1
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Wu X, Go M, Nguyen JV, Kuchel NW, Lu BGC, Zeglinski K, Lowes KN, Calleja DJ, Mitchell JP, Lessene G, Komander D, Call ME, Call MJ. Mutational profiling of SARS-CoV-2 papain-like protease reveals requirements for function, structure, and drug escape. Nat Commun 2024; 15:6219. [PMID: 39043718 PMCID: PMC11266423 DOI: 10.1038/s41467-024-50566-9] [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: 02/24/2024] [Accepted: 07/12/2024] [Indexed: 07/25/2024] Open
Abstract
Papain-like protease (PLpro) is an attractive drug target for SARS-CoV-2 because it is essential for viral replication, cleaving viral poly-proteins pp1a and pp1ab, and has de-ubiquitylation and de-ISGylation activities, affecting innate immune responses. We employ Deep Mutational Scanning to evaluate the mutational effects on PLpro enzymatic activity and protein stability in mammalian cells. We confirm features of the active site and identify mutations in neighboring residues that alter activity. We characterize residues responsible for substrate binding and demonstrate that although residues in the blocking loop are remarkably tolerant to mutation, blocking loop flexibility is important for function. We additionally find a connected network of mutations affecting activity that extends far from the active site. We leverage our library to identify drug-escape variants to a common PLpro inhibitor scaffold and predict that plasticity in both the S4 pocket and blocking loop sequence should be considered during the drug design process.
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Affiliation(s)
- Xinyu Wu
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Margareta Go
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Julie V Nguyen
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Nathan W Kuchel
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Bernadine G C Lu
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Kathleen Zeglinski
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Kym N Lowes
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Dale J Calleja
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Jeffrey P Mitchell
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Guillaume Lessene
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, Australia
| | - David Komander
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Matthew E Call
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Melissa J Call
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.
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2
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Castillo-Campos L, Velázquez-Libera JL, Caballero J. Computational study of the binding orientation and affinity of noncovalent inhibitors of the papain-like protease (PLpro) from SARS-CoV-1 considering the protein flexibility by using molecular dynamics and cross-docking. Front Mol Biosci 2023; 10:1215499. [PMID: 37426421 PMCID: PMC10326900 DOI: 10.3389/fmolb.2023.1215499] [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: 05/03/2023] [Accepted: 06/12/2023] [Indexed: 07/11/2023] Open
Abstract
The papain-like protease (PLpro) from zoonotic coronaviruses (CoVs) has been identified as a target with an essential role in viral respiratory diseases caused by Severe Acute Respiratory Syndrome-associated coronaviruses (SARS-CoVs). The design of PLpro inhibitors has been proposed as an alternative to developing potential drugs against this disease. In this work, 67 naphthalene-derived compounds as noncovalent PLpro inhibitors were studied using molecular modeling methods. Structural characteristics of the bioactive conformations of these inhibitors and their interactions at the SARS-CoV-1 PLpro binding site were reported here in detail, taking into account the flexibility of the protein residues. Firstly, a molecular docking protocol was used to obtain the orientations of the inhibitors. After this, the orientations were compared, and the recurrent interactions between the PLpro residues and ligand chemical groups were described (with LigRMSD and interaction fingerprints methods). In addition, efforts were made to find correlations between docking energy values and experimentally determined binding affinities. For this, the PLpro was sampled by using Gaussian Accelerated Molecular Dynamics (GaMD), generating multiple conformations of the binding site. Diverse protein conformations were selected and a cross-docking experiment was performed, yielding models of the 67 naphthalene-derived compounds adopting different binding modes. Representative complexes for each ligand were selected to obtain the highest correlation between docking energies and activities. A good correlation (R 2 = 0.948) was found when this flexible docking protocol was performed.
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Affiliation(s)
| | | | - Julio Caballero
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, Talca, Chile
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3
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Castillo G, Mora-Díaz JC, Breuer M, Singh P, Nelli RK, Giménez-Lirola LG. Molecular mechanisms of human coronavirus NL63 infection and replication. Virus Res 2023; 327:199078. [PMID: 36813239 PMCID: PMC9944649 DOI: 10.1016/j.virusres.2023.199078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023]
Abstract
Human coronavirus NL63 (HCoV-NL63) is spread globally, causing upper and lower respiratory tract infections mainly in young children. HCoV-NL63 shares a host receptor (ACE2) with severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 but, unlike them, HCoV-NL63 primarily develops into self-limiting mild to moderate respiratory disease. Although with different efficiency, both HCoV-NL63 and SARS-like CoVs infect ciliated respiratory cells using ACE2 as receptor for binding and cell entry. Working with SARS-like CoVs require access to BSL-3 facilities, while HCoV-NL63 research can be performed at BSL-2 laboratories. Thus, HCoV-NL63 could be used as a safer surrogate for comparative studies on receptor dynamics, infectivity and virus replication, disease mechanism, and potential therapeutic interventions against SARS-like CoVs. This prompted us to review the current knowledge on the infection mechanism and replication of HCoV-NL63. Specifically, after a brief overview on the taxonomy, genomic organization and virus structure, this review compiles the current HCoV-NL63-related research in virus entry and replication mechanism, including virus attachment, endocytosis, genome translation, and replication and transcription. Furthermore, we reviewed cumulative knowledge on the susceptibility of different cells to HCoV-NL63 infection in vitro, which is essential for successful virus isolation and propagation, and contribute to address different scientific questions from basic science to the development and assessment of diagnostic tools, and antiviral therapies. Finally, we discussed different antiviral strategies that have been explored to suppress replication of HCoV-NL63, and other related human coronaviruses, by either targeting the virus or enhancing host antiviral mechanisms.
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Affiliation(s)
- Gino Castillo
- Department of Veterinary Diagnostic and Production Animal Medicine, Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA
| | - Juan Carlos Mora-Díaz
- Department of Veterinary Diagnostic and Production Animal Medicine, Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA
| | - Mary Breuer
- Department of Veterinary Diagnostic and Production Animal Medicine, Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA
| | - Pallavi Singh
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL 60115, USA
| | - Rahul K Nelli
- Department of Veterinary Diagnostic and Production Animal Medicine, Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA
| | - Luis G Giménez-Lirola
- Department of Veterinary Diagnostic and Production Animal Medicine, Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA.
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4
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Gumede NJ. Pathfinder-Driven Chemical Space Exploration and Multiparameter Optimization in Tandem with Glide/IFD and QSAR-Based Active Learning Approach to Prioritize Design Ideas for FEP+ Calculations of SARS-CoV-2 PL pro Inhibitors. Molecules 2022; 27:8569. [PMID: 36500659 PMCID: PMC9741453 DOI: 10.3390/molecules27238569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/25/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
A global pandemic caused by the SARS-CoV-2 virus that started in 2020 and has wreaked havoc on humanity still ravages up until now. As a result, the negative impact of travel restrictions and lockdowns has underscored the importance of our preparedness for future pandemics. The main thrust of this work was based on addressing this need by traversing chemical space to design inhibitors that target the SARS-CoV-2 papain-like protease (PLpro). Pathfinder-based retrosynthesis analysis was used to generate analogs of GRL-0617 using commercially available building blocks by replacing the naphthalene moiety. A total of 10 models were built using active learning QSAR, which achieved good statistical results such as an R2 > 0.70, Q2 > 0.64, STD Dev < 0.30, and RMSE < 0.31, on average for all models. A total of 35 ideas were further prioritized for FEP+ calculations. The FEP+ results revealed that compound 45 was the most active compound in this series with a ΔG of −7.28 ± 0.96 kcal/mol. Compound 5 exhibited a ΔG of −6.78 ± 1.30 kcal/mol. The inactive compounds in this series were compound 91 and compound 23 with a ΔG of −5.74 ± 1.06 and −3.11 ± 1.45 kcal/mol. The combined strategy employed here is envisaged to be of great utility in multiparameter lead optimization efforts, to traverse chemical space, maintaining and/or improving the potency as well as the property space of synthetically aware design ideas.
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Affiliation(s)
- Njabulo Joyfull Gumede
- Department of Chemistry, Mangosuthu University of Technology, P.O. Box 12363, Jacobs 4026, South Africa
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5
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Tomazou M, Bourdakou MM, Minadakis G, Zachariou M, Oulas A, Karatzas E, Loizidou EM, Kakouri AC, Christodoulou CC, Savva K, Zanti M, Onisiforou A, Afxenti S, Richter J, Christodoulou CG, Kyprianou T, Kolios G, Dietis N, Spyrou GM. Multi-omics data integration and network-based analysis drives a multiplex drug repurposing approach to a shortlist of candidate drugs against COVID-19. Brief Bioinform 2021; 22:bbab114. [PMID: 34009288 PMCID: PMC8135326 DOI: 10.1093/bib/bbab114] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 02/01/2021] [Accepted: 03/13/2021] [Indexed: 02/06/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is undeniably the most severe global health emergency since the 1918 Influenza outbreak. Depending on its evolutionary trajectory, the virus is expected to establish itself as an endemic infectious respiratory disease exhibiting seasonal flare-ups. Therefore, despite the unprecedented rally to reach a vaccine that can offer widespread immunization, it is equally important to reach effective prevention and treatment regimens for coronavirus disease 2019 (COVID-19). Contributing to this effort, we have curated and analyzed multi-source and multi-omics publicly available data from patients, cell lines and databases in order to fuel a multiplex computational drug repurposing approach. We devised a network-based integration of multi-omic data to prioritize the most important genes related to COVID-19 and subsequently re-rank the identified candidate drugs. Our approach resulted in a highly informed integrated drug shortlist by combining structural diversity filtering along with experts' curation and drug-target mapping on the depicted molecular pathways. In addition to the recently proposed drugs that are already generating promising results such as dexamethasone and remdesivir, our list includes inhibitors of Src tyrosine kinase (bosutinib, dasatinib, cytarabine and saracatinib), which appear to be involved in multiple COVID-19 pathophysiological mechanisms. In addition, we highlight specific immunomodulators and anti-inflammatory drugs like dactolisib and methotrexate and inhibitors of histone deacetylase like hydroquinone and vorinostat with potential beneficial effects in their mechanisms of action. Overall, this multiplex drug repurposing approach, developed and utilized herein specifically for SARS-CoV-2, can offer a rapid mapping and drug prioritization against any pathogen-related disease.
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Affiliation(s)
- Marios Tomazou
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Cyprus
- The Cyprus School of Molecular Medicine, Cyprus
- Neurogenetics Department, The Cyprus Institute of Neurology and Genetics, Cyprus
| | - Marilena M Bourdakou
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Cyprus
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, Greece
| | - George Minadakis
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Cyprus
- The Cyprus School of Molecular Medicine, Cyprus
| | - Margarita Zachariou
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Cyprus
- The Cyprus School of Molecular Medicine, Cyprus
| | - Anastasis Oulas
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Cyprus
- The Cyprus School of Molecular Medicine, Cyprus
| | - Evangelos Karatzas
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Cyprus
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, Vari, Greece
| | - Eleni M Loizidou
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Cyprus
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, Vari, Greece
| | - Andrea C Kakouri
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Cyprus
- The Cyprus School of Molecular Medicine, Cyprus
- Neurogenetics Department, The Cyprus Institute of Neurology and Genetics, Cyprus
| | - Christiana C Christodoulou
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Cyprus
- The Cyprus School of Molecular Medicine, Cyprus
- Neuroepidemiology Department, The Cyprus Institute of Neurology and Genetics, Cyprus
| | - Kyriaki Savva
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Cyprus
- The Cyprus School of Molecular Medicine, Cyprus
| | - Maria Zanti
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Cyprus
- The Cyprus School of Molecular Medicine, Cyprus
- Cancer Genetics, Therapeutics … Ultrastructural Pathology, The Cyprus Institute of Neurology and Genetics, Cyprus
| | - Anna Onisiforou
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Cyprus
- The Cyprus School of Molecular Medicine, Cyprus
| | - Sotiroula Afxenti
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Cyprus
- The Cyprus School of Molecular Medicine, Cyprus
- Neuroimmunology Department, The Cyprus Institute of Neurology and Genetics, Cyprus
| | - Jan Richter
- Department of Molecular Virology, The Cyprus Institute of Neurology and Genetics, Cyprus
- The Cyprus School of Molecular Medicine, Cyprus
| | - Christina G Christodoulou
- Department of Molecular Virology, The Cyprus Institute of Neurology and Genetics, Cyprus
- The Cyprus School of Molecular Medicine, Cyprus
| | - Theodoros Kyprianou
- Medical School, University of Nicosia, Cyprus
- University Hospitals Bristol and Weston NHS Foundation Trust, United Kingdom
| | - George Kolios
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, Greece
| | - Nikolas Dietis
- Experimental Pharmacology Laboratory, Medical School, University of Cyprus, Cyprus
| | - George M Spyrou
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Cyprus
- The Cyprus School of Molecular Medicine, Cyprus
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6
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Joshi S, Joshi M, Degani MS. Tackling SARS-CoV-2: proposed targets and repurposed drugs. Future Med Chem 2020; 12:1579-1601. [PMID: 32564623 PMCID: PMC7307730 DOI: 10.4155/fmc-2020-0147] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/03/2020] [Indexed: 12/15/2022] Open
Abstract
The SARS-CoV-2 pandemic, declared as a global health emergency by the WHO in February 2020, has currently infected more than 6 million people with fatalities near 371,000 and increasing exponentially, in absence of vaccines and drugs. The pathogenesis of SARS-CoV-2 is still being elucidated. Identifying potential targets and repurposing drugs as therapeutic options is the need of the hour. In this review, we focus on potential druggable targets and suitable therapeutics, currently being explored in clinical trials, to treat SARS-CoV-2 infection. A brief understanding of the complex interactions of both viral as well as host targets, and the possible repurposed drug candidates are described with an emphasis on understanding the mechanisms at the molecular level.
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Affiliation(s)
- Siddhi Joshi
- Department of Pharmaceutical Sciences & Technology, Institute of Chemical Technology, Nathalal Parekh Marg, Mumbai, 400019, Maharashtra, India
| | - Maithili Joshi
- Department of Pharmaceutical Sciences & Technology, Institute of Chemical Technology, Nathalal Parekh Marg, Mumbai, 400019, Maharashtra, India
| | - Mariam S Degani
- Department of Pharmaceutical Sciences & Technology, Institute of Chemical Technology, Nathalal Parekh Marg, Mumbai, 400019, Maharashtra, India
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7
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Bosken YK, Cholko T, Lou YC, Wu KP, Chang CEA. Insights Into Dynamics of Inhibitor and Ubiquitin-Like Protein Binding in SARS-CoV-2 Papain-Like Protease. Front Mol Biosci 2020; 7:174. [PMID: 32850963 PMCID: PMC7417481 DOI: 10.3389/fmolb.2020.00174] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 07/06/2020] [Indexed: 11/28/2022] Open
Abstract
Covid-19 is caused by a novel form of coronavirus for which there are currently no vaccines or anti-viral drugs. This virus, termed SARS-CoV-2 (CoV2), contains Papain-like protease (PLpro) involved in viral replication and immune response evasion. Drugs targeting this protease therefore have great potential for inhibiting the virus, and have proven successful in older coronaviruses. Here, we introduce two effective inhibitors of SARS-CoV-1 (CoV1) and MERS-CoV to assess their potential for inhibiting CoV2 PLpro. We ran 1 μs molecular dynamics (MD) simulations of CoV2, CoV1, and MERS-CoV ligand-free PLpro to characterize the dynamics of CoV2 PLpro, and made comparisons between the three to elucidate important similarities and differences relevant to drug design and ubiquitin-like protein binding for deubiquitinating and deISGylating activity of CoV2. Next, we simulated the inhibitors bound to CoV1 and CoV2 PLpro in various poses and at different known binding sites to analyze their binding modes. We found that the naphthalene-based ligand shows strong potential as an inhibitor of CoV2 PLpro by binding at the putative naphthalene inhibitor binding site in both computational predictions and experimental assays. Our modeling work suggested strategies to improve naphthalene-based compounds, and our results from molecular docking showed that the newly designed compounds exhibited improved binding affinity. The other ligand, chemotherapy drug 6-mercaptopurine (6MP), showed little to no stable intermolecular interaction with PLpro and quickly dissociated or remained highly mobile. We demonstrate multiple ways to improve the binding affinity of the naphthalene-based inhibitor scaffold by engaging new residues in the unused space of the binding site. Analysis of CoV2 PLpro also brings insights into recognition of ubiquitin-like proteins that may alter innate immune response.
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Affiliation(s)
- Yuliana K Bosken
- Department of Chemistry, University of California, Riverside, Riverside, CA, United States
| | - Timothy Cholko
- Department of Chemistry, University of California, Riverside, Riverside, CA, United States
| | - Yuan-Chao Lou
- Biomedical Translation Research Center, Academia Sinica, Taipei, Taiwan
| | - Kuen-Phon Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chia-En A Chang
- Department of Chemistry, University of California, Riverside, Riverside, CA, United States
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8
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Wang L, Hu W, Fan C. Structural and biochemical characterization of SADS-CoV papain-like protease 2. Protein Sci 2020; 29:1228-1241. [PMID: 32216114 PMCID: PMC7184779 DOI: 10.1002/pro.3857] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/19/2020] [Accepted: 03/20/2020] [Indexed: 01/12/2023]
Abstract
Swine acute diarrhea syndrome coronavirus (SADS‐CoV) is a novel coronavirus that is involved in severe diarrhea disease in piglets, causing considerable agricultural and economic loss in China. The emergence of this new coronavirus increases the importance of understanding SADS‐CoV as well as antivirals. Coronaviral proteases, including main proteases and papain‐like proteases (PLP), are attractive antiviral targets because of their essential roles in polyprotein processing and thus viral maturation. Here, we describe the biochemical and structural identification of recombinant SADS papain‐like protease 2 (PLP2) domain of nsp3. The SADS‐CoV PLP2 was shown to cleave nsp1 proteins and also peptides mimicking the nsp2|nsp3 cleavage site and also had deubiquitinating and deISGynating activity by in vitro assays. The crystal structure adopts an architecture resembling that of PLPs from other coronaviruses. We characterize both conserved and unique structural features likely directing the interaction of PLP2 with the substrates, including the tentative mapping of active site and other essential residues. These results provide a foundation for understanding the molecular basis of coronaviral PLPs' catalytic mechanism and for the screening and design of therapeutics to combat infection by SADS coronavirus. PDB Code(s): http://firstglance.jmol.org/fg.htm?mol=6L5T;
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Affiliation(s)
- Lu Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesWuhan UniversityWuhanChina
| | - Weihua Hu
- Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesWuhan UniversityWuhanChina
| | - Chengpeng Fan
- Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesWuhan UniversityWuhanChina
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9
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Shanker AK, Bhanu D, Alluri A, Gupta S. Whole-genome sequence analysis and homology modelling of the main protease and non-structural protein 3 of SARS-CoV-2 reveal an aza-peptide and a lead inhibitor with possible antiviral properties. NEW J CHEM 2020. [DOI: 10.1039/d0nj00974a] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
SARS-CoV-2 3CLpro shows homology in binding to an aza-peptide epoxide (APE) known for the irreversible inhibition of main peptidase in SARS-CoV.
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Affiliation(s)
- Arun K. Shanker
- ICAR – Central Research Institute for Dryland Agriculture, Santoshnagar
- Hyderabad – 500059
- India
| | - Divya Bhanu
- ICAR – Central Research Institute for Dryland Agriculture, Santoshnagar
- Hyderabad – 500059
- India
- Centre for Plant Molecular Biology
- Osmania University
| | - Anjani Alluri
- Advanced Post Graduate Centre
- Acharya N. G. Ranga Agricultural University
- Guntur
- India
| | - Samriddhi Gupta
- Department of Biochemistry
- School of Life Sciences
- University of Hyderabad
- India
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10
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De Vita S, Chini MG, Lauro G, Bifulco G. Accelerating the repurposing of FDA-approved drugs against coronavirus disease-19 (COVID-19). RSC Adv 2020; 10:40867-40875. [PMID: 35519188 PMCID: PMC9057693 DOI: 10.1039/d0ra09010g] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 11/02/2020] [Indexed: 12/24/2022] Open
Abstract
The recent release of the main protein structures belonging to SARS CoV-2, responsible for the coronavirus disease-19 (COVID-19), strongly pushed for identifying valuable drug treatments. With this aim, we show a repurposing study on FDA-approved drugs applying a new computational protocol and introducing a novel parameter called IVSratio. Starting with a virtual screening against three SARS CoV-2 targets (main protease, papain-like protease, spike protein), the top-ranked molecules were reassessed combining the Inverse Virtual Screening novel approach and MM-GBSA calculations. Applying this protocol, a list of drugs was identified against the three investigated targets. Also, the top-ranked selected compounds on each target (rutin vs. main protease, velpatasvir vs. papain-like protease, lomitapide vs. spike protein) were further tested with molecular dynamics simulations to confirm the promising binding modes, obtaining encouraging results such as high stability of the complex during the simulation and a good protein–ligand interaction network involving some important residues of each target. Moreover, the recent outcomes highlighting the inhibitory activity of quercetin, a natural compound strictly related to rutin, on the SARS-CoV-2 main protease, strengthened the applicability of the proposed workflow. New computational protocol applied to a repurposing campaign against SARS-CoV-2.![]()
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Affiliation(s)
- Simona De Vita
- Department of Pharmacy
- University of Salerno
- Fisciano 84084
- Italy
| | - Maria Giovanna Chini
- Department of Biosciences and Territory
- University of Molise
- 86090 Pesche (IS)
- Italy
| | - Gianluigi Lauro
- Department of Pharmacy
- University of Salerno
- Fisciano 84084
- Italy
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11
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Ren J, Lee H, Kotak A, Johnson ME. MD simulations reveal alternate conformations of the oxyanion hole in the Zika virus NS2B/NS3 protease. Proteins 2019; 88:345-354. [PMID: 31461176 DOI: 10.1002/prot.25809] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 08/02/2019] [Accepted: 08/19/2019] [Indexed: 12/29/2022]
Abstract
Recent crystallography studies have shown that the binding site oxyanion hole plays an important role in inhibitor binding, but can exist in two conformations (active/inactive). We have undertaken molecular dynamics (MD) calculations to better understand oxyanion hole dynamics and thermodynamics. We find that the Zika virus (ZIKV) NS2B/NS3 protease maintains a stable closed conformation over multiple 100-ns conventional MD simulations in both the presence and absence of inhibitors. The S1, S2, and S3 pockets are stable as well. However, in two of eight simulations, the A132-G133 peptide bond in the binding pocket of S1' spontaneously flips to form a 310 -helix that corresponds to the inactive conformation of the oxyanion hole, and then maintains this conformation until the end of the 100-ns conventional MD simulations without inversion of the flip. This conformational change affects the S1' pocket in ZIKV NS2B/NS3 protease active site, which is important for small molecule binding. The simulation results provide evidence at the atomic level that the inactive conformation of the oxyanion hole is more favored energetically when no specific interactions are formed between substrate/inhibitor and oxyanion hole residues. Interestingly, however, transition between the active and inactive conformation of the oxyanion hole can be observed by boosting the valley potential in accelerated MD simulations. This supports a proposed induced-fit mechanism of ZIKV NS2B/NS3 protease from computational methods and provides useful direction to enhance inhibitor binding predictions in structure-based drug design.
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Affiliation(s)
- Jinhong Ren
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois
| | - Hyun Lee
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois.,Research Resource Center Biophysics Core, University of Illinois at Chicago, Chicago, Illinois.,Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois
| | - Alpa Kotak
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois.,Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois
| | - Michael E Johnson
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois.,Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois.,Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois
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12
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Chu HF, Chen CC, Moses DC, Chen YH, Lin CH, Tsai YC, Chou CY. Porcine epidemic diarrhea virus papain-like protease 2 can be noncompetitively inhibited by 6-thioguanine. Antiviral Res 2018; 158:199-205. [PMID: 30138642 PMCID: PMC7113753 DOI: 10.1016/j.antiviral.2018.08.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 07/09/2018] [Accepted: 08/17/2018] [Indexed: 01/25/2023]
Abstract
Porcine epidemic diarrhea virus (PEDV) is a coronavirus (CoV) discovered in the 1970s that infects the intestinal tract of pigs, resulting in diarrhea and vomiting. It can cause extreme dehydration and death in neonatal piglets. In Asia, modified live attenuated vaccines have been used to control PEDV infection in recent years. However, a new strain of PEDV that belongs to genogroup 2a appeared in the USA in 2013 and then quickly spread to Canada and Mexico as well as Asian and European countries. Due to the less effective protective immunity provided by the vaccines against this new strain, it has caused considerable agricultural and economic loss worldwide. The emergence of this new strain increases the importance of understanding PEDV as well as strategies for inhibiting it. Coronaviral proteases, including main proteases and papain-like proteases, are ideal antiviral targets because of their essential roles in viral maturation. Here we provide a first description of the expression, purification and structural characteristics of recombinant PEDV papain-like protease 2, moreover present our finding that 6-thioguanine, a chemotherapeutic drug, in contrast to its competitive inhibition on SARS- and MERS-CoV papain-like proteases, is a noncompetitive inhibitor of PEDV papain-like protease 2. PEDV PL2pro exhibits much higher DUB activity than that of other PLpros in spite of their structural similarities. In contrast to its competitive inhibition on SARS- and MERS-CoV PLpros, 6-thioguanine inhibits PEDV PL2pro allosterically. Putative 6-thioguanine binding site is proposed to render the blocking loop less flexible and therefore disfavor catalysis. 6-thioguanine can be a lead compound for anti-coronaviral drug development.
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Affiliation(s)
- Hsu-Feng Chu
- Biomedical Industry Ph.D. Program, National Yang-Ming University, Taipei 112, Taiwan; Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan
| | - Chiao-Che Chen
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan
| | - David C Moses
- Department of Chemistry, Tamkang University, Tamsui 251, Taiwan
| | - Yau-Hung Chen
- Department of Chemistry, Tamkang University, Tamsui 251, Taiwan
| | - Chao-Hsiung Lin
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan
| | - Ying-Chieh Tsai
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 112, Taiwan; Probiotic Research Center, National Yang-Ming University, Taipei 112, Taiwan
| | - Chi-Yuan Chou
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan.
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13
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Childers MC, Daggett V. Validating Molecular Dynamics Simulations against Experimental Observables in Light of Underlying Conformational Ensembles. J Phys Chem B 2018; 122:6673-6689. [PMID: 29864281 DOI: 10.1021/acs.jpcb.8b02144] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Far from the static, idealized conformations deposited into structural databases, proteins are highly dynamic molecules that undergo conformational changes on temporal and spatial scales that may span several orders of magnitude. These conformational changes, often intimately connected to the functional roles that proteins play, may be obscured by traditional biophysical techniques. Over the past 40 years, molecular dynamics (MD) simulations have complemented these techniques by providing the "hidden" atomistic details that underlie protein dynamics. However, there are limitations of the degree to which molecular simulations accurately and quantitatively describe protein motions. Here we show that although four molecular dynamics simulation packages (AMBER, GROMACS, NAMD, and ilmm) reproduced a variety of experimental observables for two different proteins (engrailed homeodomain and RNase H) equally well overall at room temperature, there were subtle differences in the underlying conformational distributions and the extent of conformational sampling obtained. This leads to ambiguity about which results are correct, as experiment cannot always provide the necessary detailed information to distinguish between the underlying conformational ensembles. However, the results with different packages diverged more when considering larger amplitude motion, for example, the thermal unfolding process and conformational states sampled, with some packages failing to allow the protein to unfold at high temperature or providing results at odds with experiment. While most differences between MD simulations performed with different packages are attributed to the force fields themselves, there are many other factors that influence the outcome, including the water model, algorithms that constrain motion, how atomic interactions are handled, and the simulation ensemble employed. Here four different MD packages were tested each using best practices as established by the developers, utilizing three different protein force fields and three different water models. Differences between the simulated protein behavior using two different packages but the same force field, as well as two different packages with different force fields but the same water models and approaches to restraining motion, show how other factors can influence the behavior, and it is incorrect to place all the blame for deviations and errors on force fields or to expect improvements in force fields alone to solve such problems.
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Affiliation(s)
- Matthew Carter Childers
- Department of Bioengineering , University of Washington , Seattle , Washington 98195-5013 , United States
| | - Valerie Daggett
- Department of Bioengineering , University of Washington , Seattle , Washington 98195-5013 , United States
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14
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Bailey-Elkin BA, Knaap RCM, Kikkert M, Mark BL. Structure and Function of Viral Deubiquitinating Enzymes. J Mol Biol 2017; 429:3441-3470. [PMID: 28625850 PMCID: PMC7094624 DOI: 10.1016/j.jmb.2017.06.010] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 06/12/2017] [Accepted: 06/13/2017] [Indexed: 01/12/2023]
Abstract
Post-translational modification of cellular proteins by ubiquitin regulates numerous cellular processes, including innate and adaptive immune responses. Ubiquitin-mediated control over these processes can be reversed by cellular deubiquitinating enzymes (DUBs), which remove ubiquitin from cellular targets and depolymerize polyubiquitin chains. The importance of protein ubiquitination to host immunity has been underscored by the discovery of viruses that encode proteases with deubiquitinating activity, many of which have been demonstrated to actively corrupt cellular ubiquitin-dependent processes to suppress innate antiviral responses and promote viral replication. DUBs have now been identified in diverse viral lineages, and their characterization is providing valuable insights into virus biology and the role of the ubiquitin system in host antiviral mechanisms. Here, we provide an overview of the structural biology of these fascinating viral enzymes and their role innate immune evasion and viral replication.
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Affiliation(s)
- Ben A Bailey-Elkin
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - Robert C M Knaap
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Marjolein Kikkert
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Brian L Mark
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada.
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15
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Zumla A, Chan JFW, Azhar EI, Hui DSC, Yuen KY. Coronaviruses - drug discovery and therapeutic options. Nat Rev Drug Discov 2016. [PMID: 26868298 DOI: 10.1038/nrd201537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
In humans, infections with the human coronavirus (HCoV) strains HCoV-229E, HCoV-OC43, HCoV-NL63 and HCoV-HKU1 usually result in mild, self-limiting upper respiratory tract infections, such as the common cold. By contrast, the CoVs responsible for severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), which were discovered in Hong Kong, China, in 2003, and in Saudi Arabia in 2012, respectively, have received global attention over the past 12 years owing to their ability to cause community and health-care-associated outbreaks of severe infections in human populations. These two viruses pose major challenges to clinical management because there are no specific antiviral drugs available. In this Review, we summarize the epidemiology, virology, clinical features and current treatment strategies of SARS and MERS, and discuss the discovery and development of new virus-based and host-based therapeutic options for CoV infections.
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Affiliation(s)
- Alimuddin Zumla
- Division of Infection and Immunity, University College London, and NIHR Biomedical Research Centre, UCL Hospitals NHS Foundation Trust, 307 Euston Road, London NW1 3AD, UK
| | - Jasper F W Chan
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Research Centre of Infection and Immunology, Department of Microbiology, University Pathology Building, Queen Mary Hospital, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong Special Administrative Region of the People's Republic of China
| | - Esam I Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Centre, and Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, P.O. Box 128442, Jeddah - 21362, Kingdom of Saudi Arabia
| | - David S C Hui
- Division of Respiratory Medicine and Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, 30-32 Ngan Shing Street, Shatin, New Territories, Hong Kong Special Administrative Region of the People's Republic of China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Research Centre of Infection and Immunology, Department of Microbiology, University Pathology Building, Queen Mary Hospital, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong Special Administrative Region of the People's Republic of China
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16
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Zumla A, Chan JFW, Azhar EI, Hui DSC, Yuen KY. Coronaviruses - drug discovery and therapeutic options. Nat Rev Drug Discov 2016; 15:327-47. [PMID: 26868298 PMCID: PMC7097181 DOI: 10.1038/nrd.2015.37] [Citation(s) in RCA: 1147] [Impact Index Per Article: 143.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) are examples of emerging zoonotic coronavirus infections capable of person-to-person transmission that result in large-scale epidemics with substantial effects on patient health and socioeconomic factors. Unlike patients with mild illnesses that are caused by other human-pathogenic coronaviruses, patients with SARS or MERS coronavirus infections may develop severe acute respiratory disease with multi-organ failure. The case–fatality rates of SARS and MERS are approximately 10% and 35%, respectively. Both SARS and MERS pose major clinical management challenges because there is no specific antiviral treatment that has been proven to be effective in randomized clinical trials for either infection. Substantial efforts are underway to discover new therapeutic agents for coronavirus infections. Virus-based therapies include monoclonal antibodies and antiviral peptides that target the viral spike glycoprotein, viral enzyme inhibitors, viral nucleic acid synthesis inhibitors and inhibitors of other viral structural and accessory proteins. Host-based therapies include agents that potentiate the interferon response or affect either host signalling pathways involved in viral replication or host factors utilized by coronaviruses for viral replication. The major challenges in the clinical development of novel anti-coronavirus drugs include the limited number of suitable animal models for the evaluation of potential treatments for SARS and MERS, the current absence of new SARS cases, the limited number of MERS cases — which are also predominantly geographically confined to the Middle East — as well as the lack of industrial incentives to develop antivirals for mild infections caused by other, less pathogenic coronaviruses. The continuing threat of MERS-CoV to global health 3 years after its discovery presents a golden opportunity to tackle current obstacles in the development of new anti-coronavirus drugs. A well-organized, multidisciplinary, international collaborative network consisting of clinicians, virologists and drug developers, coupled to political commitment, should be formed to carry out clinical trials using anti-coronavirus drugs that have already been shown to be safe and effective in vitro and/or in animal models, particularly lopinavir–ritonavir, interferon beta-1b and monoclonal antibodies and antiviral peptides targeting the viral spike glycoprotein.
Severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), which are caused by coronaviruses, have attracted substantial attention owing to their high mortality rates and potential to cause epidemics. Yuen and colleagues discuss progress with treatment options for these syndromes, including virus- and host-targeted drugs, and the challenges that need to be overcome in their further development. In humans, infections with the human coronavirus (HCoV) strains HCoV-229E, HCoV-OC43, HCoV-NL63 and HCoV-HKU1 usually result in mild, self-limiting upper respiratory tract infections, such as the common cold. By contrast, the CoVs responsible for severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), which were discovered in Hong Kong, China, in 2003, and in Saudi Arabia in 2012, respectively, have received global attention over the past 12 years owing to their ability to cause community and health-care-associated outbreaks of severe infections in human populations. These two viruses pose major challenges to clinical management because there are no specific antiviral drugs available. In this Review, we summarize the epidemiology, virology, clinical features and current treatment strategies of SARS and MERS, and discuss the discovery and development of new virus-based and host-based therapeutic options for CoV infections.
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Affiliation(s)
- Alimuddin Zumla
- Division of Infection and Immunity, University College London, and NIHR Biomedical Research Centre, UCL Hospitals NHS Foundation Trust, 307 Euston Road, London NW1 3AD, UK
| | - Jasper F W Chan
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Research Centre of Infection and Immunology, Department of Microbiology, University Pathology Building, Queen Mary Hospital, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong Special Administrative Region of the People's Republic of China
| | - Esam I Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Centre, and Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, P.O. Box 128442, Jeddah - 21362, Kingdom of Saudi Arabia
| | - David S C Hui
- Division of Respiratory Medicine and Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, 30-32 Ngan Shing Street, Shatin, New Territories, Hong Kong Special Administrative Region of the People's Republic of China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Research Centre of Infection and Immunology, Department of Microbiology, University Pathology Building, Queen Mary Hospital, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong Special Administrative Region of the People's Republic of China
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17
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Abstract
This review examines the small molecules described over the past decade as inhibitors of any of the approximately 100 human deubiquitinating enzymes (DUBs). Structures from patent publications as well as from the primary literature are included. Inhibitors of two viral DUBs are also described since these proteases share structural similarity with one of the human DUB sub-families. The structure, function and disease associations of certain DUBs are presented. The evolution of the screening assays used to identify and characterise new inhibitors is discussed. Several emerging trends in the series are highlighted and the ‘drug-likeness’ of the various inhibitors is analysed. Large pharmaceutical company collaborations have drawn attention to this field, and these recent advances are discussed in the context of the wider range of therapeutically important DUB targets.
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Affiliation(s)
- Mark Kemp
- MISSION Therapeutics, Babraham Research Campus, Cambridge, United Kingdom
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18
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Hoelz LVB, Leal VF, Rodrigues CR, Pascutti PG, Albuquerque MG, Muri EMF, Dias LRS. Molecular dynamics simulations of the free and inhibitor-bound cruzain systems in aqueous solvent: insights on the inhibition mechanism in acidic pH. J Biomol Struct Dyn 2015; 34:1969-78. [PMID: 26414241 DOI: 10.1080/07391102.2015.1100139] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The major cysteine protease of Trypanosoma cruzi, cruzain (CRZ), has been described as a therapeutic target for Chagas' disease, which affects millions of people worldwide. Thus, a series of CRZ inhibitors has been studied, including a new competitive inhibitor, Nequimed176 (NEQ176). Nevertheless, the structural and dynamic basis for CRZ inhibition remains unclear. Hoping to contribute to this ever-growing understanding of timescale dynamics in the CRZ inhibition mechanism, we have performed the first study using 100 ns of molecular dynamics (MD) simulations of two CRZ systems in an aqueous solvent under pH 5.5: CRZ in the apo form (ligand free) and CRZ complexed to NEQ176. According to the MD simulations, the enzyme adopts an open conformation in the apo form and a closed conformation in the NEQ176-CRZ complex. We also suggest that this closed conformation is related to the hydrogen-bonding interactions between NEQ176 and CRZ, which occurs through key residues, mainly Gly66, Met68, Asn69, and Leu160. In addition, the cross-correlation analysis shows evidence of the correlated motions among Ala110-Asp140, Leu160-Gly189, and Glu190-Gly215 subdomains, as well as, the movements related to Ala1-Thr59 and Asp60-Pro90 regions seem to be crucial for CRZ activity.
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Affiliation(s)
- L V B Hoelz
- a Laboratório de Química Medicinal, Faculdade de Farmácia , Universidade Federal Fluminense (UFF) , Rua Mário Viana 523, Santa Rosa , Niterói , RJ 24241-000 , Brazil
| | - V F Leal
- a Laboratório de Química Medicinal, Faculdade de Farmácia , Universidade Federal Fluminense (UFF) , Rua Mário Viana 523, Santa Rosa , Niterói , RJ 24241-000 , Brazil
| | - C R Rodrigues
- b Laboratório ModMolQSAR, Faculdade de Farmácia , Universidade Federal do Rio de Janeiro (UFRJ) , Av. Carlos Chagas Filho 373, CCS, Rio de Janeiro , RJ 21941-599 , Brazil
| | - P G Pascutti
- c Laboratório de Modelagem e Dinâmica Molecular , Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro (UFRJ) , Av. Carlos Chagas Filho 373, CCS, Rio de Janeiro , RJ 21941-902 , Brazil
| | - M G Albuquerque
- d Laboratório de Modelagem Molecular , Instituto de Química, Universidade Federal do Rio de Janeiro (UFRJ) , Av. Athos da Silveira Ramos 149, CT, Rio de Janeiro , RJ 21949-900 , Brazil
| | - E M F Muri
- a Laboratório de Química Medicinal, Faculdade de Farmácia , Universidade Federal Fluminense (UFF) , Rua Mário Viana 523, Santa Rosa , Niterói , RJ 24241-000 , Brazil
| | - L R S Dias
- a Laboratório de Química Medicinal, Faculdade de Farmácia , Universidade Federal Fluminense (UFF) , Rua Mário Viana 523, Santa Rosa , Niterói , RJ 24241-000 , Brazil
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19
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Kong L, Shaw N, Yan L, Lou Z, Rao Z. Structural view and substrate specificity of papain-like protease from avian infectious bronchitis virus. J Biol Chem 2015; 290:7160-8. [PMID: 25609249 PMCID: PMC4358136 DOI: 10.1074/jbc.m114.628636] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Papain-like protease (PLpro) of coronaviruses (CoVs) carries out proteolytic maturation of non-structural proteins that play a role in replication of the virus and performs deubiquitination of host cell factors to scuttle antiviral responses. Avian infectious bronchitis virus (IBV), the causative agent of bronchitis in chicken that results in huge economic losses every year in the poultry industry globally, encodes a PLpro. The substrate specificities of this PLpro are not clearly understood. Here, we show that IBV PLpro can degrade Lys48- and Lys63-linked polyubiquitin chains to monoubiquitin but not linear polyubiquitin. To explain the substrate specificities, we have solved the crystal structure of PLpro from IBV at 2.15-Å resolution. The overall structure is reminiscent of the structure of severe acute respiratory syndrome CoV PLpro. However, unlike the severe acute respiratory syndrome CoV PLpro that lacks blocking loop (BL) 1 of deubiquitinating enzymes, the IBV PLpro has a short BL1-like loop. Access to a conserved catalytic triad consisting of Cys101, His264, and Asp275 is regulated by the flexible BL2. A model of ubiquitin-bound IBV CoV PLpro brings out key differences in substrate binding sites of PLpros. In particular, P3 and P4 subsites as well as residues interacting with the β-barrel of ubiquitin are different, suggesting different catalytic efficiencies and substrate specificities. We show that IBV PLpro cleaves peptide substrates KKAG-7-amino-4-methylcoumarin and LRGG-7-amino-4-methylcoumarin with different catalytic efficiencies. These results demonstrate that substrate specificities of IBV PLpro are different from other PLpros and that IBV PLpro might target different ubiquitinated host factors to aid the propagation of the virus.
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Affiliation(s)
- Lingying Kong
- From the Laboratory of Structural Biology, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Neil Shaw
- College of Life Sciences, Nankai University, Tianjin 300071, China, and National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China
| | - Lingming Yan
- From the Laboratory of Structural Biology, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Zhiyong Lou
- From the Laboratory of Structural Biology, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Zihe Rao
- From the Laboratory of Structural Biology, School of Medicine, Tsinghua University, Beijing 100084, China, College of Life Sciences, Nankai University, Tianjin 300071, China, and National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China
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20
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Yuan L, Chen Z, Song S, Wang S, Tian C, Xing G, Chen X, Xiao ZX, He F, Zhang L. p53 degradation by a coronavirus papain-like protease suppresses type I interferon signaling. J Biol Chem 2014; 290:3172-82. [PMID: 25505178 PMCID: PMC4317044 DOI: 10.1074/jbc.m114.619890] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Infection by human coronaviruses is usually characterized by rampant viral replication and severe immunopathology in host cells. Recently, the coronavirus papain-like proteases (PLPs) have been identified as suppressors of the innate immune response. However, the molecular mechanism of this inhibition remains unclear. Here, we provide evidence that PLP2, a catalytic domain of the nonstructural protein 3 of human coronavirus NL63 (HCoV-NL63), deubiquitinates and stabilizes the cellular oncoprotein MDM2 and induces the proteasomal degradation of p53. Meanwhile, we identify IRF7 (interferon regulatory factor 7) as a bona fide target gene of p53 to mediate the p53-directed production of type I interferon and the innate immune response. By promoting p53 degradation, PLP2 inhibits the p53-mediated antiviral response and apoptosis to ensure viral growth in infected cells. Thus, our study reveals that coronavirus engages PLPs to escape from the innate antiviral response of the host by inhibiting p53-IRF7-IFNβ signaling.
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Affiliation(s)
- Lin Yuan
- From the State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Collaborative Innovation Center for Cancer Medicine, Beijing 100850, China, the Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning Province 116044, China
| | - Zhongbin Chen
- the Division of Infection and Immunity, Department of Electromagnetic and Laser Biology, Beijing Institute of Radiation Medicine, Beijing 100850, China, and
| | - Shanshan Song
- From the State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Collaborative Innovation Center for Cancer Medicine, Beijing 100850, China
| | - Shan Wang
- From the State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Collaborative Innovation Center for Cancer Medicine, Beijing 100850, China
| | - Chunyan Tian
- From the State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Collaborative Innovation Center for Cancer Medicine, Beijing 100850, China
| | - Guichun Xing
- From the State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Collaborative Innovation Center for Cancer Medicine, Beijing 100850, China
| | - Xiaojuan Chen
- the Division of Infection and Immunity, Department of Electromagnetic and Laser Biology, Beijing Institute of Radiation Medicine, Beijing 100850, China, and
| | - Zhi-Xiong Xiao
- the School of Life Sciences, Sichuan University, Sichuan Province, 610065, China
| | - Fuchu He
- From the State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Collaborative Innovation Center for Cancer Medicine, Beijing 100850, China
| | - Lingqiang Zhang
- From the State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Collaborative Innovation Center for Cancer Medicine, Beijing 100850, China, the Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning Province 116044, China,
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21
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Catalytic function and substrate specificity of the papain-like protease domain of nsp3 from the Middle East respiratory syndrome coronavirus. J Virol 2014; 88:12511-27. [PMID: 25142582 DOI: 10.1128/jvi.01294-14] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
UNLABELLED The papain-like protease (PLpro) domain from the deadly Middle East respiratory syndrome coronavirus (MERS-CoV) was overexpressed and purified. MERS-CoV PLpro constructs with and without the putative ubiquitin-like (UBL) domain at the N terminus were found to possess protease, deubiquitinating, deISGylating, and interferon antagonism activities in transfected HEK293T cells. The quaternary structure and substrate preferences of MERS-CoV PLpro were determined and compared to those of severe acute respiratory syndrome coronavirus (SARS-CoV) PLpro, revealing prominent differences between these closely related enzymes. Steady-state kinetic analyses of purified MERS-CoV and SARS-CoV PLpros uncovered significant differences in their rates of hydrolysis of 5-aminomethyl coumarin (AMC) from C-terminally labeled peptide, ubiquitin, and ISG15 substrates, as well as in their rates of isopeptide bond cleavage of K48- and K63-linked polyubiquitin chains. MERS-CoV PLpro was found to have 8-fold and 3,500-fold higher catalytic efficiencies for hydrolysis of ISG15-AMC than for hydrolysis of the Ub-AMC and Z-RLRGG-AMC substrates, respectively. A similar trend was observed for SARS-CoV PLpro, although it was much more efficient than MERS-CoV PLpro toward ISG15-AMC and peptide-AMC substrates. MERS-CoV PLpro was found to process K48- and K63-linked polyubiquitin chains at similar rates and with similar debranching patterns, producing monoubiquitin species. However, SARS-CoV PLpro much preferred K48-linked polyubiquitin chains to K63-linked chains, and it rapidly produced di-ubiquitin molecules from K48-linked chains. Finally, potent inhibitors of SARS-CoV PLpro were found to have no effect on MERS-CoV PLpro. A homology model of the MERS-CoV PLpro structure was generated and compared to the X-ray structure of SARS-CoV PLpro to provide plausible explanations for differences in substrate and inhibitor recognition. IMPORTANCE Unlocking the secrets of how coronavirus (CoV) papain-like proteases (PLpros) perform their multifunctional roles during viral replication entails a complete mechanistic understanding of their substrate recognition and enzymatic activities. We show that the PLpro domains from the MERS and SARS coronaviruses can recognize and process the same substrates, but with different catalytic efficiencies. The differences in substrate recognition between these closely related PLpros suggest that neither enzyme can be used as a generalized model to explain the kinetic behavior of all CoV PLpros. As a consequence, decoding the mechanisms of PLpro-mediated antagonism of the host innate immune response and the development of anti-CoV PLpro enzyme inhibitors will be a challenging undertaking. The results from this study provide valuable information for understanding how MERS-CoV PLpro-mediated antagonism of the host innate immune response is orchestrated, as well as insight into the design of inhibitors against MERS-CoV PLpro.
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22
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Carbajo-Lozoya J, Ma-Lauer Y, Malešević M, Theuerkorn M, Kahlert V, Prell E, von Brunn B, Muth D, Baumert TF, Drosten C, Fischer G, von Brunn A. Human coronavirus NL63 replication is cyclophilin A-dependent and inhibited by non-immunosuppressive cyclosporine A-derivatives including Alisporivir. Virus Res 2014; 184:44-53. [PMID: 24566223 PMCID: PMC7114444 DOI: 10.1016/j.virusres.2014.02.010] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 02/12/2014] [Accepted: 02/13/2014] [Indexed: 12/12/2022]
Abstract
Cyclophilin A (CypA) is a host factor for human coronavirus NL63 replication. CypA is a target for anti-coronaviral therapy. Non-immunosuppressive CsA derivatives (Alisporivir, NIM811) inhibit CoV replication. New classes of non-immunosuppressive CsA/FK506 derivatives inhibit CoV replication.
Until recently, there were no effective drugs available blocking coronavirus (CoV) infection in humans and animals. We have shown before that CsA and FK506 inhibit coronavirus replication (Carbajo-Lozoya, J., Müller, M.A., Kallies, S., Thiel, V., Drosten, C., von Brunn, A. Replication of human coronaviruses SARS-CoV, HCoV-NL63 and HCoV-229E is inhibited by the drug FK506. Virus Res. 2012; Pfefferle, S., Schöpf, J., Kögl, M., Friedel, C., Müller, M.A., Stellberger, T., von Dall’Armi, E., Herzog, P., Kallies, S., Niemeyer, D., Ditt, V., Kuri, T., Züst, R., Schwarz, F., Zimmer, R., Steffen, I., Weber, F., Thiel, V., Herrler, G., Thiel, H.-J., Schwegmann-Weßels, C., Pöhlmann, S., Haas, J., Drosten, C. and von Brunn, A. The SARS-Coronavirus-host interactome: identification of cyclophilins as target for pan-Coronavirus inhibitors. PLoS Pathog., 2011). Here we demonstrate that CsD Alisporivir, NIM811 as well as novel non-immunosuppressive derivatives of CsA and FK506 strongly inhibit the growth of human coronavirus HCoV-NL63 at low micromolar, non-cytotoxic concentrations in cell culture. We show by qPCR analysis that virus replication is diminished up to four orders of magnitude to background levels. Knockdown of the cellular Cyclophilin A (CypA/PPIA) gene in Caco-2 cells prevents replication of HCoV-NL63, suggesting that CypA is required for virus replication. Collectively, our results uncover Cyclophilin A as a host target for CoV infection and provide new strategies for urgently needed therapeutic approaches.
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Affiliation(s)
| | - Yue Ma-Lauer
- Max-von-Pettenkofer Institut, Ludwig-Maximilians-Universität, München, Germany
| | - Miroslav Malešević
- Martin-Luther-Universität Halle-Wittenberg, Institute of Biochemistry and Biotechnology, Division of Enzymology, Halle, Germany
| | - Martin Theuerkorn
- Max-Planck-Institute of Biophysical Chemistry Göttingen, BO Halle (Saale), Germany
| | - Viktoria Kahlert
- Max-Planck-Institute of Biophysical Chemistry Göttingen, BO Halle (Saale), Germany
| | - Erik Prell
- Max-Planck-Institute of Biophysical Chemistry Göttingen, BO Halle (Saale), Germany
| | - Brigitte von Brunn
- Max-von-Pettenkofer Institut, Ludwig-Maximilians-Universität, München, Germany
| | - Doreen Muth
- Institut für Virologie, Universität Bonn, Bonn, Germany
| | - Thomas F Baumert
- Inserm U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Université de Strasbourg, Strasbourg, France
| | | | - Gunter Fischer
- Max-Planck-Institute of Biophysical Chemistry Göttingen, BO Halle (Saale), Germany
| | - Albrecht von Brunn
- Max-von-Pettenkofer Institut, Ludwig-Maximilians-Universität, München, Germany.
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