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Wu K, Guo Y, Xu T, Huang W, Guo D, Cao L, Lei J. Structure-Based Virtual Screening for Methyltransferase Inhibitors of SARS-CoV-2 nsp14 and nsp16. Molecules 2024; 29:2312. [PMID: 38792173 PMCID: PMC11124212 DOI: 10.3390/molecules29102312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/06/2024] [Accepted: 04/18/2024] [Indexed: 05/26/2024] Open
Abstract
The ongoing COVID-19 pandemic still threatens human health around the world. The methyltransferases (MTases) of SARS-CoV-2, specifically nsp14 and nsp16, play crucial roles in the methylation of the N7 and 2'-O positions of viral RNA, making them promising targets for the development of antiviral drugs. In this work, we performed structure-based virtual screening for nsp14 and nsp16 using the screening workflow (HTVS, SP, XP) of Schrödinger 2019 software, and we carried out biochemical assays and molecular dynamics simulation for the identification of potential MTase inhibitors. For nsp14, we screened 239,000 molecules, leading to the identification of three hits A1-A3 showing N7-MTase inhibition rates greater than 60% under a concentration of 50 µM. For the SAM binding and nsp10-16 interface sites of nsp16, the screening of 210,000 and 237,000 molecules, respectively, from ZINC15 led to the discovery of three hit compounds B1-B3 exhibiting more than 45% of 2'-O-MTase inhibition under 50 µM. These six compounds with moderate MTase inhibitory activities could be used as novel candidates for the further development of anti-SARS-CoV-2 drugs.
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Affiliation(s)
- Kejue Wu
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China; (K.W.); (Y.G.); (W.H.)
| | - Yinfeng Guo
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China; (K.W.); (Y.G.); (W.H.)
| | - Tiefeng Xu
- Centre for Infection and Immunity Studies (CIIS), School of Medicine, Sun Yat-Sen University, Shenzhen 518107, China (D.G.); (L.C.)
| | - Weifeng Huang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China; (K.W.); (Y.G.); (W.H.)
| | - Deyin Guo
- Centre for Infection and Immunity Studies (CIIS), School of Medicine, Sun Yat-Sen University, Shenzhen 518107, China (D.G.); (L.C.)
- Guangzhou Laboratory, Bio-Island, Guangzhou 510320, China
| | - Liu Cao
- Centre for Infection and Immunity Studies (CIIS), School of Medicine, Sun Yat-Sen University, Shenzhen 518107, China (D.G.); (L.C.)
| | - Jinping Lei
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China; (K.W.); (Y.G.); (W.H.)
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Pojtanadithee P, Hengphasatporn K, Suroengrit A, Boonyasuppayakorn S, Wilasluck P, Deetanya P, Wangkanont K, Sukanadi IP, Chavasiri W, Wolschann P, Langer T, Shigeta Y, Maitarad P, Sanachai K, Rungrotmongkol T. Identification of Promising Sulfonamide Chalcones as Inhibitors of SARS-CoV-2 3CL pro through Structure-Based Virtual Screening and Experimental Approaches. J Chem Inf Model 2023; 63:5244-5258. [PMID: 37581276 DOI: 10.1021/acs.jcim.3c00663] [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: 08/16/2023]
Abstract
3CLpro is a viable target for developing antiviral therapies against the coronavirus. With the urgent need to find new possible inhibitors, a structure-based virtual screening approach was developed. This study recognized 75 pharmacologically bioactive compounds from our in-house library of 1052 natural product-based compounds that satisfied drug-likeness criteria and exhibited good bioavailability and membrane permeability. Among these compounds, three promising sulfonamide chalcones were identified by combined theoretical and experimental approaches, with SWC423 being the most suitable representative compound due to its competitive inhibition and low cytotoxicity in Vero E6 cells (EC50 = 0.89 ± 0.32 μM; CC50 = 25.54 ± 1.38 μM; SI = 28.70). The binding and stability of SWC423 in the 3CLpro active site were investigated through all-atom molecular dynamics simulation and fragment molecular orbital calculation, indicating its potential as a 3CLpro inhibitor for further SARS-CoV-2 therapeutic research. These findings suggested that inhibiting 3CLpro with a sulfonamide chalcone such as SWC423 may pave the effective way for developing COVID-19 treatments.
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Affiliation(s)
- Piyatida Pojtanadithee
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kowit Hengphasatporn
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Aphinya Suroengrit
- Center of Excellence in Applied Medical Virology, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Siwaporn Boonyasuppayakorn
- Center of Excellence in Applied Medical Virology, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Patcharin Wilasluck
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Center of Excellence for Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Peerapon Deetanya
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Center of Excellence for Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kittikhun Wangkanont
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Center of Excellence for Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - I Putu Sukanadi
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Warinthorn Chavasiri
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Peter Wolschann
- Department of Pharmaceutical Chemistry, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
- Institute of Theoretical Chemistry, University of Vienna, Vienna 1090, Austria
| | - Thierry Langer
- Department of Pharmaceutical Chemistry, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Phornphimon Maitarad
- Research Center of Nano Science and Technology, Department of Chemistry, College of Science, Shanghai University, Shanghai 200444, P. R. China
| | - Kamonpan Sanachai
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Thanyada Rungrotmongkol
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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Dawood AA. The efficacy of Paxlovid against COVID-19 is the result of the tight molecular docking between M pro and antiviral drugs (nirmatrelvir and ritonavir). Adv Med Sci 2023; 68:1-9. [PMID: 36368287 PMCID: PMC9626444 DOI: 10.1016/j.advms.2022.10.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/05/2022] [Accepted: 10/27/2022] [Indexed: 11/09/2022]
Abstract
Purpose Currently, a number of medications for coronavirus disease 2019 (COVID-19) treatment are tested in clinical trials; however, credible clinical studies are becoming increasingly difficult to come by. Paxlovid is a ritonavir-boosted nirmatrelvir drug that the U.S. Food and Drug Administration (FDA) authorized for the treatment of COVID-19. This study aimed to demonstrate the interaction of nirmatrelvir and ritonavir on the active site of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (Mpro). Materials and methods To locate the optimal docking between Mpro and antiviral drugs, and to conduct dynamic simulations between atoms in the fusion areas, various bioinformatics and mathematical equations were applied. Results According to the docking data, nirmatrelvir has a stronger interaction with Mpro than ritonavir, which has more multiple bonds. Molecular docking of antiviral drugs such as Paxlovid has a significant impact on the treatment of COVID-19 virus. Conclusions According to this study, Paxlovid may work on new strains, including Omicron, because the Mpro mutation P132H in the Omicron variant has no direct effect on the protein.
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