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Hu S, Zhong Q, Xie X, Zhang S, Wang J, Liu H, Dai W. Research progress on critical viral protease inhibitors for coronaviruses and enteroviruses. Bioorg Med Chem Lett 2025; 122:130168. [PMID: 40074013 DOI: 10.1016/j.bmcl.2025.130168] [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: 10/29/2024] [Revised: 03/01/2025] [Accepted: 03/04/2025] [Indexed: 03/14/2025]
Abstract
Viral infectious diseases have been seriously affecting human life and health. SARS-CoV-2 was the pathogen that caused Coronavirus Disease 2019 (COVID-19), and the impact of COVID-19 is still existing. Enterovirus 71 (EV71) is the primary pathogen of hand, foot, and mouth disease (HFMD), and no effective direct-acting antiviral drugs targeting EV71 has been approved yet. Innate antiviral strategies play an important role in preventing virus infections depending on the powerful immune regulatory system of body, while viruses have evolved to exploit diverse methods to overcome immune response. Viral proteases, which are known in cleaving viral polyproteins, have also been found to modulate the innate immunity of host cells, thereby promoting viral proliferation. Herein, we reviewed the current development of SARS-CoV-2 3CLpro, PLpro, and EV71 3Cpro and 2Apro, mainly including structure, function, modulation of immune response, and inhibitors of these four proteases, to further deepen the understanding of viral pathogenesis and provide a new perspective for subsequent corresponding drug development.
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Affiliation(s)
- Shulei Hu
- China Pharmaceutical University, 639 Longmian Avenue, Jiangning District, Nanjing 211198, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Qiuyu Zhong
- China Pharmaceutical University, 639 Longmian Avenue, Jiangning District, Nanjing 211198, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Xiong Xie
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Shurui Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Jinlin Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Hong Liu
- China Pharmaceutical University, 639 Longmian Avenue, Jiangning District, Nanjing 211198, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China.
| | - Wenhao Dai
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China.
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2
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Etori H, Asoshina R, Obita T, Okumura F. Spermidine reduces ISGylation and enhances ISG15-USP18 interaction. Sci Rep 2025; 15:17913. [PMID: 40410283 PMCID: PMC12102389 DOI: 10.1038/s41598-025-01425-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2024] [Accepted: 05/06/2025] [Indexed: 05/25/2025] Open
Abstract
The expression of ubiquitin-like molecule interferon-stimulated gene 15 kDa (ISG15) and its post-translational modification (ISGylation) are significantly activated by interferons or pathogen infections, highlighting their roles in innate immune responses. Over 1100 proteins have been identified as ISGylated. ISG15 is removed from substrates by interferon-induced ubiquitin-specific peptidase 18 (USP18) or severe acute respiratory syndrome coronavirus 2-derived papain-like protease. High ISGylation levels may help prevent the spread of coronavirus disease 2019 (COVID-19). Polyamines (spermidine and spermine) exhibit anti-inflammatory, antioxidant, and mitochondrial functions. However, the relationship between nutrients and ISGylation remains unclear. This study assessed the effects of spermine and spermidine on ISGylation. MCF10A and A549 cells were treated with interferon-alpha, spermine, or spermidine, and the expression levels of various proteins and ISGylation were measured. Spermine and spermidine dose-dependently reduced ISGylation. Additionally, spermidine directly interacted with ISG15 and USP18, enhancing their interaction and potentially reducing ISGylation. Therefore, spermidine may prevent ISGylation-related immune responses.
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Affiliation(s)
- Haruka Etori
- Department of Food and Health Sciences, International College of Arts and Sciences, Fukuoka Women's University, Fukuoka, 813-8582, Japan
| | - Riko Asoshina
- Department of Food and Health Sciences, International College of Arts and Sciences, Fukuoka Women's University, Fukuoka, 813-8582, Japan
| | - Takayuki Obita
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Fumihiko Okumura
- Department of Food and Health Sciences, International College of Arts and Sciences, Fukuoka Women's University, Fukuoka, 813-8582, Japan.
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3
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Glass AM, Navas-Martin S. Interferon-induced protein ISG15 in the central nervous system, quo vadis? FEBS Lett 2025. [PMID: 40353372 DOI: 10.1002/1873-3468.70063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2024] [Revised: 04/03/2025] [Accepted: 04/17/2025] [Indexed: 05/14/2025]
Abstract
The ubiquitin-like interferon (IFN)-stimulated gene 15 (ISG15) is a unique molecular effector that functions both intra- and extracellularly. Central to its pleiotropic nature is the ability to coordinate cellular responses following its conjugation to target proteins via ISGylation or in its free form. The activity of ISG15 is highly context-dependent: in the case of viral infections, ISG15 can serve as a pro- or antiviral factor. While ISG15 has been studied extensively, several gaps persist in our understanding of its role in dysregulated immune homeostasis. In particular, the role of ISG15 in the central nervous system (CNS), which has traditionally been considered an immune-privileged site, remains ill-defined. Interestingly, elevated ISG15 expression is observed in the CNS following instances of brain injury, autoimmunity, neurodegeneration, and viral infection. In this review, we seek to provide a comprehensive analysis of these studies as they pertain to ISG15 and its potential roles in the CNS. Furthermore, we discuss questions and challenges in the field while highlighting ISG15 as a potential diagnostic biomarker or therapeutic target. Impact statement While ISG15 has been studied extensively, several gaps remain in our understanding of its role in dysregulated immune homeostasis and its impact within the central nervous system (CNS). In this review, we provide a comprehensive analysis of the emerging roles of ISG15 in brain injury, autoimmunity, neurodegeneration, and viral infection within the CNS.
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Affiliation(s)
- Adam M Glass
- Department of Microbiology and Immunology, Centers for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Sonia Navas-Martin
- Department of Microbiology and Immunology, Centers for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
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4
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Ayala-Torres C, Liu J, Dantuma NP, Masucci MG. Regulation of N-degron recognin-mediated autophagy by the SARS-CoV-2 PLpro ubiquitin deconjugase. Autophagy 2025; 21:1019-1038. [PMID: 39723606 PMCID: PMC12013424 DOI: 10.1080/15548627.2024.2442849] [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: 10/03/2024] [Revised: 12/07/2024] [Accepted: 12/11/2024] [Indexed: 12/28/2024] Open
Abstract
Viral proteases play critical roles in the host cell and immune remodeling that allows virus production. The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) papain-like protease (PLpro) encoded in the large nonstructural protein 3 (Nsp3) also possesses isopeptidase activity with specificity for ubiquitin and ISG15 conjugates. Here, we interrogated the cellular interactome of the SARS-CoV-2 PLpro catalytic domain to gain insight into the putative substrates and cellular functions affected by the viral deubiquitinase. PLpro was detected in protein complexes that control multiple ubiquitin and ubiquitin-like (UbL) regulated signaling and effector pathways. By restricting the analysis to cytosolic and membrane-associated ubiquitin ligases, we found that PLpro interacts with N-recognin ubiquitin ligases and preferentially rescues type I N-degron substrates from proteasomal degradation. PLpro stabilized N-degron carrying HSPA5/BiP/GRP78, which is arginylated in the cytosol upon release from the endoplasmic reticulum (ER) during ER stress, and enhanced the Arg-HSPA5-driven oligomerization of the N-recognin SQSTM1/p62 that serves as a platform for phagophore assembly. However, while in addition to Arg-HSPA5 and SQSTM1/p62, ATG9A, WIPI2, and BECN1/Beclin 1 were detected in PLpro immunoprecipitates, other components of the autophagosome biogenesis machinery, such as the ATG12-ATG5-ATG16L1 complex and MAP1LC3/LC3 were absent, which correlated with proteolytic inactivation of ULK1, impaired production of lipidated LC3-II, and inhibition of reticulophagy. The findings highlight a novel mechanism by which, through the reprogramming of autophagy, the PLpro deubiquitinase may contribute to the remodeling of intracellular membranes in coronavirus-infected cells.
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Affiliation(s)
- Carlos Ayala-Torres
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna, Sweden
| | - Jiangnan Liu
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna, Sweden
| | - Nico P. Dantuma
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna, Sweden
| | - Maria G. Masucci
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna, Sweden
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Mandal M, Pires D, Azevedo-Pereira JM, Anes E. Host-Directed Therapies Based on Protease Inhibitors to Control Mycobacterium tuberculosis and HIV Coinfection. Microorganisms 2025; 13:1040. [PMID: 40431213 PMCID: PMC12113826 DOI: 10.3390/microorganisms13051040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2025] [Revised: 04/25/2025] [Accepted: 04/28/2025] [Indexed: 05/29/2025] Open
Abstract
Despite continuous and extensive global efforts in the fight against tuberculosis (TB), this infectious disease continues to exert a tremendous burden on public health concerns and deaths worldwide. TB, caused by the bacterial species Mycobacterium tuberculosis, is highly frequent in people living with HIV. The continuing epidemics of both chronic infections and the emergence of antimicrobial resistance, as well as the lack of effective diagnostic tools and drug-drug interactions, pose major challenges in the fight against these pathogens. Developing a wide range of host-directed therapies may improve treatment outcomes, helping alleviate the morbidity and mortality associated with both infections. In this review, we discuss the identification and development of new host-directed strategies based on protease inhibitors and their clinical relevance as adjunctive treatment. In the context of therapeutic agents with novel mechanisms, selective protease inhibitors, including saquinavir (SQV) and cystatins (CstC and CstF), are valuable targets that may provide effective therapeutic solutions for controlling Mtb and HIV coinfection.
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Affiliation(s)
- Manoj Mandal
- Host-Pathogen Interactions Unit, Research Institute for Medicines, iMed.ULisboa, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal; (M.M.); (D.P.); (J.M.A.-P.)
| | - David Pires
- Host-Pathogen Interactions Unit, Research Institute for Medicines, iMed.ULisboa, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal; (M.M.); (D.P.); (J.M.A.-P.)
- Center for Interdisciplinary Research in Health, Católica Medical School, Universidade Católica Portuguesa, Estrada Octávio Pato, 2635-631 Rio de Mouro, Portugal
| | - José Miguel Azevedo-Pereira
- Host-Pathogen Interactions Unit, Research Institute for Medicines, iMed.ULisboa, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal; (M.M.); (D.P.); (J.M.A.-P.)
| | - Elsa Anes
- Host-Pathogen Interactions Unit, Research Institute for Medicines, iMed.ULisboa, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal; (M.M.); (D.P.); (J.M.A.-P.)
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Napitupulu R, Maimunah, Malik A, Helianti I. Improving soluble recombinant SARS-CoV-2 papain-like protease production in Escherichia coli through chaperonin and maltose-binding protein tag: purification and kinetic characterization. Prep Biochem Biotechnol 2025:1-10. [PMID: 39889765 DOI: 10.1080/10826068.2025.2456940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2025]
Abstract
Although COVID-19 is now becoming endemic, SARS-CoV-2 persists potential jeopardy to clinically vulnerable populations. Hence, further study is still necessary to discover novel antiviral agents against SARS-CoV-2 for proactive preparedness. SARS-CoV-2 papain-like protease (PL Pro) is a target enzyme for searching anti-Covid candidates. Our prior study revealed the major formation of inclusion bodies during PL Pro expression in E. coli RIPL. In this study, we tried using chaperonin in the E. coli Arctic Express system and both codon optimization and maltose-binding protein (MBP) fusion protein to make PL Pro more soluble. Recombinant PL Pro encoded on the pET21d(+) plasmid was expressed in E. coli Arctic express. However, the soluble protein yield remained low and unstable due to suboptimal codon usage in the insert gene. Whereas, fusion of the MBP protein with optimized codon of PL Pro enhanced the enzyme expression and solubility. Recombinant PL Pro cleaved the linker between MBP and PL Pro, which served as a cleavage site recognized by PL Pro (LKGG↓A). The purified enzyme from a 200-mL culture generated 1 mL of pure PL Pro enzyme at a 1.913 mg/mL concentration. It exhibited favorable activity against the Z-RLRGG-AMC substrate, with a Km value of 33.40 μM and a Vmax of 5.10 RFU/min.
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Affiliation(s)
- Riswanto Napitupulu
- Division of Pharmaceutical Microbiology and Biotechnology, Faculty of Pharmacy, Universitas Indonesia, Depok, West Java, Indonesia
| | - Maimunah
- Division of Pharmaceutical Microbiology and Biotechnology, Faculty of Pharmacy, Universitas Indonesia, Depok, West Java, Indonesia
| | - Amarila Malik
- Division of Pharmaceutical Microbiology and Biotechnology, Faculty of Pharmacy, Universitas Indonesia, Depok, West Java, Indonesia
| | - Is Helianti
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN) Republic of Indonesia, Cibinong, West Java, Indonesia
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7
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Varghese A, Liu J, Liu B, Guo W, Dong F, Patterson TA, Hong H. Analysis of Structures of SARS-CoV-2 Papain-like Protease Bound with Ligands Unveils Structural Features for Inhibiting the Enzyme. Molecules 2025; 30:491. [PMID: 39942596 PMCID: PMC11820935 DOI: 10.3390/molecules30030491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2024] [Revised: 01/17/2025] [Accepted: 01/20/2025] [Indexed: 02/16/2025] Open
Abstract
The COVID-19 pandemic, driven by the novel coronavirus SARS-CoV-2, has drastically reshaped global health and socioeconomic landscapes. The papain-like protease (PLpro) plays a critical role in viral polyprotein cleavage and immune evasion, making it a prime target for therapeutic intervention. Numerous compounds have been identified as inhibitors of SARS-CoV-2 PLpro, with many characterized through crystallographic studies. To date, over 70 three-dimensional (3D) structures of PLpro complexed ligands have been deposited in the Protein Data Bank, offering valuable insight into ligand-binding features that could aid the discovery and development of effective COVID-19 treatments targeting PLpro. In this study, we reviewed and analyzed these 3D structures, focusing on the key residues involved in ligand interactions. Our analysis revealed that most inhibitors bind to PLpro's substrate recognition sites S3/S4 and SUb2. While these sites are highly attractive and have been extensively explored, other potential binding regions, such as SUb1 and the Zn(II) domain, are less explored and may hold untapped potential for future COVID-19 drug discovery and development. Our structural analysis provides insights into the molecular features of PLpro that could accelerate the development of novel therapeutics targeting this essential viral enzyme.
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Affiliation(s)
| | | | | | | | | | | | - Huixiao Hong
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA; (A.V.); (J.L.); (B.L.); (W.G.); (F.D.); (T.A.P.)
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Jimenez-Campos AG, Maestas LI, Velappan N, Beck B, Ye C, Wernsing K, Mata-Solis Y, Bruno WJ, Bussmann SC, Bradfute S, Baca JT, Rininsland FH. A cell-based Papain-like Protease (PLpro) activity assay for rapid detection of active SARS-CoV-2 infections and antivirals. PLoS One 2024; 19:e0309305. [PMID: 39724215 DOI: 10.1371/journal.pone.0309305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 08/09/2024] [Indexed: 12/28/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants are a continuous threat to human life. An urgent need remains for simple and fast tests that reliably detect active infections with SARS-CoV-2 and its variants in the early stage of infection. Here we introduce a simple and rapid activity-based diagnostic (ABDx) test that identifies SARS-CoV-2 infections by measuring the activity of a viral enzyme, Papain-Like protease (PLpro). The test system consists of a peptide that fluoresces when cleaved by SARS PLpro that is active in crude, unprocessed lysates from human tongue scrapes and saliva. Test results are obtained in 30 minutes or less using widely available fluorescence plate readers, or a battery-operated portable instrument for on-site testing. Proof-of-concept was obtained in a study on clinical specimens collected from patients with COVID-19 like symptoms who tested positive (n = 10) or negative (n = 10) with LIAT RT-PCR using nasal mid turbinate swabs. When saliva from these patients was tested with in-house endpoint RT-PCR, 17 were positive and only 5 specimens were negative, of which 2 became positive when tested 5 days later. PLpro activity correlated in 17 of these cases (3 out of 3 negatives and 14 out of 16 positives, with one invalid specimen). Despite the small number of samples, the agreement was significant (p value = 0.01). Two false negatives were detected, one from a sample with a late Ct value of 35 in diagnostic RT-PCR, indicating that an active infection was no longer present. The PLpro assay is easily scalable and expected to detect all viable SARS-CoV-2 variants, making it attractive as a screening and surveillance tool. Additionally, we show feasibility of the platform as a new homogeneous phenotypic assay for rapid screening of SARS-CoV-2 antiviral drugs and neutralizing antibodies.
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Affiliation(s)
- Anahi G Jimenez-Campos
- University of New Mexico Health Sciences Center, Department of Emergency Medicine, Albuquerque, New Mexico, United States of America
| | - Lucas I Maestas
- University of New Mexico Health Sciences Center, Department of Emergency Medicine, Albuquerque, New Mexico, United States of America
| | - Nileena Velappan
- Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Brian Beck
- MicroBiologics, St. Cloud, MN, United States of America
| | - Chunyan Ye
- Health Science Center, Center for Global Health and Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico, United States of America
| | | | | | | | - Silas C Bussmann
- University of New Mexico Health Sciences Center, Department of Emergency Medicine, Albuquerque, New Mexico, United States of America
| | - Steven Bradfute
- Health Science Center, Center for Global Health and Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Justin T Baca
- University of New Mexico Health Sciences Center, Department of Emergency Medicine, Albuquerque, New Mexico, United States of America
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Nemčovičová I, Lopušná K, Štibrániová I, Benedetti F, Berti F, Felluga F, Drioli S, Vidali M, Katrlík J, Pažitná L, Holazová A, Blahutová J, Lenhartová S, Sláviková M, Klempa B, Ondrejovič M, Chmelová D, Legerská B, Miertuš S, Klacsová M, Uhríková D, Kerti L, Frecer V. Identification and evaluation of antiviral activity of novel compounds targeting SARS-CoV-2 virus by enzymatic and antiviral assays, and computational analysis. J Enzyme Inhib Med Chem 2024; 39:2301772. [PMID: 38221792 PMCID: PMC10791089 DOI: 10.1080/14756366.2024.2301772] [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: 07/29/2023] [Accepted: 12/18/2023] [Indexed: 01/16/2024] Open
Abstract
The viral genome of the SARS-CoV-2 coronavirus, the aetiologic agent of COVID-19, encodes structural, non-structural, and accessory proteins. Most of these components undergo rapid genetic variations, though to a lesser extent the essential viral proteases. Consequently, the protease and/or deubiquitinase activities of the cysteine proteases Mpro and PLpro became attractive targets for the design of antiviral agents. Here, we develop and evaluate new bis(benzylidene)cyclohexanones (BBC) and identify potential antiviral compounds. Three compounds were found to be effective in reducing the SARS-CoV-2 load, with EC50 values in the low micromolar concentration range. However, these compounds also exhibited inhibitory activity IC50 against PLpro at approximately 10-fold higher micromolar concentrations. Although originally developed as PLpro inhibitors, the comparison between IC50 and EC50 of BBC indicates that the mechanism of their in vitro antiviral activity is probably not directly related to inhibition of viral cysteine proteases. In conclusion, our study has identified new potential noncytotoxic antiviral compounds suitable for in vivo testing and further improvement.
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Affiliation(s)
- Ivana Nemčovičová
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Katarína Lopušná
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Iveta Štibrániová
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Fabio Benedetti
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Federico Berti
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Fulvia Felluga
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Sara Drioli
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Mattia Vidali
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Jaroslav Katrlík
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Lucia Pažitná
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Alena Holazová
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jana Blahutová
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Simona Lenhartová
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Monika Sláviková
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Boris Klempa
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Miroslav Ondrejovič
- Department of Biotechnology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, Trnava, Slovakia
- ICARST n.o, Bratislava, Slovakia
| | - Daniela Chmelová
- Department of Biotechnology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, Trnava, Slovakia
| | - Barbora Legerská
- Department of Biotechnology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, Trnava, Slovakia
| | - Stanislav Miertuš
- Department of Biotechnology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, Trnava, Slovakia
- ICARST n.o, Bratislava, Slovakia
| | - Mária Klacsová
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University Bratislava, Bratislava, Slovakia
| | - Daniela Uhríková
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University Bratislava, Bratislava, Slovakia
| | - Lukáš Kerti
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University Bratislava, Bratislava, Slovakia
| | - Vladimír Frecer
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University Bratislava, Bratislava, Slovakia
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Kerti L, Frecer V. Design of inhibitors of SARS-CoV-2 papain-like protease deriving from GRL0617: Structure-activity relationships. Bioorg Med Chem 2024; 113:117909. [PMID: 39288705 DOI: 10.1016/j.bmc.2024.117909] [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: 06/19/2024] [Revised: 09/02/2024] [Accepted: 09/06/2024] [Indexed: 09/19/2024]
Abstract
The unique and complex structure of papain-like protease (PLpro) of the SARS-CoV-2 virus represents a difficult challenge for antiviral development, yet it offers a compelling validated target for effective therapy of COVID-19. The surge in scientific interest in inhibiting this cysteine protease emerged after its demonstrated connection to the cytokine storm in patients with COVID-19 disease. Furthermore, the development of new inhibitors against PLpro may also be beneficial for the treatment of respiratory infections caused by emerging coronavirus variants of concern. This review article provides a comprehensive overview of PLpro inhibitors, focusing on the structural framework of the known inhibitor GRL0617 and its analogs. We categorize PLpro inhibitors on the basis of their structures and binding site: Glu167 containing site, BL2 groove, Val70Ub site, and Cys111 containing catalytic site. We summarize and evaluate the majority of GRL0617-like inhibitors synthesized so far, highlighting their published biochemical parameters, which reflect their efficacy. Published research has shown that strategic modifications to GRL0617, such as decorating the naphthalene ring, extending the aromatic amino group or the orthomethyl group, can substantially decrease the IC50 from micromolar up to nanomolar concentration range. Some advantageous modifications significantly enhance inhibitory activity, paving the way for the development of new potent compounds. Our review places special emphasis on structures that involve direct modifications to the GRL0617 scaffold, including piperidine carboxamides and modified benzylmethylnaphthylethanamines (Jun9 scaffold). All these compounds are believed to inhibit the proteolytic, deubiquitination, and deISGylation activity of PLpro, biochemical processes linked to the severe progression of COVID-19. Finally, we summarize the development efforts for SARS-CoV-2 PLpro inhibitors, in detailed structure-activity relationships diagrams. This aims to inform and inspire future research in the search for potent antiviral agents against PLpro of current and emerging coronavirus threats.
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Affiliation(s)
- Lukas Kerti
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University Bratislava, SK-83232 Bratislava, Slovakia
| | - Vladimir Frecer
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University Bratislava, SK-83232 Bratislava, Slovakia.
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11
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James VK, Godula RN, Perez JM, Beckham JT, Butalewicz JP, Sipe SN, Huibregtse JM, Brodbelt JS. Native Mass Spectrometry Reveals Binding Interactions of SARS-CoV-2 PLpro with Inhibitors and Cellular Targets. ACS Infect Dis 2024; 10:3597-3606. [PMID: 39303064 PMCID: PMC11533220 DOI: 10.1021/acsinfecdis.4c00444] [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] [Indexed: 09/22/2024]
Abstract
Here we used native mass spectrometry (native MS) to probe a SARS-CoV protease, PLpro, which plays critical roles in coronavirus disease by affecting viral protein production and antagonizing host antiviral responses. Ultraviolet photodissociation (UVPD) and variable temperature electrospray ionization (vT ESI) were used to localize binding sites of PLpro inhibitors and revealed the stabilizing effects of inhibitors on protein tertiary structure. We compared PLpro from SARS-CoV-1 and SARS-CoV-2 in terms of inhibitor and ISG15 interactions to discern possible differences in protease function. A PLpro mutant lacking a single cysteine was used to localize inhibitor binding, and thermodynamic measurements revealed that inhibitor PR-619 stabilized the folded PLpro structure. These results will inform further development of PLpro as a therapeutic target against SARS-CoV-2 and other emerging coronaviruses.
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Affiliation(s)
- Virginia K. James
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Rianna N. Godula
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jessica M. Perez
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Josh T. Beckham
- Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jamie P. Butalewicz
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Sarah N. Sipe
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jon M. Huibregtse
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer S. Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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12
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Nazir F, John Kombe Kombe A, Khalid Z, Bibi S, Zhang H, Wu S, Jin T. SARS-CoV-2 replication and drug discovery. Mol Cell Probes 2024; 77:101973. [PMID: 39025272 DOI: 10.1016/j.mcp.2024.101973] [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: 01/11/2024] [Revised: 07/14/2024] [Accepted: 07/15/2024] [Indexed: 07/20/2024]
Abstract
The coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has killed millions of people and continues to wreak havoc across the globe. This sudden and deadly pandemic emphasizes the necessity for anti-viral drug development that can be rapidly administered to reduce morbidity, mortality, and virus propagation. Thus, lacking efficient anti-COVID-19 treatment, and especially given the lengthy drug development process as well as the critical death tool that has been associated with SARS-CoV-2 since its outbreak, drug repurposing (or repositioning) constitutes so far, the ideal and ready-to-go best approach in mitigating viral spread, containing the infection, and reducing the COVID-19-associated death rate. Indeed, based on the molecular similarity approach of SARS-CoV-2 with previous coronaviruses (CoVs), repurposed drugs have been reported to hamper SARS-CoV-2 replication. Therefore, understanding the inhibition mechanisms of viral replication by repurposed anti-viral drugs and chemicals known to block CoV and SARS-CoV-2 multiplication is crucial, and it opens the way for particular treatment options and COVID-19 therapeutics. In this review, we highlighted molecular basics underlying drug-repurposing strategies against SARS-CoV-2. Notably, we discussed inhibition mechanisms of viral replication, involving and including inhibition of SARS-CoV-2 proteases (3C-like protease, 3CLpro or Papain-like protease, PLpro) by protease inhibitors such as Carmofur, Ebselen, and GRL017, polymerases (RNA-dependent RNA-polymerase, RdRp) by drugs like Suramin, Remdesivir, or Favipiravir, and proteins/peptides inhibiting virus-cell fusion and host cell replication pathways, such as Disulfiram, GC376, and Molnupiravir. When applicable, comparisons with SARS-CoV inhibitors approved for clinical use were made to provide further insights to understand molecular basics in inhibiting SARS-CoV-2 replication and draw conclusions for future drug discovery research.
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Affiliation(s)
- Farah Nazir
- Center of Disease Immunity and Investigation, College of Medicine, Lishui University, Lishui, 323000, China
| | - Arnaud John Kombe Kombe
- Laboratory of Structural Immunology, Key Laboratory of Immune Response and Immunotherapy, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Zunera Khalid
- Laboratory of Structural Immunology, Key Laboratory of Immune Response and Immunotherapy, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Shaheen Bibi
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, University of Science and Technology of China, Anhui, China
| | - Hongliang Zhang
- Center of Disease Immunity and Investigation, College of Medicine, Lishui University, Lishui, 323000, China
| | - Songquan Wu
- Center of Disease Immunity and Investigation, College of Medicine, Lishui University, Lishui, 323000, China.
| | - Tengchuan Jin
- Center of Disease Immunity and Investigation, College of Medicine, Lishui University, Lishui, 323000, China; Laboratory of Structural Immunology, Key Laboratory of Immune Response and Immunotherapy, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China; Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, University of Science and Technology of China, Anhui, China; Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, Anhui, China; Biomedical Sciences and Health Laboratory of Anhui Province, University of Science & Technology of China, Hefei, 230027, China; Clinical Research Hospital of Chinese Academy of Sciences (Hefei), University of Science and Technology of China, Hefei, 230001, China.
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13
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Jhanwar A, Sharma D, Das U. Unraveling the structural and functional dimensions of SARS-CoV2 proteins in the context of COVID-19 pathogenesis and therapeutics. Int J Biol Macromol 2024; 278:134850. [PMID: 39168210 DOI: 10.1016/j.ijbiomac.2024.134850] [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: 01/12/2024] [Revised: 08/14/2024] [Accepted: 08/16/2024] [Indexed: 08/23/2024]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2) has emerged as the causative agent behind the global pandemic of Coronavirus Disease 2019 (COVID-19). As the scientific community strives to comprehend the intricate workings of this virus, a fundamental aspect lies in deciphering the myriad proteins it expresses. This knowledge is pivotal in unraveling the complexities of the viral machinery and devising targeted therapeutic interventions. The proteomic landscape of SARS-CoV2 encompasses structural, non-structural, and open-reading frame proteins, each playing crucial roles in viral replication, host interactions, and the pathogenesis of COVID-19. This comprehensive review aims to provide an updated and detailed examination of the structural and functional attributes of SARS-CoV2 proteins. By exploring the intricate molecular architecture, we have highlighted the significance of these proteins in viral biology. Insights into their roles and interplay contribute to a deeper understanding of the virus's mechanisms, thereby paving the way for the development of effective therapeutic strategies. As the global scientific community strives to combat the ongoing pandemic, this synthesis of knowledge on SARS-CoV2 proteins serves as a valuable resource, fostering informed approaches toward mitigating the impact of COVID-19 and advancing the frontier of antiviral research.
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Affiliation(s)
- Aniruddh Jhanwar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Dipika Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Uddipan Das
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
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14
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Rahebi P, Aryapour H. Reconstruction of the unbinding pathways of new inhibitors of the SARS-CoV-2 papain-like protease using molecular dynamics simulation. J Biomol Struct Dyn 2024; 42:7501-7514. [PMID: 37505097 DOI: 10.1080/07391102.2023.2240424] [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: 05/12/2023] [Accepted: 07/18/2023] [Indexed: 07/29/2023]
Abstract
Developing novel antiviral drugs against the SARS-CoV-2 virus and COVID-19 disease is imperative as the vaccines may not offer absolute protection. PLpro plays a crucial role in the viral life cycle, making it an attractive target for drug development. Several PLpro inhibitors have been developed, and their 3D structures in complex with PLpro are available. In this work, we employed Supervised Molecular Dynamics (SuMD), a specific Unbiased Molecular Dynamics (UMD) method, to investigate unbinding pathways of the novel inhibitors of PLpro (PDB IDs: 7LBR, 7RZC, 7SDR and 7E35) and GRL0617 (PDB ID: 7JRN) as a reference. We conducted three simulations for each ligand and achieved unbinding events in the nanosecond timescale in all simulations. We found that unbinding events are commonly affected by altering the conformation of the BL2 loop, which is caused by the natural fluctuations of the loop that are required to trap the substrate and throw out the product. BL2 loop is crucial for keeping the ligand and unbinding and acts as a double-edged sword. Any inhibitor designed to be effective must prevent the loop's natural fluctuations. We perceived that increasing ligands interactions with the binding pocket interior and the BL2 loop will help prevent natural fluctuation of the BL2 loop, Although the interactions with the binding pocket's inner side are more critical than the BL2 loop. These findings may be helpful in developing more potent inhibitors against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Pouya Rahebi
- Department of Biology, Faculty of Science, Golestan University, Gorgan, Iran
| | - Hassan Aryapour
- Department of Biology, Faculty of Science, Golestan University, Gorgan, Iran
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15
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Garnsey MR, Robinson MC, Nguyen LT, Cardin R, Tillotson J, Mashalidis E, Yu A, Aschenbrenner L, Balesano A, Behzadi A, Boras B, Chang JS, Eng H, Ephron A, Foley T, Ford KK, Frick JM, Gibson S, Hao L, Hurst B, Kalgutkar AS, Korczynska M, Lengyel-Zhand Z, Gao L, Meredith HR, Patel NC, Polivkova J, Rai D, Rose CR, Rothan H, Sakata SK, Vargo TR, Qi W, Wu H, Liu Y, Yurgelonis I, Zhang J, Zhu Y, Zhang L, Lee AA. Discovery of SARS-CoV-2 papain-like protease (PL pro) inhibitors with efficacy in a murine infection model. SCIENCE ADVANCES 2024; 10:eado4288. [PMID: 39213347 PMCID: PMC11364104 DOI: 10.1126/sciadv.ado4288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 07/26/2024] [Indexed: 09/04/2024]
Abstract
Vaccines and first-generation antiviral therapeutics have provided important protection against COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, there remains a need for additional therapeutic options that provide enhanced efficacy and protection against potential viral resistance. The SARS-CoV-2 papain-like protease (PLpro) is one of the two essential cysteine proteases involved in viral replication. While inhibitors of the SARS-CoV-2 main protease have demonstrated clinical efficacy, known PLpro inhibitors have, to date, lacked the inhibitory potency and requisite pharmacokinetics to demonstrate that targeting PLpro translates to in vivo efficacy in a preclinical setting. Here, we report the machine learning-driven discovery of potent, selective, and orally available SARS-CoV-2 PLpro inhibitors, with lead compound PF-07957472 (4) providing robust efficacy in a mouse-adapted model of COVID-19 infection.
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Affiliation(s)
| | | | | | - Rhonda Cardin
- Pfizer Global Research and Development, Pearl River, NY 10965, USA
| | - Joseph Tillotson
- Pfizer Global Research and Development, Cambridge, MA 02139, USA
| | | | - Aijia Yu
- WuXi, WuXi AppTec (Shanghai) Co. Ltd. Shanghai 200131, China
| | | | - Amanda Balesano
- Pfizer Global Research and Development, Groton, CT 06340, USA
| | - Amin Behzadi
- Pfizer Global Research and Development, Pearl River, NY 10965, USA
| | - Britton Boras
- Pfizer Global Research and Development, La Jolla, CA 92121, USA
| | - Jeanne S. Chang
- Pfizer Global Research and Development, Groton, CT 06340, USA
| | - Heather Eng
- Pfizer Global Research and Development, Groton, CT 06340, USA
| | - Andrew Ephron
- Pfizer Global Research and Development, Groton, CT 06340, USA
| | - Tim Foley
- Pfizer Global Research and Development, Groton, CT 06340, USA
| | - Kristen K. Ford
- Pfizer Global Research and Development, Groton, CT 06340, USA
| | - James M. Frick
- PostEra, 1 Broadway, 14th floor, Cambridge, MA 02142, USA
| | - Scott Gibson
- Institute for Antiviral Research, Department of Animal, Dairy, and Veterinary Sciences,Utah State University, Logan, UT 84322, USA
| | - Li Hao
- Pfizer Global Research and Development, Pearl River, NY 10965, USA
| | - Brett Hurst
- Institute for Antiviral Research, Department of Animal, Dairy, and Veterinary Sciences,Utah State University, Logan, UT 84322, USA
| | | | | | | | - Liping Gao
- WuXi, WuXi AppTec (Shanghai) Co. Ltd. Shanghai 200131, China
| | | | - Nandini C. Patel
- Pfizer Global Research and Development, Cambridge, MA 02139, USA
| | - Jana Polivkova
- Pfizer Global Research and Development, Groton, CT 06340, USA
| | - Devendra Rai
- Pfizer Global Research and Development, Groton, CT 06340, USA
| | - Colin R. Rose
- Pfizer Global Research and Development, Groton, CT 06340, USA
| | - Hussin Rothan
- Pfizer Global Research and Development, Pearl River, NY 10965, USA
| | | | | | - Wenying Qi
- WuXi, WuXi AppTec (Shanghai) Co. Ltd. Shanghai 200131, China
| | - Huixian Wu
- Pfizer Global Research and Development, Groton, CT 06340, USA
| | - Yiping Liu
- WuXi, WuXi AppTec (Shanghai) Co. Ltd. Shanghai 200131, China
| | - Irina Yurgelonis
- Pfizer Global Research and Development, Pearl River, NY 10965, USA
| | - Jinzhi Zhang
- Pfizer Global Research and Development, Shanghai 201210, China
| | - Yuao Zhu
- Pfizer Global Research and Development, Pearl River, NY 10965, USA
| | - Lei Zhang
- Pfizer Global Research and Development, Cambridge, MA 02139, USA
| | - Alpha A. Lee
- PostEra, 1 Broadway, 14th floor, Cambridge, MA 02142, USA
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16
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Velma G, Shen Z, Holberg C, Fu J, Soleymani F, Cooper L, Ramos OL, Indukuri D, Musku SR, Rychetsky P, Slilaty S, Li Z, Ratia K, Rong L, Schenten D, Xiong R, J Thatcher GR. Non-Covalent Inhibitors of SARS-CoV-2 Papain-Like Protease (PLpro): In Vitro and In Vivo Antiviral Activity. J Med Chem 2024; 67:13681-13702. [PMID: 39102360 PMCID: PMC11345844 DOI: 10.1021/acs.jmedchem.4c00378] [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: 02/13/2024] [Revised: 07/01/2024] [Accepted: 07/22/2024] [Indexed: 08/07/2024]
Abstract
The SARS-CoV-2 papain-like protease (PLpro), essential for viral processing and immune response disruption, is a promising target for treating acute infection of SARS-CoV-2. To date, there have been no reports of PLpro inhibitors with both submicromolar potency and animal model efficacy. To address the challenge of PLpro's featureless active site, a noncovalent inhibitor library with over 50 new analogs was developed, targeting the PLpro active site by modulating the BL2-loop and engaging the BL2-groove. Notably, compounds 42 and 10 exhibited strong antiviral effects and were further analyzed pharmacokinetically. 10, in particular, showed a significant lung accumulation, up to 12.9-fold greater than plasma exposure, and was effective in a mouse model of SARS-CoV-2 infection, as well as against several SARS-CoV-2 variants. These findings highlight the potential of 10 as an in vivo chemical probe for studying PLpro inhibition in SARS-CoV-2 infection.
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Affiliation(s)
- Ganga
Reddy Velma
- Department
of Pharmacology & Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson 85721, Arizona, United States
| | - Zhengnan Shen
- Department
of Pharmacology & Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson 85721, Arizona, United States
| | - Cameron Holberg
- Department
of Pharmacology & Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson 85721, Arizona, United States
| | - Jiqiang Fu
- Department
of Pharmacology & Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson 85721, Arizona, United States
| | - Farinaz Soleymani
- Department
of Chemistry & Biochemistry, Colleges of Science and Medicine, University of Arizona, Tucson 85721, Arizona, United States
| | - Laura Cooper
- Department
of Microbiology, College of Medicine, University
of Illinois at Chicago (UIC), Chicago 60612, Illinois, United States
| | - Omar Lozano Ramos
- Department
of Pharmacology & Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson 85721, Arizona, United States
| | - Divakar Indukuri
- Department
of Pharmacology & Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson 85721, Arizona, United States
| | - Soumya Reddy Musku
- Department
of Pharmacology & Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson 85721, Arizona, United States
| | - Pavel Rychetsky
- Department
of Pharmacology & Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson 85721, Arizona, United States
| | - Steve Slilaty
- Sunshine
Biopharma Inc, 333 Las Olas Way, CU4 Suite 433, Fort Lauderdale 33301, Florida, United States
| | - Zuomei Li
- Sunshine
Biopharma Inc, 333 Las Olas Way, CU4 Suite 433, Fort Lauderdale 33301, Florida, United States
| | - Kiira Ratia
- Research
Resources Center, University of Illinois
at Chicago (UIC), Chicago 60612, Illinois, United States
| | - Lijun Rong
- Department
of Microbiology, College of Medicine, University
of Illinois at Chicago (UIC), Chicago 60612, Illinois, United States
| | - Dominik Schenten
- Department
of Immunology, College of Medicine, University
of Arizona, Tucson 85721, Arizona, United States
| | - Rui Xiong
- Department
of Pharmacology & Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson 85721, Arizona, United States
| | - Gregory R. J Thatcher
- Department
of Pharmacology & Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson 85721, Arizona, United States
- Department
of Chemistry & Biochemistry, Colleges of Science and Medicine, University of Arizona, Tucson 85721, Arizona, United States
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17
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Samrat SK, Kumar P, Liu Y, Chen K, Lee H, Li Z, Chen Y, Li H. An ISG15-Based High-Throughput Screening Assay for Identification and Characterization of SARS-CoV-2 Inhibitors Targeting Papain-like Protease. Viruses 2024; 16:1239. [PMID: 39205213 PMCID: PMC11359932 DOI: 10.3390/v16081239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 07/18/2024] [Accepted: 07/25/2024] [Indexed: 09/04/2024] Open
Abstract
Emergence of newer variants of SARS-CoV-2 underscores the need for effective antivirals to complement the vaccination program in managing COVID-19. The multi-functional papain-like protease (PLpro) of SARS-CoV-2 is an essential viral protein that not only regulates the viral replication but also modulates the host immune system, making it a promising therapeutic target. To this end, we developed an in vitro interferon stimulating gene 15 (ISG15)-based Förster resonance energy transfer (FRET) assay and screened the National Cancer Institute (NCI) Diversity Set VI compound library, which comprises 1584 small molecules. Subsequently, we assessed the PLpro enzymatic activity in the presence of screened molecules. We identified three potential PLpro inhibitors, namely, NSC338106, 651084, and 679525, with IC50 values in the range from 3.3 to 6.0 µM. These molecules demonstrated in vitro inhibition of the enzyme activity and exhibited antiviral activity against SARS-CoV-2, with EC50 values ranging from 0.4 to 4.6 µM. The molecular docking of all three small molecules to PLpro suggested their specificity towards the enzyme's active site. Overall, our study contributes promising prospects for further developing potential antivirals to combat SARS-CoV-2 infection.
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Affiliation(s)
- Subodh Kumar Samrat
- Department of Pharmacology and Toxicology, R Ken Coit College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson, AZ 85721, USA; (P.K.); (Y.L.); (K.C.); (Z.L.); (Y.C.)
| | - Prashant Kumar
- Department of Pharmacology and Toxicology, R Ken Coit College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson, AZ 85721, USA; (P.K.); (Y.L.); (K.C.); (Z.L.); (Y.C.)
| | - Yuchen Liu
- Department of Pharmacology and Toxicology, R Ken Coit College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson, AZ 85721, USA; (P.K.); (Y.L.); (K.C.); (Z.L.); (Y.C.)
| | - Ke Chen
- Department of Pharmacology and Toxicology, R Ken Coit College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson, AZ 85721, USA; (P.K.); (Y.L.); (K.C.); (Z.L.); (Y.C.)
| | - Hyun Lee
- Department of Pharmaceutical Sciences, College of Pharmacy and Biophysics Core, Research Resources Center, University of Illinois at Chicago, Chicago, IL 60607, USA;
| | - Zhong Li
- Department of Pharmacology and Toxicology, R Ken Coit College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson, AZ 85721, USA; (P.K.); (Y.L.); (K.C.); (Z.L.); (Y.C.)
| | - Yin Chen
- Department of Pharmacology and Toxicology, R Ken Coit College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson, AZ 85721, USA; (P.K.); (Y.L.); (K.C.); (Z.L.); (Y.C.)
| | - Hongmin Li
- Department of Pharmacology and Toxicology, R Ken Coit College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson, AZ 85721, USA; (P.K.); (Y.L.); (K.C.); (Z.L.); (Y.C.)
- Department of Chemistry and Biochemistry, College of Science & College of Medicine, The University of Arizona, Tucson, AZ 85721, USA
- The BIO5 Institute, The University of Arizona, Tucson, AZ 85721, USA
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18
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Fan J, Xi P, Liu H, Song X, Zhao X, Zhou X, Zou Y, Fu Y, Li L, Jia R, Yin Z. Myricetin inhibits transmissible gastroenteritis virus replication by targeting papain-like protease deubiquitinating enzyme activity. Front Microbiol 2024; 15:1433664. [PMID: 39050632 PMCID: PMC11266173 DOI: 10.3389/fmicb.2024.1433664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 06/24/2024] [Indexed: 07/27/2024] Open
Abstract
Myricetin, a natural flavonoid found in various foods, was investigated for its antiviral effect against transmissible gastroenteritis virus (TGEV). This α-coronavirus causes significant economic losses in the global swine industry. The study focused on the papain-like protease (PLpro), which plays a crucial role in coronavirus immune evasion by mediating deubiquitination. Targeting PLpro could potentially disrupt viral replication and enhance antiviral responses. The results demonstrated that myricetin effectively inhibited TGEV-induced cytopathic effects in a dose-dependent manner, with an EC50 value of 31.19 μM. Myricetin significantly reduced TGEV viral load within 48 h after an 8-h co-incubation period. Further investigations revealed that myricetin at a concentration of 100 μM directly inactivated TGEV and suppressed its intracellular replication stage. Moreover, pretreatment with 100 μM myricetin conferred a protective effect on PK-15 cells against TGEV infection. Myricetin competitively inhibited PLpro with an IC50 value of 6.563 μM. Molecular docking experiments show that myricetin binds to the Cys102 residue of PLpro through conventional hydrogen bonds, Pi-sulfur, and Pi-alkyl interactions. This binding was confirmed through site-directed mutagenesis experiments, indicating myricetin as a potential candidate for preventing and treating TGEV infection.
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Affiliation(s)
- Jiahao Fan
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Pengyuan Xi
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Huimao Liu
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xu Song
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xinghong Zhao
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xun Zhou
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yuanfeng Zou
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yuping Fu
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Lixia Li
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Renyong Jia
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Zhongqiong Yin
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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19
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Li Y, Lu SM, Wang JL, Yao HP, Liang LG. Progress in SARS-CoV-2, diagnostic and clinical treatment of COVID-19. Heliyon 2024; 10:e33179. [PMID: 39021908 PMCID: PMC11253070 DOI: 10.1016/j.heliyon.2024.e33179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 06/13/2024] [Accepted: 06/15/2024] [Indexed: 07/20/2024] Open
Abstract
Background Corona Virus Disease 2019(COVID-19)is a global pandemic novel coronavirus infection disease caused by Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2). Although rapid, large-scale testing plays an important role in patient management and slowing the spread of the disease. However, there has been no good and widely used drug treatment for infection and transmission of SARS-CoV-2. Key findings Therefore, this review updates the body of knowledge on viral structure, infection routes, detection methods, and clinical treatment, with the aim of responding to the large-section caused by SARS-CoV-2. This paper focuses on the structure of SARS-CoV-2 viral protease, RNA polymerase, serine protease and main proteinase-like protease as well as targeted antiviral drugs. Conclusion In vitro or clinical trials have been carried out to provide deeper thinking for the pathogenesis, clinical diagnosis, vaccine development and treatment of SARS-CoV-2.
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Affiliation(s)
- Yang Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Si-Ming Lu
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Key Laboratory of Clinical in Vitro Diagnostic Techniques, Hangzhou, China
- Institute of Laboratory Medicine, Zhejiang University, Hangzhou, China
| | - Jia-Long Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hang-Ping Yao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Li-Guo Liang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Centre for Clinical Laboratory, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
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20
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Qin B, Wu C, Zhao B, Li G, Wang B, Ou M, Li Z, Lang X, Li P, Liu J, Cui S, Huang H. Design, Synthesis, and Biological Evaluation of 1,2,4-Oxadiazole Derivatives Containing an Aryl Carboxylic Acid Moiety as Potent Sarbecovirus Papain-like Protease Inhibitors. J Med Chem 2024; 67:10211-10232. [PMID: 38871484 DOI: 10.1021/acs.jmedchem.4c00534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
Papain-like protease (PLpro) is a promising therapeutic target for its pivotal role in the life cycle of SARS-CoV-2. A series of 1,2,4-oxadiazole derivatives was designed and synthesized via a ring formation strategy based on SARS-CoV-2 PLpro-GRL0617 complex structure. Systematic structure-activity relationship studies revealed that introducing oxadiazole and aryl carboxylic acid moieties to GRL0617 enhanced the enzymatic inhibition activity, affinity, and deubiquitination capacity toward PLpro. 1,2,4-Oxadiazole compounds 13f and 26r, which had PLpro inhibition activity (IC50 = 1.8 and 1.0 μM) and antiviral activity against SARS-CoV-2 (EC50 = 5.4 and 4.3 μM), exhibited good metabolic stability (t1/2 > 93.2 min) and higher plasma exposure (AUC0-t = 17,380.08 and 24,289.76 ng·h/mL) in mice. Especially, compound 26r with moderate oral bioavailability of 39.1% and potent antiviral activity is worthy of further studies in vivo. Our findings provide a new insight for the discovery of antiviral agents targeting PLpro.
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Affiliation(s)
- Bo Qin
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, P. R. China
| | - Chengwei Wu
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, P. R. China
| | - Binbin Zhao
- National Center of Technology Innovation for Animal Models, NHC Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing 100021, P. R. China
| | - Gang Li
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, P. R. China
- State Key Laboratory of Respiratory Health and Multimorbidity, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, P. R. China
| | - Baolian Wang
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, P. R. China
| | - Mengdie Ou
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, P. R. China
| | - Ziheng Li
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, P. R. China
| | - Xuli Lang
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, P. R. China
| | - Peng Li
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, P. R. China
| | - Jiangning Liu
- National Center of Technology Innovation for Animal Models, NHC Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing 100021, P. R. China
| | - Sheng Cui
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, P. R. China
- State Key Laboratory of Respiratory Health and Multimorbidity, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, P. R. China
| | - Haihong Huang
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, P. R. China
- State Key Laboratory of Respiratory Health and Multimorbidity, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, P. R. China
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21
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Ferdoush J, Abdul Kadir R, Simay Kaplanoglu S, Osborn M. SARS-CoV-2 and UPS with potentials for therapeutic interventions. Gene 2024; 912:148377. [PMID: 38490508 DOI: 10.1016/j.gene.2024.148377] [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: 01/19/2024] [Revised: 03/09/2024] [Accepted: 03/12/2024] [Indexed: 03/17/2024]
Abstract
The Ubiquitin proteasome system (UPS), an essential eukaryotic/host/cellular post-translational modification (PTM), plays a critical role in the regulation of diverse cellular functions including regulation of protein stability, immune signaling, antiviral activity, as well as virus replication. Although UPS regulation of viral proteins may be utilized by the host as a defense mechanism to invade viruses, viruses may have adapted to take advantage of the host UPS. This system can be manipulated by viruses such as the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) to stimulate various steps of the viral replication cycle and facilitate pathogenesis, thereby causing the respiratory disease COVID-19. Many SARS-CoV-2 encoded proteins including open reading frame 3a (ORF3a), ORF6, ORF7a, ORF9b, and ORF10 interact with the host's UPS machinery, influencing host immune signaling and apoptosis. Moreover, SARS-CoV-2 encoded papain-like protease (PLpro) interferes with the host UPS to facilitate viral replication and to evade the host's immune system. These alterations in SARS-CoV-2 infected cells have been revealed by various proteomic studies, suggesting potential targets for clinical treatment. To provide insight into the underlying causes of COVID-19 and suggest possible directions for therapeutic interventions, this paper reviews the intricate relationship between SARS-CoV-2 and UPS. Promising treatment strategies are also investigated in this paper including targeting PLpro with zinc-ejector drugs, as well as targeting viral non-structural protein (nsp12) via heat treatment associated ubiquitin-mediated proteasomal degradation to reduce viral pathogenesis.
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Affiliation(s)
- Jannatul Ferdoush
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga 615 McCallie Ave, Chattanooga, TN 37403, USA.
| | - Rizwaan Abdul Kadir
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga 615 McCallie Ave, Chattanooga, TN 37403, USA
| | - Selin Simay Kaplanoglu
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga 615 McCallie Ave, Chattanooga, TN 37403, USA
| | - Morgan Osborn
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga 615 McCallie Ave, Chattanooga, TN 37403, USA
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22
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Li CW, Chao TL, Lai CL, Lin CC, Pan MYC, Cheng CL, Kuo CJ, Wang LHC, Chang SY, Liang PH. Systematic Studies on the Anti-SARS-CoV-2 Mechanisms of Tea Polyphenol-Related Natural Products. ACS OMEGA 2024; 9:23984-23997. [PMID: 38854515 PMCID: PMC11154727 DOI: 10.1021/acsomega.4c02392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/22/2024] [Accepted: 05/09/2024] [Indexed: 06/11/2024]
Abstract
The causative pathogen of COVID-19, severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), utilizes the receptor-binding domain (RBD) of the spike protein to bind to human receptor angiotensin-converting enzyme 2 (ACE2). Further cleavage of spike by human proteases furin, TMPRSS2, and/or cathepsin L facilitates viral entry into the host cells for replication, where the maturation of polyproteins by 3C-like protease (3CLpro) and papain-like protease (PLpro) yields functional nonstructural proteins (NSPs) such as RNA-dependent RNA polymerase (RdRp) to synthesize mRNA of structural proteins. By testing the tea polyphenol-related natural products through various assays, we found that the active antivirals prevented SARS-CoV-2 entry by blocking the RBD/ACE2 interaction and inhibiting the relevant human proteases, although some also inhibited the viral enzymes essential for replication. Due to their multitargeting properties, these compounds were often misinterpreted for their antiviral mechanisms. In this study, we provide a systematic protocol to check and clarify their anti-SARS-CoV-2 mechanisms, which should be applicable for all of the antivirals.
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Affiliation(s)
- Chen-Wei Li
- Institute
of Biochemical Sciences, National Taiwan
University, Taipei 10617, Taiwan
| | - Tai-Ling Chao
- Department
of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei 10048, Taiwan
| | - Chin-Lan Lai
- Institute
of Biochemical Sciences, National Taiwan
University, Taipei 10617, Taiwan
| | - Cheng-Chin Lin
- Institute
of Biochemical Sciences, National Taiwan
University, Taipei 10617, Taiwan
| | - Max Yu-Chen Pan
- Institute
of Molecular and Cellular Biology, National
Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chieh-Ling Cheng
- Institute
of Biochemical Sciences, National Taiwan
University, Taipei 10617, Taiwan
| | - Chih-Jung Kuo
- Department
of Veterinary Medicine, National Chung Hsing
University, Taichung 40227, Taiwan
| | - Lily Hui-Ching Wang
- Institute
of Molecular and Cellular Biology, National
Tsing Hua University, Hsinchu 30013, Taiwan
| | - Sui-Yuan Chang
- Department
of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei 10048, Taiwan
- Department
of Laboratory Medicine, National Taiwan
University Hospital, Taipei 10002, Taiwan
| | - Po-Huang Liang
- Institute
of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Institute
of Biochemical Sciences, National Taiwan
University, Taipei 10617, Taiwan
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23
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van Vliet VJE, De Silva A, Mark BL, Kikkert M. Viral deubiquitinating proteases and the promising strategies of their inhibition. Virus Res 2024; 344:199368. [PMID: 38588924 PMCID: PMC11025011 DOI: 10.1016/j.virusres.2024.199368] [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: 11/30/2023] [Revised: 03/01/2024] [Accepted: 04/05/2024] [Indexed: 04/10/2024]
Abstract
Several viruses are now known to code for deubiquitinating proteases in their genomes. Ubiquitination is an essential post-translational modification of cellular substrates involved in many processes in the cell, including in innate immune signalling. This post-translational modification is regulated by the ubiquitin conjugation machinery, as well as various host deubiquitinating enzymes. The conjugation of ubiquitin chains to several innate immune related factors is often needed to induce downstream signalling, shaping the antiviral response. Viral deubiquitinating proteins, besides often having a primary function in the viral replication cycle by cleaving the viral polyprotein, are also able to cleave ubiquitin chains from such host substrates, in that way exerting a function in innate immune evasion. The presence of viral deubiquitinating enzymes has been firmly established for numerous animal-infecting viruses, such as some well-researched and clinically important nidoviruses, and their presence has now been confirmed in several plant viruses as well. Viral proteases in general have long been highlighted as promising drug targets, with a current focus on small molecule inhibitors. In this review, we will discuss the range of viral deubiquitinating proteases known to date, summarise the various avenues explored to inhibit such proteases and discuss novel strategies and models intended to inhibit and study these specific viral enzymes.
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Affiliation(s)
- Vera J E van Vliet
- Department of Medical Microbiology, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, South Holland, the Netherlands; The Roslin Institute, University of Edinburgh, Midlothian, Scotland, United Kingdom
| | - Anuradha De Silva
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Brian L Mark
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Marjolein Kikkert
- Department of Medical Microbiology, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, South Holland, the Netherlands.
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24
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Hoenigsperger H, Sivarajan R, Sparrer KM. Differences and similarities between innate immune evasion strategies of human coronaviruses. Curr Opin Microbiol 2024; 79:102466. [PMID: 38555743 DOI: 10.1016/j.mib.2024.102466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/20/2024] [Accepted: 03/12/2024] [Indexed: 04/02/2024]
Abstract
So far, seven coronaviruses have emerged in humans. Four recurring endemic coronaviruses cause mild respiratory symptoms. Infections with epidemic Middle East respiratory syndrome-related coronavirus or severe acute respiratory syndrome coronavirus (SARS-CoV)-1 are associated with high mortality rates. SARS-CoV-2 is the causative agent of the coronavirus disease 2019 pandemic. To establish an infection, coronaviruses evade restriction by human innate immune defenses, such as the interferon system, autophagy and the inflammasome. Here, we review similar and distinct innate immune manipulation strategies employed by the seven human coronaviruses. We further discuss the impact on pathogenesis, zoonotic emergence and adaptation. Understanding the nature of the interplay between endemic/epidemic/pandemic coronaviruses and host defenses may help to better assess the pandemic potential of emerging coronaviruses.
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Affiliation(s)
- Helene Hoenigsperger
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Rinu Sivarajan
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
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25
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Kiba Y, Tanikawa T, Hayashi T, Yokogawa T, Sano A, Suzuki R, Kitamura M. Inhibitory effects of senkyuchachosan on SARS-CoV-2 papain-like protease activity in vitro. J Nat Med 2024; 78:784-791. [PMID: 38512650 DOI: 10.1007/s11418-024-01788-0] [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: 08/19/2023] [Accepted: 02/02/2024] [Indexed: 03/23/2024]
Abstract
Papain-like protease (PLpro) enzyme plays a vital role in viral replication as it breaks down polyproteins and disrupts the host's immune response. There are few reports on Kampo formulas that focus on PLpro activity. In this study, we evaluated the inhibitory effects of senkyuchachosan, a traditional Japanese medicine, on PLpro of SARS-CoV-2, the virus responsible for causing COVID-19. We purified the PLpro enzyme and conducted in vitro enzymatic assays using specific substrates. Among the nine crude drugs present in senkyuchachosan, four (Cyperi Rhizoma, Schizonepetae Spica, Menthae Herba, and Camelliae sinensis Folium [CsF]) strongly inhibited PLpro activity. CsF, derived from Camellia sinensis (green tea), contains polyphenols, including catechins and tannins. To confirm that the PLpro inhibitory effects of senkyuchachosan predominantly stem from tannins, the tannins were removed from the decoction using polyvinylpolypyrrolidone (PVPP). The inhibitory effect of senkyuchachosan on PLpro activity was reduced by the removal of PVPP. In addition, the tannin fraction obtained from the CsF extracts showed significant PLpro inhibitory effects. These findings lay the groundwork for the potential development of therapeutic agents that target SARS-CoV-2 infection by intervening in proteolytic cleavage of the virus.
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Affiliation(s)
- Yuka Kiba
- School of Pharmacy, Faculty of Pharmacy and Pharmaceutical Sciences, Josai University, 1-1, Keyakidai, Sakado, Saitama, 350-0295, Japan
| | - Takashi Tanikawa
- School of Pharmacy, Faculty of Pharmacy and Pharmaceutical Sciences, Josai University, 1-1, Keyakidai, Sakado, Saitama, 350-0295, Japan
| | - Tsuyoshi Hayashi
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takami Yokogawa
- School of Pharmacy, Faculty of Pharmacy and Pharmaceutical Sciences, Josai University, 1-1, Keyakidai, Sakado, Saitama, 350-0295, Japan
| | - Aiko Sano
- Department of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, Josai University, 1-1, Keyakidai, Sakado, Saitama, 350-0295, Japan
| | - Ryuichiro Suzuki
- Department of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, Josai University, 1-1, Keyakidai, Sakado, Saitama, 350-0295, Japan
| | - Masashi Kitamura
- School of Pharmacy, Faculty of Pharmacy and Pharmaceutical Sciences, Josai University, 1-1, Keyakidai, Sakado, Saitama, 350-0295, Japan.
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26
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Sabadini G, Mellado M, Morales C, Mella J. Arylamines QSAR-Based Design and Molecular Dynamics of New Phenylthiophene and Benzimidazole Derivatives with Affinity for the C111, Y268, and H73 Sites of SARS-CoV-2 PLpro Enzyme. Pharmaceuticals (Basel) 2024; 17:606. [PMID: 38794177 PMCID: PMC11124164 DOI: 10.3390/ph17050606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/01/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
A non-structural SARS-CoV-2 protein, PLpro, is involved in post-translational modifications in cells, allowing the evasion of antiviral immune response mechanisms. In this study, potential PLpro inhibitory drugs were designed using QSAR, molecular docking, and molecular dynamics. A combined QSAR equation with physicochemical and Free-Wilson descriptors was formulated. The r2, q2, and r2test values were 0.833, 0.770, and 0.721, respectively. From the equation, it was found that the presence of an aromatic ring and a basic nitrogen atom is crucial for obtaining good antiviral activity. Then, a series of structures for the binding sites of C111, Y268, and H73 of PLpro were created. The best compounds were found to exhibit pIC50 values of 9.124 and docking scoring values of -14 kcal/mol. The stability of the compounds in the cavities was confirmed by molecular dynamics studies. A high number of stable contacts and good interactions over time were exhibited by the aryl-thiophenes Pred14 and Pred15, making them potential antiviral candidates.
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Affiliation(s)
- Gianfranco Sabadini
- Instituto de Química y Bioquímica, Facultad de Ciencias, Universidad de Valparaíso, Av. Gran Bretaña 1111, Valparaíso 2360102, Chile;
| | - Marco Mellado
- Instituto de Investigación y Postgrado, Facultad de Ciencias de la Salud, Universidad Central de Chile, Santiago 8330507, Chile
| | - César Morales
- Laboratorio de Materiales Funcionales, Centro Integrativo de Biología y Química Aplicada (CIBQA), Facultad de Ciencias de la Salud, Universidad Bernardo OHiggins, General Gana 1702, Santiago 8320000, Chile;
| | - Jaime Mella
- Instituto de Química y Bioquímica, Facultad de Ciencias, Universidad de Valparaíso, Av. Gran Bretaña 1111, Valparaíso 2360102, Chile;
- Centro de Investigación, Desarrollo e Innovación de Productos Bioactivos (CInBIO), Universidad de Valparaíso, Av. Gran Bretaña 1111, Valparaíso 2360102, Chile
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27
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Jové V, Wheeler H, Lee CW, Healy DR, Levine K, Ralph EC, Yamaguchi M, Jiang ZK, Cabral E, Xu Y, Stock J, Yang B, Giddabasappa A, Loria P, Casimiro-Garcia A, Kessler BM, Pinto-Fernández A, Frattini V, Wes PD, Wang F. Type I interferon regulation by USP18 is a key vulnerability in cancer. iScience 2024; 27:109593. [PMID: 38632987 PMCID: PMC11022047 DOI: 10.1016/j.isci.2024.109593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 01/12/2024] [Accepted: 03/25/2024] [Indexed: 04/19/2024] Open
Abstract
Precise regulation of Type I interferon signaling is crucial for combating infection and cancer while avoiding autoimmunity. Type I interferon signaling is negatively regulated by USP18. USP18 cleaves ISG15, an interferon-induced ubiquitin-like modification, via its canonical catalytic function, and inhibits Type I interferon receptor activity through its scaffold role. USP18 loss-of-function dramatically impacts immune regulation, pathogen susceptibility, and tumor growth. However, prior studies have reached conflicting conclusions regarding the relative importance of catalytic versus scaffold function. Here, we develop biochemical and cellular methods to systematically define the physiological role of USP18. By comparing a patient-derived mutation impairing scaffold function (I60N) to a mutation disrupting catalytic activity (C64S), we demonstrate that scaffold function is critical for cancer cell vulnerability to Type I interferon. Surprisingly, we discovered that human USP18 exhibits minimal catalytic activity, in stark contrast to mouse USP18. These findings resolve human USP18's mechanism-of-action and enable USP18-targeted therapeutics.
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Affiliation(s)
- Veronica Jové
- Centers for Therapeutic Innovation, Pfizer, New York City, NY 10016, USA
| | - Heather Wheeler
- Discovery Sciences, Medicine Design, Pfizer, Groton, CT 06340, USA
| | | | - David R. Healy
- Discovery Sciences, Medicine Design, Pfizer, Groton, CT 06340, USA
| | - Kymberly Levine
- Centers for Therapeutic Innovation, Pfizer, New York City, NY 10016, USA
| | - Erik C. Ralph
- Discovery Sciences, Medicine Design, Pfizer, Groton, CT 06340, USA
| | - Masaya Yamaguchi
- Discovery Sciences, Medicine Design, Pfizer, Groton, CT 06340, USA
| | | | - Edward Cabral
- Comparative Medicine, Pfizer, La Jolla, CA 92121, USA
| | - Yingrong Xu
- Discovery Sciences, Medicine Design, Pfizer, Groton, CT 06340, USA
| | - Jeffrey Stock
- Discovery Sciences, Medicine Design, Pfizer, Groton, CT 06340, USA
| | - Bing Yang
- Comparative Medicine, Pfizer, La Jolla, CA 92121, USA
| | | | - Paula Loria
- Discovery Sciences, Medicine Design, Pfizer, Groton, CT 06340, USA
| | | | - Benedikt M. Kessler
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Adán Pinto-Fernández
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Véronique Frattini
- Centers for Therapeutic Innovation, Pfizer, New York City, NY 10016, USA
| | - Paul D. Wes
- Centers for Therapeutic Innovation, Pfizer, New York City, NY 10016, USA
| | - Feng Wang
- Discovery Sciences, Medicine Design, Pfizer, Groton, CT 06340, USA
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28
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Schmedtje JF, Ciske F, Muzzarelli KM, Assar Z. Novel nitric oxide donors are coronary vasodilators that also bind to the papain-like protease of SARS-CoV-2. Biomed Pharmacother 2024; 173:116378. [PMID: 38492437 DOI: 10.1016/j.biopha.2024.116378] [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: 12/10/2023] [Revised: 02/24/2024] [Accepted: 02/29/2024] [Indexed: 03/18/2024] Open
Abstract
Several investigational nitric oxide donors were originally created to correct vascular endothelial dysfunction in cardiovascular diseases. These 48 compounds contain an urea-like moiety attached to the well-known NO donors isosorbide 2- and 5-mononitrate. CR-0305 and CR-0202 were synthesized and found to be nontoxic in the cell lines HMEC-1, A549/hACE2 and VeroE6. CR-0305 induced vasodilation in human coronary arteries ex vivo. Since NO can also have antiviral properties, a study of drug-protein interactions with SARS-CoV-2 was undertaken using in silico modeling. CR-0305 experimentally outperformed the other compounds, including CR-0202, in binding the catalytic site of SARS-CoV-2 papain-like protease (PLpro). PLpro is a primary target for therapeutic inhibition of SARS-CoV-2 as it mediates viral replication and modulates host innate immune responses. CR-0305 is predicted to sit firmly in the PLpro catalytic pocket as confirmed by molecular dynamics simulations, wherein stability of binding to the catalytic site of PLpro induces a conformational change in the BL2 loop to a more closed conformation as observed previously with GRL0617. Surface plasmon resonance was performed with CR-0305 and CR-0202 to characterize binding affinity to purified SARS-CoV-2 PLpro protein. CR-0305 and CR-0202 also inhibited SARS-CoV-2 infection compared to vehicle as measured by virus N protein staining with a specific antibody in A549-ACE2 and VeroE6 cells at 20 µM. CR-0305 is a coronary vasodilator that appears to bind to the catalytic site of the PLpro of SARS-CoV-2 while targeting delivery of antiviral NO to cells infected by SARS-CoV-2, suggesting multiple indications for future development.
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Affiliation(s)
- John F Schmedtje
- Coeurative, Inc., 201 McClanahan St. SW, Roanoke, VA 24014, USA.
| | - Fred Ciske
- Cayman Chemical Co., 1180 East Ellsworth Road, Ann Arbor, MI 48108, USA
| | | | - Zahra Assar
- Cayman Chemical Co., 1180 East Ellsworth Road, Ann Arbor, MI 48108, USA
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29
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Nguyen TH, Thai QM, Pham MQ, Minh PTH, Phung HTT. Machine learning combines atomistic simulations to predict SARS-CoV-2 Mpro inhibitors from natural compounds. Mol Divers 2024; 28:553-561. [PMID: 36823394 PMCID: PMC9950021 DOI: 10.1007/s11030-023-10601-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/04/2023] [Indexed: 02/25/2023]
Abstract
To date, the COVID-19 pandemic has still been infectious around the world, continuously causing social and economic damage on a global scale. One of the most important therapeutic targets for the treatment of COVID-19 is the main protease (Mpro) of SARS-CoV-2. In this study, we combined machine-learning (ML) model with atomistic simulations to computationally search for highly promising SARS-CoV-2 Mpro inhibitors from the representative natural compounds of the National Cancer Institute (NCI) Database. First, the trained ML model was used to scan the library quickly and reliably for possible Mpro inhibitors. The ML output was then confirmed using atomistic simulations integrating molecular docking and molecular dynamic simulations with the linear interaction energy scheme. The results turned out to show that there was evidently good agreement between ML and atomistic simulations. Ten substances were proposed to be able to inhibit SARS-CoV-2 Mpro. Seven of them have high-nanomolar affinity and are very potential inhibitors. The strategy has been proven to be reliable and appropriate for fast prediction of SARS-CoV-2 Mpro inhibitors, benefiting for new emerging SARS-CoV-2 variants in the future accordingly.
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Affiliation(s)
- Trung Hai Nguyen
- Laboratory of Theoretical and Computational Biophysics, Advanced Institute of Materials Science, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Quynh Mai Thai
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Minh Quan Pham
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Pham Thi Hong Minh
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Huong Thi Thu Phung
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
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van Huizen M, Bloeme - ter Horst JR, de Gruyter HLM, Geurink PP, van der Heden van Noort GJ, Knaap RCM, Nelemans T, Ogando NS, Leijs AA, Urakova N, Mark BL, Snijder EJ, Myeni SK, Kikkert M. Deubiquitinating activity of SARS-CoV-2 papain-like protease does not influence virus replication or innate immune responses in vivo. PLoS Pathog 2024; 20:e1012100. [PMID: 38527094 PMCID: PMC10994560 DOI: 10.1371/journal.ppat.1012100] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/04/2024] [Accepted: 03/04/2024] [Indexed: 03/27/2024] Open
Abstract
The coronavirus papain-like protease (PLpro) is crucial for viral replicase polyprotein processing. Additionally, PLpro can subvert host defense mechanisms by its deubiquitinating (DUB) and deISGylating activities. To elucidate the role of these activities during SARS-CoV-2 infection, we introduced mutations that disrupt binding of PLpro to ubiquitin or ISG15. We identified several mutations that strongly reduced DUB activity of PLpro, without affecting viral polyprotein processing. In contrast, mutations that abrogated deISGylating activity also hampered viral polyprotein processing and when introduced into the virus these mutants were not viable. SARS-CoV-2 mutants exhibiting reduced DUB activity elicited a stronger interferon response in human lung cells. In a mouse model of severe disease, disruption of PLpro DUB activity did not affect lethality, virus replication, or innate immune responses in the lungs. This suggests that the DUB activity of SARS-CoV-2 PLpro is dispensable for virus replication and does not affect innate immune responses in vivo. Interestingly, the DUB mutant of SARS-CoV replicated to slightly lower titers in mice and elicited a diminished immune response early in infection, although lethality was unaffected. We previously showed that a MERS-CoV mutant deficient in DUB and deISGylating activity was strongly attenuated in mice. Here, we demonstrate that the role of PLpro DUB activity during infection can vary considerably between highly pathogenic coronaviruses. Therefore, careful considerations should be taken when developing pan-coronavirus antiviral strategies targeting PLpro.
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Affiliation(s)
- Mariska van Huizen
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
| | - Jonna R. Bloeme - ter Horst
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
| | - Heidi L. M. de Gruyter
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
| | - Paul P. Geurink
- Department of Cell and Chemical Biology, Division of Chemical Biology and Drug Discovery, Leiden University Medical Centre, Leiden, The Netherlands
| | - Gerbrand J. van der Heden van Noort
- Department of Cell and Chemical Biology, Division of Chemical Biology and Drug Discovery, Leiden University Medical Centre, Leiden, The Netherlands
| | - Robert C. M. Knaap
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
| | - Tessa Nelemans
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
| | - Natacha S. Ogando
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
| | - Anouk A. Leijs
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
| | - Nadya Urakova
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
| | - Brian L. Mark
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Eric J. Snijder
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
| | - Sebenzile K. Myeni
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
| | - Marjolein Kikkert
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
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31
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Chan HTH, Brewitz L, Lukacik P, Strain-Damerell C, Walsh MA, Schofield CJ, Duarte F. Studies on the selectivity of the SARS-CoV-2 papain-like protease reveal the importance of the P2' proline of the viral polyprotein. RSC Chem Biol 2024; 5:117-130. [PMID: 38333195 PMCID: PMC10849127 DOI: 10.1039/d3cb00128h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/13/2023] [Indexed: 02/10/2024] Open
Abstract
The SARS-CoV-2 papain-like protease (PLpro) is an antiviral drug target that catalyzes the hydrolysis of the viral polyproteins pp1a/1ab, so releasing the non-structural proteins (nsps) 1-3 that are essential for the coronavirus lifecycle. The LXGG↓X motif in pp1a/1ab is crucial for recognition and cleavage by PLpro. We describe molecular dynamics, docking, and quantum mechanics/molecular mechanics (QM/MM) calculations to investigate how oligopeptide substrates derived from the viral polyprotein bind to PLpro. The results reveal how the substrate sequence affects the efficiency of PLpro-catalyzed hydrolysis. In particular, a proline at the P2' position promotes catalysis, as validated by residue substitutions and mass spectrometry-based analyses. Analysis of PLpro catalyzed hydrolysis of LXGG motif-containing oligopeptides derived from human proteins suggests that factors beyond the LXGG motif and the presence of a proline residue at P2' contribute to catalytic efficiency, possibly reflecting the promiscuity of PLpro. The results will help in identifying PLpro substrates and guiding inhibitor design.
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Affiliation(s)
- H T Henry Chan
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Lennart Brewitz
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Petra Lukacik
- Diamond Light Source Ltd., Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - Claire Strain-Damerell
- Diamond Light Source Ltd., Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - Martin A Walsh
- Diamond Light Source Ltd., Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Fernanda Duarte
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
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32
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Abbasi M, Mansourian M, Oskouie AA, Taheri S, Mahnam K. In-silico study MM/GBSA binding free energy and molecular dynamics simulation of some designed remdesivir derivatives as the inhibitory potential of SARS-CoV-2 main protease. Res Pharm Sci 2024; 19:29-41. [PMID: 39006973 PMCID: PMC11244705 DOI: 10.4103/1735-5362.394818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/16/2023] [Accepted: 01/17/2024] [Indexed: 07/16/2024] Open
Abstract
Background and purpose Coronavirus disease (COVID-19) is one of the greatest challenges of the twentieth century. Recently, in silico tools help to predict new inhibitors of SARS-CoV-2. In this study, the new compounds based on the remdesivir structure (12 compounds) were designed. Experimental approach The main interactions of remdesivir and designed compounds were investigated in the 3CLpro active site. The binding free energy of compounds by the MM-GBSA method was calculated and the best compound (compound 12 with the value of -88.173 kcal/mol) was introduced to the molecular dynamics simulation study. Findings/Results The simulation results were compared with the results of protein simulation without the presence of an inhibitor and in the presence of remdesivir. Additionally, the RMSD results for the protein backbone showed that compound 12 in the second 50 nanoseconds has less fluctuation than the protein alone and in the presence of remdesivir, which indicates the stability of the compound in the active site of the Mpro protein. Furthermore, protein compactness was investigated in the absence of compounds and the presence of compound 12 and remdesivir. The Rg diagram shows a fluctuation of approximately 0.05 A, which indicates the compressibility of the protein in the presence and absence of compounds. The results of the RMSF plot also show the stability of essential amino acids during protein binding. Conclusion and implications Supported by the theoretical results, compound 12 could have the potential to inhibit the 3CLpro enzyme, which requires further in vitro studies and enzyme inhibition must also be confirmed at protein levels.
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Affiliation(s)
- Maryam Abbasi
- Department of Pharmaceutical Chemistry, School of Pharmacy, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Mahboubeh Mansourian
- Medicinal Plants Research Center, Yasuj University of Medical Sciences, Yasuj, I.R. Iran
- Department of Pharmacology, Faculty of Medicine, Yasuj University of Medical Sciences, Yasuj, I.R. Iran
| | - Afsaneh Arefi Oskouie
- Department of Basic Sciences, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, I.R. Iran
| | - Salman Taheri
- Chemistry & Chemical Engineering Research Center of Iran, P.O. Box 14335-186, Tehran, I.R. Iran
| | - Karim Mahnam
- Faculty of Science, Department of Biology, Shahrekord University, Shahrekord, I.R. Iran
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33
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Kralj S, Jukič M, Bahun M, Kranjc L, Kolarič A, Hodošček M, Ulrih NP, Bren U. Identification of Triazolopyrimidinyl Scaffold SARS-CoV-2 Papain-Like Protease (PL pro) Inhibitor. Pharmaceutics 2024; 16:169. [PMID: 38399230 PMCID: PMC10893172 DOI: 10.3390/pharmaceutics16020169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
The global impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its companion disease, COVID-19, has reminded us of the importance of basic coronaviral research. In this study, a comprehensive approach using molecular docking, in vitro assays, and molecular dynamics simulations was applied to identify potential inhibitors for SARS-CoV-2 papain-like protease (PLpro), a key and underexplored viral enzyme target. A focused protease inhibitor library was initially created and molecular docking was performed using CmDock software (v0.2.0), resulting in the selection of hit compounds for in vitro testing on the isolated enzyme. Among them, compound 372 exhibited promising inhibitory properties against PLpro, with an IC50 value of 82 ± 34 μM. The compound also displayed a new triazolopyrimidinyl scaffold not yet represented within protease inhibitors. Molecular dynamics simulations demonstrated the favorable binding properties of compound 372. Structural analysis highlighted its key interactions with PLpro, and we stress its potential for further optimization. Moreover, besides compound 372 as a candidate for PLpro inhibitor development, this study elaborates on the PLpro binding site dynamics and provides a valuable contribution for further efforts in pan-coronaviral PLpro inhibitor development.
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Affiliation(s)
- Sebastjan Kralj
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova Ulica 17, SI-2000 Maribor, Slovenia
| | - Marko Jukič
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova Ulica 17, SI-2000 Maribor, Slovenia
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška Ulica 8, SI-6000 Koper, Slovenia
- Institute of Enviormental Protection and Sensors, Beloruska Ulica 7, SI-2000 Maribor, Slovenia
| | - Miha Bahun
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Luka Kranjc
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
- National Institute of Biology, Večna Pot 111, SI-1000 Ljubljana, Slovenia
| | - Anja Kolarič
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova Ulica 17, SI-2000 Maribor, Slovenia
| | - Milan Hodošček
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Nataša Poklar Ulrih
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Urban Bren
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova Ulica 17, SI-2000 Maribor, Slovenia
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška Ulica 8, SI-6000 Koper, Slovenia
- Institute of Enviormental Protection and Sensors, Beloruska Ulica 7, SI-2000 Maribor, Slovenia
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34
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Li J, Zhong X, Li H, Yu Z, Li J, Duan Q, Li Y, Chen F, Wang Y, Wu Z, Liu Y, Peng Z, Song D. Design, synthesis and biological evaluation of biaryl amide derivatives against SARS-CoV-2 with dual-target mechanism. Eur J Med Chem 2024; 264:115978. [PMID: 38061229 DOI: 10.1016/j.ejmech.2023.115978] [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: 09/07/2023] [Revised: 11/14/2023] [Accepted: 11/18/2023] [Indexed: 12/30/2023]
Abstract
The COVID-19 pandemic highlights the urgent need to develop effective small-molecule antivirals. Thirty-three novel biaryl amide derivatives were synthesized and evaluated for anti-coronaviral activity. Some significant SARs were uncovered and the intensive structure modifications led to the most active compounds 8b and 8h. The broad-spectrum anti-coronaviral effects of 8h were validated at RNA and protein levels. 8h inhibits coronavirus replication at multiple stages, from virus entry to virus dsRNA synthesis. The mechanism of action showed that 8h may simultaneously act on 3CLpro and TMPRSS2 to display anti-coronaviral effects. 8h combined with RdRp inhibitor showed synergistic inhibitory activity against coronavirus. This study confirmed that biaryl amide derivatives may be a new class of potential therapeutic agents against coronavirus with multiple target effect, worthy of further investigation.
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Affiliation(s)
- Jiayu Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Xiuli Zhong
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Hongying Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Zhihui Yu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Jianrui Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Qionglu Duan
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Yinghong Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Fenbei Chen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Yanxiang Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Zhiyun Wu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Yonghua Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| | - Zonggen Peng
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| | - Danqing Song
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
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35
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Gavilán E, Medina-Guzman R, Bahatyrevich-Kharitonik B, Ruano D. Protein Quality Control Systems and ER Stress as Key Players in SARS-CoV-2-Induced Neurodegeneration. Cells 2024; 13:123. [PMID: 38247815 PMCID: PMC10814689 DOI: 10.3390/cells13020123] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/03/2024] [Accepted: 01/08/2024] [Indexed: 01/23/2024] Open
Abstract
The COVID-19 pandemic has brought to the forefront the intricate relationship between SARS-CoV-2 and its impact on neurological complications, including potential links to neurodegenerative processes, characterized by a dysfunction of the protein quality control systems and ER stress. This review article explores the role of protein quality control systems, such as the Unfolded Protein Response (UPR), the Endoplasmic Reticulum-Associated Degradation (ERAD), the Ubiquitin-Proteasome System (UPS), autophagy and the molecular chaperones, in SARS-CoV-2 infection. Our hypothesis suggests that SARS-CoV-2 produces ER stress and exploits the protein quality control systems, leading to a disruption in proteostasis that cannot be solved by the host cell. This disruption culminates in cell death and may represent a link between SARS-CoV-2 and neurodegeneration.
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Affiliation(s)
- Elena Gavilán
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Sevilla (US), 41012 Sevilla, Spain; (R.M.-G.); (B.B.-K.); (D.R.)
- Instituto de Biomedicina de Sevilla, IBIS, Hospital Universitario Virgen del Rocío, Junta de Andalucía, CSIC, University of Seville (US), 41013 Sevilla, Spain
| | - Rafael Medina-Guzman
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Sevilla (US), 41012 Sevilla, Spain; (R.M.-G.); (B.B.-K.); (D.R.)
| | - Bazhena Bahatyrevich-Kharitonik
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Sevilla (US), 41012 Sevilla, Spain; (R.M.-G.); (B.B.-K.); (D.R.)
- Instituto de Biomedicina de Sevilla, IBIS, Hospital Universitario Virgen del Rocío, Junta de Andalucía, CSIC, University of Seville (US), 41013 Sevilla, Spain
| | - Diego Ruano
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Sevilla (US), 41012 Sevilla, Spain; (R.M.-G.); (B.B.-K.); (D.R.)
- Instituto de Biomedicina de Sevilla, IBIS, Hospital Universitario Virgen del Rocío, Junta de Andalucía, CSIC, University of Seville (US), 41013 Sevilla, Spain
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36
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Harding SD, Armstrong JF, Faccenda E, Southan C, Alexander SH, Davenport AP, Spedding M, Davies JA. The IUPHAR/BPS Guide to PHARMACOLOGY in 2024. Nucleic Acids Res 2024; 52:D1438-D1449. [PMID: 37897341 PMCID: PMC10767925 DOI: 10.1093/nar/gkad944] [Citation(s) in RCA: 84] [Impact Index Per Article: 84.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/09/2023] [Accepted: 10/18/2023] [Indexed: 10/30/2023] Open
Abstract
The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb; https://www.guidetopharmacology.org) is an open-access, expert-curated, online database that provides succinct overviews and key references for pharmacological targets and their recommended experimental ligands. It includes over 3039 protein targets and 12 163 ligand molecules, including approved drugs, small molecules, peptides and antibodies. Here, we report recent developments to the resource and describe expansion in content over the six database releases made during the last two years. The database update section of this paper focuses on two areas relating to important global health challenges. The first, SARS-CoV-2 COVID-19, remains a major concern and we describe our efforts to expand the database to include a new family of coronavirus proteins. The second area is antimicrobial resistance, for which we have extended our coverage of antibacterials in partnership with AntibioticDB, a collaboration that has continued through support from GARDP. We discuss other areas of curation and also focus on our external links to resources such as PubChem that bring important synergies to the resources.
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Affiliation(s)
- Simon D Harding
- Centre for Discovery Brain Science, Deanery of Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Jane F Armstrong
- Centre for Discovery Brain Science, Deanery of Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Elena Faccenda
- Centre for Discovery Brain Science, Deanery of Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Christopher Southan
- Centre for Discovery Brain Science, Deanery of Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Stephen P H Alexander
- School of Life Sciences, University of Nottingham Medical School, Nottingham NG7 2UH, UK
| | - Anthony P Davenport
- Experimental Medicine and Immunotherapeutics, University of Cambridge, Cambridge CB2 0QQ, UK
| | | | - Jamie A Davies
- Centre for Discovery Brain Science, Deanery of Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
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37
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Li X, Song Y. Targeting SARS-CoV-2 nonstructural protein 3: Function, structure, inhibition, and perspective in drug discovery. Drug Discov Today 2024; 29:103832. [PMID: 37977285 PMCID: PMC10872262 DOI: 10.1016/j.drudis.2023.103832] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/06/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
As a highly contagious human pathogen, severe acute respiratory syndrome-associated coronavirus-2 (SARS-CoV-2) has infected billions of people worldwide with more than 6 million deaths. With several effective vaccines and antiviral drugs now available, the SARS-CoV-2 pandemic been brought under control. However, a new pathogenic coronavirus could emerge in the future, given the zoonotic nature of this virus. Natural evolution and drug-induced mutations of SARS-CoV-2 also require continued efforts for new anti-coronavirus drugs. Nonstructural protein (nsp) 3 of CoVs is a large, multifunctional protein, containing a papain-like protease (PLpro) and a macrodomain (Mac1), which are essential for viral replication. Here, we provide a comprehensive review of the function, structure, and inhibition of SARS-CoV/-CoV-2 PLpro and Mac1. We also discuss advances in, and challenges to, the discovery of drugs against these targets.
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Affiliation(s)
- Xin Li
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA.
| | - Yongcheng Song
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA.
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38
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Yang M, Mariano J, Su R, Smith CE, Das S, Gill C, Andresson T, Loncarek J, Tsai YC, Weissman AM. SARS-CoV-2 papain-like protease plays multiple roles in regulating cellular proteins in the endoplasmic reticulum. J Biol Chem 2023; 299:105346. [PMID: 37838170 PMCID: PMC10692909 DOI: 10.1016/j.jbc.2023.105346] [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: 05/30/2023] [Revised: 10/01/2023] [Accepted: 10/03/2023] [Indexed: 10/16/2023] Open
Abstract
Nsp3s are the largest nonstructural proteins of coronaviruses. These transmembrane proteins include papain-like proteases (PLpro) that play essential roles in cleaving viral polyproteins into their mature units. The PLpro of SARS-CoV viruses also have deubiquitinating and deISGylating activities. As Nsp3 is an endoplasmic reticulum (ER)-localized protein, we asked if the deubiquitinating activity of SARS-CoV-2 PLpro affects proteins that are substrates for ER-associated degradation (ERAD). Using full-length Nsp3 as well as a truncated transmembrane form we interrogated, by coexpression, three potential ERAD substrates, all of which play roles in regulating lipid biosynthesis. Transmembrane PLpro increases the level of INSIG-1 and decreases its ubiquitination. However, different effects were seen with SREBP-1 and SREBP-2. Transmembrane PLpro cleaves SREBP-1 at three sites, including two noncanonical sites in the N-terminal half of the protein, resulting in a decrease in precursors of the active transcription factor. Conversely, cleavage of SREBP-2 occurs at a single canonical site that disrupts a C-terminal degron, resulting in increased SREBP-2 levels. When this site is mutated and the degron can no longer be interrupted, SREBP-2 is still stabilized by transmembrane PLpro, which correlates with a decrease in SREBP-2 ubiquitination. All of these observations are dependent on PLpro catalytic activity. Our findings demonstrate that, when anchored to the ER membrane, SARS-CoV-2 Nsp3 PLpro can function as a deubiquitinating enzyme to stabilize ERAD substrates. Additionally, SARS-CoV-2 Nsp3 PLpro can cleave ER-resident proteins, including at sites that could escape analyses based on the established consensus sequence.
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Affiliation(s)
- Mei Yang
- Cancer Innovation Laboratory, Center for Cancer Research, National Institutes of Health, Frederick, Maryland, USA
| | - Jennifer Mariano
- Cancer Innovation Laboratory, Center for Cancer Research, National Institutes of Health, Frederick, Maryland, USA
| | - Rebecca Su
- Cancer Innovation Laboratory, Center for Cancer Research, National Institutes of Health, Frederick, Maryland, USA
| | - Christopher E Smith
- Cancer Innovation Laboratory, Center for Cancer Research, National Institutes of Health, Frederick, Maryland, USA
| | - Sudipto Das
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Catherine Gill
- Cancer Innovation Laboratory, Center for Cancer Research, National Institutes of Health, Frederick, Maryland, USA
| | - Thorkell Andresson
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Jadranka Loncarek
- Cancer Innovation Laboratory, Center for Cancer Research, National Institutes of Health, Frederick, Maryland, USA
| | - Yien Che Tsai
- Cancer Innovation Laboratory, Center for Cancer Research, National Institutes of Health, Frederick, Maryland, USA
| | - Allan M Weissman
- Cancer Innovation Laboratory, Center for Cancer Research, National Institutes of Health, Frederick, Maryland, USA.
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Ghosh AK, Shahabi D, Imhoff MEC, Kovela S, Sharma A, Hattori SI, Higashi-Kuwata N, Mitsuya H, Mesecar AD. SARS-CoV-2 papain-like protease (PLpro) inhibitory and antiviral activity of small molecule derivatives for drug leads. Bioorg Med Chem Lett 2023; 96:129489. [PMID: 37770002 PMCID: PMC10842477 DOI: 10.1016/j.bmcl.2023.129489] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 10/03/2023]
Abstract
We report here the synthesis and biological evaluation of a series of small molecule SARS-CoV-2 PLpro inhibitors. We compared the activity of selected compounds in both SARS-CoV-1 and SARS-CoV-2 PLpro inhibitory and antiviral assays. We have synthesized and evaluated several new structural variants of previous leads against SARS-CoV-2 PLpro. The replacement of the carboxamide functionality with sulfonamide derivatives resulted in PLpro inhibitors with potent PLpro inhibitory and antiviral activity in VeroE6 cells similar to GRL0617. To obtain molecular insight, we created an optimized model of a potent sulfonamide derivative in the SARS-CoV-2 PLpro active site.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 USA.
| | - Dana Shahabi
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 USA
| | | | - Satish Kovela
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 USA
| | - Ashish Sharma
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 USA
| | - Shin-Ichiro Hattori
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine, Shinjuku, Tokyo 162-8655 Japan
| | - Nobuyo Higashi-Kuwata
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine, Shinjuku, Tokyo 162-8655 Japan
| | - Hiroaki Mitsuya
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine, Shinjuku, Tokyo 162-8655 Japan; Department of Clinical Sciences, Kumamoto University Hospital, Kumamoto 860-8556 Japan; Experimental Retrovirology Section, HIV and AIDS Malignancy Branch National Cancer Institute, Bethesda, MD 20892 USA
| | - Andrew D Mesecar
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907 USA
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Brewitz L, Henry Chan HT, Lukacik P, Strain-Damerell C, Walsh MA, Duarte F, Schofield CJ. Mass spectrometric assays monitoring the deubiquitinase activity of the SARS-CoV-2 papain-like protease inform on the basis of substrate selectivity and have utility for substrate identification. Bioorg Med Chem 2023; 95:117498. [PMID: 37857256 PMCID: PMC10933793 DOI: 10.1016/j.bmc.2023.117498] [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: 08/21/2023] [Revised: 10/07/2023] [Accepted: 10/10/2023] [Indexed: 10/21/2023]
Abstract
The SARS-CoV-2 papain-like protease (PLpro) and main protease (Mpro) are nucleophilic cysteine enzymes that catalyze hydrolysis of the viral polyproteins pp1a/1ab. By contrast with Mpro, PLpro is also a deubiquitinase (DUB) that accepts post-translationally modified human proteins as substrates. Here we report studies on the DUB activity of PLpro using synthetic Nε-lysine-branched oligopeptides as substrates that mimic post-translational protein modifications by ubiquitin (Ub) or Ub-like modifiers (UBLs), such as interferon stimulated gene 15 (ISG15). Mass spectrometry (MS)-based assays confirm the DUB activity of isolated recombinant PLpro. They reveal that the sequence of both the peptide fragment derived from the post-translationally modified protein and that derived from the UBL affects PLpro catalysis; the nature of substrate binding in the S sites appears to be more important for catalytic efficiency than binding in the S' sites. Importantly, the results reflect the reported cellular substrate selectivity of PLpro, i.e. human proteins conjugated to ISG15 are better substrates than those conjugated to Ub or other UBLs. The combined experimental and modelling results imply that PLpro catalysis is affected not only by the identity of the substrate residues binding in the S and S' sites, but also by the substrate fold and the conformational dynamics of the blocking loop 2 of the PLpro:substrate complex. Nε-Lysine-branched oligopeptides thus have potential to help the identification of PLpro substrates. More generally, the results imply that MS-based assays with Nε-lysine-branched oligopeptides have potential to monitor catalysis by human DUBs and hence to inform on their substrate preferences.
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Affiliation(s)
- Lennart Brewitz
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom; The Ineos Oxford Institute for Antimicrobial Research, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom.
| | - H T Henry Chan
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Petra Lukacik
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom; Research Complex at Harwell, Harwell Science and Innovation Campus, OX11 0FA Didcot, United Kingdom
| | - Claire Strain-Damerell
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom; Research Complex at Harwell, Harwell Science and Innovation Campus, OX11 0FA Didcot, United Kingdom
| | - Martin A Walsh
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom; Research Complex at Harwell, Harwell Science and Innovation Campus, OX11 0FA Didcot, United Kingdom
| | - Fernanda Duarte
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom; The Ineos Oxford Institute for Antimicrobial Research, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom.
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41
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Justo Arevalo S, Castillo-Chávez A, Uribe Calampa CS, Zapata Sifuentes D, Huallpa CJ, Landa Bianchi G, Garavito-Salini Casas R, Quiñones Aguilar M, Pineda Chavarría R. What do we know about the function of SARS-CoV-2 proteins? Front Immunol 2023; 14:1249607. [PMID: 37790934 PMCID: PMC10544941 DOI: 10.3389/fimmu.2023.1249607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/30/2023] [Indexed: 10/05/2023] Open
Abstract
The COVID-19 pandemic has highlighted the importance in the understanding of the biology of SARS-CoV-2. After more than two years since the first report of COVID-19, it remains crucial to continue studying how SARS-CoV-2 proteins interact with the host metabolism to cause COVID-19. In this review, we summarize the findings regarding the functions of the 16 non-structural, 6 accessory and 4 structural SARS-CoV-2 proteins. We place less emphasis on the spike protein, which has been the subject of several recent reviews. Furthermore, comprehensive reviews about COVID-19 therapeutic have been also published. Therefore, we do not delve into details on these topics; instead we direct the readers to those other reviews. To avoid confusions with what we know about proteins from other coronaviruses, we exclusively report findings that have been experimentally confirmed in SARS-CoV-2. We have identified host mechanisms that appear to be the primary targets of SARS-CoV-2 proteins, including gene expression and immune response pathways such as ribosome translation, JAK/STAT, RIG-1/MDA5 and NF-kβ pathways. Additionally, we emphasize the multiple functions exhibited by SARS-CoV-2 proteins, along with the limited information available for some of these proteins. Our aim with this review is to assist researchers and contribute to the ongoing comprehension of SARS-CoV-2's pathogenesis.
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Affiliation(s)
- Santiago Justo Arevalo
- Facultad de Ciencias Biológicas, Universidad Ricardo Palma, Lima, Peru
- Departmento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, São Paulo, Brazil
| | | | | | - Daniela Zapata Sifuentes
- Facultad de Ciencias Biológicas, Universidad Ricardo Palma, Lima, Peru
- Departmento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, São Paulo, Brazil
| | - César J. Huallpa
- Facultad de Ciencias, Universidad Nacional Agraria La Molina, Lima, Peru
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Bajaj T, Wehri E, Suryawanshi RK, King E, Pardeshi KS, Behrouzi K, Khodabakhshi Z, Schulze-Gahmen U, Kumar GR, Mofrad MRK, Nomura DK, Ott M, Schaletzky J, Murthy N. Mercapto-pyrimidines are reversible covalent inhibitors of the papain-like protease (PLpro) and inhibit SARS-CoV-2 (SCoV-2) replication. RSC Adv 2023; 13:17667-17677. [PMID: 37312993 PMCID: PMC10259201 DOI: 10.1039/d3ra01915b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/01/2023] [Indexed: 06/15/2023] Open
Abstract
The papain-like protease (PLpro) plays a critical role in SARS-CoV-2 (SCoV-2) pathogenesis and is essential for viral replication and for allowing the virus to evade the host immune response. Inhibitors of PLpro have great therapeutic potential, however, developing them has been challenging due to PLpro's restricted substrate binding pocket. In this report, we screened a 115 000-compound library for PLpro inhibitors and identified a new pharmacophore, based on a mercapto-pyrimidine fragment that is a reversible covalent inhibitor (RCI) of PLpro and inhibits viral replication in cells. Compound 5 had an IC50 of 5.1 μM for PLpro inhibition and hit optimization yielded a derivative with increased potency (IC50 0.85 μM, 6-fold higher). Activity based profiling of compound 5 demonstrated that it reacts with PLpro cysteines. We show here that compound 5 represents a new class of RCIs, which undergo an addition elimination reaction with cysteines in their target proteins. We further show that their reversibility is catalyzed by exogenous thiols and is dependent on the size of the incoming thiol. In contrast, traditional RCIs are all based upon the Michael addition reaction mechanism and their reversibility is base-catalyzed. We identify a new class of RCIs that introduces a more reactive warhead with a pronounced selectivity profile based on thiol ligand size. This could allow the expansion of RCI modality use towards a larger group of proteins important for human disease.
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Affiliation(s)
- Teena Bajaj
- Graduate Program of Comparative Biochemistry, University of California Berkeley CA USA
| | - Eddie Wehri
- The Henry Wheeler Center of Emerging and Neglected Diseases 344 Li Ka Shing Berkeley CA USA
| | | | - Elizabeth King
- Chemical Biology Graduate Program, University of California Berkeley CA USA
| | | | - Kamyar Behrouzi
- Department of Mechanical Engineering, University of California Berkeley CA USA
| | | | | | - G Renuka Kumar
- Gladstone Institute of Virology Gladstone Institutes San Francisco CA USA
| | | | - Daniel K Nomura
- Department of Chemistry, University of California Berkeley CA USA
| | - Melanie Ott
- Gladstone Institute of Virology Gladstone Institutes San Francisco CA USA
- Department of Medicine, University of California San Francisco CA USA
- Chan Zuckerberg Biohub San Francisco CA USA
| | - Julia Schaletzky
- The Henry Wheeler Center of Emerging and Neglected Diseases 344 Li Ka Shing Berkeley CA USA
| | - Niren Murthy
- Department of Bioengineering, University of California Berkeley CA USA
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43
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Zhao M, Zhang M, Yang Z, Zhou Z, Huang J, Zhao B. Role of E3 ubiquitin ligases and deubiquitinating enzymes in SARS-CoV-2 infection. Front Cell Infect Microbiol 2023; 13:1217383. [PMID: 37360529 PMCID: PMC10288995 DOI: 10.3389/fcimb.2023.1217383] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 05/29/2023] [Indexed: 06/28/2023] Open
Abstract
Ever since its emergence in 2019, COVID-19 has rapidly disseminated worldwide, engendering a pervasive pandemic that has profoundly impacted healthcare systems and the socio-economic milieu. A plethora of studies has been conducted targeting its pathogenic virus, SARS-CoV-2, to find ways to combat COVID-19. The ubiquitin-proteasome system (UPS) is widely recognized as a crucial mechanism that regulates human biological activities by maintaining protein homeostasis. Within the UPS, the ubiquitination and deubiquitination, two reversible modifications, of substrate proteins have been extensively studied and implicated in the pathogenesis of SARS-CoV-2. The regulation of E3 ubiquitin ligases and DUBs(Deubiquitinating enzymes), which are key enzymes involved in the two modification processes, determines the fate of substrate proteins. Proteins associated with the pathogenesis of SARS-CoV-2 may be retained, degraded, or even activated, thus affecting the ultimate outcome of the confrontation between SARS-CoV-2 and the host. In other words, the clash between SARS-CoV-2 and the host can be viewed as a battle for dominance over E3 ubiquitin ligases and DUBs, from the standpoint of ubiquitin modification regulation. This review primarily aims to clarify the mechanisms by which the virus utilizes host E3 ubiquitin ligases and DUBs, along with its own viral proteins that have similar enzyme activities, to facilitate invasion, replication, escape, and inflammation. We believe that gaining a better understanding of the role of E3 ubiquitin ligases and DUBs in COVID-19 can offer novel and valuable insights for developing antiviral therapies.
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Affiliation(s)
- Mingjiu Zhao
- National Clinical Research Center for Metabolic Diseases, Metabolic Syndrome Research Center, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Mengdi Zhang
- National Clinical Research Center for Metabolic Diseases, Metabolic Syndrome Research Center, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Zhou Yang
- National Clinical Research Center for Metabolic Diseases, Metabolic Syndrome Research Center, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Zhiguang Zhou
- National Clinical Research Center for Metabolic Diseases, Metabolic Syndrome Research Center, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Jiaqi Huang
- National Clinical Research Center for Metabolic Diseases, Metabolic Syndrome Research Center, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Xiangya School of Public Health, Central South University, Changsha, China
| | - Bin Zhao
- National Clinical Research Center for Metabolic Diseases, Metabolic Syndrome Research Center, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Furong Laboratory, Central South University, Changsha, China
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Zmudzinski M, Rut W, Olech K, Granda J, Giurg M, Burda-Grabowska M, Kaleta R, Zgarbova M, Kasprzyk R, Zhang L, Sun X, Lv Z, Nayak D, Kesik-Brodacka M, Olsen SK, Weber J, Hilgenfeld R, Jemielity J, Drag M. Ebselen derivatives inhibit SARS-CoV-2 replication by inhibition of its essential proteins: PL pro and M pro proteases, and nsp14 guanine N7-methyltransferase. Sci Rep 2023; 13:9161. [PMID: 37280236 DOI: 10.1038/s41598-023-35907-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/25/2023] [Indexed: 06/08/2023] Open
Abstract
Proteases encoded by SARS-CoV-2 constitute a promising target for new therapies against COVID-19. SARS-CoV-2 main protease (Mpro, 3CLpro) and papain-like protease (PLpro) are responsible for viral polyprotein cleavage-a process crucial for viral survival and replication. Recently it was shown that 2-phenylbenzisoselenazol-3(2H)-one (ebselen), an organoselenium anti-inflammatory small-molecule drug, is a potent, covalent inhibitor of both the proteases and its potency was evaluated in enzymatic and antiviral assays. In this study, we screened a collection of 34 ebselen and ebselen diselenide derivatives for SARS-CoV-2 PLpro and Mpro inhibitors. Our studies revealed that ebselen derivatives are potent inhibitors of both the proteases. We identified three PLpro and four Mpro inhibitors superior to ebselen. Independently, ebselen was shown to inhibit the N7-methyltransferase activity of SARS-CoV-2 nsp14 protein involved in viral RNA cap modification. Hence, selected compounds were also evaluated as nsp14 inhibitors. In the second part of our work, we employed 11 ebselen analogues-bis(2-carbamoylaryl)phenyl diselenides-in biological assays to evaluate their anti-SARS-CoV-2 activity in Vero E6 cells. We present their antiviral and cytoprotective activity and also low cytotoxicity. Our work shows that ebselen, its derivatives, and diselenide analogues constitute a promising platform for development of new antivirals targeting the SARS-CoV-2 virus.
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Affiliation(s)
- Mikolaj Zmudzinski
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland.
| | - Wioletta Rut
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Kamila Olech
- Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Jarosław Granda
- Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Mirosław Giurg
- Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Małgorzata Burda-Grabowska
- Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Rafał Kaleta
- Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Michala Zgarbova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nám. 2, 16610, Prague, Czech Republic
| | - Renata Kasprzyk
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland
| | - Linlin Zhang
- Institute of Molecular Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Xinyuanyuan Sun
- Institute of Molecular Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Zongyang Lv
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Digant Nayak
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | | | - Shaun K Olsen
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Jan Weber
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nám. 2, 16610, Prague, Czech Republic
| | - Rolf Hilgenfeld
- Institute of Molecular Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, 23562, Lübeck, Germany
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland
| | - Marcin Drag
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland.
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45
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Xue Y, Mei H, Chen Y, Griffin JD, Liu Q, Weisberg E, Yang J. Repurposing clinically available drugs and therapies for pathogenic targets to combat SARS-CoV-2. MedComm (Beijing) 2023; 4:e254. [PMID: 37193304 PMCID: PMC10183156 DOI: 10.1002/mco2.254] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/11/2023] [Accepted: 03/07/2023] [Indexed: 05/18/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has affected a large portion of the global population, both physically and mentally. Current evidence suggests that the rapidly evolving coronavirus subvariants risk rendering vaccines and antibodies ineffective due to their potential to evade existing immunity, with enhanced transmission activity and higher reinfection rates that could lead to new outbreaks across the globe. The goal of viral management is to disrupt the viral life cycle as well as to relieve severe symptoms such as lung damage, cytokine storm, and organ failure. In the fight against viruses, the combination of viral genome sequencing, elucidation of the structure of viral proteins, and identifying proteins that are highly conserved across multiple coronaviruses has revealed many potential molecular targets. In addition, the time- and cost-effective repurposing of preexisting antiviral drugs or approved/clinical drugs for these targets offers considerable clinical advantages for COVID-19 patients. This review provides a comprehensive overview of various identified pathogenic targets and pathways as well as corresponding repurposed approved/clinical drugs and their potential against COVID-19. These findings provide new insight into the discovery of novel therapeutic strategies that could be applied to the control of disease symptoms emanating from evolving SARS-CoV-2 variants.
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Affiliation(s)
- Yiying Xue
- Department of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Husheng Mei
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical ScienceChinese Academy of SciencesHefeiChina
- University of Science and Technology of ChinaHefeiAnhuiChina
| | - Yisa Chen
- Department of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - James D. Griffin
- Department of Medical Oncology, Dana‐Farber Cancer InstituteBostonMassachusettsUSA
- Department of Medicine, Harvard Medical SchoolBostonMassachusettsUSA
| | - Qingsong Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical ScienceChinese Academy of SciencesHefeiChina
- University of Science and Technology of ChinaHefeiAnhuiChina
- Hefei Cancer HospitalChinese Academy of SciencesHefeiChina
| | - Ellen Weisberg
- Department of Medical Oncology, Dana‐Farber Cancer InstituteBostonMassachusettsUSA
- Department of Medicine, Harvard Medical SchoolBostonMassachusettsUSA
| | - Jing Yang
- Department of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical ScienceChinese Academy of SciencesHefeiChina
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46
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Zhang Z, Zhang H, Zhang Y, Zhang Q, Liu Q, Hu Y, Chen X, Wang J, Shi Y, Deng C, Gong P, Zhang B, Li X, Zhu B, Ye H. Oridonin inhibits SARS-CoV-2 replication by targeting viral proteinase and polymerase. Virol Sin 2023; 38:470-479. [PMID: 37127212 PMCID: PMC10148713 DOI: 10.1016/j.virs.2023.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 04/27/2023] [Indexed: 05/03/2023] Open
Abstract
COVID-19 has become a global public health crisis since its outbreak in China in December 2019. Currently there are few clinically effective drugs to combat SARS-CoV-2 infection. The main protein (Mpro), papain-like protease (PLpro) and RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 are involved in the viral replication, and might be prospective targets for anti-coronavirus drug development. Here, we investigated the antiviral activity of oridonin, a natural small-molecule compound, against SARS-CoV-2 infection in vitro. The time-of-addition analysis showed that oridonin efficiently inhibited SARS-CoV-2 infection by interfering with the genome replication at the post-entry stage. Mechanistically, the inhibition of viral replication by oridonin depends on the oxidation activity of α, β-unsaturated carbonyl. Further experiments showed that oridonin not only effectively inhibited SARS-CoV-2 Mpro activity, but also had some inhibitory effects on PLpro-mediated deubiquitinating and viral polymerase-catalyzed RNA elongation activities at high concentrations. In particular, oridonin could inhibit the bat SARS-like CoV and the newly emerged SARS-CoV-2 omicron variants (BA.1 and BA.2), which highlights its potential as a pan-coronavirus antiviral agent. Overall, our data provide strong evidence that oridonin is an efficient antiviral agent against SARS-CoV-2 infection.
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Affiliation(s)
- Zherui Zhang
- Virus Laboratory, Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China; Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Hongqing Zhang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanan Zhang
- Virus Laboratory, Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China; Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Qiuyan Zhang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Qiaojie Liu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yanyan Hu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoling Chen
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Wang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yujia Shi
- Hunan Normal University, School of Medicine, Changsha, 410081, China
| | - Chenglin Deng
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Peng Gong
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bo Zhang
- Virus Laboratory, Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China; Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xiaodan Li
- Hunan Normal University, School of Medicine, Changsha, 410081, China.
| | - Bing Zhu
- Virus Laboratory, Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China.
| | - Hanqing Ye
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China.
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47
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Falqui M, Perdiguero B, Coloma R, Albert M, Marcos-Villar L, McGrail JP, Sorzano CÓS, Esteban M, Gómez CE, Guerra S. An MVA-based vector expressing cell-free ISG15 increases IFN-I production and improves HIV-1-specific CD8 T cell immune responses. Front Cell Infect Microbiol 2023; 13:1187193. [PMID: 37313341 PMCID: PMC10258332 DOI: 10.3389/fcimb.2023.1187193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 04/17/2023] [Indexed: 06/15/2023] Open
Abstract
The human immunodeficiency virus (HIV), responsible of the Acquired Immune Deficiency Syndrome (AIDS), continues to be a major global public health issue with any cure or vaccine available. The Interferon-stimulated gene 15 (ISG15) encodes a ubiquitin-like protein that is induced by interferons and plays a critical role in the immune response. ISG15 is a modifier protein that covalently binds to its targets via a reversible bond, a process known as ISGylation, which is the best-characterized activity of this protein to date. However, ISG15 can also interact with intracellular proteins via non-covalent binding or act as a cytokine in the extracellular space after secretion. In previous studies we proved the adjuvant effect of ISG15 when delivered by a DNA-vector in heterologous prime-boost combination with a Modified Vaccinia virus Ankara (MVA)-based recombinant virus expressing HIV-1 antigens Env/Gag-Pol-Nef (MVA-B). Here we extended these results evaluating the adjuvant effect of ISG15 when expressed by an MVA vector. For this, we generated and characterized two novel MVA recombinants expressing different forms of ISG15, the wild-type ISG15GG (able to perform ISGylation) or the mutated ISG15AA (unable to perform ISGylation). In mice immunized with the heterologous DNA prime/MVA boost regimen, the expression of the mutant ISG15AA from MVA-Δ3-ISG15AA vector in combination with MVA-B induced an increase in the magnitude and quality of HIV-1-specific CD8 T cells as well as in the levels of IFN-I released, providing a better immunostimulatory activity than the wild-type ISG15GG. Our results confirm the importance of ISG15 as an immune adjuvant in the vaccine field and highlights its role as a potential relevant component in HIV-1 immunization protocols.
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Affiliation(s)
- Michela Falqui
- Department of Preventive Medicine, Public Health and Microbiology, Universidad Autónoma de Madrid, Madrid, Spain
| | - Beatriz Perdiguero
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Rocio Coloma
- Department of Preventive Medicine, Public Health and Microbiology, Universidad Autónoma de Madrid, Madrid, Spain
| | - Manuel Albert
- Department of Preventive Medicine, Public Health and Microbiology, Universidad Autónoma de Madrid, Madrid, Spain
| | - Laura Marcos-Villar
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Joseph Patrick McGrail
- Department of Preventive Medicine, Public Health and Microbiology, Universidad Autónoma de Madrid, Madrid, Spain
| | - Carlos Óscar S. Sorzano
- Biocomputing Unit and Computational Genomics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Mariano Esteban
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Carmen Elena Gómez
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Susana Guerra
- Department of Preventive Medicine, Public Health and Microbiology, Universidad Autónoma de Madrid, Madrid, Spain
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48
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Wang Q, Chen G, He J, Li J, Xiong M, Su H, Li M, Hu H, Xu Y. Structure-Based Design of Potent Peptidomimetic Inhibitors Covalently Targeting SARS-CoV-2 Papain-like Protease. Int J Mol Sci 2023; 24:ijms24108633. [PMID: 37239980 DOI: 10.3390/ijms24108633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/05/2023] [Accepted: 05/07/2023] [Indexed: 05/28/2023] Open
Abstract
The papain-like protease (PLpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays a critical role in the proteolytic processing of viral polyproteins and the dysregulation of the host immune response, providing a promising therapeutic target. Here, we report the structure-guide design of novel peptidomimetic inhibitors covalently targeting SARS-CoV-2 PLpro. The resulting inhibitors demonstrate submicromolar potency in the enzymatic assay (IC50 = 0.23 μM) and significant inhibition of SARS-CoV-2 PLpro in the HEK293T cells using a cell-based protease assay (EC50 = 3.61 μM). Moreover, an X-ray crystal structure of SARS-CoV-2 PLpro in complex with compound 2 confirms the covalent binding of the inhibitor to the catalytic residue cysteine 111 (C111) and emphasizes the importance of interactions with tyrosine 268 (Y268). Together, our findings reveal a new scaffold of SARS-CoV-2 PLpro inhibitors and provide an attractive starting point for further optimization.
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Affiliation(s)
- Qian Wang
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Guofeng Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian He
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiameng Li
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Muya Xiong
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haixia Su
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Minjun Li
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Hangchen Hu
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Yechun Xu
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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49
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Shao Q, Xiong M, Li J, Hu H, Su H, Xu Y. Unraveling the catalytic mechanism of SARS-CoV-2 papain-like protease with allosteric modulation of C270 mutation using multiscale computational approaches. Chem Sci 2023; 14:4681-4696. [PMID: 37181765 PMCID: PMC10171076 DOI: 10.1039/d3sc00166k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/10/2023] [Indexed: 05/16/2023] Open
Abstract
Papain-like protease (PLpro) is a promising therapeutic target against SARS-CoV-2, but its restricted S1/S2 subsites pose an obstacle in developing active site-directed inhibitors. We have recently identified C270 as a novel covalent allosteric site for SARS-CoV-2 PLpro inhibitors. Here we present a theoretical investigation of the proteolysis reaction catalyzed by the wild-type SARS-CoV-2 PLpro as well as the C270R mutant. Enhanced sampling MD simulations were first performed to explore the influence of C270R mutation on the protease dynamics, and sampled thermodynamically favorable conformations were then submitted to MM/PBSA and QM/MM MD simulations for thorough characterization of the protease-substrate binding and covalent reactions. The disclosed proteolysis mechanism of PLpro, as characterized by the occurrence of proton transfer from the catalytic C111 to H272 prior to the substrate binding and with deacylation being the rate-determining step of the whole proteolysis process, is not completely identical to that of the 3C-like protease, another key cysteine protease of coronaviruses. The C270R mutation alters the structural dynamics of the BL2 loop that indirectly impairs the catalytic function of H272 and reduces the binding of the substrate with the protease, ultimately showing an inhibitory effect on PLpro. Together, these results provide a comprehensive understanding at the atomic level of the key aspects of SARS-CoV-2 PLpro proteolysis, including the catalytic activity allosterically regulated by C270 modification, which is crucial to the follow-up inhibitor design and development.
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Affiliation(s)
- Qiang Shao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Muya Xiong
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Jiameng Li
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Hangchen Hu
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences Hangzhou 310024 China
| | - Haixia Su
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
| | - Yechun Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
- University of Chinese Academy of Sciences Beijing 100049 China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine Nanjing 210023 China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences Hangzhou 310024 China
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50
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Kattula B, Reddi B, Jangam A, Naik L, Adimoolam BM, Vavilapalli S, Are S, Thota JR, Jadav SS, Arifuddin M, Addlagatta A. Development of 2-chloroquinoline based heterocyclic frameworks as dual inhibitors of SARS-CoV-2 M Pro and PL Pro. Int J Biol Macromol 2023; 242:124772. [PMID: 37172706 PMCID: PMC10171901 DOI: 10.1016/j.ijbiomac.2023.124772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 04/21/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023]
Abstract
Evolution of new variants of SARS-CoV-2 warrant the need for the continued efforts in identifying target-oriented new drugs. Dual targeting agents against MPro and PLPro not only overcome the incomplete efficacy but also the drug resistance, which is common problem. Since both these are cysteine proteases, we designed 2-chloroquinoline based molecules with additional imine moiety in the middle as possible nucleophilic warheads. In the first round of design and synthesis, three molecules (C3, C4 and C5) inhibited (Ki < 2 μM) only MPro by binding covalently to C145 and one molecule (C10) inhibited both the proteases non-covalently (Ki < 2 μM) with negligible cytotoxicity. Further conversion of the imine in C10 to azetidinone (C11) improved the potency against both the enzymes in the nanomolar range (820 nM against MPro and 350 nM against PLPro) with no cytotoxicity. Conversion of imine to thiazolidinone (C12), reduced the inhibition by 3-5 folds against both the enzymes. Biochemical and computational studies suggest that C10-C12 bind in the substrate binding pocket of MPro and in the BL2 loop of the PLPro. Since these dual inhibitors have least cytotoxicity, they could be further explored as therapeutics against the SARS-CoV-2 and other analogous viruses.
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Affiliation(s)
- Bhavita Kattula
- Division of Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Rafi Marg, New Delhi 110001, India
| | - Bharati Reddi
- Division of Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Rafi Marg, New Delhi 110001, India
| | - Aruna Jangam
- Division of Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Rafi Marg, New Delhi 110001, India
| | - Lekhika Naik
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500 037, Telangana, India
| | - Bala Manikanta Adimoolam
- Analytical and Structural Chemistry Department, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Rafi Marg, New Delhi 110001, India
| | - Suresh Vavilapalli
- Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Rafi Marg, New Delhi 110001, India
| | - Sayanna Are
- Division of Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, Telangana, India
| | - Jagadeshwar Reddy Thota
- Analytical and Structural Chemistry Department, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, Telangana, India; Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, Telangana, India
| | - Surender Singh Jadav
- Department of Natural Products and Medicinal Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Rafi Marg, New Delhi 110001, India.
| | - Mohammed Arifuddin
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500 037, Telangana, India.
| | - Anthony Addlagatta
- Division of Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Rafi Marg, New Delhi 110001, India.
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