de Ciências Biológicas/Universidade Feral do Pará - ICB/UFPA), Rua Augusto Corrêa, 1 - Guamá, Belém, PA 66075-110, Brazil.
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48
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Rumlová M, Ruml T. In vitro methods for testing antiviral drugs. Biotechnol Adv 2018; 36:557-576. [PMID: 29292156 PMCID: PMC7127693 DOI: 10.1016/j.biotechadv.2017.12.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 12/22/2017] [Accepted: 12/27/2017] [Indexed: 12/24/2022]
Abstract
Despite successful vaccination programs and effective treatments for some viral infections, humans are still losing the battle with viruses. Persisting human pandemics, emerging and re-emerging viruses, and evolution of drug-resistant strains impose continuous search for new antiviral drugs. A combination of detailed information about the molecular organization of viruses and progress in molecular biology and computer technologies has enabled rational antivirals design. Initial step in establishing efficacy of new antivirals is based on simple methods assessing inhibition of the intended target. We provide here an overview of biochemical and cell-based assays evaluating the activity of inhibitors of clinically important viruses.
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Affiliation(s)
- Michaela Rumlová
- Department of Biotechnology, University of Chemistry and Technology, Prague 166 28, Czech Republic.
| | - Tomáš Ruml
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague 166 28, Czech Republic.
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49
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Dai X, Gong D, Lim H, Jih J, Wu TT, Sun R, Zhou ZH. Structure and mutagenesis reveal essential capsid protein interactions for KSHV replication. Nature 2018; 553:521-525. [PMID: 29342139 DOI: 10.1038/nature25438] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 12/06/2017] [Indexed: 12/31/2022]
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) causes Kaposi's sarcoma, a cancer that commonly affects patients with AIDS and which is endemic in sub-Saharan Africa. The KSHV capsid is highly pressurized by its double-stranded DNA genome, as are the capsids of the eight other human herpesviruses. Capsid assembly and genome packaging of herpesviruses are prone to interruption and can therefore be targeted for the structure-guided development of antiviral agents. However, herpesvirus capsids-comprising nearly 3,000 proteins and over 1,300 Å in diameter-present a formidable challenge to atomic structure determination and functional mapping of molecular interactions. Here we report a 4.2 Å resolution structure of the KSHV capsid, determined by electron-counting cryo-electron microscopy, and its atomic model, which contains 46 unique conformers of the major capsid protein (MCP), the smallest capsid protein (SCP) and the triplex proteins Tri1 and Tri2. Our structure and mutagenesis results reveal a groove in the upper domain of the MCP that contains hydrophobic residues that interact with the SCP, which in turn crosslinks with neighbouring MCPs in the same hexon to stabilize the capsid. Multiple levels of MCP-MCP interaction-including six sets of stacked hairpins lining the hexon channel, disulfide bonds across channel and buttress domains in neighbouring MCPs, and an interaction network forged by the N-lasso domain and secured by the dimerization domain-define a robust capsid that is resistant to the pressure exerted by the enclosed genome. The triplexes, each composed of two Tri2 molecules and a Tri1 molecule, anchor to the capsid floor via a Tri1 N-anchor to plug holes in the MCP network and rivet the capsid floor. These essential roles of the MCP N-lasso and Tri1 N-anchor are verified by serial-truncation mutageneses. Our proof-of-concept demonstration of the use of polypeptides that mimic the smallest capsid protein to inhibit KSHV lytic replication highlights the potential for exploiting the interaction hotspots revealed in our atomic structure to develop antiviral agents.
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Affiliation(s)
- Xinghong Dai
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, California 90095, USA.,The California NanoSystems Institute (CNSI), University of California, Los Angeles (UCLA), Los Angeles, California 90095, USA.,Department of Molecular and Medical Pharmacology, University of California, Los Angeles (UCLA), Los Angeles, California 90095, USA
| | - Danyang Gong
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles (UCLA), Los Angeles, California 90095, USA
| | - Hanyoung Lim
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, California 90095, USA
| | - Jonathan Jih
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, California 90095, USA
| | - Ting-Ting Wu
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles (UCLA), Los Angeles, California 90095, USA
| | - Ren Sun
- The California NanoSystems Institute (CNSI), University of California, Los Angeles (UCLA), Los Angeles, California 90095, USA.,Department of Molecular and Medical Pharmacology, University of California, Los Angeles (UCLA), Los Angeles, California 90095, USA
| | - Z Hong Zhou
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, California 90095, USA.,The California NanoSystems Institute (CNSI), University of California, Los Angeles (UCLA), Los Angeles, California 90095, USA
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50
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Wapling J, Srivastava S, Shehu-Xhilaga M, Tachedjian G. Targeting Human Immunodeficiency Virus Type 1 Assembly, Maturation and Budding. Drug Target Insights 2017. [DOI: 10.1177/117739280700200020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Johanna Wapling
- Molecular Interactions Group, Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, 3004, Australia
- Department of Microbiology, Monash University, Clayton, Victoria 3168, Australia
| | - Seema Srivastava
- Molecular Interactions Group, Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, 3004, Australia
| | - Miranda Shehu-Xhilaga
- Department of Medicine, Monash University, Prahran, Victoria 3181, Australia
- Infectious Diseases Unit, Alfred Hospital, Prahran, Victoria 3181, Australia
| | - Gilda Tachedjian
- Molecular Interactions Group, Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, 3004, Australia
- Department of Microbiology, Monash University, Clayton, Victoria 3168, Australia
- Department of Medicine, Monash University, Prahran, Victoria 3181, Australia
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