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Toopradab B, Xie W, Duan L, Hengphasatporn K, Harada R, Sinsulpsiri S, Shigeta Y, Shi L, Maitarad P, Rungrotmongkol T. Machine learning-based QSAR and LB-PaCS-MD guided design of SARS-CoV-2 main protease inhibitors. Bioorg Med Chem Lett 2024; 110:129852. [PMID: 38925524 DOI: 10.1016/j.bmcl.2024.129852] [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: 02/20/2024] [Revised: 05/17/2024] [Accepted: 06/19/2024] [Indexed: 06/28/2024]
Abstract
The global outbreak of the COVID-19 pandemic caused by the SARS-CoV-2 virus had led to profound respiratory health implications. This study focused on designing organoselenium-based inhibitors targeting the SARS-CoV-2 main protease (Mpro). The ligand-binding pathway sampling method based on parallel cascade selection molecular dynamics (LB-PaCS-MD) simulations was employed to elucidate plausible paths and conformations of ebselen, a synthetic organoselenium drug, within the Mpro catalytic site. Ebselen effectively engaged the active site, adopting proximity to H41 and interacting through the benzoisoselenazole ring in a π-π T-shaped arrangement, with an additional π-sulfur interaction with C145. In addition, the ligand-based drug design using the QSAR with GFA-MLR, RF, and ANN models were employed for biological activity prediction. The QSAR-ANN model showed robust statistical performance, with an r2training exceeding 0.98 and an RMSEtest of 0.21, indicating its suitability for predicting biological activities. Integration the ANN model with the LB-PaCS-MD insights enabled the rational design of novel compounds anchored in the ebselen core structure, identifying promising candidates with favorable predicted IC50 values. The designed compounds exhibited suitable drug-like characteristics and adopted an active conformation similar to ebselen, inhibiting Mpro function. These findings represent a synergistic approach merging ligand and structure-based drug design; with the potential to guide experimental synthesis and enzyme assay testing.
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Affiliation(s)
- Borwornlak Toopradab
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand; Center of Excellence in Biocatalyst and Sustainable Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Wanting Xie
- Research Center of Nano Science and Technology, Department of Chemistry, College of Science, Shanghai University, Shanghai, 200444 PR China
| | - Lian Duan
- Center for Computational Sciences (CCS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan; Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Ibaraki 305-8571, Japan
| | - Kowit Hengphasatporn
- Center for Computational Sciences (CCS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Ryuhei Harada
- Center for Computational Sciences (CCS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Silpsiri Sinsulpsiri
- Center of Excellence in Biocatalyst and Sustainable Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Yasuteru Shigeta
- Center for Computational Sciences (CCS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Liyi Shi
- Research Center of Nano Science and Technology, Department of Chemistry, College of Science, Shanghai University, Shanghai, 200444 PR China; Emerging Industries Institute Shanghai University, Jiaxing, Zhejiang 314006, PR China
| | - Phornphimon Maitarad
- Research Center of Nano Science and Technology, Department of Chemistry, College of Science, Shanghai University, Shanghai, 200444 PR China.
| | - Thanyada Rungrotmongkol
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand; Center of Excellence in Biocatalyst and Sustainable Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
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2
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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.
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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
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3
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Meng Z, Wang S, Chen F, Zhang Z, Zhang Y, Yin Z, Duan Y, Zheng N, Wang Q, Liao C, Chen Y, Xie Z. Discovery of Highly Selective, Potent, Covalent, and Orally Bioavailable Factor XIIa Inhibitors for the Treatment of Thrombo-Inflammation. J Med Chem 2024; 67:10946-10966. [PMID: 38913497 DOI: 10.1021/acs.jmedchem.4c00475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Thrombo-inflammation is closely associated with a few severe cardiovascular and infectious diseases. Factor XIIa (FXIIa) in the intrinsic coagulation pathway plays a pivotal role in the development of thrombo-inflammation and its inhibition has emerged as a potential therapeutic approach for thrombo-inflammatory disorders. Nonetheless, as of now, few small-molecule FXIIa inhibitors have demonstrated notable effectiveness against thrombo-inflammation, with none progressing into clinical stages. Herein, we present potent, covalent, reversible, and selective small-molecule FXIIa inhibitors such as 4a and 4j obtained through structure-based drug design. Compounds 4a and 4j showed significant anticoagulation and substantial anti-inflammatory effects in vitro, coupled with exceptional plasma stability. Furthermore, in carrageenan-induced thrombosis models, 4a and 4j demonstrated remarkable dual antithrombotic and anti-inflammatory activity when administered orally. Compound 4j exhibited a favorable safety profile without obvious tissue toxicity in mice, suggesting its potential as an oral therapeutic option for thrombo-inflammation.
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Affiliation(s)
- Zhiwei Meng
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Shengnan Wang
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Fangrong Chen
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Zhenzhen Zhang
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Yajing Zhang
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Zequn Yin
- The First Affiliated Hospital of University of Science and Technology of China, Hefei 230001, China
| | - Yajun Duan
- The First Affiliated Hospital of University of Science and Technology of China, Hefei 230001, China
| | - Nan Zheng
- The First Affiliated Hospital of University of Science and Technology of China, Hefei 230001, China
| | - Qin Wang
- Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - Chenzhong Liao
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Yuanli Chen
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Zhouling Xie
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
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Dobrydnev AV, Popova MV, Volovenko YM. Cyclic Sulfinamides. CHEM REC 2024; 24:e202300221. [PMID: 37594737 DOI: 10.1002/tcr.202300221] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/09/2023] [Indexed: 08/19/2023]
Abstract
The literature on cyclic sulfinamides (put simply, sultims) published from 1989 to 2022 has been summarized and reviewed. The information is divided into two sections: the analysis of synthetic methods on the preparation of cyclic sulfinamides and the discussion of the chemical properties of cyclic sulfinamides focusing on their reactions and applications. The survey of the reaction conditions, provided in the most detailed way, and a critical view of the reaction mechanisms add an extra dimension to the text. The data presented will be useful to specialists in different areas, especially those who work in the field of synthetic organic and pharmaceutical chemistry.
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Affiliation(s)
- Alexey V Dobrydnev
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv, 01033, Ukraine
- Enamine Ltd., Chervonotkatska Street 78, Kyiv, 02094, Ukraine
| | - Maria V Popova
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv, 01033, Ukraine
- Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128, Mainz, Germany
| | - Yulian M Volovenko
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv, 01033, Ukraine
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Ali F, Alom S, Ali SR, Kondoli B, Sadhu P, Borah C, Kakoti BB, Ghosh SK, Shakya A, Ahmed AB, Singh UP, Bhat HR. Ebselen: A Review on its Synthesis, Derivatives, Anticancer Efficacy and Utility in Combating SARS-COV-2. Mini Rev Med Chem 2024; 24:1203-1225. [PMID: 37711004 DOI: 10.2174/1389557523666230914103339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/26/2023] [Accepted: 06/16/2023] [Indexed: 09/16/2023]
Abstract
Ebselen is a selenoorganic chiral compound with antioxidant properties comparable to glutathione peroxidase. It is also known as 2-phenyl-1,2-benzisoselenazol-3(2H)-one. In studies examining its numerous pharmacological activities, including antioxidant, anticancer, antiviral, and anti- Alzheimer's, ebselen has demonstrated promising results. This review's primary objective was to emphasize the numerous synthesis pathways of ebselen and their efficacy in fighting cancer. The data were collected from multiple sources, including Scopus, PubMed, Google Scholar, Web of Science, and Publons. The starting reagents for the synthesis of ebselen are 2-aminobenzoic acid and N-phenyl benzamide. It was discovered that ebselen has the ability to initiate apoptosis in malignant cells and prevent the formation of new cancer cells by scavenging free radicals. In addition, ebselen increases tumor cell susceptibility to apoptosis by inhibiting TNF-α mediated NF-kB activation. Ebselen can inhibit both doxorubicin and daunorubicin-induced cardiotoxicity. Allopurinol and ebselen administered orally can be used to suppress renal ototoxicity and nephrotoxicity. Due to excessive administration, diclofenac can induce malignancy of the gastrointestinal tract, which ebselen can effectively suppress. Recent research has demonstrated ebselen to inhibit viral function by binding to cysteinecontaining catalytic domains of various viral proteases. It was discovered that ebselen could inhibit the catalytic dyad function of Mpro by forming an irreversible covalent bond between Se and Cys145, thereby altering protease function and inhibiting SARS-CoV-2. Ebselen may also inhibit the activation of endosomal NADPH oxidase of vascular endothelial cells, which is believed to be required for thrombotic complications in COVID-19. In this review, we have included various studies conducted on the anticancer effect of ebselen as well as its inhibition of SARS-CoV-2.
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Affiliation(s)
- Farak Ali
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh, Assam, 786004, India
- Girijananda Chowdhury Institute of Pharmaceutical Science, Tezpur Medical College and Hospital, Tezpur, Sonitpur Assam, 784501,India
| | - Shahnaz Alom
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh, Assam, 786004, India
- Girijananda Chowdhury Institute of Pharmaceutical Science, Tezpur Medical College and Hospital, Tezpur, Sonitpur Assam, 784501,India
| | - Sheikh Rezzak Ali
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh, Assam, 786004, India
| | - Biswanarayan Kondoli
- Department of Pharmacy, Tripura University, Suryamani Nagar, Agartala, Tripura 799022, India
| | - Prativa Sadhu
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh, Assam, 786004, India
| | - Chinmoyee Borah
- Girijananda Chowdhury Institute of Pharmaceutical Science, Guwahati, Kamrup, Assam, 781017, India
| | - Bibhuti Bushan Kakoti
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh, Assam, 786004, India
| | - Surajit Kumar Ghosh
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh, Assam, 786004, India
| | - Anshul Shakya
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh, Assam, 786004, India
| | - Abdul Baquee Ahmed
- Girijananda Chowdhury Institute of Pharmaceutical Science,Tezpur Medical College and Hospital, Tezpur, Sonitpur-784501, Assam, India
| | - Udaya Pratap Singh
- Drug Design & Discovery Laboratory, Department of Pharmaceutical Sciences, Sam Higginbottom University of Agriculture, Technology & Sciences, Allahabad, Uttar Pradesh, 211007, India
| | - Hans Raj Bhat
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh, Assam, 786004, India
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Viçozzi GP, de Oliveira Pereira FS, da Silva RS, Leal JG, Sarturi JM, Nogara PA, Rodrigues OED, Teixeira da Rocha JB, Ávila DS. In silico evidences of Mpro inhibition by a series of organochalcogen-AZT derivatives and their safety in Caenorhabditis elegans. J Trace Elem Med Biol 2023; 80:127297. [PMID: 37716209 DOI: 10.1016/j.jtemb.2023.127297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/02/2023] [Accepted: 08/29/2023] [Indexed: 09/18/2023]
Abstract
BACKGROUND The new coronavirus (SARS-CoV-2) pandemic emerged in 2019 causing millions of deaths. Vaccines were quickly developed and made available in 2021. Despite the availability of vaccines, some subjects refuse to take the immunizing or present comorbities, therefore developing serious cases of COVID-19, which makes necessary the development of antiviral drugs. Previous studies have demonstrated that ebselen, a selenium-containing molecule, can inhibit SARS-CoV-2 Mpro. In addition, selenium is a trace element that has antiviral and anti-inflammatory properties. Zidovudine (AZT) has been widely used against HIV infections and its action against SARS-CoV-2 may be altered by the structural modification with organochalcogen moieties, but this hypothesis still needs to be tested. METHODS In the present work we evaluated the Mpro inhibition capacity (in silico), the safety and antioxidant effect of six organochalcogen AZT-derivatives using the free-living nematode Caenorhabditis elegans, through acute (30 min) and chronic (48) exposure protocols. RESULTS We observed that the molecules were safe at a concentration range of 1-500 µM and did not alter any toxicological endpoint evaluated. Furthermore, the molecules are capable to decrease the ROS formation stimulated by hydrogen peroxide, to modulate the expression of important antioxidant enzymes such superoxide-dismutase-3 and glutathione S-transferese-4 and to stimulate the translocation of the DAF-16 to the cell nucleus. In addition, the molecules did not deplete thiol groups, which reinforces their safety and contribution to oxidative stress resistance. CONCLUSIONS We have found that compounds S116l (a Tellurium AZT-derivative) and S116h (a Selenium-AZT derivative) presented more promising effects both in silico and in vivo, being strong candidates for further in vivo studies.
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Affiliation(s)
- Gabriel Pedroso Viçozzi
- Grupo de Pesquisa em Bioquímica e Toxicologia em Caenorhabditis elegans (GBToxCE), Universidade Federal do Pampa - UNIPAMPA, CEP 97500-970 Uruguaiana, RS, Brazil; Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria (UFSM), Av. Roraima 1000, 97105-900 Santa Maria, RS, Brazil
| | - Flávia Suelen de Oliveira Pereira
- Grupo de Pesquisa em Bioquímica e Toxicologia em Caenorhabditis elegans (GBToxCE), Universidade Federal do Pampa - UNIPAMPA, CEP 97500-970 Uruguaiana, RS, Brazil
| | - Rafael Santos da Silva
- LabSelen-NanoBio - Departamento de Química, Universidade Federal de Santa Maria, Santa Maria, Brazil
| | - Julliano Guerin Leal
- LabSelen-NanoBio - Departamento de Química, Universidade Federal de Santa Maria, Santa Maria, Brazil
| | - Joelma Menegazzi Sarturi
- LabSelen-NanoBio - Departamento de Química, Universidade Federal de Santa Maria, Santa Maria, Brazil
| | - Pablo Andrei Nogara
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria (UFSM), Av. Roraima 1000, 97105-900 Santa Maria, RS, Brazil; Instituto Federal de Educação, Ciência e Tecnologia Sul-rio-grandense (IFSul), Av. Leonel de Moura Brizola, 2501, 96418-400 Bagé, RS, Brazil
| | | | - João Batista Teixeira da Rocha
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria (UFSM), Av. Roraima 1000, 97105-900 Santa Maria, RS, Brazil
| | - Daiana Silva Ávila
- Grupo de Pesquisa em Bioquímica e Toxicologia em Caenorhabditis elegans (GBToxCE), Universidade Federal do Pampa - UNIPAMPA, CEP 97500-970 Uruguaiana, RS, Brazil; Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria (UFSM), Av. Roraima 1000, 97105-900 Santa Maria, RS, Brazil.
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7
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Li X, Song Y. Structure and function of SARS-CoV and SARS-CoV-2 main proteases and their inhibition: A comprehensive review. Eur J Med Chem 2023; 260:115772. [PMID: 37659195 PMCID: PMC10529944 DOI: 10.1016/j.ejmech.2023.115772] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/24/2023] [Accepted: 08/26/2023] [Indexed: 09/04/2023]
Abstract
Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) identified in 2003 infected ∼8000 people in 26 countries with 800 deaths, which was soon contained and eradicated by syndromic surveillance and enhanced quarantine. A closely related coronavirus SARS-CoV-2, the causative agent of COVID-19 identified in 2019, has been dramatically more contagious and catastrophic. It has infected and caused various flu-like symptoms of billions of people in >200 countries, including >6 million people died of or with the virus. Despite the availability of several vaccines and antiviral drugs against SARS-CoV-2, finding new therapeutics is needed because of viral evolution and a possible emerging coronavirus in the future. The main protease (Mpro) of these coronaviruses plays important roles in their life cycle and is essential for the viral replication. This article represents a comprehensive review of the function, structure and inhibition of SARS-CoV and -CoV-2 Mpro, including structure-activity relationships, protein-inhibitor interactions and clinical trial status.
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Affiliation(s)
- Xin Li
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
| | - Yongcheng Song
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
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8
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Ren P, Li H, Nie T, Jian X, Yu C, Li J, Su H, Zhang X, Li S, Yang X, Peng C, Yin Y, Zhang L, Xu Y, Liu H, Bai F. Discovery and Mechanism Study of SARS-CoV-2 3C-like Protease Inhibitors with a New Reactive Group. J Med Chem 2023; 66:12266-12283. [PMID: 37594952 DOI: 10.1021/acs.jmedchem.3c00818] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2023]
Abstract
3CLpro is an attractive target for the treatment of COVID-19. Using the scaffold hopping strategy, we identified a potent inhibitor of 3CLpro (3a) that contains a thiocyanate moiety as a novel warhead that can form a covalent bond with Cys145 of the protein. Tandem mass spectrometry (MS/MS) and X-ray crystallography confirmed the mechanism of covalent formation between 3a and the protein in its catalytic pocket. Moreover, several analogues of compound 3a were designed and synthesized. Among them, compound 3h shows the best inhibition of 3CLpro with an IC50 of 0.322 μM and a kinact/Ki value of 1669.34 M-1 s-1, and it exhibits good target selectivity for 3CLpro against host proteases. Compound 3c inhibits SARS-CoV-2 in Vero E6 cells (EC50 = 2.499 μM) with low cytotoxicity (CC50 > 200 μM). These studies provide ideas and insights to explore and develop new 3CLpro inhibitors in the future.
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Affiliation(s)
- Pengxuan Ren
- School of Life Science and Technology, and Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Hui Li
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Tianqing Nie
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xiaoqin Jian
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
| | - Changyue Yu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jian Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Haixia Su
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xianglei Zhang
- School of Life Science and Technology, and Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Shiwei Li
- School of Life Science and Technology, and Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Xin Yang
- School of Life Science and Technology, and Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Chao Peng
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China
| | - Yue Yin
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China
| | - Leike Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
| | - Yechun Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Hong Liu
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Fang Bai
- School of Life Science and Technology, and Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
- School of Information Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
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Citarella A, Dimasi A, Moi D, Passarella D, Scala A, Piperno A, Micale N. Recent Advances in SARS-CoV-2 Main Protease Inhibitors: From Nirmatrelvir to Future Perspectives. Biomolecules 2023; 13:1339. [PMID: 37759739 PMCID: PMC10647625 DOI: 10.3390/biom13091339] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/28/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
The main protease (Mpro) plays a pivotal role in the replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is considered a highly conserved viral target. Disruption of the catalytic activity of Mpro produces a detrimental effect on the course of the infection, making this target one of the most attractive for the treatment of COVID-19. The current success of the SARS-CoV-2 Mpro inhibitor Nirmatrelvir, the first oral drug for the treatment of severe forms of COVID-19, has further focused the attention of researchers on this important viral target, making the search for new Mpro inhibitors a thriving and exciting field for the development of antiviral drugs active against SARS-CoV-2 and related coronaviruses.
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Affiliation(s)
- Andrea Citarella
- Department of Chemistry, University of Milan, Via Golgi 19, 20133 Milano, Italy; (A.D.); (D.P.)
| | - Alessandro Dimasi
- Department of Chemistry, University of Milan, Via Golgi 19, 20133 Milano, Italy; (A.D.); (D.P.)
| | - Davide Moi
- Department of Chemical and Geological Sciences, University of Cagliari, S.P. 8 CA, 09042 Cagliari, Italy;
| | - Daniele Passarella
- Department of Chemistry, University of Milan, Via Golgi 19, 20133 Milano, Italy; (A.D.); (D.P.)
| | - Angela Scala
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno D’Alcontres 31, 98166 Messina, Italy; (A.S.); (A.P.)
| | - Anna Piperno
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno D’Alcontres 31, 98166 Messina, Italy; (A.S.); (A.P.)
| | - Nicola Micale
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno D’Alcontres 31, 98166 Messina, Italy; (A.S.); (A.P.)
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10
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Anton DB, Galvez Bulhões Pedreira J, Zvirtes ML, Laufer SA, Ducati RG, Goettert M, Saraiva Macedo Timmers LF. Targeting SARS-CoV-2 Main Protease (MPro) with Kinase Inhibitors: A Promising Approach for Discovering Antiviral and Anti-inflammatory Molecules against SARS-CoV-2. J Chem Inf Model 2023. [PMID: 37329322 DOI: 10.1021/acs.jcim.3c00324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus infected over 688 million people worldwide, causing public health concern and approximately 6.8 million deaths due to COVID-19. COVID-19, especially severe cases, is characterized by exacerbated lung inflammation with an increase of pro-inflammatory cytokines. In addition to antiviral drugs, there is a need for anti-inflammatory therapies to treat all phases of COVID-19. One of the most attractive drug targets for COVID-19 is the SARS-CoV-2 main protease (MPro), an enzyme responsible for cleaving polyproteins formed after the translation of viral RNA, which is essential for viral replication. MPro inhibitors, therefore, have the potential to stop viral replication and act as antiviral drugs. Considering that several kinase inhibitors are known for their action in inflammatory pathways, this could also be investigated toward a potential anti-inflammatory treatment for COVID-19. Therefore, the use of kinase inhibitors against SARS-CoV-2 MPro may be a promising strategy to find molecules with dual activity─antiviral and anti-inflammatory. Considering this, the potential of six kinase inhibitors against SARS-CoV-2 MPro were evaluated in silico and in vitro, including Baricitinib, Tofacitinib, Ruxolitinib, BIRB-796, Skepinone-L, and Sorafenib. To assess the inhibitory potential of the kinase inhibitors, a continuous fluorescent-based enzyme activity assay was optimized with SARS-CoV-2 MPro and MCA-AVLQSGFR-K(Dnp)-K-NH2 (substrate). BIRB-796 and Baricitinib were identified as inhibitors of SARS-CoV-2 MPro, presenting IC50 values of 7.99 and 25.31 μM, respectively. As they are also known for their anti-inflammatory action, both are prototype compounds with the potential to present antiviral and anti-inflammatory activity against SARS-CoV-2 infection.
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Affiliation(s)
- Débora Bublitz Anton
- Biotechnology Graduate Program, Universidade do Vale do Taquari (Univates), Lajeado CEP 95914-014, Brazil
| | - Júlia Galvez Bulhões Pedreira
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen 72076, Germany
| | - Maria Luiza Zvirtes
- Department of Medicine, Universidade do Vale do Taquari (Univates), Lajeado CEP 95914-014, Brazil
| | - Stefan A Laufer
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen 72076, Germany
| | - Rodrigo Gay Ducati
- Biotechnology Graduate Program, Universidade do Vale do Taquari (Univates), Lajeado CEP 95914-014, Brazil
- Department of Medicine, Universidade do Vale do Taquari (Univates), Lajeado CEP 95914-014, Brazil
| | - Márcia Goettert
- Biotechnology Graduate Program, Universidade do Vale do Taquari (Univates), Lajeado CEP 95914-014, Brazil
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen 72076, Germany
- Medical Science Graduate Program, Universidade do Vale do Taquari (Univates), Lajeado CEP 95914-014, Brazil
| | - Luis Fernando Saraiva Macedo Timmers
- Biotechnology Graduate Program, Universidade do Vale do Taquari (Univates), Lajeado CEP 95914-014, Brazil
- Department of Medicine, Universidade do Vale do Taquari (Univates), Lajeado CEP 95914-014, Brazil
- Medical Science Graduate Program, Universidade do Vale do Taquari (Univates), Lajeado CEP 95914-014, Brazil
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11
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Tumber A, Salah E, Brewitz L, Corner TP, Schofield CJ. Kinetic and inhibition studies on human Jumonji-C (JmjC) domain-containing protein 5. RSC Chem Biol 2023; 4:399-413. [PMID: 37292060 PMCID: PMC10246557 DOI: 10.1039/d2cb00249c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/19/2023] [Indexed: 06/10/2023] Open
Abstract
Jumonji-C (JmjC) domain-containing protein 5 (JMJD5) is a human 2-oxoglutarate (2OG) and Fe(ii)-dependent oxygenase which catalyses the post-translational C3 hydroxylation of arginyl-residues and which is linked to the circadian rhythm and to cancer biology through as yet unidentified mechanisms. We report robust solid phase extraction coupled to mass spectrometry (SPE-MS)-based JMJD5 assays which enable kinetic and high-throughput inhibition studies. The kinetic studies reveal that some synthetic 2OG derivatives, notably including a 2OG derivative with a cyclic carbon backbone (i.e. (1R)-3-(carboxycarbonyl)cyclopentane-1-carboxylic acid), are efficient alternative cosubstrates of JMJD5 and of factor inhibiting hypoxia-inducible transcription factor HIF-α (FIH), but not of the Jumonji-C (JmjC) histone Nε-methyl lysine demethylase KDM4E, apparently reflecting the closer structural similarity of JMJD5 and FIH. The JMJD5 inhibition assays were validated by investigating the effect of reported 2OG oxygenase inhibitors on JMJD5 catalysis; the results reveal that broad-spectrum 2OG oxygenase inhibitors are also efficient JMJD5 inhibitors (e.g. N-oxalylglycine, pyridine-2,4-dicarboxylic acid, ebselen) whereas most 2OG oxygenase inhibitors that are in clinical use (e.g. roxadustat) do not inhibit JMJD5. The SPE-MS assays will help enable the development of efficient and selective JMJD5 inhibitors for investigating the biochemical functions of JMJD5 in cellular studies.
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Affiliation(s)
- Anthony Tumber
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford UK
| | - Eidarus Salah
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford UK
| | - Lennart Brewitz
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford UK
| | - Thomas P Corner
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford UK
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12
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Pang X, Xu W, Liu Y, Li H, Chen L. The research progress of SARS-CoV-2 main protease inhibitors from 2020 to 2022. Eur J Med Chem 2023; 257:115491. [PMID: 37244162 DOI: 10.1016/j.ejmech.2023.115491] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/06/2023] [Accepted: 05/14/2023] [Indexed: 05/29/2023]
Abstract
The novel coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide. The main protease (Mpro) of SARS-CoV-2 plays a central role in viral replication and transcription and represents an attractive drug target for fighting COVID-19. Many SARS-CoV-2 Mpro inhibitors have been reported, including covalent and noncovalent inhibitors. The SARS-CoV-2 Mpro inhibitor PF-07321332 (Nirmatrelvir) designed by Pfizer has been put on the market. This paper briefly introduces the structural characteristics of SARS-CoV-2 Mpro and summarizes the research progress of SARS-CoV-2 Mpro inhibitors from the aspects of drug repurposing and drug design. These information will provide a basis for the drug development of treating the infection of SARS-CoV-2 and even other coronaviruses in the future.
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Affiliation(s)
- Xiaojing Pang
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Wei Xu
- Institute of Structural Pharmacology & TCM Chemical Biology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, 350122, China
| | - Yang Liu
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Hua Li
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China; Institute of Structural Pharmacology & TCM Chemical Biology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, 350122, China.
| | - Lixia Chen
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China.
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13
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Kronenberger T, Laufer SA, Pillaiyar T. COVID-19 therapeutics: small-molecule drug development targeting SARS-CoV-2 main protease. Drug Discov Today 2023; 28:103579. [PMID: 37028502 PMCID: PMC10074736 DOI: 10.1016/j.drudis.2023.103579] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 03/14/2023] [Accepted: 03/28/2023] [Indexed: 04/09/2023]
Abstract
The severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) is the causative factor behind the 2019 global coronavirus pandemic (COVID-19). The main protease, known as Mpro, is encoded by the viral genome and is essential for viral replication. It has also been an effective target for drug development. In this review, we discuss the rationale for inhibitors that specifically target SARS-CoV-2 Mpro. Small molecules and peptidomimetic inhibitors are two types of inhibitor with various modes of action and we focus here on novel inhibitors that were only discovered during the COVID-19 pandemic highlighting their binding modes and structures.
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Affiliation(s)
- Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tuebingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany; School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, PO Box 1627, FI-70211 Kuopio, Finland; Cluster of Excellence iFIT (EXC 2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, 72076 Tübingen, Germany
| | - Stefan A Laufer
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tuebingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany; Cluster of Excellence iFIT (EXC 2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, 72076 Tübingen, Germany
| | - Thanigaimalai Pillaiyar
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tuebingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
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14
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Brewitz L, Dumjahn L, Zhao Y, Owen CD, Laidlaw SM, Malla TR, Nguyen D, Lukacik P, Salah E, Crawshaw AD, Warren AJ, Trincao J, Strain-Damerell C, Carroll MW, Walsh MA, Schofield CJ. Alkyne Derivatives of SARS-CoV-2 Main Protease Inhibitors Including Nirmatrelvir Inhibit by Reacting Covalently with the Nucleophilic Cysteine. J Med Chem 2023; 66:2663-2680. [PMID: 36757959 PMCID: PMC9924091 DOI: 10.1021/acs.jmedchem.2c01627] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Indexed: 02/10/2023]
Abstract
Nirmatrelvir (PF-07321332) is a nitrile-bearing small-molecule inhibitor that, in combination with ritonavir, is used to treat infections by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Nirmatrelvir interrupts the viral life cycle by inhibiting the SARS-CoV-2 main protease (Mpro), which is essential for processing viral polyproteins into functional nonstructural proteins. We report studies which reveal that derivatives of nirmatrelvir and other Mpro inhibitors with a nonactivated terminal alkyne group positioned similarly to the electrophilic nitrile of nirmatrelvir can efficiently inhibit isolated Mpro and SARS-CoV-2 replication in cells. Mass spectrometric and crystallographic evidence shows that the alkyne derivatives inhibit Mpro by apparent irreversible covalent reactions with the active site cysteine (Cys145), while the analogous nitriles react reversibly. The results highlight the potential for irreversible covalent inhibition of Mpro and other nucleophilic cysteine proteases by alkynes, which, in contrast to nitriles, can be functionalized at their terminal position to optimize inhibition and selectivity, as well as pharmacodynamic and pharmacokinetic properties.
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Affiliation(s)
- Lennart Brewitz
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Leo Dumjahn
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Yilin Zhao
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - C. David Owen
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research
Complex at Harwell, Harwell Science and
Innovation Campus, Didcot OX11 0FA, United
Kingdom
| | - Stephen M. Laidlaw
- Wellcome
Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Tika R. Malla
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Dung Nguyen
- Wellcome
Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Petra Lukacik
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research
Complex at Harwell, Harwell Science and
Innovation Campus, Didcot OX11 0FA, United
Kingdom
| | - Eidarus Salah
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Adam D. Crawshaw
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Anna J. Warren
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Jose Trincao
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Claire Strain-Damerell
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research
Complex at Harwell, Harwell Science and
Innovation Campus, Didcot OX11 0FA, United
Kingdom
| | - Miles W. Carroll
- Wellcome
Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Martin A. Walsh
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research
Complex at Harwell, Harwell Science and
Innovation Campus, Didcot OX11 0FA, United
Kingdom
| | - Christopher J. Schofield
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
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15
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Khanfar MA, Salaas N, Abumostafa R. Discovery of natural-derived M pro inhibitors as therapeutic candidates for COVID-19: Structure-based pharmacophore screening combined with QSAR analysis. Mol Inform 2023; 42:e2200198. [PMID: 36762567 DOI: 10.1002/minf.202200198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 12/26/2022] [Accepted: 01/05/2023] [Indexed: 02/11/2023]
Abstract
The main protease (Mpro ) is an essential enzyme for the life cycle of SARS-CoV-2 and a validated target for treatment of COVID-19 infection. Structure-based pharmacophore modeling combined with QSAR calculations were employed to identify new chemical scaffolds of Mpro inhibitors from natural products repository. Hundreds of pharmacophore models were manually built from their corresponding X-ray crystallographic structures. A pharmacophore model that was validated by receiver operating characteristic (ROC) curve analysis and selected using the statistically optimum QSAR equation was implemented as a 3D-search tool to mine AnalytiCon Discovery database of natural products. Captured hits that showed the highest predicted inhibitory activities were bioassayed. Three active Mpro inhibitors (pseurotin A, lactupicrin, and alpinetin) were successfully identified with IC50 values in low micromolar range.
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Affiliation(s)
- Mohammad A Khanfar
- College of Pharmacy, Alfaisal University, Al Takhassusi Rd, P. O. Box 50927, Riyadh, 11533, Saudi Arabia.,Department of Pharmaceutical Sciences, Faculty of Pharmacy, The University of Jordan, P.O Box 13140, Amman, 11942, Jordan
| | - Nada Salaas
- College of Pharmacy, Alfaisal University, Al Takhassusi Rd, P. O. Box 50927, Riyadh, 11533, Saudi Arabia
| | - Reem Abumostafa
- College of Pharmacy, Alfaisal University, Al Takhassusi Rd, P. O. Box 50927, Riyadh, 11533, Saudi Arabia
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16
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Karges J, Giardini MA, Blacque O, Woodworth B, Siqueira-Neto JL, Cohen SM. Enantioselective inhibition of the SARS-CoV-2 main protease with rhenium(i) picolinic acid complexes. Chem Sci 2023; 14:711-720. [PMID: 36741526 PMCID: PMC9848156 DOI: 10.1039/d2sc05473f] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 12/12/2022] [Indexed: 12/14/2022] Open
Abstract
Infections of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have triggered a global pandemic with millions of deaths worldwide. Herein, the synthesis of functionalized Re(i) tricarbonyl complexes as inhibitors of the SARS-CoV-2 main protease, also referred to as the 3-chymotrypsin-like protease (3CLpro), is presented. The metal complexes were found to inhibit the activity of the enzyme with IC50 values in the low micromolar range. Mass spectrometry revealed that the metal complexes formed a coordinate covalent bond with the enzyme. Chiral separation of the enantiomers of the lead compound showed that one enantiomer was significantly more active than the other, consistent with specific binding and much like that observed for conventional organic small molecule inhibitors and druglike compounds. Evaluation of the lead compound against SARS-CoV-2 in a cell-based infection assay confirmed enantiospecific inhibition against the virus. This study represents a significant advancement in the use of metal complexes as coordinate covalent inhibitors of enzymes, as well as a novel starting point for the development of novel SARS-CoV-2 inhibitors.
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Affiliation(s)
- Johannes Karges
- Department of Chemistry and Biochemistry, University of CaliforniaLa JollaSan DiegoCalifornia 92093USA
| | - Miriam A. Giardini
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of CaliforniaLa JollaSan DiegoCalifornia 92093USA
| | - Olivier Blacque
- Department of Chemistry, University of ZurichWinterthurerstrasse 190CH-8057ZurichSwitzerland
| | - Brendon Woodworth
- Department of Medicine, Division of Infectious Diseases, University of California San DiegoLa JollaCalifornia 92093USA
| | - Jair L. Siqueira-Neto
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of CaliforniaLa JollaSan DiegoCalifornia 92093USA
| | - Seth M. Cohen
- Department of Chemistry and Biochemistry, University of CaliforniaLa JollaSan DiegoCalifornia 92093USA
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17
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Moreira JS, Galvão DS, Xavier CFC, Cunha S, Pita SSDR, Reis JN, Freitas HFD. Phenotypic and in silico studies for a series of synthetic thiosemicarbazones as New Delhi metallo-beta-lactamase carbapenemase inhibitors. J Biomol Struct Dyn 2022; 40:14223-14235. [PMID: 34766882 DOI: 10.1080/07391102.2021.2001379] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The past two decades have been marked by a global spread of bacterial resistance to β-lactam drugs and carbapenems derivatives are the ultimate treatment against multidrug-resistant bacteria. β-lactamase expression is related to resistance which demands the development of bacterial resistance blockers. Drug inhibitor combinations of serine-β-lactamase and β-lactam were successful employed in therapy despite their inactivity against New Delhi metallo-beta-lactamase (NDM). Until now, few compounds are active against NDM-producing bacteria and no specific inhibitors are available yet. The rational strategy for NDM inhibitors development starts with in vitro assays aiming to seek compounds that could act synergistically with β-lactam antibiotics. Thus, eight thiosemicarbazone derivatives were synthesized and investigated for their ability to reverse the resistant phenotype in NDM in Enterobacter cloacae. Phenotypic screening indicated that four isatin-beta-thiosemicarbazones showed Fractional Inhibitory Concentration (FIC) ≤ 250 µM in the presence of meropenem (4 µg/mL). The most promising compound (FIC= 31.25 µM) also presented synergistic effect (FICI = 0.34). Docking and molecular dynamics studies on NDM-thiosemicarbazone complex suggested that 2,3-dihydro-1H-indol-2-one subunit interacts with catalytic zinc and interacted through hydrogen bonds with Asp124 acting like a carboxylic acid bioisostere. Additionally, thiosemicarbazone tautomer with oxidized sulfur (thione) seems to act as a spacer rather than zinc chelator, and the aromatic moieties are stabilized by pi-pi and cation-pi interactions with His189 and Lys221 residues. Our results addressed some thiosemicarbazone structural changes to increase its biological activity against NDM and highlight its scaffold as promising alternatives to treat bacterial resistance.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jonatham Souza Moreira
- Post-Graduation Program in Pharmacy, Pharmacy College, Federal University of Bahia, Salvador, Bahia, Brazil
| | | | | | - Silvio Cunha
- Chemistry Institute, Federal University of Bahia, Ondina, Salvador, Bahia, Brazil
| | - Samuel Silva da Rocha Pita
- Pharmacy College, Federal University of Bahia, Salvador, Bahia, Brazil.,Bioinformatics and Molecular Modeling Laboratory (LaBiMM), Federal University of Bahia, Salvador, Bahia, Brazil
| | - Joice Neves Reis
- Post-Graduation Program in Pharmacy, Pharmacy College, Federal University of Bahia, Salvador, Bahia, Brazil.,Pharmacy College, Federal University of Bahia, Salvador, Bahia, Brazil
| | - Humberto Fonseca de Freitas
- Post-Graduation Program in Pharmacy, Pharmacy College, Federal University of Bahia, Salvador, Bahia, Brazil.,Pharmacy College, Federal University of Bahia, Salvador, Bahia, Brazil.,Bioinformatics and Molecular Modeling Laboratory (LaBiMM), Federal University of Bahia, Salvador, Bahia, Brazil
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18
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Xie H, Qiang P, Wang Y, Xia F, Liu P, Li M. Discovery and mechanism studies of a novel ATG4B inhibitor Ebselen by drug repurposing and its anti-colorectal cancer effects in mice. Cell Biosci 2022; 12:206. [PMID: 36539845 PMCID: PMC9767854 DOI: 10.1186/s13578-022-00944-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Cysteine protease ATG4B, a key autophagy protein, is an attractive target for colorectal cancer therapy. However, ATG4B inhibitors with higher efficiency, safety, and clear mechanism are still limited. In this study, we discovered ATG4B inhibitors based on the FDA-approved drug library through FRET-based high-throughput screening and gel-based analysis. Among the nine hits, compound Ebselen showed the most potent ATG4B inhibitory activity (IC50 = 189 nM) and exhibited controllable selectivity and structural optimizable possibility against ATG4A and caspases. We then performed mass spectrometry assay and cysteine mutations to confirm that Ebselen could covalently bind to ATG4B at Cys74. Moreover, Cys292 and Cys361 instead of Cys74 are responsible for the redox-oligomerization and efficient activity inhibition of ATG4B. Ultimately through cell culture and mouse xenograft tumor models, we established the impact of Ebselen on autophagy and tumor suppression via ATG4B inhibition other than apoptosis. These results suggest that old drug Ebselen as an ATG4B inhibitor through oxidative modification may be repurposed as a promising anti-colorectal cancer drug.
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Affiliation(s)
- Huazhong Xie
- grid.12981.330000 0001 2360 039XSchool of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Pengfei Qiang
- grid.12981.330000 0001 2360 039XSchool of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Yao Wang
- grid.12981.330000 0001 2360 039XSchool of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Fan Xia
- grid.12981.330000 0001 2360 039XSchool of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Peiqing Liu
- grid.12981.330000 0001 2360 039XSchool of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Min Li
- grid.12981.330000 0001 2360 039XSchool of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
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19
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Jansen-van Vuuren RD, Jedlovčnik L, Košmrlj J, Massey TE, Derdau V. Deuterated Drugs and Biomarkers in the COVID-19 Pandemic. ACS OMEGA 2022; 7:41840-41858. [PMID: 36440130 PMCID: PMC9685803 DOI: 10.1021/acsomega.2c04160] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 10/18/2022] [Indexed: 06/07/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is a highly contagious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Initially identified in Wuhan (China) in December 2019, COVID-19 rapidly spread globally, resulting in the COVID-19 pandemic. Carriers of the SARS-CoV-2 can experience symptoms ranging from mild to severe (or no symptoms whatsoever). Although vaccination provides extra immunity toward SARS-CoV-2, there has been an urgent need to develop treatments for COVID-19 to alleviate symptoms for carriers of the disease. In seeking a potential treatment, deuterated compounds have played a critical role either as therapeutic agents or as internal MS standards for studying the pharmacological properties of new drugs by quantifying the parent compounds and metabolites. We have identified >70 examples of deuterium-labeled compounds associated with treatment of COVID-19. Of these, we found 9 repurposed drugs and >20 novel drugs studied for potential therapeutic roles along with a total of 38 compounds (drugs, biomarkers, and lipids) explored as internal mass spectrometry standards. This review details the synthetic pathways and modes of action of these compounds (if known), and a brief analysis of each study.
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Affiliation(s)
- Ross D. Jansen-van Vuuren
- Faculty
of Chemistry and Chemical Technology, University
of Ljubljana, Večna pot 113, Ljubljana 1000, Slovenia
- Department
of Chemistry, Queen’s University, 90 Bader Lane, Kingston, Ontario K7L
3N6, Canada
| | - Luka Jedlovčnik
- Faculty
of Chemistry and Chemical Technology, University
of Ljubljana, Večna pot 113, Ljubljana 1000, Slovenia
| | - Janez Košmrlj
- Faculty
of Chemistry and Chemical Technology, University
of Ljubljana, Večna pot 113, Ljubljana 1000, Slovenia
| | - Thomas E. Massey
- Department
of Biomedical and Molecular Sciences, School of Medicine, Queen’s University, Botterell Hall, 18 Stuart Street, Kingston, Ontario K7L 3N6, Canada
| | - Volker Derdau
- Research
& Development, Integrated Drug Discovery, Isotope Chemistry, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst G876, Frankfurt/Main 65926, Germany
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20
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La Monica G, Bono A, Lauria A, Martorana A. Targeting SARS-CoV-2 Main Protease for Treatment of COVID-19: Covalent Inhibitors Structure-Activity Relationship Insights and Evolution Perspectives. J Med Chem 2022; 65:12500-12534. [PMID: 36169610 PMCID: PMC9528073 DOI: 10.1021/acs.jmedchem.2c01005] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Indexed: 02/07/2023]
Abstract
The viral main protease is one of the most attractive targets among all key enzymes involved in the SARS-CoV-2 life cycle. Covalent inhibition of the cysteine145 of SARS-CoV-2 MPRO with selective antiviral drugs will arrest the replication process of the virus without affecting human catalytic pathways. In this Perspective, we analyzed the in silico, in vitro, and in vivo data of the most representative examples of covalent SARS-CoV-2 MPRO inhibitors reported in the literature to date. In particular, the studied molecules were classified into eight different categories according to their reactive electrophilic warheads, highlighting the differences between their reversible/irreversible mechanism of inhibition. Furthermore, the analyses of the most recurrent pharmacophoric moieties and stereochemistry of chiral carbons were reported. The analyses of noncovalent and covalent in silico protocols, provided in this Perspective, would be useful for the scientific community to discover new and more efficient covalent SARS-CoV-2 MPRO inhibitors.
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Affiliation(s)
| | | | - Antonino Lauria
- Dipartimento di Scienze e
Tecnologie Biologiche Chimiche e Farmaceutiche, University of Palermo, Viale delle Scienze, Ed. 17, I-90128 Palermo, Italy
| | - Annamaria Martorana
- Dipartimento di Scienze e
Tecnologie Biologiche Chimiche e Farmaceutiche, University of Palermo, Viale delle Scienze, Ed. 17, I-90128 Palermo, Italy
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21
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Hu Q, Xiong Y, Zhu G, Zhang Y, Zhang Y, Huang P, Ge G. The SARS-CoV-2 main protease (M pro): Structure, function, and emerging therapies for COVID-19. MedComm (Beijing) 2022; 3:e151. [PMID: 35845352 PMCID: PMC9283855 DOI: 10.1002/mco2.151] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/06/2022] [Accepted: 06/06/2022] [Indexed: 12/21/2022] Open
Abstract
The main proteases (Mpro), also termed 3-chymotrypsin-like proteases (3CLpro), are a class of highly conserved cysteine hydrolases in β-coronaviruses. Increasing evidence has demonstrated that 3CLpros play an indispensable role in viral replication and have been recognized as key targets for preventing and treating coronavirus-caused infectious diseases, including COVID-19. This review is focused on the structural features and biological function of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease Mpro (also known as 3CLpro), as well as recent advances in discovering and developing SARS-CoV-2 3CLpro inhibitors. To better understand the characteristics of SARS-CoV-2 3CLpro inhibitors, the inhibition activities, inhibitory mechanisms, and key structural features of various 3CLpro inhibitors (including marketed drugs, peptidomimetic, and non-peptidomimetic synthetic compounds, as well as natural compounds and their derivatives) are summarized comprehensively. Meanwhile, the challenges in this field are highlighted, while future directions for designing and developing efficacious 3CLpro inhibitors as novel anti-coronavirus therapies are also proposed. Collectively, all information and knowledge presented here are very helpful for understanding the structural features and inhibitory mechanisms of SARS-CoV-2 3CLpro inhibitors, which offers new insights or inspiration to medicinal chemists for designing and developing more efficacious 3CLpro inhibitors as novel anti-coronavirus agents.
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Affiliation(s)
- Qing Hu
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
- Clinical Pharmacy CenterCancer CenterDepartment of PharmacyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical College, HangzhouZhejiangChina
| | - Yuan Xiong
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Guang‐Hao Zhu
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Ya‐Ni Zhang
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Yi‐Wen Zhang
- Clinical Pharmacy CenterCancer CenterDepartment of PharmacyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical College, HangzhouZhejiangChina
| | - Ping Huang
- Clinical Pharmacy CenterCancer CenterDepartment of PharmacyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical College, HangzhouZhejiangChina
| | - Guang‐Bo Ge
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
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22
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Bresinsky M, Strasser JM, Hubmann A, Vallaster B, McCue WM, Fuller J, Singh G, Nelson KM, Cuellar ME, Finzel BC, Ashe KH, Walters MA, Pockes S. Characterization of caspase-2 inhibitors based on specific sites of caspase-2-mediated proteolysis. Arch Pharm (Weinheim) 2022; 355:e2200095. [PMID: 35642311 PMCID: PMC9616052 DOI: 10.1002/ardp.202200095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/30/2022] [Accepted: 05/04/2022] [Indexed: 02/04/2023]
Abstract
Since the discovery of the caspase-2 (Casp2)-mediated ∆tau314 cleavage product and its associated impact on tauopathies such as Alzheimer's disease, the design of selective Casp2 inhibitors has become a focus in medicinal chemistry research. In the search for new lead structures with respect to Casp2 selectivity and drug-likeness, we have taken an approach by looking more closely at the specific sites of Casp2-mediated proteolysis. Using seven selected protein cleavage sequences, we synthesized a peptide series of 53 novel molecules and studied them using in vitro pharmacology, molecular modeling, and crystallography. Regarding Casp2 selectivity, AcITV(Dab)D-CHO (23) and AcITV(Dap)D-CHO (26) demonstrated the best selectivity (1-6-fold), although these trends were only moderate. However, some analogous tetrapeptides, most notably AcDKVD-CHO (45), showed significantly increased Casp3 selectivities (>100-fold). Tetra- and tripeptides display decreased or no Casp2 affinity, supporting the assumption that a motif of five amino acids is required for efficient Casp2 inhibition. Overall, the results provide a reasonable basis for the development of both selective Casp2 and Casp3 inhibitors.
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Affiliation(s)
- Merlin Bresinsky
- Institute of Pharmacy, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Jessica M. Strasser
- Department of Medicinal Chemistry, Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN 55414, USA
| | - Alexander Hubmann
- Institute of Pharmacy, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Bernadette Vallaster
- Institute of Pharmacy, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - William M. McCue
- Department of Medicinal Chemistry, Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN 55414, USA
| | - Jessica Fuller
- Department of Medicinal Chemistry, Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN 55414, USA
| | - Gurpreet Singh
- Department of Medicinal Chemistry, Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN 55414, USA
| | - Kathryn M. Nelson
- Department of Medicinal Chemistry, Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN 55414, USA
| | - Matthew E. Cuellar
- Department of Medicinal Chemistry, Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN 55414, USA
| | - Barry C. Finzel
- Department of Medicinal Chemistry, Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN 55414, USA
| | - Karen H. Ashe
- Department of Neurology, University of Minnesota, 2101 6th Street SE, Minneapolis, MN 55455, USA
- GRECC, Minneapolis VA Hospital, 1 Veterans Drive, Minneapolis, MN 55417, USA
| | - Michael A. Walters
- Department of Medicinal Chemistry, Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN 55414, USA
| | - Steffen Pockes
- Institute of Pharmacy, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
- Department of Medicinal Chemistry, Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN 55414, USA
- Department of Neurology, University of Minnesota, 2101 6th Street SE, Minneapolis, MN 55455, USA
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23
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Xu YS, Chigan JZ, Li JQ, Ding HH, Sun LY, Liu L, Hu Z, Yang KW. Hydroxamate and thiosemicarbazone: Two highly promising scaffolds for the development of SARS-CoV-2 antivirals. Bioorg Chem 2022; 124:105799. [PMID: 35462235 PMCID: PMC9014651 DOI: 10.1016/j.bioorg.2022.105799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/31/2022] [Accepted: 04/07/2022] [Indexed: 01/09/2023]
Abstract
The emerging COVID-19 pandemic generated by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has severely threatened human health. The main protease (Mpro) of SARS-CoV-2 is promising target for antiviral drugs, which plays a vital role for viral duplication. Development of the inhibitor against Mpro is an ideal strategy to combat COVID-19. In this work, twenty-three hydroxamates 1a-i and thiosemicarbazones 2a-n were identified by FRET screening to be the potent inhibitors of Mpro, which exhibited more than 94% (except 1c) and more than 69% inhibition, and an IC50 value in the range of 0.12-31.51 and 2.43-34.22 μM, respectively. 1a and 2b were found to be the most effective inhibitors in the hydroxamates and thiosemicarbazones, with an IC50 of 0.12 and 2.43 μM, respectively. Enzyme kinetics, jump dilution and thermal shift assays revealed that 2b is a competitive inhibitor of Mpro, while 1a is a time-dependently inhibitor; 2b reversibly but 1a irreversibly bound to the target; the binding of 2b increased but 1a decreased stability of the target, and DTT assays indicate that 1a is the promiscuous cysteine protease inhibitor. Cytotoxicity assays showed that 1a has low, but 2b has certain cytotoxicity on the mouse fibroblast cells (L929). Docking studies revealed that the benzyloxycarbonyl carbon of 1a formed thioester with Cys145, while the phenolic hydroxyl oxygen of 2b formed H-bonds with Cys145 and Asn142. This work provided two promising scaffolds for the development of Mpro inhibitors to combat COVID-19.
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Affiliation(s)
- Yin-Sui Xu
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Jia-Zhu Chigan
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Jia-Qi Li
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Huan-Huan Ding
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Le-Yun Sun
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Lu Liu
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Zhenxin Hu
- Suzhou Genevide Biotechnology Co., Ltd, Suzhou 215123, PR China
| | - Ke-Wu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China.
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24
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Li H, Yuan S, Wei X, Sun H. Metal-based strategies for the fight against COVID-19. Chem Commun (Camb) 2022; 58:7466-7482. [PMID: 35730442 DOI: 10.1039/d2cc01772e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The emerging COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has claimed over six million lives globally to date. Despite the availability of vaccines, the pandemic still cannot be fully controlled owing to rapid mutation of the virus that renders enhanced transmissibility and antibody evasion. This is thus an unmet need to develop safe and effective therapeutic options for COVID-19, in particular, remedies that can be used at home. Considering the great success of multi-targeted cocktail therapy for the treatment of viral infections, metal-based drugs might represent a unique and new source of antivirals that resemble a cocktail therapy in terms of their mode of actions. In this review, we first summarize the role that metal ions played in SARS-CoV-2 viral replication and pathogenesis, then highlight the chemistry of metal-based strategies in the fight against SARS-CoV-2 infection, including both metal displacement and chelation based approaches. Finally, we outline a perspective and direction on how to design and develop metal-based antivirals for the fight against the current or future coronavirus pandemic.
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Affiliation(s)
- Hongyan Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry and CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
| | - Shuofeng Yuan
- Department of Microbiology and State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Xueying Wei
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry and CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pokfulam, Hong Kong SAR, China. .,Department of Microbiology and State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Hongzhe Sun
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry and CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
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25
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Malla TR, Brewitz L, Muntean DG, Aslam H, Owen CD, Salah E, Tumber A, Lukacik P, Strain-Damerell C, Mikolajek H, Walsh MA, Schofield CJ. Penicillin Derivatives Inhibit the SARS-CoV-2 Main Protease by Reaction with Its Nucleophilic Cysteine. J Med Chem 2022; 65:7682-7696. [PMID: 35549342 PMCID: PMC9115881 DOI: 10.1021/acs.jmedchem.1c02214] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Indexed: 12/05/2022]
Abstract
The SARS-CoV-2 main protease (Mpro) is a medicinal chemistry target for COVID-19 treatment. Given the clinical efficacy of β-lactams as inhibitors of bacterial nucleophilic enzymes, they are of interest as inhibitors of viral nucleophilic serine and cysteine proteases. We describe the synthesis of penicillin derivatives which are potent Mpro inhibitors and investigate their mechanism of inhibition using mass spectrometric and crystallographic analyses. The results suggest that β-lactams have considerable potential as Mpro inhibitors via a mechanism involving reaction with the nucleophilic cysteine to form a stable acyl-enzyme complex as shown by crystallographic analysis. The results highlight the potential for inhibition of viral proteases employing nucleophilic catalysis by β-lactams and related acylating agents.
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Affiliation(s)
- Tika R. Malla
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Lennart Brewitz
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Dorian-Gabriel Muntean
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Hiba Aslam
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - C. David Owen
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, OX11
0FA Didcot, United Kingdom
| | - Eidarus Salah
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Anthony Tumber
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Petra Lukacik
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, OX11
0FA Didcot, United Kingdom
| | - Claire Strain-Damerell
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, OX11
0FA Didcot, United Kingdom
| | - Halina Mikolajek
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, OX11
0FA Didcot, United Kingdom
| | - Martin A. Walsh
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, OX11
0FA Didcot, United Kingdom
| | - Christopher J. Schofield
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
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26
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Brewitz L, Kamps JJAG, Lukacik P, Strain‐Damerell C, Zhao Y, Tumber A, Malla TR, Orville AM, Walsh MA, Schofield CJ. Mass Spectrometric Assays Reveal Discrepancies in Inhibition Profiles for the SARS-CoV-2 Papain-Like Protease. ChemMedChem 2022; 17:e202200016. [PMID: 35085423 PMCID: PMC9015526 DOI: 10.1002/cmdc.202200016] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 01/26/2022] [Indexed: 11/20/2022]
Abstract
The two SARS-CoV-2 proteases, i. e. the main protease (Mpro ) and the papain-like protease (PLpro ), which hydrolyze the viral polypeptide chain giving functional non-structural proteins, are essential for viral replication and are medicinal chemistry targets. We report a high-throughput mass spectrometry (MS)-based assay which directly monitors PLpro catalysis in vitro. The assay was applied to investigate the effect of reported small-molecule PLpro inhibitors and selected Mpro inhibitors on PLpro catalysis. The results reveal that some, but not all, PLpro inhibitor potencies differ substantially from those obtained using fluorescence-based assays. Some substrate-competing Mpro inhibitors, notably PF-07321332 (nirmatrelvir) which is in clinical development, do not inhibit PLpro . Less selective Mpro inhibitors, e. g. auranofin, inhibit PLpro , highlighting the potential for dual PLpro /Mpro inhibition. MS-based PLpro assays, which are orthogonal to widely employed fluorescence-based assays, are of utility in validating inhibitor potencies, especially for inhibitors operating by non-covalent mechanisms.
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Affiliation(s)
- Lennart Brewitz
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of Oxford12 Mansfield RoadOX1 3TAOxfordUK
| | - Jos J. A. G. Kamps
- Diamond Light Source Ltd.Harwell Science and Innovation CampusOX11 0DEDidcotUK
- Research Complex at HarwellHarwell Science and Innovation CampusOX11 0FADidcotUK
| | - Petra Lukacik
- Diamond Light Source Ltd.Harwell Science and Innovation CampusOX11 0DEDidcotUK
- Research Complex at HarwellHarwell Science and Innovation CampusOX11 0FADidcotUK
| | - Claire Strain‐Damerell
- Diamond Light Source Ltd.Harwell Science and Innovation CampusOX11 0DEDidcotUK
- Research Complex at HarwellHarwell Science and Innovation CampusOX11 0FADidcotUK
| | - Yilin Zhao
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of Oxford12 Mansfield RoadOX1 3TAOxfordUK
| | - Anthony Tumber
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of Oxford12 Mansfield RoadOX1 3TAOxfordUK
| | - Tika R. Malla
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of Oxford12 Mansfield RoadOX1 3TAOxfordUK
| | - Allen M. Orville
- Diamond Light Source Ltd.Harwell Science and Innovation CampusOX11 0DEDidcotUK
- Research Complex at HarwellHarwell Science and Innovation CampusOX11 0FADidcotUK
| | - Martin A. Walsh
- Diamond Light Source Ltd.Harwell Science and Innovation CampusOX11 0DEDidcotUK
- Research Complex at HarwellHarwell Science and Innovation CampusOX11 0FADidcotUK
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of Oxford12 Mansfield RoadOX1 3TAOxfordUK
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27
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Ramli FF, Cowen PJ, Godlewska BR. The Potential Use of Ebselen in Treatment-Resistant Depression. Pharmaceuticals (Basel) 2022; 15:485. [PMID: 35455482 PMCID: PMC9030939 DOI: 10.3390/ph15040485] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 02/01/2023] Open
Abstract
Ebselen is an organoselenium compound developed as an antioxidant and subsequently shown to be a glutathione peroxidase (GPx) mimetic. Ebselen shows some efficacy in post-stroke neuroprotection and is currently in trial for the treatment and prevention of hearing loss, Meniere's Disease and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In vitro screening studies show that ebselen is also an effective inhibitor of the enzyme inositol monophosphatase (IMPase), which is a key target of the mood-stabilising drug lithium. Further, in animal experimental studies, ebselen produces effects on the serotonin system very similar to those of lithium and also decreases behavioural impulsivity. The antidepressant effects of lithium in treatment-resistant depression (TRD) have been attributed to its ability to facilitate presynaptic serotonin activity; this suggests that ebselen might also have a therapeutic role in this condition. Human studies utilising magnetic resonance spectroscopy support the notion that ebselen, at therapeutic doses, inhibits IMPase in the human brain. Moreover, neuropsychological studies support an antidepressant profile for ebselen based on positive effects on emotional processing and reward seeking. Ebselen also lowers a human laboratory measure of impulsivity, a property that has been associated with lithium's anti-suicidal effects in patients with mood disorders. Current clinical studies are directed towards assessment of the neuropsychological effects of ebselen in TRD patients. It will also be important to ascertain whether ebselen is able to lower impulsivity and suicidal behaviour in clinical populations. The objective of this review is to summarise the developmental history, pre-clinical and clinical psychopharmacological properties of ebselen in psychiatric disorders and its potential application as a treatment for TRD.
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Affiliation(s)
- Fitri Fareez Ramli
- Clinical Psychopharmacology Research Group, Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford OX3 7JX, UK; (F.F.R.); (P.J.C.)
- Department of Pharmacology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia
| | - Philip J. Cowen
- Clinical Psychopharmacology Research Group, Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford OX3 7JX, UK; (F.F.R.); (P.J.C.)
| | - Beata R. Godlewska
- Clinical Psychopharmacology Research Group, Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford OX3 7JX, UK; (F.F.R.); (P.J.C.)
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28
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Agost-Beltrán L, de la Hoz-Rodríguez S, Bou-Iserte L, Rodríguez S, Fernández-de-la-Pradilla A, González FV. Advances in the Development of SARS-CoV-2 Mpro Inhibitors. Molecules 2022; 27:2523. [PMID: 35458721 PMCID: PMC9026863 DOI: 10.3390/molecules27082523] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 02/01/2023] Open
Abstract
Since the outbreak of COVID-19, one of the strategies used to search for new drugs has been to find inhibitors of the main protease (Mpro) of the virus SARS-CoV-2. Initially, previously reported inhibitors of related proteases such as the main proteases of SARS-CoV and MERS-CoV were tested. A huge effort was then carried out by the scientific community to design, synthesize and test new small molecules acting as inactivators of SARS-CoV-2 Mpro. From the chemical structure view, these compounds can be classified into two main groups: one corresponds to modified peptides displaying an adequate sequence for high affinity and a reactive warhead; and the second is a diverse group including chemical compounds that do not have a peptide framework. Although a drug including a SARS-CoV-2 main protease inhibitor has already been commercialized, denoting the importance of this field, more compounds have been demonstrated to be promising potent inhibitors as potential antiviral drugs.
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Affiliation(s)
- Laura Agost-Beltrán
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, 12080 Castelló, Spain; (L.A.-B.); (S.d.l.H.-R.); (L.B.-I.); (S.R.)
| | - Sergio de la Hoz-Rodríguez
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, 12080 Castelló, Spain; (L.A.-B.); (S.d.l.H.-R.); (L.B.-I.); (S.R.)
| | - Lledó Bou-Iserte
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, 12080 Castelló, Spain; (L.A.-B.); (S.d.l.H.-R.); (L.B.-I.); (S.R.)
| | - Santiago Rodríguez
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, 12080 Castelló, Spain; (L.A.-B.); (S.d.l.H.-R.); (L.B.-I.); (S.R.)
| | | | - Florenci V. González
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, 12080 Castelló, Spain; (L.A.-B.); (S.d.l.H.-R.); (L.B.-I.); (S.R.)
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29
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Ma C, Tan H, Choza J, Wang Y, Wang J. Validation and invalidation of SARS-CoV-2 main protease inhibitors using the Flip-GFP and Protease-Glo luciferase assays. Acta Pharm Sin B 2022; 12:1636-1651. [PMID: 34745850 PMCID: PMC8558150 DOI: 10.1016/j.apsb.2021.10.026] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/24/2021] [Accepted: 10/14/2021] [Indexed: 12/14/2022] Open
Abstract
SARS-CoV-2 main protease (Mpro) is one of the most extensively exploited drug targets for COVID-19. Structurally disparate compounds have been reported as Mpro inhibitors, raising the question of their target specificity. To elucidate the target specificity and the cellular target engagement of the claimed Mpro inhibitors, we systematically characterize their mechanism of action using the cell-free FRET assay, the thermal shift-binding assay, the cell lysate Protease-Glo luciferase assay, and the cell-based FlipGFP assay. Collectively, our results have shown that majority of the Mpro inhibitors identified from drug repurposing including ebselen, carmofur, disulfiram, and shikonin are promiscuous cysteine inhibitors that are not specific to Mpro, while chloroquine, oxytetracycline, montelukast, candesartan, and dipyridamole do not inhibit Mpro in any of the assays tested. Overall, our study highlights the need of stringent hit validation at the early stage of drug discovery.
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30
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Thun‐Hohenstein STD, Suits TF, Malla TR, Tumber A, Brewitz L, Choudhry H, Salah E, Schofield CJ. Structure-Activity Studies Reveal Scope for Optimisation of Ebselen-Type Inhibition of SARS-CoV-2 Main Protease. ChemMedChem 2022; 17:e202100582. [PMID: 34850566 PMCID: PMC9015279 DOI: 10.1002/cmdc.202100582] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Indexed: 11/08/2022]
Abstract
The reactive organoselenium compound ebselen is being investigated for treatment of coronavirus disease 2019 (COVID-19) and other diseases. We report structure-activity studies on sulfur analogues of ebselen with the Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) main protease (Mpro ), employing turnover and protein-observed mass spectrometry-based assays. The results reveal scope for optimisation of ebselen/ebselen derivative- mediated inhibition of Mpro , particularly with respect to improved selectivity.
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Affiliation(s)
- Siegfried T. D. Thun‐Hohenstein
- Department of ChemistryUniversity of OxfordChemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research12 Mansfield RoadOxfordOX1 3TAUK
| | - Timothy F. Suits
- Department of ChemistryUniversity of OxfordChemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research12 Mansfield RoadOxfordOX1 3TAUK
| | - Tika R. Malla
- Department of ChemistryUniversity of OxfordChemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research12 Mansfield RoadOxfordOX1 3TAUK
| | - Anthony Tumber
- Department of ChemistryUniversity of OxfordChemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research12 Mansfield RoadOxfordOX1 3TAUK
| | - Lennart Brewitz
- Department of ChemistryUniversity of OxfordChemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research12 Mansfield RoadOxfordOX1 3TAUK
| | - Hani Choudhry
- Department of BiochemistryCenter for Artificial Intelligence in Precision MedicinesKing Abdulaziz UniversityJeddahSaudi Arabia
| | - Eidarus Salah
- Department of ChemistryUniversity of OxfordChemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research12 Mansfield RoadOxfordOX1 3TAUK
| | - Christopher J. Schofield
- Department of ChemistryUniversity of OxfordChemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research12 Mansfield RoadOxfordOX1 3TAUK
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31
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Emert-Sedlak LA, Moukha-Chafiq O, Shi H, Du S, Alvarado JJ, Pathak V, Tanner SG, Hunter RN, Nebane M, Chen L, Ilina TV, Ishima R, Zhang S, Kuzmichev YV, Wonderlich ER, Schader SM, Augelli-Szafran CE, Ptak RG, Smithgall TE. Inhibitors of HIV-1 Nef-Mediated Activation of the Myeloid Src-Family Kinase Hck Block HIV-1 Replication in Macrophages and Disrupt MHC-I Downregulation. ACS Infect Dis 2022; 8:91-105. [PMID: 34985256 PMCID: PMC9274903 DOI: 10.1021/acsinfecdis.1c00288] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
HIV-1 Nef is an attractive target for antiretroviral drug discovery because of its role in promoting HIV-1 infectivity, replication, and host immune system avoidance. Here, we applied a screening strategy in which recombinant HIV-1 Nef protein was coupled to activation of the Src-family tyrosine kinase Hck, which enhances the HIV-1 life cycle in macrophages. Nef stimulates recombinant Hck activity in vitro, providing a robust assay for chemical library screening. High-throughput screening of more than 730 000 compounds using the Nef·Hck assay identified six unique hit compounds that bound directly to recombinant Nef by surface plasmon resonance (SPR) in vitro and inhibited HIV-1 replication in primary macrophages in the 0.04 to 5 μM range without cytotoxicity. Eighty-four analogs were synthesized around an isothiazolone scaffold from this series, many of which bound to recombinant Nef and inhibited HIV-1 infectivity in the low to submicromolar range. Compounds in this series restored MHC-I to the surface of HIV-infected primary cells and disrupted a recombinant protein complex of Nef with the C-terminal tail of MHC-I and the μ1 subunit of the AP-1 endocytic trafficking protein. Nef inhibitors in this class have the potential to block HIV-1 replication in myeloid cells and trigger recognition of HIV-infected cells by the adaptive immune system in vivo.
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Affiliation(s)
- Lori A. Emert-Sedlak
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA 15219
| | - Omar Moukha-Chafiq
- Department of Chemistry, Southern Research Institute, 2000 Ninth Avenue South, Birmingham, AL 35205
| | - Haibin Shi
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA 15219
| | - Shoucheng Du
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA 15219
| | - John J. Alvarado
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA 15219
| | - Vibha Pathak
- Department of Chemistry, Southern Research Institute, 2000 Ninth Avenue South, Birmingham, AL 35205
| | - Samuel G. Tanner
- Department of Chemistry, Southern Research Institute, 2000 Ninth Avenue South, Birmingham, AL 35205
| | - Robert N. Hunter
- Department of Chemistry, Southern Research Institute, 2000 Ninth Avenue South, Birmingham, AL 35205
| | - Miranda Nebane
- Department of High-throughput Screening, Drug Discovery Division, Southern Research Institute, 2000 Ninth Avenue South, Birmingham, AL 35205
| | - Li Chen
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA 15219
| | - Tatiana V. Ilina
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260
| | - Rieko Ishima
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260
| | - Sixue Zhang
- Department of High-throughput Screening, Drug Discovery Division, Southern Research Institute, 2000 Ninth Avenue South, Birmingham, AL 35205
| | - Yury V. Kuzmichev
- Department of Infectious Disease Research, Drug Development Division, Southern Research Institute, 431 Aviation Way, Frederick, MD 21701
| | - Elizabeth R. Wonderlich
- Department of Infectious Disease Research, Drug Development Division, Southern Research Institute, 431 Aviation Way, Frederick, MD 21701
| | - Susan M. Schader
- Department of Infectious Disease Research, Drug Development Division, Southern Research Institute, 431 Aviation Way, Frederick, MD 21701
| | | | - Roger G. Ptak
- Department of Infectious Disease Research, Drug Development Division, Southern Research Institute, 431 Aviation Way, Frederick, MD 21701
| | - Thomas E. Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA 15219
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32
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Chen W, Feng B, Han S, Wang P, Chen W, Zang Y, Li J, Hu Y. Discovery of highly potent SARS-CoV-2 M pro inhibitors based on benzoisothiazolone scaffold. Bioorg Med Chem Lett 2022; 58:128526. [PMID: 34998903 PMCID: PMC8730469 DOI: 10.1016/j.bmcl.2022.128526] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/27/2021] [Accepted: 01/01/2022] [Indexed: 12/13/2022]
Abstract
The COVID-19 pandemic has drastically impacted global economies and public health. Although vaccine development has been successful, it was not sufficient against more infectious mutant strains including the Delta variant indicating a need for alternative treatment strategies such as small molecular compound development. In this work, a series of SARS-CoV-2 main protease (Mpro) inhibitors were designed and tested based on the active compound from high-throughput diverse compound library screens. The most efficacious compound (16b-3) displayed potent SARS-CoV-2 Mpro inhibition with an IC50 value of 116 nM and selectivity against SARS-CoV-2 Mpro when compared to PLpro and RdRp. This new class of compounds could be used as potential leads for further optimization in anti COVID-19 drug discovery.
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Affiliation(s)
- Weixiong Chen
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Bo Feng
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, No.103 Wenhua Road, Shenyang 110016, China
| | - Sheng Han
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Peipei Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Wuhong Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yi Zang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China.
| | - Jia Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, No.103 Wenhua Road, Shenyang 110016, China; Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Aoshanwei Jimo, Qingdao 266237, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China.
| | - Youhong Hu
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China.
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33
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Macip G, Garcia-Segura P, Mestres-Truyol J, Saldivar-Espinoza B, Pujadas G, Garcia-Vallvé S. A Review of the Current Landscape of SARS-CoV-2 Main Protease Inhibitors: Have We Hit the Bullseye Yet? Int J Mol Sci 2021; 23:259. [PMID: 35008685 PMCID: PMC8745775 DOI: 10.3390/ijms23010259] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/24/2021] [Accepted: 12/25/2021] [Indexed: 01/01/2023] Open
Abstract
In this review, we collected 1765 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) M-pro inhibitors from the bibliography and other sources, such as the COVID Moonshot project and the ChEMBL database. This set of inhibitors includes only those compounds whose inhibitory capacity, mainly expressed as the half-maximal inhibitory concentration (IC50) value, against M-pro from SARS-CoV-2 has been determined. Several covalent warheads are used to treat covalent and non-covalent inhibitors separately. Chemical space, the variation of the IC50 inhibitory activity when measured by different methods or laboratories, and the influence of 1,4-dithiothreitol (DTT) are discussed. When available, we have collected the values of inhibition of viral replication measured with a cellular antiviral assay and expressed as half maximal effective concentration (EC50) values, and their possible relationship to inhibitory potency against M-pro is analyzed. Finally, the most potent covalent and non-covalent inhibitors that simultaneously inhibit the SARS-CoV-2 M-pro and the virus replication in vitro are discussed.
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Affiliation(s)
| | | | | | | | - Gerard Pujadas
- Research Group in Cheminformatics & Nutrition, Departament de Bioquímica i Biotecnologia, Campus Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Catalonia, Spain; (G.M.); (P.G.-S.); (J.M.-T.); (B.S.-E.)
| | - Santiago Garcia-Vallvé
- Research Group in Cheminformatics & Nutrition, Departament de Bioquímica i Biotecnologia, Campus Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Catalonia, Spain; (G.M.); (P.G.-S.); (J.M.-T.); (B.S.-E.)
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34
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Maehara S, Kobayashi M, Kuwada M, Choshi T, Inoue H, Hieda Y, Nishiyama T, Hata T. In vitro and in silico studies of potential coronavirus-specific 3C-like protease inhibitors. Chem Pharm Bull (Tokyo) 2021; 70:195-198. [PMID: 34955489 DOI: 10.1248/cpb.c21-01002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We investigated similar compounds to ebselen and tideglusib, which exhibit strong activity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), using MACCS keys. Four candidate compounds were identified. One of them, phenyl-benzothiazol-3-one, showed coronavirus-specific 3C-like (3CL) protease inhibitory activity. The results indicated that a similarity score above 0.81 is a good indicator of activity for ebselen-and-tideglusib-like compounds. Subsequently, we simulated the ring-cleavage Michael reaction of ebselen at the Se center, which is responsible for its 3CL protease inhibitory activity, and determined the activation free energy of the reaction. The results showed that reaction simulation is a useful tool for estimating the activity of inhibitory compounds that undergo Michael addition reactions with the relevant cysteine S atom of 3CL proteases.
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Affiliation(s)
- Shoji Maehara
- Faculty of Pharmacy and Pharmaceutical Sciences, Fukuyama University
| | - Manami Kobayashi
- Faculty of Pharmacy and Pharmaceutical Sciences, Fukuyama University
| | - Mari Kuwada
- Faculty of Pharmacy and Pharmaceutical Sciences, Fukuyama University
| | - Tominari Choshi
- Faculty of Pharmacy and Pharmaceutical Sciences, Fukuyama University
| | - Hirohumi Inoue
- Faculty of Pharmacy and Pharmaceutical Sciences, Fukuyama University
| | - Yuzou Hieda
- Faculty of Pharmacy and Pharmaceutical Sciences, Fukuyama University
| | - Takashi Nishiyama
- Faculty of Pharmacy and Pharmaceutical Sciences, Fukuyama University
| | - Toshiyuki Hata
- Faculty of Pharmacy and Pharmaceutical Sciences, Fukuyama University
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35
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Abstract
The main protease (Mpro) plays a crucial role in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication and is highly conserved, rendering it one of the most attractive therapeutic targets for SARS-CoV-2 inhibition. Currently, although two drug candidates targeting SARS-CoV-2 Mpro designed by Pfizer are under clinical trials, no SARS-CoV-2 medication is approved due to the long period of drug development. Here, we collect a comprehensive list of 817 available SARS-CoV-2 and SARS-CoV Mpro inhibitors from the literature or databases and analyze their molecular mechanisms of action. The structure-activity relationships (SARs) among each series of inhibitors are discussed. Additionally, we broadly examine available antiviral activity, ADMET (absorption, distribution, metabolism, excretion, and toxicity), and animal tests of these inhibitors. We comment on their druggability or drawbacks that prevent them from becoming drugs. This Perspective sheds light on the future development of Mpro inhibitors for SARS-CoV-2 and future coronavirus diseases.
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Affiliation(s)
- Kaifu Gao
- Department of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Rui Wang
- Department of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiahui Chen
- Department of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jetze J Tepe
- Department of Chemistry and Pharmacology & Toxicology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Faqing Huang
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Guo-Wei Wei
- Department of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, United States
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36
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The Mpro structure-based modifications of ebselen derivatives for improved antiviral activity against SARS-CoV-2 virus. Bioorg Chem 2021; 117:105455. [PMID: 34740055 PMCID: PMC8556866 DOI: 10.1016/j.bioorg.2021.105455] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/13/2021] [Accepted: 10/22/2021] [Indexed: 12/17/2022]
Abstract
The main protease (Mpro or 3CLpro) of
SARS-CoV-2 virus is a cysteine enzyme critical for viral replication and
transcription, thus indicating a potential target for antiviral therapy.
A recent repurposing effort has identified ebselen, a multifunctional
drug candidate as an inhibitor of Mpro. Our docking of ebselen to the
binding pocket of Mpro crystal structure suggests a noncovalent
interaction for improvement of potency, antiviral activity and
selectivity. To test this hypothesis, we designed and synthesized ebselen
derivatives aimed at enhancing their non-covalent bonds within Mpro. The
inhibition of Mpro by ebselen derivatives (0.3 μM) was screened in both
HPLC and FRET assays. Nine ebselen derivatives (EBs) exhibited stronger
inhibitory effect on Mpro with IC50 of
0.07–0.38 μM. Further evaluation of three derivatives showed that EB2-7
exhibited the most potent inhibition of SARS-CoV-2 viral replication with
an IC50 value of 4.08 µM in HPAepiC cells, as
compared to the prototype ebselen at 24.61 μM. Mechanistically, EB2-7
functions as a noncovalent Mpro inhibitor in LC-MS/MS assay. Taken
together, our identification of ebselen derivatives with improved
antiviral activity may lead to developmental potential for treatment of
COVID-19 and SARS-CoV-2 infection.
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37
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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: 2.0] [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.
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38
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Seliem IA, Panda SS, Girgis AS, Moatasim Y, Kandeil A, Mostafa A, Ali MA, Nossier ES, Rasslan F, Srour AM, Sakhuja R, Ibrahim TS, Abdel-Samii ZKM, Al-Mahmoudy AMM. New quinoline-triazole conjugates: Synthesis, and antiviral properties against SARS-CoV-2. Bioorg Chem 2021; 114:105117. [PMID: 34214752 PMCID: PMC8219945 DOI: 10.1016/j.bioorg.2021.105117] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/08/2021] [Accepted: 06/19/2021] [Indexed: 01/25/2023]
Abstract
At present therapeutic options for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) are very limited. We designed and synthesized three sets of small molecules using quinoline scaffolds. A series of quinoline conjugates (10a-l, 11a-c, and 12a-e) by incorporating 1,2,3-triazole were synthesized via a modified microwave-assisted click chemistry technique. Among the synthesized conjugates, 4-((1-(2-chlorophenyl)-1H-1,2,3-triazol-4-yl)methoxy)-6-fluoro-2-(trifluoromethyl)quinoline (10g) and 6-fluoro-4-(2-(1-(4-methoxyphenyl)-1H-1,2,3-triazol-4-yl)ethoxy)-2-(trifluoromethyl)quinoline (12c) show high potency against SARS-CoV-2. The selectivity index (SI) of compounds 10g and 12c also indicates the significant efficacy compared to the reference drugs.
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Affiliation(s)
- Israa A Seliem
- Department of Chemistry and Physics, Augusta University, Augusta, GA 30912, USA; Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Siva S Panda
- Department of Chemistry and Physics, Augusta University, Augusta, GA 30912, USA.
| | - Adel S Girgis
- Department of Pesticide Chemistry, National Research Centre, Dokki, Giza 12622, Egypt
| | - Yassmin Moatasim
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt
| | - Ahmed Kandeil
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt
| | - Ahmed Mostafa
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt
| | - Mohamed A Ali
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt
| | - Eman S Nossier
- Department of Pharmaceutical Medicinal Chemistry and Drug Design, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
| | - Fatma Rasslan
- Department of Microbiology and Immunology, Faculty of Pharmacy (Girls), Al Azhar University, Cairo, Egypt
| | - Aladdin M Srour
- Department of Therapeutic Chemistry, National Research Centre, Dokki, Giza 12622, Egypt
| | - Rajeev Sakhuja
- Department of Chemistry, Birla Institute of Technology and Science, Pilani, India
| | - Tarek S Ibrahim
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Zakaria K M Abdel-Samii
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Amany M M Al-Mahmoudy
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
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39
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Nogara PA, Omage FB, Bolzan GR, Delgado CP, Aschner M, Orian L, Teixeira Rocha JB. In silico Studies on the Interaction between Mpro and PLpro From SARS-CoV-2 and Ebselen, its Metabolites and Derivatives. Mol Inform 2021; 40:e2100028. [PMID: 34018687 PMCID: PMC8236915 DOI: 10.1002/minf.202100028] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 04/11/2021] [Indexed: 12/20/2022]
Abstract
The COVID-19 pandemic caused by the SARS-CoV-2 has mobilized scientific attention in search of a treatment. The cysteine-proteases, main protease (Mpro) and papain-like protease (PLpro) are important targets for antiviral drugs. In this work, we simulate the interactions between the Mpro and PLpro with Ebselen, its metabolites and derivatives with the aim of finding molecules that can potentially inhibit these enzymes. The docking data demonstrate that there are two main interactions between the thiol (-SH) group of Cys (from the protease active sites) and the electrophilic centers of the organoselenium molecules, i. e. the interaction with the carbonyl group (O=C… SH) and the interaction with the Se moiety (Se… SH). Both interactions may lead to an adduct formation and enzyme inhibition. Density Functional Theory (DFT) calculations with Ebselen indicate that the energetics of the thiol nucleophilic attack is more favorable on Se than on the carbonyl group, which is in accordance with experimental data (Jin et al. Nature, 2020, 582, 289-293). Therefore, organoselenium molecules should be further explored as inhibitors of the SARS-CoV-2 proteases. Furthermore, we suggest that some metabolites of Ebselen (e. g. Ebselen diselenide and methylebselenoxide) and derivatives ethaselen and ebsulfur should be tested in vitro as inhibitors of virus replication and its proteases.
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Affiliation(s)
- Pablo Andrei Nogara
- Departamento de Bioquímica e Biologia MolecularUniversidade Federal de Santa Maria (UFSM)Santa Maria97105-900RSBrazil
| | - Folorunsho Bright Omage
- Departamento de Bioquímica e Biologia MolecularUniversidade Federal de Santa Maria (UFSM)Santa Maria97105-900RSBrazil
| | - Gustavo Roni Bolzan
- Departamento de Bioquímica e Biologia MolecularUniversidade Federal de Santa Maria (UFSM)Santa Maria97105-900RSBrazil
| | - Cássia Pereira Delgado
- Departamento de Bioquímica e Biologia MolecularUniversidade Federal de Santa Maria (UFSM)Santa Maria97105-900RSBrazil
| | - Michael Aschner
- Department of Molecular PharmacologyAlbert Einstein College of Medicine1300 Morris Park Avenue, BronxNY10461USA
| | - Laura Orian
- Dipartimento di Scienze ChimicheUniversità degli Studi di PadovaVia Marzolo 135131PadovaItaly
| | - João Batista Teixeira Rocha
- Departamento de Bioquímica e Biologia MolecularUniversidade Federal de Santa Maria (UFSM)Santa Maria97105-900RSBrazil
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Botteselle GV, Elias WC, Bettanin L, Canto RFS, Salin DNO, Barbosa FAR, Saba S, Gallardo H, Ciancaleoni G, Domingos JB, Rafique J, Braga AL. Catalytic Antioxidant Activity of Bis-Aniline-Derived Diselenides as GPx Mimics. Molecules 2021; 26:molecules26154446. [PMID: 34361597 PMCID: PMC8347129 DOI: 10.3390/molecules26154446] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/14/2021] [Accepted: 07/20/2021] [Indexed: 12/02/2022] Open
Abstract
Herein, we describe a simple and efficient route to access aniline-derived diselenides and evaluate their antioxidant/GPx-mimetic properties. The diselenides were obtained in good yields via ipso-substitution/reduction from the readily available 2-nitroaromatic halides (Cl, Br, I). These diselenides present GPx-mimetic properties, showing better antioxidant activity than the standard GPx-mimetic compounds, ebselen and diphenyl diselenide. DFT analysis demonstrated that the electronic properties of the substituents determine the charge delocalization and the partial charge on selenium, which correlate with the catalytic performances. The amino group concurs in the stabilization of the selenolate intermediate through a hydrogen bond with the selenium.
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Affiliation(s)
- Giancarlo V. Botteselle
- Departamento de Química, Universidade Estadual do Centro-Oeste (UNICENTRO), Guarapuava 85040-167, PR, Brazil
- Correspondence: (G.V.B.); (J.R.); (A.L.B.)
| | - Welman C. Elias
- Departamento de Química, Universidade Federal de Santa Catarina (UFSC), Florianópolis 88040-970, SC, Brazil; (W.C.E.); (L.B.); (D.N.O.S.); (F.A.R.B.); (H.G.); (J.B.D.)
| | - Luana Bettanin
- Departamento de Química, Universidade Federal de Santa Catarina (UFSC), Florianópolis 88040-970, SC, Brazil; (W.C.E.); (L.B.); (D.N.O.S.); (F.A.R.B.); (H.G.); (J.B.D.)
| | - Rômulo F. S. Canto
- Programa de Pós-Graduação em Ciências da Saúde, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre 90050-170, RS, Brazil;
| | - Drielly N. O. Salin
- Departamento de Química, Universidade Federal de Santa Catarina (UFSC), Florianópolis 88040-970, SC, Brazil; (W.C.E.); (L.B.); (D.N.O.S.); (F.A.R.B.); (H.G.); (J.B.D.)
| | - Flavio A. R. Barbosa
- Departamento de Química, Universidade Federal de Santa Catarina (UFSC), Florianópolis 88040-970, SC, Brazil; (W.C.E.); (L.B.); (D.N.O.S.); (F.A.R.B.); (H.G.); (J.B.D.)
| | - Sumbal Saba
- Instituto de Química—IQ, Universidade Federal de Goiás—(UFG), Goiânia 74690-900, GO, Brazil;
| | - Hugo Gallardo
- Departamento de Química, Universidade Federal de Santa Catarina (UFSC), Florianópolis 88040-970, SC, Brazil; (W.C.E.); (L.B.); (D.N.O.S.); (F.A.R.B.); (H.G.); (J.B.D.)
| | - Gianluca Ciancaleoni
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy;
| | - Josiel B. Domingos
- Departamento de Química, Universidade Federal de Santa Catarina (UFSC), Florianópolis 88040-970, SC, Brazil; (W.C.E.); (L.B.); (D.N.O.S.); (F.A.R.B.); (H.G.); (J.B.D.)
| | - Jamal Rafique
- Instituto de Química—INQUI, Universidade Federal do Mato Grosso do Sul (UFMS), Campo Grande 79074-460, MS, Brazil
- Correspondence: (G.V.B.); (J.R.); (A.L.B.)
| | - Antonio L. Braga
- Departamento de Química, Universidade Federal de Santa Catarina (UFSC), Florianópolis 88040-970, SC, Brazil; (W.C.E.); (L.B.); (D.N.O.S.); (F.A.R.B.); (H.G.); (J.B.D.)
- Department of Chemical Sciences, Faculty of Science, University of Johannesburg, Doornfontein 2028, South Africa
- Correspondence: (G.V.B.); (J.R.); (A.L.B.)
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Santi C, Scimmi C, Sancineto L. Ebselen and Analogues: Pharmacological Properties and Synthetic Strategies for Their Preparation. Molecules 2021; 26:4230. [PMID: 34299505 PMCID: PMC8306772 DOI: 10.3390/molecules26144230] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 02/06/2023] Open
Abstract
Ebselen is the leader of selenorganic compounds, and starting from its identification as mimetic of the key antioxidant enzyme glutathione peroxidase, several papers have appeared in literature claiming its biological activities. It was the subject of several clinical trials and it is currently in clinical evaluation for the treatment of COVID-19 patients. Given our interest in the synthesis and pharmacological evaluation of selenorganic derivatives with this review, we aimed to collect all the papers focused on the biological evaluation of ebselen and its close analogues, covering the timeline between 2016 and most of 2021. Our analysis evidences that, even if it lacks specificity when tested in vitro, being able to bind to every reactive cysteine, it proved to be always well tolerated in vivo, exerting no sign of toxicity whatever the administered doses. Besides, looking at the literature, we realized that no review article dealing with the synthetic approaches for the construction of the benzo[d][1,2]-selenazol-3(2H)-one scaffold is available; thus, a section of the present review article is completely devoted to this specific topic.
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Affiliation(s)
| | | | - Luca Sancineto
- Group of Catalysis and Green Organic Chemistry, Department of Pharmaceutical Sciences, University of Perugia Via del Liceo 1, 06122 Perugia, Italy; (C.S.); (C.S.)
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Mechanistic Insight into SARS-CoV-2 Mpro Inhibition by Organoselenides: The Ebselen Case Study. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11146291] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The main protease (Mpro) of SARS-CoV-2 is a current target for the inhibition of viral replication. Through a combined Docking and Density Functional Theory (DFT) approach, we investigated in-silico the molecular mechanism by which ebselen (IUPAC: 2-phenyl-1,2-benzoselenazol-3-one), the most famous and pharmacologically active organoselenide, inhibits Mpro. For the first time, we report on a mechanistic investigation in an enzyme for the formation of the covalent -S-Se- bond between ebselen and a key enzymatic cysteine. The results highlight the strengths and weaknesses of ebselen and provide hints for a rational drug design of bioorganic selenium-based inhibitors.
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