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Zhang J, Li Q, Cruz Cosme RS, Gerzanich V, Tang Q, Simard JM, Zhao RY. Genome-Wide Characterization of SARS-CoV-2 Cytopathogenic Proteins in the Search of Antiviral Targets. mBio 2021; 13:e0016922. [PMID: 35164548 PMCID: PMC8844912 DOI: 10.1128/mbio.00169-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 12/11/2022] Open
Abstract
Therapeutic inhibition of critical viral functions is important for curtailing coronavirus disease 2019 (COVID-19). We sought to identify antiviral targets through the genome-wide characterization of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins that are crucial for viral pathogenesis and that cause harmful cytopathogenic effects. All 29 viral proteins were tested in a fission yeast cell-based system using inducible gene expression. Twelve proteins, including eight nonstructural proteins (NSP1, NSP3, NSP4, NSP5, NSP6, NSP13, NSP14, and NSP15) and four accessory proteins (ORF3a, ORF6, ORF7a, and ORF7b), were identified that altered cellular proliferation and integrity and induced cell death. Cell death correlated with the activation of cellular oxidative stress. Of the 12 proteins, ORF3a was chosen for further study in mammalian cells because it plays an important role in viral pathogenesis and its activities are linked to lung tissue damage and a cytokine storm. In human pulmonary and kidney epithelial cells, ORF3a induced cellular oxidative stress associated with apoptosis and necrosis and caused activation of proinflammatory response with production of the cytokines tumor necrosis factor alpha (TNF-α), interleukin-6 (IL-6), and IFN-β1, possibly through the activation of nuclear factor kappa B (NF-κB). To further characterize the mechanism, we tested a natural ORF3a Beta variant, Q57H, and a mutant with deletion of the highly conserved residue, ΔG188. Compared with wild-type ORF3a, the ΔG188 variant yielded more robust activation of cellular oxidative stress, cell death, and innate immune response. Since cellular oxidative stress and inflammation contribute to cell death and tissue damage linked to the severity of COVID-19, our findings suggest that ORF3a is a promising, novel therapeutic target against COVID-19. IMPORTANCE The ongoing COVID-19 pandemic caused by SARS-CoV-2 has claimed over 5.5 million lives with more than 300 million people infected worldwide. While vaccines are effective, the emergence of new viral variants could jeopardize vaccine protection. Treatment of COVID-19 by antiviral drugs provides an alternative to battle against the disease. The goal of this study was to identify viral therapeutic targets that can be used in antiviral drug discovery. Utilizing a genome-wide functional analysis in a fission yeast cell-based system, we identified 12 viral candidates, including ORF3a, which cause cellular oxidative stress, inflammation, apoptosis, and necrosis that contribute to cytopathogenicity and COVID-19. Our findings indicate that antiviral agents targeting ORF3a could have a great impact on COVID-19.
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Affiliation(s)
- Jiantao Zhang
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Research & Development Service, VA Maryland Health Care System, Baltimore, Maryland, USA
| | - Qi Li
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Ruth S. Cruz Cosme
- Surgical Care Clinical Center, VA Maryland Health Care System, Baltimore, Maryland, USA
| | - Volodymyr Gerzanich
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Research & Development Service, VA Maryland Health Care System, Baltimore, Maryland, USA
| | - Qiyi Tang
- Department of Microbiology, Howard University College of Medicine, Washington, DC, USA
| | - J. Marc Simard
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Surgical Care Clinical Center, VA Maryland Health Care System, Baltimore, Maryland, USA
| | - Richard Y. Zhao
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Institute of Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Research & Development Service, VA Maryland Health Care System, Baltimore, Maryland, USA
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Bonar MM, Tabler CO, Haqqani AA, Lapointe LE, Galiatsos JA, Joussef-Piña S, Quiñones-Mateu ME, Tilton JC. Nanoscale flow cytometry reveals interpatient variability in HIV protease activity that correlates with viral infectivity and identifies drug-resistant viruses. Sci Rep 2020; 10:18101. [PMID: 33093566 PMCID: PMC7583244 DOI: 10.1038/s41598-020-75118-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 10/06/2020] [Indexed: 11/26/2022] Open
Abstract
HIV encodes an aspartyl protease that is activated during, or shortly after, budding of viral particles from the surface of infected cells. Protease-mediated cleavage of viral polyproteins is essential to generating infectious viruses, a process known as ‘maturation’ that is the target of FDA-approved antiretroviral drugs. Most assays to monitor protease activity rely on bulk analysis of millions of viruses and obscure potential heterogeneity of protease activation within individual particles. In this study we used nanoscale flow cytometry in conjunction with an engineered FRET reporter called VIral ProteasE Reporter (VIPER) to investigate heterogeneity of protease activation in individual, patient-derived viruses. We demonstrate previously unappreciated interpatient variation in HIV protease processing efficiency that impacts viral infectivity. Additionally, monitoring of protease activity in individual virions distinguishes between drug sensitivity or resistance to protease inhibitors in patient-derived samples. These findings demonstrate the feasibility of monitoring enzymatic processes using nanoscale flow cytometry and highlight the potential of this technology for translational clinical discovery, not only for viruses but also other submicron particles including exosomes, microvesicles, and bacteria.
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Affiliation(s)
- Michał M Bonar
- Center for Proteomics and Bioinformatics, Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Caroline O Tabler
- Center for Proteomics and Bioinformatics, Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Aiman A Haqqani
- Center for Proteomics and Bioinformatics, Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Lauren E Lapointe
- Center for Proteomics and Bioinformatics, Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Jake A Galiatsos
- Center for Proteomics and Bioinformatics, Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Samira Joussef-Piña
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Miguel E Quiñones-Mateu
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.,Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - John C Tilton
- Center for Proteomics and Bioinformatics, Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.
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Lawal MM, Sanusi ZK, Govender T, Maguire GE, Honarparvar B, Kruger HG. From Recognition to Reaction Mechanism: An Overview on the Interactions between HIV-1 Protease and its Natural Targets. Curr Med Chem 2020; 27:2514-2549. [DOI: 10.2174/0929867325666181113122900] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 11/04/2018] [Accepted: 11/07/2018] [Indexed: 12/28/2022]
Abstract
Current investigations on the Human Immunodeficiency Virus Protease (HIV-1
PR) as a druggable target towards the treatment of AIDS require an update to facilitate further
development of promising inhibitors with improved inhibitory activities. For the past two
decades, up to 100 scholarly reports appeared annually on the inhibition and catalytic mechanism
of HIV-1 PR. A fundamental literature review on the prerequisite of HIV-1 PR action
leading to the release of the infectious virion is absent. Herein, recent advances (both computationally
and experimentally) on the recognition mode and reaction mechanism of HIV-1 PR
involving its natural targets are provided. This review features more than 80 articles from
reputable journals. Recognition of the natural Gag and Gag-Pol cleavage junctions by this
enzyme and its mutant analogs was first addressed. Thereafter, a comprehensive dissect of
the enzymatic mechanism of HIV-1 PR on its natural polypeptide sequences from literature
was put together. In addition, we highlighted ongoing research topics in which in silico
methods could be harnessed to provide deeper insights into the catalytic mechanism of the
HIV-1 protease in the presence of its natural substrates at the molecular level. Understanding
the recognition and catalytic mechanism of HIV-1 PR leading to the release of an infective
virion, which advertently affects the immune system, will assist in designing mechanismbased
inhibitors with improved bioactivity.
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Affiliation(s)
- Monsurat M. Lawal
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Zainab K. Sanusi
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Thavendran Govender
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Glenn E.M. Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Bahareh Honarparvar
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Hendrik G. Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
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Lawal MM, Sanusi ZK, Govender T, Tolufashe GF, Maguire GEM, Honarparvar B, Kruger HG. Unraveling the concerted catalytic mechanism of the human immunodeficiency virus type 1 (HIV-1) protease: a hybrid QM/MM study. Struct Chem 2018. [DOI: 10.1007/s11224-018-1251-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Abstract
Transition state theory teaches that chemically stable mimics of enzymatic transition states will bind tightly to their cognate enzymes. Kinetic isotope effects combined with computational quantum chemistry provides enzymatic transition state information with sufficient fidelity to design transition state analogues. Examples are selected from various stages of drug development to demonstrate the application of transition state theory, inhibitor design, physicochemical characterization of transition state analogues, and their progress in drug development.
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Affiliation(s)
- Vern L. Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
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Manasa J, Varghese V, Pond SLK, Rhee SY, Tzou PL, Fessel WJ, Jang KS, White E, Rögnvaldsson T, Katzenstein DA, Shafer RW. Evolution of gag and gp41 in Patients Receiving Ritonavir-Boosted Protease Inhibitors. Sci Rep 2017; 7:11559. [PMID: 28912582 PMCID: PMC5599673 DOI: 10.1038/s41598-017-11893-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 08/31/2017] [Indexed: 11/15/2022] Open
Abstract
Several groups have proposed that genotypic determinants in gag and the gp41 cytoplasmic domain (gp41-CD) reduce protease inhibitor (PI) susceptibility without PI-resistance mutations in protease. However, no gag and gp41-CD mutations definitively responsible for reduced PI susceptibility have been identified in individuals with virological failure (VF) while receiving a boosted PI (PI/r)-containing regimen. To identify gag and gp41 mutations under selective PI pressure, we sequenced gag and/or gp41 in 61 individuals with VF on a PI/r (n = 40) or NNRTI (n = 20) containing regimen. We quantified nonsynonymous and synonymous changes in both genes and identified sites exhibiting signal for directional or diversifying selection. We also used published gag and gp41 polymorphism data to highlight mutations displaying a high selection index, defined as changing from a conserved to an uncommon amino acid. Many amino acid mutations developed in gag and in gp41-CD in both the PI- and NNRTI-treated groups. However, in neither gene, were there discernable differences between the two groups in overall numbers of mutations, mutations displaying evidence of diversifying or directional selection, or mutations with a high selection index. If gag and/or gp41 encode PI-resistance mutations, they may not be confined to consistent mutations at a few sites.
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Affiliation(s)
- Justen Manasa
- Division of Infectious Diseases, Department of Medicine Stanford University, Stanford, CA, USA
| | - Vici Varghese
- Division of Infectious Diseases, Department of Medicine Stanford University, Stanford, CA, USA
| | | | - Soo-Yon Rhee
- Division of Infectious Diseases, Department of Medicine Stanford University, Stanford, CA, USA
| | - Philip L Tzou
- Division of Infectious Diseases, Department of Medicine Stanford University, Stanford, CA, USA
| | - W Jeffrey Fessel
- Department of Internal Medicine, Kaiser Permanente Medical Care Program - Northern California, San Francisco, CA, United States
| | - Karen S Jang
- Division of Infectious Diseases, Department of Medicine Stanford University, Stanford, CA, USA
| | - Elizabeth White
- Division of Infectious Diseases, Department of Medicine Stanford University, Stanford, CA, USA
| | | | - David A Katzenstein
- Division of Infectious Diseases, Department of Medicine Stanford University, Stanford, CA, USA
| | - Robert W Shafer
- Division of Infectious Diseases, Department of Medicine Stanford University, Stanford, CA, USA.
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Chauhan J, Chen SE, Fenstermacher KJ, Naser-Tavakolian A, Reingewertz T, Salmo R, Lee C, Williams E, Raje M, Sundberg E, DeStefano JJ, Freire E, Fletcher S. Synthetic, structural mimetics of the β-hairpin flap of HIV-1 protease inhibit enzyme function. Bioorg Med Chem 2015; 23:7095-109. [PMID: 26474665 DOI: 10.1016/j.bmc.2015.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 08/20/2015] [Accepted: 09/03/2015] [Indexed: 01/11/2023]
Abstract
Small-molecule mimetics of the β-hairpin flap of HIV-1 protease (HIV-1 PR) were designed based on a 1,4-benzodiazepine scaffold as a strategy to interfere with the flap-flap protein-protein interaction, which functions as a gated mechanism to control access to the active site. Michaelis-Menten kinetics suggested our small-molecules are competitive inhibitors, which indicates the mode of inhibition is through binding the active site or sterically blocking access to the active site and preventing flap closure, as designed. More generally, a new bioactive scaffold for HIV-1PR inhibition has been discovered, with the most potent compound inhibiting the protease with a modest K(i) of 11 μM.
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Affiliation(s)
- Jay Chauhan
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 N. Pine St., Baltimore, MD 21201, USA
| | - Shen-En Chen
- Department of Biology, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Katherine J Fenstermacher
- Department of Cell Biology & Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Aurash Naser-Tavakolian
- Department of Biology, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Tali Reingewertz
- Department of Microbiology and Immunology, University of Maryland School of Medicine, 725 West Lombard St., Baltimore, MD 21201, USA
| | - Rosene Salmo
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 N. Pine St., Baltimore, MD 21201, USA
| | - Christian Lee
- PharmD Program, University of Maryland School of Pharmacy, 20 N. Pine St., Baltimore, MD 21201, USA
| | - Emori Williams
- Vivien T Thomas Medical Arts Academy, 100 N Calhoun St., Baltimore, MD 21223, USA
| | - Mithun Raje
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 N. Pine St., Baltimore, MD 21201, USA
| | - Eric Sundberg
- Department of Microbiology and Immunology, University of Maryland School of Medicine, 725 West Lombard St., Baltimore, MD 21201, USA
| | - Jeffrey J DeStefano
- Department of Cell Biology & Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Ernesto Freire
- Department of Biology, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Steven Fletcher
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 N. Pine St., Baltimore, MD 21201, USA; University of Maryland Greenebaum Cancer Center, 22 S. Greene St., Baltimore, MD 21201, USA.
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