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Abstract
The main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease (COVID-19), is an ideal target for pharmaceutical inhibition. Mpro is conserved among coronaviruses and distinct from human proteases. Viral replication depends on the cleavage of the viral polyprotein at multiple sites. We present crystal structures of SARS-CoV-2 Mpro bound to two viral substrate peptides. The structures show how Mpro recognizes distinct substrates and how subtle changes in substrate accommodation can drive large changes in catalytic efficiency. One peptide, constituting the junction between viral nonstructural proteins 8 and 9 (nsp8/9), has P1' and P2' residues that are unique among the SARS-CoV-2 Mpro cleavage sites but conserved among homologous junctions in coronaviruses. Mpro cleaves nsp8/9 inefficiently, and amino acid substitutions at P1' or P2' can enhance catalysis. Visualization of Mpro with intact substrates provides new templates for antiviral drug design and suggests that the coronavirus lifecycle selects for finely tuned substrate-dependent catalytic parameters.
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Affiliation(s)
| | - Gary Frey
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- ICCB-Longwood Screening Facility, Harvard Medical School, Boston, MA, 02115, USA
| | - Mark N. Namchuk
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Stephen C. Harrison
- Laboratory of Molecular Medicine, Boston Children′s Hospital, Boston, MA, 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Stephen M. Hinshaw
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Ian W. Windsor
- Laboratory of Molecular Medicine, Boston Children′s Hospital, Boston, MA, 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
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2
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Eche S, Gordon ML. Recombinant expression of HIV-1 protease using soluble fusion tags in Escherichia coli: A vital tool for functional characterization of HIV-1 protease. Virus Res 2021; 295:198289. [PMID: 33418026 DOI: 10.1016/j.virusres.2020.198289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 12/23/2020] [Accepted: 12/25/2020] [Indexed: 10/22/2022]
Abstract
HIV-1 protease expression in the laboratory is demanding because of its high cytotoxicity, making it difficult to express in bacterial expression systems such as Escherichia coli. To overcome these challenges, HIV-1 protease fusion with solubility enhancing tags helps to mitigate its cytotoxic effect and drive its expression as a soluble protein. Therefore, this review focuses on the expression of bioactive HIV-1 protease using solubility-enhancing fusion tags in Escherichia coli and summarises the characteristic features of the different common fusion tags that have been used in the expression of HIV-1 protease. This review will assist researchers with their choice of protein fusion tag for HIV-1 protease expression.
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Affiliation(s)
- Simeon Eche
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa.
| | - Michelle L Gordon
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa.
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3
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Abstract
Proteases drive the life cycle of all proteins, ensuring the transportation and activation of newly minted, would-be proteins into their functional form while recycling spent or unneeded proteins. Far from their image as engines of protein digestion, proteases play fundamental roles in basic physiology and regulation at multiple levels of systems biology. Proteases are intimately associated with disease and modulation of proteolytic activity is the presumed target for successful therapeutics. "Proteases: Pivot Points in Functional Proteomics" examines the crucial roles of proteolysis across a wide range of physiological processes and diseases. The existing and potential impacts of proteolysis-related activity on drug and biomarker development are presented in detail. All told the decisive roles of proteases in four major categories comprising 23 separate subcategories are addressed. Within this construct, 15 sets of subject-specific, tabulated data are presented that include identification of proteases, protease inhibitors, substrates, and their actions. Said data are derived from and confirmed by over 300 references. Cross comparison of datasets indicates that proteases, their inhibitors/promoters and substrates intersect over a range of physiological processes and diseases, both chronic and pathogenic. Indeed, "Proteases: Pivot Points …" closes by dramatizing this very point through association of (pro)Thrombin and Fibrin(ogen) with: hemostasis, innate immunity, cardiovascular and metabolic disease, cancer, neurodegeneration, and bacterial self-defense.
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Affiliation(s)
- Ingrid M Verhamme
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA.
| | - Sarah E Leonard
- Chemical and Biomolecular Engineering, University of Illinois Champaign-Urbana School of Chemical Sciences, Champaign, IL, USA
| | - Ray C Perkins
- New Liberty Proteomics Corporation, New Liberty, KY, USA.
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4
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Vadhadiya PM, Jean MA, Bouzriba C, Tremblay T, Lagüe P, Fortin S, Boukouvalas J, Giguère D. Diversity-Oriented Synthesis of Diol-Based Peptidomimetics as Potential HIV Protease Inhibitors and Antitumor Agents. Chembiochem 2018; 19:1779-1791. [PMID: 29858881 DOI: 10.1002/cbic.201800247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Indexed: 12/15/2022]
Abstract
Peptidomimetic HIV protease inhibitors are an important class of drugs used in the treatment of AIDS. The synthesis of a new type of diol-based peptidomimetics is described. Our route is flexible, uses d-glucal as an inexpensive starting material, and makes minimal use of protection/deprotection cycles. Binding affinities from molecular docking simulations suggest that these compounds are potential inhibitors of HIV protease. Moreover, the antiproliferative activities of compounds 33 a, 35 a, and 35 b on HT-29, M21, and MCF7 cancer cell lines are in the low micromolar range. The results provide a platform that could facilitate the development of medically relevant asymmetrical diol-based peptidomimetics.
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Affiliation(s)
- Paresh M Vadhadiya
- Département de Chimie, Université Laval-RQRM, 1045 Avenue de la Médecine, Quebec City, QC, G1V 0A6, Canada
| | - Marc-Alexandre Jean
- Département de Chimie, Université Laval-RQRM, 1045 Avenue de la Médecine, Quebec City, QC, G1V 0A6, Canada
| | - Chahrazed Bouzriba
- CHU de Québec-Université Laval Research Center, Oncology Division, Hôpital Saint-François d'Assise, 10 rue de l'Espinay, Quebec City, QC, G1L 3L5, Canada
- Faculté de Pharmacie, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - Thomas Tremblay
- Département de Chimie, Université Laval-RQRM, 1045 Avenue de la Médecine, Quebec City, QC, G1V 0A6, Canada
| | - Patrick Lagüe
- Départment de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, 1045, Avenue de la Médecine, Quebec City, QC, G1V 0A6, Canada
| | - Sébastien Fortin
- CHU de Québec-Université Laval Research Center, Oncology Division, Hôpital Saint-François d'Assise, 10 rue de l'Espinay, Quebec City, QC, G1L 3L5, Canada
- Faculté de Pharmacie, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - John Boukouvalas
- Département de Chimie, Université Laval-RQRM, 1045 Avenue de la Médecine, Quebec City, QC, G1V 0A6, Canada
| | - Denis Giguère
- Département de Chimie, Université Laval-RQRM, 1045 Avenue de la Médecine, Quebec City, QC, G1V 0A6, Canada
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