1
|
Atatreh N, Mahgoub RE, Ghattas MA. Exploring covalent inhibitors of SARS-CoV-2 main protease: from peptidomimetics to novel scaffolds. J Enzyme Inhib Med Chem 2025; 40:2460045. [PMID: 39912405 PMCID: PMC11803818 DOI: 10.1080/14756366.2025.2460045] [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: 07/30/2024] [Revised: 01/16/2025] [Accepted: 01/24/2025] [Indexed: 02/07/2025] Open
Abstract
Peptidomimetic inhibitors mimic natural peptide substrates, employing electrophilic warheads to covalently interact with the catalytic Cys145 of Mpro. Examples include aldehydes, α-ketoamides, and aza-peptides, with discussions on their mechanisms of action, potency, and structural insights. Non-peptidomimetic inhibitors utilise diverse scaffolds and mechanisms, achieving covalent modification of Mpro.
Collapse
Affiliation(s)
- Noor Atatreh
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
- AAU Health and Biomedical Research Centre, Al Ain University, Abu Dhabi, United Arab Emirates
| | - Radwa E. Mahgoub
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
- AAU Health and Biomedical Research Centre, Al Ain University, Abu Dhabi, United Arab Emirates
| | - Mohammad A. Ghattas
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
- AAU Health and Biomedical Research Centre, Al Ain University, Abu Dhabi, United Arab Emirates
| |
Collapse
|
2
|
Oruçoğlu B, Çetin İ, Şimşek H, Topçul M, Çalışkan M, Aydın C, Kavaklı IH, Okyar A, Gül Ş. Identification of potential SARS-CoV-2 inhibitors among well-tolerated drugs using drug repurposing and in vitro approaches. Sci Rep 2025; 15:13975. [PMID: 40263343 PMCID: PMC12015351 DOI: 10.1038/s41598-025-88388-4] [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: 10/09/2024] [Accepted: 01/28/2025] [Indexed: 04/24/2025] Open
Abstract
The 3C-like protease (3CLpro) is essential in the SARS-CoV-2 life cycle and a promising target for antiviral drug discovery, as no similar proteases exist in humans. This study aimed to identify effective SARS-CoV-2 inhibitors among FDA-approved drugs. Previous computational analysis revealed several drugs with high binding affinity to the 3CLpro active site. In vitro enzymatic assays confirmed that ten of these drugs effectively inhibited the enzyme. To evaluate their impact on viral replication, we used non-infectious SARS-CoV-2 sub-genomic replicons in lung and intestinal cells. Amcinonide, eltrombopag, lumacaftor, candesartan, and nelfinavir inhibited replication at low micromolar concentrations. Lumacaftor showed IC50 values of 964 nM in Caco-2 cells and 458 nM in Calu-3 cells, while candesartan had IC50 values of 714 nM and 1.05 µM, respectively. Furthermore, dual combination experiments revealed that amcinonide, pimozide, lumacaftor, and eltrombopag acted as potent inhibitors at nanomolar concentrations when combined with candesartan. This study highlights lumacaftor, candesartan, and nelfinavir as effective inhibitors of SARS-CoV-2 replication in vitro and emphasizes their potential for repurposing as antiviral treatments. These findings support future clinical trials and may lead to breakthroughs in COVID-19 treatment strategies.
Collapse
Affiliation(s)
- Betül Oruçoğlu
- Biotechnology Division, Department of Biology, Istanbul University, Istanbul, Türkiye
- Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Istanbul, Türkiye
| | - İdil Çetin
- Biotechnology Division, Department of Biology, Istanbul University, Istanbul, Türkiye
| | - Handan Şimşek
- Biotechnology Division, Department of Biology, Istanbul University, Istanbul, Türkiye
| | - Mehmet Topçul
- Biotechnology Division, Department of Biology, Istanbul University, Istanbul, Türkiye
| | - Mahmut Çalışkan
- Biotechnology Division, Department of Biology, Istanbul University, Istanbul, Türkiye
| | - Cihan Aydın
- Department of Molecular Biology, Faculty of Engineering and Natural Sciences, Istanbul Medeniyet University, Istanbul, Türkiye
- Istanbul Medeniyet University Science and Advanced Technology Research Center (IMU-BILTAM), Istanbul, Türkiye
| | - I Halil Kavaklı
- Department of Molecular Biology and Genetics, Koc University, Istanbul, Türkiye
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Türkiye
| | - Alper Okyar
- Faculty of Pharmacy, Department of Pharmacology, İstanbul University, Istanbul, Türkiye
| | - Şeref Gül
- Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Istanbul, Türkiye.
| |
Collapse
|
3
|
Gu X, Zhang X, Zhang X, Wang X, Sun W, Zhang Y, Hu Z. Unveiling the mechanism of action of a novel natural dual inhibitor of SARS-CoV-2 Mpro and PLpro with molecular dynamics simulations. NATURAL PRODUCTS AND BIOPROSPECTING 2025; 15:3. [PMID: 39753911 PMCID: PMC11699025 DOI: 10.1007/s13659-024-00486-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2024] [Accepted: 11/27/2024] [Indexed: 01/06/2025]
Abstract
In the twenty-first century, we have witnessed multiple coronavirus pandemics. Despite declining SARS-CoV-2 cases, continued research remains vital. We report the discovery of sydowiol B, a natural product, as a dual inhibitor of SARS-CoV-2 main protease (Mpro) and papain-like protease (PLpro). Sydowiol B interacts with the nano-channel at the Mpro dimer interface and the PLpro active site. Molecular dynamics simulations suggest that sydowiol B inhibits Mpro by limiting active site expansion rather than inducing collapse. Furthermore, sydowiol B binding may amplify the fluctuation of two loops coordinating with the structural Zn2+ in PLpro, displacing Zn2+ from the zinc finger domain to the S2 helix. Sydowiol B and its analogue, violaceol I, exhibit broad-spectrum antiviral activity against homologous coronaviruses. Given the conservation of Mpro and PLpro, sydowiol B and violaceol I are promising leads for designing and developing anti-coronavirus therapies.
Collapse
Affiliation(s)
- Xiaoxia Gu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Xiaotian Zhang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Xueke Zhang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Xinyu Wang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Weiguang Sun
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China.
| | - Yonghui Zhang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China.
| | - Zhengxi Hu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China.
| |
Collapse
|
4
|
Thuy La VN, Kang L, Minh DDL. Enzyme kinetics model for the coronavirus main protease including dimerization and ligand binding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.01.631001. [PMID: 39803422 PMCID: PMC11722214 DOI: 10.1101/2025.01.01.631001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2025]
Abstract
The coronavirus main protease (MPro) plays a pivotal role in viral replication and is the target of several antivirals against SARS-CoV-2. In some species, CRCs of MPro enzymatic activity can exhibit biphasic behavior in which low ligand concentrations activate the enzyme whereas higher ones inhibit it. While this behavior has been attributed to ligand-induced dimerization, quantitative enzyme kinetics models have not been fit to it. Here, we develop a kinetic model integrating dimerization and ligand binding. We perform a Bayesian regression to globally fit the model to multiple types of biochemical and biophysical data. The reversible covalent inhibitor GC376 strongly induces dimerization and binds to the dimer with no cooperativity. In contrast, the fluorescent peptide substrate has a minor effect on dimerization but binds to the dimer with positive cooperativity. The biphasic concentration response curve occurs because compared to substrate, the inhibitor accelerates turnover in the opposite catalytic site.
Collapse
Affiliation(s)
- Van Ngoc Thuy La
- Department of Biology, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Lulu Kang
- Department of Mathematics and Statistics, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - David D L Minh
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL 60616, USA
| |
Collapse
|
5
|
Shawky AM, Almalki FA, Alzahrani HA, Abdalla AN, Youssif BGM, Ibrahim NA, Gamal M, El-Sherief HAM, Abdel-Fattah MM, Hefny AA, Abdelazeem AH, Gouda AM. Covalent small-molecule inhibitors of SARS-CoV-2 Mpro: Insights into their design, classification, biological activity, and binding interactions. Eur J Med Chem 2024; 277:116704. [PMID: 39121741 DOI: 10.1016/j.ejmech.2024.116704] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/10/2024] [Accepted: 07/19/2024] [Indexed: 08/12/2024]
Abstract
Since 2020, many compounds have been investigated for their potential use in the treatment of SARS-CoV-2 infection. Among these agents, a huge number of natural products and FDA-approved drugs have been evaluated as potential therapeutics for SARS-CoV-2 using virtual screening and docking studies. However, the identification of the molecular targets involved in viral replication led to the development of rationally designed anti-SARS-CoV-2 agents. Among these targets, the main protease (Mpro) is one of the key enzymes needed in the replication of the virus. The data gleaned from the crystal structures of SARS-CoV-2 Mpro complexes with small-molecule covalent inhibitors has been used in the design and discovery of many highly potent and broad-spectrum Mpro inhibitors. The current review focuses mainly on the covalent type of SARS-CoV-2 Mpro inhibitors. The design, chemistry, and classification of these inhibitors were also in focus. The biological activity of these inhibitors, including their inhibitory activities against Mpro, their antiviral activities, and the SAR studies, were discussed. The review also describes the potential mechanism of the interaction between these inhibitors and the catalytic Cys145 residue in Mpro. Moreover, the binding modes and key binding interactions of these covalent inhibitors were also illustrated. The covalent inhibitors discussed in this review were of diverse chemical nature and origin. Their antiviral activity was mediated mainly by the inhibition of SARS-CoV-2 Mpro, with IC50 values in the micromolar to the nanomolar range. Many of these inhibitors exhibited broad-spectrum inhibitory activity against the Mpro enzymes of other coronaviruses (SARS-CoV-1 and MERS-CoV). The dual inhibition of the Mpro and PLpro enzymes of SARS-CoV-2 could also provide higher therapeutic benefits than Mpro inhibition. Despite the approval of nirmatrelvir by the FDA, many mutations in the Mpro enzyme of SARS-CoV-2 have been reported. Although some of these mutations did not affect the potency of nirmatrelvir, there is an urgent need to develop a second generation of Mpro inhibitors. We hope that the data summarized in this review could help researchers in the design of a new potent generation of SARS-CoV-2 Mpro inhibitors.
Collapse
Affiliation(s)
- Ahmed M Shawky
- Science and Technology Unit (STU), Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Faisal A Almalki
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Hayat Ali Alzahrani
- Applied Medical Science College, Medical Laboratory Technology Department, Northern Border University, Arar, Saudi Arabia
| | - Ashraf N Abdalla
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Umm Al-Qura University, Makkah, 21955, Saudi Arabia; Department of Pharmacology and Toxicology, Medicinal And Aromatic Plants Research Institute, National Center for Research, Khartoum, 2404, Sudan
| | - Bahaa G M Youssif
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut, 71526, Egypt.
| | - Nashwa A Ibrahim
- Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt
| | - Mohammed Gamal
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt
| | - Hany A M El-Sherief
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Deraya University, Minia, Egypt
| | - Maha M Abdel-Fattah
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt
| | - Ahmed A Hefny
- Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt; School of Pharmacy, University of Waterloo, Kitchener, Ontario, N2G 1C5, Canada
| | - Ahmed H Abdelazeem
- Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt; Pharmacy Department, College of Pharmacy, Nursing and Medical Sciences, Riyadh Elm University, Riyadh, 11681, Saudi Arabia
| | - Ahmed M Gouda
- Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt.
| |
Collapse
|
6
|
Leusciatti M, Macchi B, Marino-Merlo F, Stefanizzi V, Mastino A, Morra G, Quadrelli P. Inhibition of the SARS-CoV-2 Non-structural Protein 5 (NSP5) Protease by Nitrosocarbonyl-Bases Small Molecules. ACS OMEGA 2024; 9:41599-41615. [PMID: 39398138 PMCID: PMC11465462 DOI: 10.1021/acsomega.4c05480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 08/09/2024] [Accepted: 08/20/2024] [Indexed: 10/15/2024]
Abstract
In the present work, we have designed and synthesized potential NSP5 protease allosteric inhibitors exploiting both docking and molecular dynamic data on SARS-CoV-2. The chemical protocols were developed on the basis of 1,3-dipolar cycloaddition reactions as well as the chemistry of nitrosocarbonyl intermediates. Computational studies were first conducted for determining the best candidate for SARS-CoV-2 NSP5 protease inhibition. Selected compounds were submitted to biological tests, showing low cytotoxicity and moderate activity.
Collapse
Affiliation(s)
- Marco Leusciatti
- Department
of Chemistry, INSTM Research Unit of Pavia;
University of Pavia, Viale Taramelli 10-12, Pavia 27100, Italy
- Biocomputing
Lab, SCITEC-Istituto di Scienze e Tecnologie
Chimiche CNR, Via Mario
Bianco 9, Milano 20131, Italy
| | - Beatrice Macchi
- Department
of Chemical Science and Technology, University
of Rome Tor Vergata, Via della ricerca scientifica 1, Roma 00133, Italy
| | - Francesca Marino-Merlo
- Department
of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres, 31, Messina 98166, Italy
| | - Valeria Stefanizzi
- Department
of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres, 31, Messina 98166, Italy
| | - Antonio Mastino
- Department
of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres, 31, Messina 98166, Italy
- The
Institute of Translational Pharmacology, CNR, Via Fosso del Cavaliere 100, Roma 00133, Italy
| | - Giulia Morra
- Biocomputing
Lab, SCITEC-Istituto di Scienze e Tecnologie
Chimiche CNR, Via Mario
Bianco 9, Milano 20131, Italy
| | - Paolo Quadrelli
- Department
of Chemistry, INSTM Research Unit of Pavia;
University of Pavia, Viale Taramelli 10-12, Pavia 27100, Italy
| |
Collapse
|
7
|
Duvvuri V, Shire F, Isabel S, Braukmann T, Clark S, Marchand-Austin A, Eshaghi A, Bandukwala H, Varghese N, Li Y, Sivaraman K, Hussain H, Cronin K, Sullivan A, Li A, Zygmunt A, Ramotar K, Kus J, Hasso M, Corbeil A, Gubbay J, Patel S. Large scale analysis of the SARS-CoV-2 main protease reveals marginal presence of nirmatrelvir-resistant SARS-CoV-2 Omicron mutants in Ontario, Canada, December 2021-September 2023. CANADA COMMUNICABLE DISEASE REPORT = RELEVE DES MALADIES TRANSMISSIBLES AU CANADA 2024; 50:365-374. [PMID: 39386278 PMCID: PMC11464099 DOI: 10.14745/ccdr.v50i10a05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Background In response to the COVID-19 pandemic, a new oral antiviral called nirmatrelvir-ritonavir (PaxlovidTM) was authorized for use in Canada in January 2022. In vitro studies have reported mutations in Mpro protein that may be associated with the development of nirmatrelvir resistance. Objectives To survey the prevalence, relevance and temporal patterns of Mpro mutations among SARS-CoV-2 Omicron lineages in Ontario, Canada. Methods A total of 93,082 Mpro gene sequences from December 2021 to September 2023 were analyzed. Reported in vitro Mpro mutations were screened against our database using in-house data science pipelines to determine the nirmatrelvir resistance. Negative binomial regression was conducted to analyze the temporal trends in Mpro mutation counts over the study time period. Results A declining trend was observed in non-synonymous mutations of Mpro sequences, showing a 7.9% reduction (95% CI: 6.5%-9.4%; p<0.001) every 30 days. The P132H was the most prevalent mutation (higher than 95%) in all Omicron lineages. In vitro nirmatrelvir-resistant mutations were found in 3.12% (n=29/929) Omicron lineages with very low counts, ranging from one to 19. Only two mutations, A7T (n=19) and M82I (n=9), showed temporal presence among the BA.1.1 in 2022 and the BQ.1.2.3 in 2022, respectively. Conclusion The observations suggest that, as of September 2023, no significant or widespread resistance to nirmatrelvir has developed among SARS-CoV-2 Omicron variants in Ontario. This study highlights the importance of creating automated monitoring systems to track the emergence of nirmatrelvir-resistant mutations within the SARS-CoV-2 virus, utilizing genomic data generated in real-time.
Collapse
Affiliation(s)
- Venkata Duvvuri
- Public Health Ontario, Toronto, ON
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON
| | - Fatima Shire
- Public Health Ontario, Toronto, ON
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON
| | | | | | | | | | | | | | | | - Ye Li
- Public Health Ontario, Toronto, ON
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON
| | | | | | | | | | - Aimin Li
- Public Health Ontario, Toronto, ON
| | - Austin Zygmunt
- Public Health Ontario, Toronto, ON
- Department of Family Medicine, University of Ottawa, Ottawa, ON
| | | | - Julianne Kus
- Public Health Ontario, Toronto, ON
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON
| | | | | | | | - Samir Patel
- Public Health Ontario, Toronto, ON
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON
| |
Collapse
|
8
|
Diogo MA, Cabral AGT, de Oliveira RB. Advances in the Search for SARS-CoV-2 M pro and PL pro Inhibitors. Pathogens 2024; 13:825. [PMID: 39452697 PMCID: PMC11510351 DOI: 10.3390/pathogens13100825] [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: 08/20/2024] [Revised: 09/19/2024] [Accepted: 09/22/2024] [Indexed: 10/26/2024] Open
Abstract
SARS-CoV-2 is a spherical, positive-sense, single-stranded RNA virus with a large genome, responsible for encoding both structural proteins, vital for the viral particle's architecture, and non-structural proteins, critical for the virus's replication cycle. Among the non-structural proteins, two cysteine proteases emerge as promising molecular targets for the design of new antiviral compounds. The main protease (Mpro) is a homodimeric enzyme that plays a pivotal role in the formation of the viral replication-transcription complex, associated with the papain-like protease (PLpro), a cysteine protease that modulates host immune signaling by reversing post-translational modifications of ubiquitin and interferon-stimulated gene 15 (ISG15) in host cells. Due to the importance of these molecular targets for the design and development of novel anti-SARS-CoV-2 drugs, the purpose of this review is to address aspects related to the structure, mechanism of action and strategies for the design of inhibitors capable of targeting the Mpro and PLpro. Examples of covalent and non-covalent inhibitors that are currently being evaluated in preclinical and clinical studies or already approved for therapy will be also discussed to show the advances in medicinal chemistry in the search for new molecules to treat COVID-19.
Collapse
Affiliation(s)
| | | | - Renata Barbosa de Oliveira
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (M.A.D.); (A.G.T.C.)
| |
Collapse
|
9
|
Vlasiou MC, Nikolaou G, Spanoudes K, Mavrides DE. β-Tocotrienol and δ-Tocotrienol as Additional Inhibitors of the Main Protease of Feline Infectious Peritonitis Virus: An In Silico Analysis. Vet Sci 2024; 11:424. [PMID: 39330803 PMCID: PMC11435718 DOI: 10.3390/vetsci11090424] [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: 07/08/2024] [Revised: 09/06/2024] [Accepted: 09/09/2024] [Indexed: 09/28/2024] Open
Abstract
Feline infectious peritonitis (FIP) is a severe and invariably fatal disease affecting both domestic and wild felines with limited effective therapeutic options available. By considering the significant immunomodulatory effects of vitamin E observed in both animal and human models under physiological and pathological conditions, we have provided a full in silico investigation of vitamin E and related compounds and their effect on the crystal structure of feline infectious peritonitis virus 3C-like protease (FIPV-3CLpro). This work revealed the β-tocotrienol and δ-tocotrienol analogs as inhibitor candidates for this protein, suggesting their potential as possible drug compounds against FIP or their supplementary use with current medicines against this disease.
Collapse
Affiliation(s)
- Manos C Vlasiou
- Department of Veterinary Medicine, University of Nicosia School of Veterinary Medicine, 2414 Nicosia, Cyprus
| | - Georgios Nikolaou
- Department of Veterinary Medicine, University of Nicosia School of Veterinary Medicine, 2414 Nicosia, Cyprus
| | - Kyriakos Spanoudes
- Department of Veterinary Medicine, University of Nicosia School of Veterinary Medicine, 2414 Nicosia, Cyprus
| | - Daphne E Mavrides
- Department of Veterinary Medicine, University of Nicosia School of Veterinary Medicine, 2414 Nicosia, Cyprus
| |
Collapse
|
10
|
Al Adem K, Ferreira J, Villanueva A, Fadl S, El-Sadaany F, Masmoudi I, Gidiya Y, Gurudza T, Cardoso T, Saksena N, Rabeh W. 3-chymotrypsin-like protease in SARS-CoV-2. Biosci Rep 2024; 44:BSR20231395. [PMID: 39036877 PMCID: PMC11300678 DOI: 10.1042/bsr20231395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 07/16/2024] [Accepted: 07/19/2024] [Indexed: 07/23/2024] Open
Abstract
Coronaviruses constitute a significant threat to the human population. Severe acute respiratory syndrome coronavirus-2, SARS-CoV-2, is a highly pathogenic human coronavirus that has caused the coronavirus disease 2019 (COVID-19) pandemic. It has led to a global viral outbreak with an exceptional spread and a high death toll, highlighting the need for effective antiviral strategies. 3-Chymotrypsin-like protease (3CLpro), the main protease in SARS-CoV-2, plays an indispensable role in the SARS-CoV-2 viral life cycle by cleaving the viral polyprotein to produce 11 individual non-structural proteins necessary for viral replication. 3CLpro is one of two proteases that function to produce new viral particles. It is a highly conserved cysteine protease with identical structural folds in all known human coronaviruses. Inhibitors binding with high affinity to 3CLpro will prevent the cleavage of viral polyproteins, thus impeding viral replication. Multiple strategies have been implemented to screen for inhibitors against 3CLpro, including peptide-like and small molecule inhibitors that covalently and non-covalently bind the active site, respectively. In addition, allosteric sites of 3CLpro have been identified to screen for small molecules that could make non-competitive inhibitors of 3CLpro. In essence, this review serves as a comprehensive guide to understanding the structural intricacies and functional dynamics of 3CLpro, emphasizing key findings that elucidate its role as the main protease of SARS-CoV-2. Notably, the review is a critical resource in recognizing the advancements in identifying and developing 3CLpro inhibitors as effective antiviral strategies against COVID-19, some of which are already approved for clinical use in COVID-19 patients.
Collapse
Affiliation(s)
- Kenana Al Adem
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Juliana C. Ferreira
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Adrian J. Villanueva
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Samar Fadl
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Farah El-Sadaany
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Imen Masmoudi
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Yugmee Gidiya
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Tariro Gurudza
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Thyago H.S. Cardoso
- OMICS Centre of Excellence, G42 Healthcare, Masdar City, Abu Dhabi, United Arab Emirates
| | - Nitin K. Saksena
- Victoria University, Footscray Campus, Melbourne, VIC. Australia
| | - Wael M. Rabeh
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| |
Collapse
|
11
|
Chen P, Van Oers TJ, Arutyunova E, Fischer C, Wang C, Lamer T, van Belkum MJ, Young HS, Vederas JC, Lemieux MJ. A Structural Comparison of Oral SARS-CoV-2 Drug Candidate Ibuzatrelvir Complexed with the Main Protease (M pro) of SARS-CoV-2 and MERS-CoV. JACS AU 2024; 4:3217-3227. [PMID: 39211604 PMCID: PMC11350714 DOI: 10.1021/jacsau.4c00508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/21/2024] [Accepted: 07/22/2024] [Indexed: 09/04/2024]
Abstract
Ibuzatrelvir (1) was recently disclosed and patented by Pfizer for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It has received fast-track status from the USA Food and Drug Administration (FDA) and has entered phase III clinical trials as a possible replacement for Paxlovid. Like nirmatrelvir (2) in Paxlovid, this orally active drug candidate is designed to target viral main proteases (Mpro) through reversible covalent interaction of its nitrile warhead with the active site thiol of the chymotrypsin-like cysteine protease (3CL protease). Inhibition of Mpro hinders the processing of the proteins essential for viral replication in vivo. However, ibuzatrelvir apparently does not require ritonavir (3), which is coadministered in Paxlovid to block human oxidative metabolism of nirmatrelvir. Here, we report the crystal structure of the complex of ibuzatrelvir with the active site of SARS-CoV-2 Mpro at 2.0 Å resolution. In addition, we show that ibuzatrelvir also potently inhibits the Mpro of Middle East respiratory syndrome-related coronavirus (MERS-CoV), which is fortunately not widespread but can be dangerously lethal (∼36% mortality). Co-crystal structures show that the binding mode of the drug to both active sites is similar and that the trifluoromethyl group of the inhibitor fits precisely into a critical S2 substrate binding pocket of the main proteases. However, our results also provide a rationale for the differences in potency of ibuzatrelvir for these two proteases due to minor differences in the substrate preferences leading to a weaker H-bond network in MERS-CoV Mpro. In addition, we examined the reversibility of compound binding to both proteases, which is an important parameter in reducing off-target effects as well as the potential immunogenicity. The crystal structures of the ibuzatrelvir complexes with Mpro of SARS-CoV-2 and of MERS-CoV will further assist drug design for coronaviral infections in humans and animals.
Collapse
Affiliation(s)
- Pu Chen
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li Ka
Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Tayla J. Van Oers
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Elena Arutyunova
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li Ka
Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Conrad Fischer
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Chaoxiang Wang
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Tess Lamer
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Marco J. van Belkum
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Howard S. Young
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - John C. Vederas
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - M. Joanne Lemieux
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li Ka
Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| |
Collapse
|
12
|
Yang Y, Luo YD, Zhang CB, Xiang Y, Bai XY, Zhang D, Fu ZY, Hao RB, Liu XL. Progress in Research on Inhibitors Targeting SARS-CoV-2 Main Protease (M pro). ACS OMEGA 2024; 9:34196-34219. [PMID: 39157135 PMCID: PMC11325518 DOI: 10.1021/acsomega.4c03023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 07/12/2024] [Accepted: 07/19/2024] [Indexed: 08/20/2024]
Abstract
Since 2019, the novel coronavirus (SARS-CoV-2) has caused significant morbidity and millions of deaths worldwide. The Coronavirus Disease 2019 (COVID-19), caused by SARS-CoV-2 and its variants, has further highlighted the urgent need for the development of effective therapeutic agents. Currently, the highly conserved and broad-spectrum nature of main proteases (Mpro) renders them of great importance in the field of inhibitor study. In this study, we categorize inhibitors targeting Mpro into three major groups: mimetic, nonmimetic, and natural inhibitors. We then present the research progress of these inhibitors in detail, including their mechanism of action, antiviral activity, pharmacokinetic properties, animal experiments, and clinical studies. This review aims to provide valuable insights and potential avenues for the development of more effective antiviral drugs against SARS-CoV-2.
Collapse
Affiliation(s)
- Yue Yang
- School
of Medicine, Yan’an University, Yan’an 716000, China
| | - Yi-Dan Luo
- School
of Medicine, Yan’an University, Yan’an 716000, China
| | - Chen-Bo Zhang
- School
of Medicine, Yan’an University, Yan’an 716000, China
| | - Yang Xiang
- School
of Medicine, Yan’an University, Yan’an 716000, China
- College
of Physical Education, Yan’an University, Yan’an 716000, China
| | - Xin-Yue Bai
- School
of Medicine, Yan’an University, Yan’an 716000, China
| | - Die Zhang
- School
of Medicine, Yan’an University, Yan’an 716000, China
| | - Zhao-Ying Fu
- School
of Medicine, Yan’an University, Yan’an 716000, China
| | - Ruo-Bing Hao
- School
of Medicine, Yan’an University, Yan’an 716000, China
| | - Xiao-Long Liu
- School
of Medicine, Yan’an University, Yan’an 716000, China
| |
Collapse
|
13
|
Huang L, Gish M, Boehlke J, Jeep RH, Chen C. Assay Development and Validation for Innovative Antiviral Development Targeting the N-Terminal Autoprocessing of SARS-CoV-2 Main Protease Precursors. Viruses 2024; 16:1218. [PMID: 39205192 PMCID: PMC11359197 DOI: 10.3390/v16081218] [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: 06/04/2024] [Revised: 07/14/2024] [Accepted: 07/23/2024] [Indexed: 09/04/2024] Open
Abstract
The SARS-CoV-2 main protease (Mpro) is initially synthesized as part of polyprotein precursors that undergo autoproteolysis to release the free mature Mpro. To investigate the autoprocessing mechanism in transfected mammalian cells, we examined several fusion precursors, with the mature SARS-CoV-2 Mpro along with the flanking amino acids (to keep the native substrate sequences) sandwiched between different tags. Our analyses revealed differential proteolysis kinetics at the N- and C-terminal cleavage sites. Particularly, N-terminal processing is differentially influenced by various upstream fusion tags (GST, sGST, CD63, and Nsp4) and amino acid variations at the N-terminal P1 position, suggesting that precursor catalysis is flexible and subject to complex regulation. Mutating Q to E at the N-terminal P1 position altered both precursor catalysis and the properties of the released Mpro. Interestingly, the wild-type precursors exhibited different enzymatic activities compared to those of the released Mpro, displaying much lower susceptibility to known inhibitors targeting the mature form. These findings suggest the precursors as alternative targets for antiviral development. Accordingly, we developed and validated a high-throughput screening (HTS)-compatible platform for functional screening of compounds targeting either the N-terminal processing of the SARS-CoV-2 Mpro precursor autoprocessing or the released mature Mpro through different mechanisms of action.
Collapse
Affiliation(s)
| | | | | | | | - Chaoping Chen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA; (L.H.); (M.G.); (J.B.); (R.H.J.)
| |
Collapse
|
14
|
Lin C, Zhu Z, Jiang H, Zou X, Zeng X, Wang J, Zeng P, Li W, Zhou X, Zhang J, Wang Q, Li J. Structural Basis for Coronaviral Main Proteases Inhibition by the 3CLpro Inhibitor GC376. J Mol Biol 2024; 436:168474. [PMID: 38311236 DOI: 10.1016/j.jmb.2024.168474] [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: 01/09/2024] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 02/10/2024]
Abstract
The main protease (Mpro) of coronaviruses participates in viral replication, serving as a hot target for drug design. GC376 is able to effectively inhibit the activity of Mpro, which is due to nucleophilic addition of GC376 by binding covalently with Cys145 in Mpro active site. Here, we used fluorescence resonance energy transfer (FRET) assay to analyze the IC50 values of GC376 against Mpros from six different coronaviruses (SARS-CoV-2, HCoV-229E, HCoV-HUK1, MERS-CoV, SARS-CoV, HCoV-NL63) and five Mpro mutants (G15S, M49I, K90R, P132H, S46F) from SARS-CoV-2 variants. The results showed that GC376 displays effective inhibition to various coronaviral Mpros and SARS-CoV-2 Mpro mutants. In addition, the crystal structures of SARS-CoV-2 Mpro (wide type)-GC376, SARS-CoV Mpro-GC376, MERS-CoV Mpro-GC376, and SARS-CoV-2 Mpro mutants (G15S, M49I, S46F, K90R, and P132H)-GC376 complexes were solved. We found that GC376 is able to fit into the active site of Mpros from different coronaviruses and different SARS-CoV-2 variants properly. Detailed structural analysis revealed key molecular determinants necessary for inhibition and illustrated the binding patterns of GC376 to these different Mpros. In conclusion, we not only proved the inhibitory activity of GC376 against different Mpros including SARS-CoV-2 Mpro mutants, but also revealed the molecular mechanism of inhibition by GC376, which will provide scientific guidance for the development of broad-spectrum drugs against SARS-CoV-2 as well as other coronaviruses.
Collapse
Affiliation(s)
- Cheng Lin
- College of Pharmacy, Gannan Medical University, Ganzhou 341000, China
| | - Zhimin Zhu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Haihai Jiang
- School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330031, China
| | - Xiaofang Zou
- Shenzhen Crystalo Biopharmaceutical Co, Ltd, Shenzhen 518118, China; Jiangxi Jmerry Biopharmaceutical Co, Ltd, Ganzhou 341000, China
| | - Xiangyi Zeng
- Shenzhen Crystalo Biopharmaceutical Co, Ltd, Shenzhen 518118, China; Jiangxi Jmerry Biopharmaceutical Co, Ltd, Ganzhou 341000, China
| | - Jie Wang
- Shenzhen Crystalo Biopharmaceutical Co, Ltd, Shenzhen 518118, China; Jiangxi Jmerry Biopharmaceutical Co, Ltd, Ganzhou 341000, China
| | - Pei Zeng
- Shenzhen Crystalo Biopharmaceutical Co, Ltd, Shenzhen 518118, China; Jiangxi Jmerry Biopharmaceutical Co, Ltd, Ganzhou 341000, China
| | - Wenwen Li
- Shenzhen Crystalo Biopharmaceutical Co, Ltd, Shenzhen 518118, China; Jiangxi Jmerry Biopharmaceutical Co, Ltd, Ganzhou 341000, China
| | - Xuelan Zhou
- Shenzhen Crystalo Biopharmaceutical Co, Ltd, Shenzhen 518118, China; Jiangxi Jmerry Biopharmaceutical Co, Ltd, Ganzhou 341000, China
| | - Jin Zhang
- School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330031, China.
| | - Qisheng Wang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China; Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China.
| | - Jian Li
- College of Pharmacy, Gannan Medical University, Ganzhou 341000, China.
| |
Collapse
|
15
|
Nguyen HH, Tufts J, Minh DDL. On Inactivation of the Coronavirus Main Protease. J Chem Inf Model 2024; 64:1644-1656. [PMID: 38423522 PMCID: PMC10936523 DOI: 10.1021/acs.jcim.3c01518] [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: 10/05/2023] [Revised: 01/12/2024] [Accepted: 01/24/2024] [Indexed: 03/02/2024]
Abstract
A deeper understanding of the inactive conformations of the coronavirus main protease (MPro) could inform the design of allosteric drugs. Based on extensive molecular dynamics simulations, we built a Markov State Model to investigate structural changes that can inactivate the SARS-CoV-2 MPro. In a subset of structures, one subunit of the homodimer assumes an inactive conformation that resembles an inactive crystal structure. However, contradicting the widely held half-of-sites activity hypothesis, the most populated enzyme structures have two active subunits. We then used transition path theory (TPT) and the Jensen-Shannon Divergence (JSD) to pinpoint residues involved in the inactivation process. A π stack between Phe140 and His163 is a key feature that can distinguish active and inactive conformations of MPro. Each subunit has unique inactive conformations stabilized by π stacking interactions involving residues Phe140, Tyr118, His163, and His172, a hydrogen bonding network centered around His163 and His172, and a modified network of interactions in the dimer interface. The importance of these residues in maintaining an active structure explains the sensitivity of enzymatic activity to site-directed mutagenesis.
Collapse
Affiliation(s)
- Hong Ha Nguyen
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - Jim Tufts
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - David D. L. Minh
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| |
Collapse
|
16
|
Albani S, Costanzi E, Hoang GL, Kuzikov M, Frings M, Ansari N, Demitri N, Nguyen TT, Rizzi V, Schulz JB, Bolm C, Zaliani A, Carloni P, Storici P, Rossetti G. Unexpected Single-Ligand Occupancy and Negative Cooperativity in the SARS-CoV-2 Main Protease. J Chem Inf Model 2024; 64:892-904. [PMID: 38051605 PMCID: PMC10865365 DOI: 10.1021/acs.jcim.3c01497] [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: 09/22/2023] [Revised: 11/20/2023] [Accepted: 11/20/2023] [Indexed: 12/07/2023]
Abstract
Many homodimeric enzymes tune their functions by exploiting either negative or positive cooperativity between subunits. In the SARS-CoV-2 Main protease (Mpro) homodimer, the latter has been suggested by symmetry in most of the 500 reported protease/ligand complex structures solved by macromolecular crystallography (MX). Here we apply the latter to both covalent and noncovalent ligands in complex with Mpro. Strikingly, our experiments show that the occupation of both active sites of the dimer originates from an excess of ligands. Indeed, cocrystals obtained using a 1:1 ligand/protomer stoichiometry lead to single occupation only. The empty binding site exhibits a catalytically inactive geometry in solution, as suggested by molecular dynamics simulations. Thus, Mpro operates through negative cooperativity with the asymmetric activity of the catalytic sites. This allows it to function with a wide range of substrate concentrations, making it resistant to saturation and potentially difficult to shut down, all properties advantageous for the virus' adaptability and resistance.
Collapse
Affiliation(s)
- Simone Albani
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich 52425, Germany
- Faculty
of Mathematics, Computer Science and Natural Sciences, RWTH Aachen, Aachen 52062, Germany
| | - Elisa Costanzi
- Elettra–Sincrotrone
Trieste S.C.p.A., SS 14 – km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Gia Linh Hoang
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
| | - Maria Kuzikov
- Fraunhofer
Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, Frankfurt 60590, Germany
- Constructor University, School of Science, Campus Ring 1, Bremen 28759, Germany
| | - Marcus Frings
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, Aachen 52074, Germany
| | - Narjes Ansari
- Atomistic
Simulations, Italian Institute of Technology, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Nicola Demitri
- Elettra–Sincrotrone
Trieste S.C.p.A., SS 14 – km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Toan T. Nguyen
- Key
Laboratory for Multiscale Simulation of Complex Systems, and Department
of Theoretical Physics, Faculty of Physics, University of Science, Vietnam National University – Hanoi, 334 Nguyen Trai Street, Thanh Xuan, Hanoi 11400, Vietnam
| | - Valerio Rizzi
- School
of Pharmaceutical Sciences, University of
Geneva, Rue Michel Servet 1, 1206 Genève, Switzerland
| | - Jörg B. Schulz
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
- Department
of Neurology, Medical Faculty, RWTH Aachen
University, Aachen 52074, Germany
| | - Carsten Bolm
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, Aachen 52074, Germany
| | - Andrea Zaliani
- Fraunhofer
Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, Hamburg 22525, Germany
- Fraunhofer
Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, Frankfurt 60590, Germany
| | - Paolo Carloni
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich 52425, Germany
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
- Key
Laboratory for Multiscale Simulation of Complex Systems, and Department
of Theoretical Physics, Faculty of Physics, University of Science, Vietnam National University – Hanoi, 334 Nguyen Trai Street, Thanh Xuan, Hanoi 11400, Vietnam
| | - Paola Storici
- Elettra–Sincrotrone
Trieste S.C.p.A., SS 14 – km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Giulia Rossetti
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich 52425, Germany
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
- Department
of Neurology, Medical Faculty, RWTH Aachen
University, Aachen 52074, Germany
- Jülich
Supercomputing Center (JSC), Forschungszentrum
Jülich, Jülich 52425, Germany
| |
Collapse
|
17
|
Samrat SK, Bashir Q, Zhang R, Huang Y, Liu Y, Wu X, Brown T, Wang W, Zheng YG, Zhang QY, Chen Y, Li Z, Li H. A universal fluorescence polarization high throughput screening assay to target the SAM-binding sites of SARS-CoV-2 and other viral methyltransferases. Emerg Microbes Infect 2023; 12:2204164. [PMID: 37060263 PMCID: PMC10165934 DOI: 10.1080/22221751.2023.2204164] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 04/16/2023]
Abstract
SARS-CoV-2 has caused a global pandemic with significant humanity and economic loss since 2020. Currently, only limited options are available to treat SARS-CoV-2 infections for vulnerable populations. In this study, we report a universal fluorescence polarization (FP)-based high throughput screening (HTS) assay for SAM-dependent viral methyltransferases (MTases), using a fluorescent SAM-analogue, FL-NAH. We performed the assay against a reference MTase, NSP14, an essential enzyme for SARS-CoV-2 to methylate the N7 position of viral 5'-RNA guanine cap. The assay is universal and suitable for any SAM-dependent viral MTases such as the SARS-CoV-2 NSP16/NSP10 MTase complex and the NS5 MTase of Zika virus (ZIKV). Pilot screening demonstrated that the HTS assay was very robust and identified two candidate inhibitors, NSC 111552 and 288387. The two compounds inhibited the FL-NAH binding to the NSP14 MTase with low micromolar IC50. We used three functional MTase assays to unambiguously verified the inhibitory potency of these molecules for the NSP14 N7-MTase function. Binding studies indicated that these molecules are bound directly to the NSP14 MTase with similar low micromolar affinity. Moreover, we further demonstrated that these molecules significantly inhibited the SARS-CoV-2 replication in cell-based assays at concentrations not causing cytotoxicity. Furthermore, NSC111552 significantly synergized with known SARS-CoV-2 drugs including nirmatrelvir and remdesivir. Finally, docking suggested that these molecules bind specifically to the SAM-binding site on the NSP14 MTase. Overall, these molecules represent novel and promising candidates to further develop broad-spectrum inhibitors for the management of viral infections.
Collapse
Affiliation(s)
- Subodh Kumar Samrat
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Qamar Bashir
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Ran Zhang
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Yiding Huang
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Yuchen Liu
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Xiangmeng Wu
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Tyler Brown
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA, USA
| | - Wei Wang
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Y. George Zheng
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA, USA
| | - Qing-Yu Zhang
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Yin Chen
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Zhong Li
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Hongmin Li
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
- Department of Chemistry and Biochemistry, College of Science & College of Medicine, The University of Arizona, Tucson, AZ, USA
- The BIO5 Institute, The University of Arizona, Tucson, AZ, USA
| |
Collapse
|
18
|
Reinke PYA, de Souza EE, Günther S, Falke S, Lieske J, Ewert W, Loboda J, Herrmann A, Rahmani Mashhour A, Karničar K, Usenik A, Lindič N, Sekirnik A, Botosso VF, Santelli GMM, Kapronezai J, de Araújo MV, Silva-Pereira TT, Filho AFDS, Tavares MS, Flórez-Álvarez L, de Oliveira DBL, Durigon EL, Giaretta PR, Heinemann MB, Hauser M, Seychell B, Böhler H, Rut W, Drag M, Beck T, Cox R, Chapman HN, Betzel C, Brehm W, Hinrichs W, Ebert G, Latham SL, Guimarães AMDS, Turk D, Wrenger C, Meents A. Calpeptin is a potent cathepsin inhibitor and drug candidate for SARS-CoV-2 infections. Commun Biol 2023; 6:1058. [PMID: 37853179 PMCID: PMC10584882 DOI: 10.1038/s42003-023-05317-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 09/01/2023] [Indexed: 10/20/2023] Open
Abstract
Several drug screening campaigns identified Calpeptin as a drug candidate against SARS-CoV-2. Initially reported to target the viral main protease (Mpro), its moderate activity in Mpro inhibition assays hints at a second target. Indeed, we show that Calpeptin is an extremely potent cysteine cathepsin inhibitor, a finding additionally supported by X-ray crystallography. Cell infection assays proved Calpeptin's efficacy against SARS-CoV-2. Treatment of SARS-CoV-2-infected Golden Syrian hamsters with sulfonated Calpeptin at a dose of 1 mg/kg body weight reduces the viral load in the trachea. Despite a higher risk of side effects, an intrinsic advantage in targeting host proteins is their mutational stability in contrast to highly mutable viral targets. Here we show that the inhibition of cathepsins, a protein family of the host organism, by calpeptin is a promising approach for the treatment of SARS-CoV-2 and potentially other viral infections.
Collapse
Affiliation(s)
- Patrick Y A Reinke
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Edmarcia Elisa de Souza
- Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil
| | - Sebastian Günther
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Sven Falke
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Julia Lieske
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Wiebke Ewert
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Jure Loboda
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Jamova 39, Ljubljana, Slovenia
| | | | - Aida Rahmani Mashhour
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Katarina Karničar
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000, Ljubljana, Slovenia
| | - Aleksandra Usenik
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000, Ljubljana, Slovenia
| | - Nataša Lindič
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia
| | - Andreja Sekirnik
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia
| | - Viviane Fongaro Botosso
- Virology Laboratory, Center of Development and Innovation, Butantan Institute, São Paulo, Brazil
| | - Gláucia Maria Machado Santelli
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Josana Kapronezai
- Virology Laboratory, Center of Development and Innovation, Butantan Institute, São Paulo, Brazil
| | - Marcelo Valdemir de Araújo
- Virology Laboratory, Center of Development and Innovation, Butantan Institute, São Paulo, Brazil
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Taiana Tainá Silva-Pereira
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, São Paulo, Brazil
| | | | - Mariana Silva Tavares
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Lizdany Flórez-Álvarez
- Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil
| | | | - Edison Luiz Durigon
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Paula Roberta Giaretta
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, 4474 TAMU, School Station, TX, USA
| | - Marcos Bryan Heinemann
- Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, São Paulo, Brazil
| | - Maurice Hauser
- Institute for Organic Chemistry and BMWZ, Leibniz University of Hannover, Schneiderberg 38, 30167, Hannover, Germany
| | - Brandon Seychell
- Department of Chemistry, Institute of Physical Chemistry, Universität Hamburg, Grindelallee 117, 20146, Hamburg, Germany
| | - Hendrik Böhler
- Department of Chemistry, Institute of Physical Chemistry, Universität Hamburg, Grindelallee 117, 20146, Hamburg, Germany
| | - Wioletta Rut
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - Marcin Drag
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - Tobias Beck
- Department of Chemistry, Institute of Physical Chemistry, Universität Hamburg, Grindelallee 117, 20146, Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Russell Cox
- Institute for Organic Chemistry and BMWZ, Leibniz University of Hannover, Schneiderberg 38, 30167, Hannover, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Christian Betzel
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Universität Hamburg, 22607, Hamburg, Germany
| | - Wolfgang Brehm
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Winfried Hinrichs
- Universität Greifswald, Institute of Biochemistry, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Gregor Ebert
- Institute of Virology, Helmholtz Munich, Munich, Germany
- Institute of Virology, Technical University of Munich, Munich, Germany
| | - Sharissa L Latham
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent's Hospital Clinical School, UNSW, Sydney, NSW, Australia
| | - Ana Marcia de Sá Guimarães
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Dusan Turk
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia.
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000, Ljubljana, Slovenia.
| | - Carsten Wrenger
- Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil.
| | - Alke Meents
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.
| |
Collapse
|
19
|
Van Oers TJ, Piercey A, Belovodskiy A, Reiz B, Donnelly BL, Vuong W, Lemieux MJ, Nieman JA, Auclair K, Vederas JC. Deuteration for Metabolic Stabilization of SARS-CoV-2 Inhibitors GC373 and Nirmatrelvir. Org Lett 2023; 25:5885-5889. [PMID: 37523471 DOI: 10.1021/acs.orglett.3c02140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Nirmatrelvir and GC373 inhibit the SARS-CoV-2 3CL protease and hinder viral replication in COVID-19. As nirmatrelvir in Paxlovid is oxidized by cytochrome P450 3A4, ritonavir is coadministered to block this. However, ritonavir undesirably alters the metabolism of other drugs. Hydrogens can be replaced with deuterium in nirmatrelvir and GC373 to slow oxidation. Results show that deuterium slows oxidation of nirmatrelvir adjacent to nitrogen by ∼40% and that the type of warhead can switch the site of oxidative metabolism.
Collapse
Affiliation(s)
- Tayla J Van Oers
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Alexia Piercey
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Alexandr Belovodskiy
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Béla Reiz
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Bethan L Donnelly
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Wayne Vuong
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - James A Nieman
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Karine Auclair
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - John C Vederas
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| |
Collapse
|
20
|
Chen S, Arutyunova E, Lu J, Khan MB, Rut W, Zmudzinski M, Shahbaz S, Iyyathurai J, Moussa EW, Turner Z, Bai B, Lamer T, Nieman JA, Vederas JC, Julien O, Drag M, Elahi S, Young HS, Lemieux MJ. SARS-CoV-2 M pro Protease Variants of Concern Display Altered Viral Substrate and Cell Host Target Galectin-8 Processing but Retain Sensitivity toward Antivirals. ACS CENTRAL SCIENCE 2023; 9:696-708. [PMID: 37122453 PMCID: PMC10042146 DOI: 10.1021/acscentsci.3c00054] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Indexed: 05/03/2023]
Abstract
The main protease of SARS-CoV-2 (Mpro) is the most promising drug target against coronaviruses due to its essential role in virus replication. With newly emerging variants there is a concern that mutations in Mpro may alter the structural and functional properties of protease and subsequently the potency of existing and potential antivirals. We explored the effect of 31 mutations belonging to 5 variants of concern (VOCs) on catalytic parameters and substrate specificity, which revealed changes in substrate binding and the rate of cleavage of a viral peptide. Crystal structures of 11 Mpro mutants provided structural insight into their altered functionality. Additionally, we show Mpro mutations influence proteolysis of an immunomodulatory host protein Galectin-8 (Gal-8) and a subsequent significant decrease in cytokine secretion, providing evidence for alterations in the escape of host-antiviral mechanisms. Accordingly, mutations associated with the Gamma VOC and highly virulent Delta VOC resulted in a significant increase in Gal-8 cleavage. Importantly, IC50s of nirmatrelvir (Pfizer) and our irreversible inhibitor AVI-8053 demonstrated no changes in potency for both drugs for all mutants, suggesting Mpro will remain a high-priority antiviral drug candidate as SARS-CoV-2 evolves.
Collapse
Affiliation(s)
- Sizhu
Amelia Chen
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Elena Arutyunova
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Jimmy Lu
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Muhammad Bashir Khan
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Wioletta Rut
- Department
of Chemical Biology and Bioimaging, Wroclaw
University of Science and Technology, Wroclaw, 50-370, Poland
| | - Mikolaj Zmudzinski
- Department
of Chemical Biology and Bioimaging, Wroclaw
University of Science and Technology, Wroclaw, 50-370, Poland
| | - Shima Shahbaz
- Department
of Dentistry & Dental Hygiene, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Jegan Iyyathurai
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Eman W. Moussa
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Zoe Turner
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Bing Bai
- Li
Ka Shing Applied Virology Institute, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
- Department
of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Tess Lamer
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - James A. Nieman
- Li
Ka Shing Applied Virology Institute, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
- Department
of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - John C. Vederas
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Olivier Julien
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Marcin Drag
- Department
of Chemical Biology and Bioimaging, Wroclaw
University of Science and Technology, Wroclaw, 50-370, Poland
| | - Shokrollah Elahi
- Department
of Dentistry & Dental Hygiene, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Howard S. Young
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - M. Joanne Lemieux
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| |
Collapse
|
21
|
Paciaroni A, Libera V, Ripanti F, Orecchini A, Petrillo C, Francisci D, Schiaroli E, Sabbatini S, Gidari A, Bianconi E, Macchiarulo A, Hussain R, Silvestrini L, Moretti P, Belhaj N, Vercelli M, Roque Y, Mariani P, Comez L, Spinozzi F. Stabilization of the Dimeric State of SARS-CoV-2 Main Protease by GC376 and Nirmatrelvir. Int J Mol Sci 2023; 24:ijms24076062. [PMID: 37047038 PMCID: PMC10093836 DOI: 10.3390/ijms24076062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/10/2023] [Accepted: 03/21/2023] [Indexed: 04/14/2023] Open
Abstract
The main protease (Mpro or 3CLpro) is an enzyme that is evolutionarily conserved among different genera of coronaviruses. As it is essential for processing and maturing viral polyproteins, Mpro has been identified as a promising target for the development of broad-spectrum drugs against coronaviruses. Like SARS-CoV and MERS-CoV, the mature and active form of SARS-CoV-2 Mpro is a dimer composed of identical subunits, each with a single active site. Individual monomers, however, have very low or no catalytic activity. As such, inhibition of Mpro can be achieved by molecules that target the substrate binding pocket to block catalytic activity or target the dimerization process. In this study, we investigated GC376, a transition-state analog inhibitor of the main protease of feline infectious peritonitis coronavirus, and Nirmatrelvir (NMV), an oral, bioavailable SARS-CoV-2 Mpro inhibitor with pan-human coronavirus antiviral activity. Our results show that both GC376 and NMV are capable of strongly binding to SARS-CoV-2 Mpro and altering the monomer-dimer equilibrium by stabilizing the dimeric state. This behavior is proposed to be related to a structured hydrogen-bond network established at the Mpro active site, where hydrogen bonds between Ser1' and Glu166/Phe140 are formed in addition to those achieved by the latter residues with GC376 or NMV.
Collapse
Affiliation(s)
- Alessandro Paciaroni
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Valeria Libera
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
- Istituto Officina dei Materiali-IOM, National Research Council-CNR, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Francesca Ripanti
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Andrea Orecchini
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Caterina Petrillo
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Daniela Francisci
- Department of Medicine and Surgery, Clinic of Infectious Diseases, University of Perugia, Piazzale Gambuli, 06129 Perugia, Italy
| | - Elisabetta Schiaroli
- Department of Medicine and Surgery, Clinic of Infectious Diseases, University of Perugia, Piazzale Gambuli, 06129 Perugia, Italy
| | - Samuele Sabbatini
- Department of Medicine and Surgery, Medical Microbiology Section, University of Perugia, Piazzale Gambuli, 06129 Perugia, Italy
| | - Anna Gidari
- Department of Medicine and Surgery, Clinic of Infectious Diseases, University of Perugia, Piazzale Gambuli, 06129 Perugia, Italy
| | - Elisa Bianconi
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo, 06123 Perugia, Italy
| | - Antonio Macchiarulo
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo, 06123 Perugia, Italy
| | - Rohanah Hussain
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Lucia Silvestrini
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 12, 60131 Ancona, Italy
| | - Paolo Moretti
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 12, 60131 Ancona, Italy
| | - Norhan Belhaj
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 12, 60131 Ancona, Italy
| | - Matteo Vercelli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 12, 60131 Ancona, Italy
| | - Yessica Roque
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 12, 60131 Ancona, Italy
| | - Paolo Mariani
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 12, 60131 Ancona, Italy
| | - Lucia Comez
- Istituto Officina dei Materiali-IOM, National Research Council-CNR, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Francesco Spinozzi
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 12, 60131 Ancona, Italy
| |
Collapse
|
22
|
Zvornicanin SN, Shaqra AM, Huang QJ, Ornelas E, Moghe M, Knapp M, Moquin S, Dovala D, Schiffer CA, Kurt Yilmaz N. Crystal Structures of Inhibitor-Bound Main Protease from Delta- and Gamma-Coronaviruses. Viruses 2023; 15:781. [PMID: 36992489 PMCID: PMC10059799 DOI: 10.3390/v15030781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 03/31/2023] Open
Abstract
With the spread of SARS-CoV-2 throughout the globe causing the COVID-19 pandemic, the threat of zoonotic transmissions of coronaviruses (CoV) has become even more evident. As human infections have been caused by alpha- and beta-CoVs, structural characterization and inhibitor design mostly focused on these two genera. However, viruses from the delta and gamma genera also infect mammals and pose a potential zoonotic transmission threat. Here, we determined the inhibitor-bound crystal structures of the main protease (Mpro) from the delta-CoV porcine HKU15 and gamma-CoV SW1 from the beluga whale. A comparison with the apo structure of SW1 Mpro, which is also presented here, enabled the identification of structural arrangements upon inhibitor binding at the active site. The cocrystal structures reveal binding modes and interactions of two covalent inhibitors, PF-00835231 (active form of lufotrelvir) bound to HKU15, and GC376 bound to SW1 Mpro. These structures may be leveraged to target diverse coronaviruses and toward the structure-based design of pan-CoV inhibitors.
Collapse
Affiliation(s)
- Sarah N. Zvornicanin
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Ala M. Shaqra
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Qiuyu J. Huang
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Elizabeth Ornelas
- Novartis Institutes for Biomedical Research, Emeryville, CA 94608, USA
| | - Mallika Moghe
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Mark Knapp
- Novartis Institutes for Biomedical Research, Emeryville, CA 94608, USA
| | - Stephanie Moquin
- Novartis Institutes for Biomedical Research, Emeryville, CA 94608, USA
| | - Dustin Dovala
- Novartis Institutes for Biomedical Research, Emeryville, CA 94608, USA
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| |
Collapse
|
23
|
Massai L, Grifagni D, De Santis A, Geri A, Cantini F, Calderone V, Banci L, Messori L. Gold-Based Metal Drugs as Inhibitors of Coronavirus Proteins: The Inhibition of SARS-CoV-2 Main Protease by Auranofin and Its Analogs. Biomolecules 2022; 12:1675. [PMID: 36421689 PMCID: PMC9687241 DOI: 10.3390/biom12111675] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/04/2022] [Accepted: 11/08/2022] [Indexed: 08/08/2023] Open
Abstract
Gold compounds have a long tradition in medicine and offer many opportunities for new therapeutic applications. Herein, we evaluated the lead compound Auranofin and five related gold(I) complexes as possible inhibitors of SARS-CoV-2 Main Protease (SARS-CoV-2 Mpro), a validated drug target for the COVID-19 disease. The investigational panel of gold compounds included Auranofin; three halido analogues, i.e., Au(PEt3)Cl, Au(PEt3)Br, and Au(PEt3)I; and two gold carbene complexes, i.e., Au(NHC)Cl and [Au(NHC)2]PF6. Notably, all these gold compounds, with the only exception of [Au(NHC)2]PF6, turned out to be potent inhibitors of the catalytic activity of SARS-CoV-2 Mpro: the measured Ki values were in the range 2.1-0.4 μM. The reactions of the various gold compounds with SARS-CoV-2 Mpro were subsequently investigated through electrospray ionization (ESI) mass spectrometry (MS) upon a careful optimization of the experimental conditions; the ESI MS spectra provided clear evidence for the formation of tight metallodrug-protein adducts and for the coordination of well defined gold-containing fragments to the SARS-CoV-2 Mpro, again with the only exception of [Au(NHC)2]PF6, The metal-protein stoichiometry was unambiguously determined for the resulting species. The crystal structures of the metallodrug- Mpro adducts were solved in the case of Au(PEt3)Br and Au(NHC)Cl. These crystal structures show that gold coordination occurs at the level of catalytic Cys 145 in the case of Au(NHC)Cl and at the level of both Cys 145 and Cys 156 for Au(PEt3)Br. Tight coordination of gold atoms to functionally relevant cysteine residues is believed to represent the true molecular basis of strong enzyme inhibition.
Collapse
Affiliation(s)
- Lara Massai
- Department of Chemistry “Ugo Schiff”, University of Florence, Via Della Lastruccia 3, 50019 Florence, Italy
| | - Deborah Grifagni
- Department of Chemistry “Ugo Schiff”, University of Florence, Via Della Lastruccia 3, 50019 Florence, Italy
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Alessia De Santis
- Department of Chemistry “Ugo Schiff”, University of Florence, Via Della Lastruccia 3, 50019 Florence, Italy
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Andrea Geri
- Department of Chemistry “Ugo Schiff”, University of Florence, Via Della Lastruccia 3, 50019 Florence, Italy
| | - Francesca Cantini
- Department of Chemistry “Ugo Schiff”, University of Florence, Via Della Lastruccia 3, 50019 Florence, Italy
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), University of Florence, Via L. Sacconi 6, 50019 Florence, Italy
| | - Vito Calderone
- Department of Chemistry “Ugo Schiff”, University of Florence, Via Della Lastruccia 3, 50019 Florence, Italy
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), University of Florence, Via L. Sacconi 6, 50019 Florence, Italy
| | - Lucia Banci
- Department of Chemistry “Ugo Schiff”, University of Florence, Via Della Lastruccia 3, 50019 Florence, Italy
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), University of Florence, Via L. Sacconi 6, 50019 Florence, Italy
| | - Luigi Messori
- Department of Chemistry “Ugo Schiff”, University of Florence, Via Della Lastruccia 3, 50019 Florence, Italy
| |
Collapse
|
24
|
Abstract
SignificanceThe coronavirus main protease (Mpro) is required for viral replication. Here, we obtained the extended conformation of the native monomer of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Mpro by trapping it with nanobodies and found that the catalytic domain and the helix domain dissociate, revealing allosteric targets. Another monomeric state is termed compact conformation and is similar to one protomer of the dimeric form. We designed a Nanoluc Binary Techonology (NanoBiT)-based high-throughput allosteric inhibitor assay based on structural conformational change. Our results provide insight into the maturation, dimerization, and catalysis of the coronavirus Mpro and pave a way to develop an anticoronaviral drug through targeting the maturation process to inhibit the autocleavage of Mpro.
Collapse
|
25
|
Lu J, Chen SA, Khan MB, Brassard R, Arutyunova E, Lamer T, Vuong W, Fischer C, Young HS, Vederas JC, Lemieux MJ. Crystallization of Feline Coronavirus M pro With GC376 Reveals Mechanism of Inhibition. Front Chem 2022; 10:852210. [PMID: 35281564 PMCID: PMC8907848 DOI: 10.3389/fchem.2022.852210] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/01/2022] [Indexed: 12/28/2022] Open
Abstract
Coronaviruses infect a variety of hosts in the animal kingdom, and while each virus is taxonomically different, they all infect their host via the same mechanism. The coronavirus main protease (Mpro, also called 3CLpro), is an attractive target for drug development due to its essential role in mediating viral replication and transcription. An Mpro inhibitor, GC376, has been shown to treat feline infectious peritonitis (FIP), a fatal infection in cats caused by internal mutations in the feline enteric coronavirus (FECV). Recently, our lab demonstrated that the feline drug, GC373, and prodrug, GC376, are potent inhibitors of SARS-CoV-2 Mpro and solved the structures in complex with the drugs; however, no crystal structures of the FIP virus (FIPV) Mpro with the feline drugs have been published so far. Here, we present crystal structures of FIPV Mpro-GC373/GC376 complexes, revealing the inhibitors covalently bound to Cys144 in the active site, similar to SARS-CoV-2 Mpro. Additionally, GC376 has a higher affinity for FIPV Mpro with lower nanomolar Ki values compared to SARS-CoV and SARS-CoV-2 Mpro. We also show that improved derivatives of GC376 have higher potency for FIPV Mpro. Since GC373 and GC376 represent strong starting points for structure-guided drug design, determining the crystal structures of FIPV Mpro with these inhibitors are important steps in drug optimization and structure-based broad-spectrum antiviral drug discovery.
Collapse
Affiliation(s)
- Jimmy Lu
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
| | - Sizhu Amelia Chen
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
| | | | - Raelynn Brassard
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
| | - Elena Arutyunova
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
| | - Tess Lamer
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Wayne Vuong
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Conrad Fischer
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Howard S. Young
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - John C. Vederas
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - M. Joanne Lemieux
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
| |
Collapse
|
26
|
Bai B, Belovodskiy A, Hena M, Kandadai AS, Joyce MA, Saffran HA, Shields JA, Khan MB, Arutyunova E, Lu J, Bajwa SK, Hockman D, Fischer C, Lamer T, Vuong W, van Belkum MJ, Gu Z, Lin F, Du Y, Xu J, Rahim M, Young HS, Vederas JC, Tyrrell DL, Lemieux MJ, Nieman JA. Peptidomimetic α-Acyloxymethylketone Warheads with Six-Membered Lactam P1 Glutamine Mimic: SARS-CoV-2 3CL Protease Inhibition, Coronavirus Antiviral Activity, and in Vitro Biological Stability. J Med Chem 2022; 65:2905-2925. [PMID: 34242027 PMCID: PMC8291138 DOI: 10.1021/acs.jmedchem.1c00616] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Indexed: 12/11/2022]
Abstract
Recurring coronavirus outbreaks, such as the current COVID-19 pandemic, establish a necessity to develop direct-acting antivirals that can be readily administered and are active against a broad spectrum of coronaviruses. Described in this Article are novel α-acyloxymethylketone warhead peptidomimetic compounds with a six-membered lactam glutamine mimic in P1. Compounds with potent SARS-CoV-2 3CL protease and in vitro viral replication inhibition were identified with low cytotoxicity and good plasma and glutathione stability. Compounds 15e, 15h, and 15l displayed selectivity for SARS-CoV-2 3CL protease over CatB and CatS and superior in vitro SARS-CoV-2 antiviral replication inhibition compared with the reported peptidomimetic inhibitors with other warheads. The cocrystallization of 15l with SARS-CoV-2 3CL protease confirmed the formation of a covalent adduct. α-Acyloxymethylketone compounds also exhibited antiviral activity against an alphacoronavirus and non-SARS betacoronavirus strains with similar potency and a better selectivity index than remdesivir. These findings demonstrate the potential of the substituted heteroaromatic and aliphatic α-acyloxymethylketone warheads as coronavirus inhibitors, and the described results provide a basis for further optimization.
Collapse
Affiliation(s)
- Bing Bai
- Li Ka Shing Applied Virology Institute,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
| | - Alexandr Belovodskiy
- Li Ka Shing Applied Virology Institute,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
| | - Mostofa Hena
- Li Ka Shing Applied Virology Institute,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
| | - Appan Srinivas Kandadai
- Li Ka Shing Applied Virology Institute,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
| | - Michael A. Joyce
- Li Ka Shing Institute of Virology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
| | - Holly A. Saffran
- Li Ka Shing Institute of Virology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
| | - Justin A. Shields
- Li Ka Shing Institute of Virology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
| | - Muhammad Bashir Khan
- Department of Biochemistry, University of
Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Elena Arutyunova
- Li Ka Shing Institute of Virology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Biochemistry, University of
Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Jimmy Lu
- Li Ka Shing Institute of Virology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Biochemistry, University of
Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Sardeev K. Bajwa
- Department of Biochemistry, University of
Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Darren Hockman
- Li Ka Shing Applied Virology Institute,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
| | - Conrad Fischer
- Department of Chemistry, University of
Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Tess Lamer
- Department of Chemistry, University of
Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Wayne Vuong
- Department of Chemistry, University of
Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Marco J. van Belkum
- Department of Chemistry, University of
Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Zhengxian Gu
- WuXi AppTec (Shanghai) Co., Ltd.,
G Warehouse #101, No. 10 Building, #227 Meisheng Road, WaiGaoQiao Free Trade Zone,
Shanghai 200131, China
| | - Fusen Lin
- WuXi AppTec (Shanghai) Co., Ltd.,
G Warehouse #101, No. 10 Building, #227 Meisheng Road, WaiGaoQiao Free Trade Zone,
Shanghai 200131, China
| | - Yanhua Du
- WuXi AppTec (Shanghai) Co., Ltd.,
G Warehouse #101, No. 10 Building, #227 Meisheng Road, WaiGaoQiao Free Trade Zone,
Shanghai 200131, China
| | - Jia Xu
- WuXi AppTec (Shanghai) Co., Ltd.,
G Warehouse #101, No. 10 Building, #227 Meisheng Road, WaiGaoQiao Free Trade Zone,
Shanghai 200131, China
| | - Mohammad Rahim
- Rane Pharmaceuticals, Inc.
4290 91a Street NW, Edmonton, Alberta T6E 5V2, Canada
| | - Howard S. Young
- Department of Biochemistry, University of
Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - John C. Vederas
- Department of Chemistry, University of
Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - D. Lorne Tyrrell
- Li Ka Shing Applied Virology Institute,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Li Ka Shing Institute of Virology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
| | - M. Joanne Lemieux
- Li Ka Shing Institute of Virology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Biochemistry, University of
Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - James A. Nieman
- Li Ka Shing Applied Virology Institute,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
| |
Collapse
|
27
|
Pro108Ser mutation of SARS-CoV-2 3CL pro reduces the enzyme activity and ameliorates the clinical severity of COVID-19. Sci Rep 2022; 12:1299. [PMID: 35079088 PMCID: PMC8789791 DOI: 10.1038/s41598-022-05424-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 01/12/2022] [Indexed: 11/13/2022] Open
Abstract
Recently, an international randomized controlled clinical trial showed that patients with SARS-CoV-2 infection treated orally with the 3-chymotrypsin-like protease (3CLpro) inhibitor PF-07321332 within three days of symptom onset showed an 89% lower risk of COVID-19-related hospital admission/ death from any cause as compared with the patients who received placebo. Lending support to this critically important result of the aforementioned trial, we demonstrated in our study that patients infected with a SARS-Cov-2 sub-lineage (B.1.1.284) carrying the Pro108Ser mutation in 3CLpro tended to have a comparatively milder clinical course (i.e., a smaller proportion of patients required oxygen supplementation during the clinical course) than patients infected with the same sub-lineage of virus not carrying the mutation. Characterization of the mutant 3CLpro revealed that the Kcat/Km of the 3CLpro enzyme containing Ser108 was 58% lower than that of Pro108 3CLpro. Hydrogen/deuterium-exchange mass spectrometry (HDX-MS) revealed that the reduced activity was associated with structural perturbation surrounding the substrate-binding region of the enzyme, which is positioned behind and distant from the 108th amino acid residue. Our findings of the attenuated clinical course of COVID-19 in patients infected with SARS-CoV-2 strains with reduced 3CLpro enzymatic activity greatly endorses the promising result of the aforementioned clinical trial of the 3CLpro inhibitor.
Collapse
|
28
|
Chen J, Zhang Y, Zeng D, Zhang B, Ye X, Zeng Z, Zhang XK, Wang Z, Zhou H. Merbromin is a mixed-type inhibitor of 3-chyomotrypsin like protease of SARS-CoV-2. Biochem Biophys Res Commun 2021; 591:118-123. [PMID: 35007835 PMCID: PMC8716398 DOI: 10.1016/j.bbrc.2021.12.108] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 12/27/2021] [Indexed: 12/23/2022]
Abstract
3-chyomotrypsin like protease (3CLpro) has been considered as a promising target for developing anti-SARS-CoV-2 drugs. Herein, about 6000 compounds were analyzed by high-throughput screening using enzyme activity model, and Merbromin, an antibacterial agent, was identified as a potent inhibitor of 3CLpro. Merbromin strongly inhibited the proteolytic activity of 3CLpro but not the other three proteases Proteinase K, Trypsin and Papain. Michaelis-Menten kinetic analysis showed that Merbromin was a mixed-type inhibitor of 3CLpro, due to its ability of increasing the KM and decreasing the Kcat of 3CLpro. The binding assays and molecular docking suggested that 3CLpro possessed two binding sites for Merbromin. Consistently, Merbromin showed a weak binding to the other three proteases. Together, these findings demonstrated that Merbromin is a selective inhibitor of 3CLpro and provided a scaffold to design effective inhibitors of SARS-CoV-2.
Collapse
Affiliation(s)
- Junjie Chen
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, China; High Throughput Drug Screening Platform of Xiamen University, China
| | - Yaya Zhang
- Department of Neurosurgery, Xiamen Key Laboratory of Brain Center, The First Affiliated Hospital of Xiamen University, China
| | - Dequan Zeng
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, China; High Throughput Drug Screening Platform of Xiamen University, China
| | - Bingchang Zhang
- Department of Neurosurgery, Xiamen Key Laboratory of Brain Center, The First Affiliated Hospital of Xiamen University, China
| | - Xiaohong Ye
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, China; High Throughput Drug Screening Platform of Xiamen University, China
| | - Zhiping Zeng
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, China; High Throughput Drug Screening Platform of Xiamen University, China
| | - Xiao-Kun Zhang
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, China; High Throughput Drug Screening Platform of Xiamen University, China
| | - Zhanxiang Wang
- Department of Neurosurgery, Xiamen Key Laboratory of Brain Center, The First Affiliated Hospital of Xiamen University, China; School of Medicine, Xiamen University, Xiamen, Fujian, 361102, China.
| | - Hu Zhou
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, China; High Throughput Drug Screening Platform of Xiamen University, China.
| |
Collapse
|
29
|
A fluorescence-based, gain-of-signal, live cell system to evaluate SARS-CoV-2 main protease inhibition. Antiviral Res 2021; 195:105183. [PMID: 34626674 PMCID: PMC8495046 DOI: 10.1016/j.antiviral.2021.105183] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/17/2021] [Accepted: 09/25/2021] [Indexed: 02/03/2023]
Abstract
The likelihood of continued circulation of COVID-19 and its variants, and novel coronaviruses due to future zoonotic transmissions, combined with the current paucity of coronavirus antivirals, emphasize the need for improved screening in developing effective antivirals for the treatment of infection by SARS-CoV-2 (CoV2) and other coronaviruses. Here we report the development of a live-cell based assay for evaluating the intracellular function of the critical, highly-conserved CoV2 target, the Main 3C-like protease (Mpro). This assay is based on expression of native wild-type mature CoV2 Mpro, the function of which is quantitatively evaluated in living cells through cleavage of a biosensor leading to loss of fluorescence. Evaluation does not require cell harvesting, allowing for multiple measurements from the same cells facilitating quantification of Mpro inhibition, as well as recovery of function upon removal of inhibitory drugs. The pan-coronavirus Mpro inhibitor, GC376, was utilized in this assay and effective inhibition of intracellular CoV2 Mpro was found to be consistent with levels required to inhibit CoV2 infection of human lung cells. We demonstrate that GC376 is an effective inhibitor of intracellular CoV2 Mpro at low micromolar levels, while other predicted Mpro inhibitors, bepridil and alverine, are not. Results indicate this system can provide a highly effective high-throughput coronavirus Mpro screening system.
Collapse
|
30
|
Bai B, Arutyunova E, Khan MB, Lu J, Joyce MA, Saffran HA, Shields JA, Kandadai AS, Belovodskiy A, Hena M, Vuong W, Lamer T, Young HS, Vederas JC, Tyrrell DL, Lemieux MJ, Nieman JA. Peptidomimetic nitrile warheads as SARS-CoV-2 3CL protease inhibitors. RSC Med Chem 2021; 12:1722-1730. [PMID: 34778773 PMCID: PMC8529539 DOI: 10.1039/d1md00247c] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 08/20/2021] [Indexed: 12/12/2022] Open
Abstract
Tragically, the death toll from the COVID-19 pandemic continues to rise, and with variants being observed around the globe new therapeutics, particularly direct-acting antivirals that are easily administered, are desperately needed. Studies targeting the SARS-CoV-2 3CL protease, which is critical for viral replication, with different peptidomimetics and warheads is an active area of research for development of potential drugs. To date, however, only a few publications have evaluated the nitrile warhead as a viral 3CL protease inhibitor, with only modest activity reported. This article describes our investigation of P3 4-methoxyindole peptidomimetic analogs with select P1 and P2 groups with a nitrile warhead that are potent inhibitors of SARS-CoV-2 3CL protease and demonstrate in vitro SARS-CoV-2 antiviral activity. A selectivity for SARS-CoV-2 3CL protease over human cathepsins B, S and L was also observed with the nitrile warhead, which was superior to that with the aldehyde warhead. A co-crystal structure with SARS-CoV-2 3CL protease and a reversibility study indicate that a reversible, thioimidate adduct is formed when the catalytic sulfur forms a covalent bond with the carbon of the nitrile. This effort also identified efflux as a property limiting antiviral activity of these compounds, and together with the positive attributes described these results provide insight for further drug development of novel nitrile peptidomimetics targeting SARS-CoV-2 3CL protease.
Collapse
Affiliation(s)
- Bing Bai
- Li Ka Shing Applied Virology Institute, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Elena Arutyunova
- Department of Biochemistry, University of Alberta Edmonton Alberta T6G 2H7 Canada
- Li Ka Shing Institute of Virology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Muhammad Bashir Khan
- Department of Biochemistry, University of Alberta Edmonton Alberta T6G 2H7 Canada
| | - Jimmy Lu
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Li Ka Shing Institute of Virology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Michael A Joyce
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Li Ka Shing Institute of Virology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Holly A Saffran
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Li Ka Shing Institute of Virology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Justin A Shields
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Li Ka Shing Institute of Virology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Appan Srinivas Kandadai
- Li Ka Shing Applied Virology Institute, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Alexandr Belovodskiy
- Li Ka Shing Applied Virology Institute, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Mostofa Hena
- Li Ka Shing Applied Virology Institute, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Wayne Vuong
- Department of Chemistry, University of Alberta Edmonton Alberta T6G 2G2 Canada
| | - Tess Lamer
- Department of Chemistry, University of Alberta Edmonton Alberta T6G 2G2 Canada
| | - Howard S Young
- Li Ka Shing Institute of Virology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - John C Vederas
- Department of Chemistry, University of Alberta Edmonton Alberta T6G 2G2 Canada
| | - D Lorne Tyrrell
- Li Ka Shing Applied Virology Institute, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Li Ka Shing Institute of Virology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta Edmonton Alberta T6G 2H7 Canada
- Li Ka Shing Institute of Virology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - James A Nieman
- Li Ka Shing Applied Virology Institute, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| |
Collapse
|
31
|
Vuong W, Fischer C, Khan MB, van Belkum MJ, Lamer T, Willoughby KD, Lu J, Arutyunova E, Joyce MA, Saffran HA, Shields JA, Young HS, Nieman JA, Tyrrell DL, Lemieux MJ, Vederas JC. Improved SARS-CoV-2 M pro inhibitors based on feline antiviral drug GC376: Structural enhancements, increased solubility, and micellar studies. Eur J Med Chem 2021; 222:113584. [PMID: 34118724 PMCID: PMC8164773 DOI: 10.1016/j.ejmech.2021.113584] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/03/2021] [Accepted: 05/22/2021] [Indexed: 12/31/2022]
Abstract
Replication of SARS-CoV-2, the coronavirus causing COVID-19, requires a main protease (Mpro) to cleave viral proteins. Consequently, Mpro is a target for antiviral agents. We and others previously demonstrated that GC376, a bisulfite prodrug with efficacy as an anti-coronaviral agent in animals, is an effective inhibitor of Mpro in SARS-CoV-2. Here, we report structure-activity studies of improved GC376 derivatives with nanomolar affinities and therapeutic indices >200. Crystallographic structures of inhibitor-Mpro complexes reveal that an alternative binding pocket in Mpro, S4, accommodates the P3 position. Alternative binding is induced by polar P3 groups or a nearby methyl. NMR and solubility studies with GC376 show that it exists as a mixture of stereoisomers and forms colloids in aqueous media at higher concentrations, a property not previously reported. Replacement of its Na+ counter ion with choline greatly increases solubility. The physical, biochemical, crystallographic, and cellular data reveal new avenues for Mpro inhibitor design.
Collapse
Affiliation(s)
- Wayne Vuong
- Department of Chemistry, University of Alberta, Edmonton AB, T6G 2G2, Canada
| | - Conrad Fischer
- Department of Chemistry, University of Alberta, Edmonton AB, T6G 2G2, Canada
| | - Muhammad Bashir Khan
- Department of Biochemistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton AB, T6G 2R3, Canada
| | - Marco J van Belkum
- Department of Chemistry, University of Alberta, Edmonton AB, T6G 2G2, Canada
| | - Tess Lamer
- Department of Chemistry, University of Alberta, Edmonton AB, T6G 2G2, Canada
| | - Kurtis D Willoughby
- Department of Chemistry, University of Alberta, Edmonton AB, T6G 2G2, Canada
| | - Jimmy Lu
- Department of Biochemistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton AB, T6G 2R3, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton AB, T6G 2E1, Canada
| | - Elena Arutyunova
- Department of Biochemistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton AB, T6G 2R3, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton AB, T6G 2E1, Canada
| | - Michael A Joyce
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton AB, T6G 2R3, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton AB, T6G 2E1, Canada
| | - Holly A Saffran
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton AB, T6G 2R3, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton AB, T6G 2E1, Canada
| | - Justin A Shields
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton AB, T6G 2R3, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton AB, T6G 2E1, Canada
| | - Howard S Young
- Department of Biochemistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton AB, T6G 2R3, Canada
| | - James A Nieman
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton AB, T6G 2R3, Canada; Li Ka Shing Applied Virology Institute, University of Alberta, Edmonton AB, T6G 2E1, Canada
| | - D Lorne Tyrrell
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton AB, T6G 2R3, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton AB, T6G 2E1, Canada
| | - M Joanne Lemieux
- Department of Biochemistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton AB, T6G 2R3, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton AB, T6G 2E1, Canada
| | - John C Vederas
- Department of Chemistry, University of Alberta, Edmonton AB, T6G 2G2, Canada.
| |
Collapse
|
32
|
Vuong W, Vederas JC. Improved Synthesis of a Cyclic Glutamine Analogue Used in Antiviral Agents Targeting 3C and 3CL Proteases Including SARS-CoV-2 M pro. J Org Chem 2021; 86:13104-13110. [PMID: 34459196 PMCID: PMC8425337 DOI: 10.1021/acs.joc.1c01299] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Indexed: 11/28/2022]
Abstract
An intermediate in the synthesis of numerous antiviral protease inhibitors is the glutamine analogue, (3S)-pyrrolid-2-one-3-yl-l-alanine. Preparations of compounds based on this pharmacophore are hindered by the lack of a reliably high yielding synthesis of protected forms of this amino acid. We describe an improved scalable route with readily available reagents and facile purification. This methodology employs γ-allylation of dimethyl N-BocGlu, further Boc N-protection, OsO4-periodate oxidation, O-Me oxime formation, and RaNi-catalyzed hydrogenolysis with concomitant cyclization under basic conditions.
Collapse
Affiliation(s)
- Wayne Vuong
- Department of Chemistry, University of
Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - John C. Vederas
- Department of Chemistry, University of
Alberta, Edmonton, Alberta, Canada T6G 2G2
| |
Collapse
|