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Zhou J, Zhao Y, Yang R, Zhang Z, Jin Y, Wang L, Huang M. Structure-based virtual screening and fragment replacement to design novel inhibitors of Coxsackievirus A16 (CVA16). J Biomol Struct Dyn 2023:1-13. [PMID: 37811547 DOI: 10.1080/07391102.2023.2263890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 09/21/2023] [Indexed: 10/10/2023]
Abstract
Numerous studies have shown that hand, foot and mouth disease (HFMD) pathogen Coxsackievirus A16 (CVA16) can also cause severe neurological complications and even death. Currently, there is no effective drugs and vaccines for CVA16. Therefore, developing a drug against CVA16 has become critical. In this study, we conducted two strategies-virtual screening (VS) and fragment replacement to obtain better candidates than the known drug GPP3. Through VS, 37 candidate drugs were screened (exhibiting a lower binding energy than GPP3). After toxicity evaluations, we obtained five candidates, analysed their binding modes and found that four candidates could enter the binding pocket of the GPP3. In another strategy, we analysed the four positions in GPP3 structures by the FragRep webserver and obtained a large number of candidates after replacing different functional groups, we obtained eight candidates (that target the four positions above) with the combined binding score and synthetic accessibility evaluations. AMDock software was uniformly utilized to perform molecular docking evaluation of the candidates with binding activity superior to that of GPP3. Finally, the selected top three molecules (Lapatinib, B001 and C001) and its interaction with CAV16 were validated by molecular dynamics (MD) simulation. The results indicated that all three molecules retain inside the pocket of CAV16 receptor throughout the simulation process, and he binding energy calculated from the MD simulation trajectories also support the strong affinity of the top three molecules towards the CVA16. These results will provide new ideas and technical guidance for designing and applying CVA16 therapeutics.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jing Zhou
- Department of Prevention and Healthcare, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Yangyang Zhao
- Department of Prevention and Healthcare, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Ruizhe Yang
- Department of Prevention and Healthcare, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Zhong Zhang
- Department of Prevention and Healthcare, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Yan Jin
- Department of Prevention and Healthcare, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Lei Wang
- Department of Prevention and Healthcare, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Min Huang
- Department of Prevention and Healthcare, Children's Hospital of Nanjing Medical University, Nanjing, China
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Boonthaworn K, Hengphasatporn K, Shigeta Y, Chavasiri W, Rungrotmongkol T, Ounjai P. In silico screening of chalcones and flavonoids as potential inhibitors against yellow head virus 3C-like protease. PeerJ 2023; 11:e15086. [PMID: 37123012 PMCID: PMC10135407 DOI: 10.7717/peerj.15086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 02/26/2023] [Indexed: 05/02/2023] Open
Abstract
Yellow head virus (YHV) is one of the most important pathogens in prawn cultivation. The outbreak of YHV could potentially result in collapses in aquaculture industries. Although a flurry of development has been made in searching for preventive and therapeutic approaches against YHV, there is still no effective therapy available in the market. Previously, computational screening has suggested a few cancer drugs to be used as YHV protease (3CLpro) inhibitors. However, their toxic nature is still of concern. Here, we exploited various computational approaches, such as deep learning-based structural modeling, molecular docking, pharmacological prediction, and molecular dynamics simulation, to search for potential YHV 3CLpro inhibitors. A total of 272 chalcones and flavonoids were in silico screened using molecular docking. The bioavailability, toxicity, and specifically drug-likeness of hits were predicted. Among the hits, molecular dynamics simulation and trajectory analysis were performed to scrutinize the compounds with high binding affinity. Herein, the four selected compounds including chalcones cpd26, cpd31 and cpd50, and a flavonoid DN071_f could be novel potent compounds to prevent YHV and GAV propagation in shrimp. The molecular mechanism at the atomistic level is also enclosed that can be used to further antiviral development.
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Affiliation(s)
- Kanpong Boonthaworn
- Department of Biology, Faculty of Science, Mahidol University, Ratchathewi, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology, Ministry of Education, Ratchathewi, Bangkok, Thailand
| | - Kowit Hengphasatporn
- Center of Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yasuteru Shigeta
- Center of Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Warinthorn Chavasiri
- Department of Chemistry, Faculty of Science, Center of Excellence in Natural Products Chemistry, Chulalongkorn University, Pathum Wan, Bangkok, Thailand
| | - Thanyada Rungrotmongkol
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathum Wan, Bangkok, Thailand
| | - Puey Ounjai
- Department of Biology, Faculty of Science, Mahidol University, Ratchathewi, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology, Ministry of Education, Ratchathewi, Bangkok, Thailand
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Yuan X, Liu Z, Wan L, Liu W, Huang Y, Cao S. Recent advances in anti-coxsackievirus A16 viral drug research. Future Med Chem 2023; 15:97-117. [PMID: 36538291 DOI: 10.4155/fmc-2022-0195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Hand, foot and mouth disease, a childhood disorder caused by enteroviruses, is intermittently endemic in the Asia-Pacific region and endangers the lives of many infants and young children. Coxsackievirus A16 (CV-A16) is one of the major pathogens causing hand, foot, and mouth disease on occasion, resulting in catastrophic neurological sequelae and patient death. Currently, no clinical interventions are available that completely block the CV-A16 infection. Therefore, research on anti-CV-A16 treatment continues to be a significant focus of interest. This report provides a detailed background on and an introduction to CV-A16; a description of the viral gene and protein structures and a summary of the current advances in pharmaceutical targets, drug research and other related areas.
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Suriya U, Mahalapbutr P, Rungrotmongkol T. Integration of In Silico Strategies for Drug Repositioning towards P38α Mitogen-Activated Protein Kinase (MAPK) at the Allosteric Site. Pharmaceutics 2022; 14:pharmaceutics14071461. [PMID: 35890356 PMCID: PMC9321129 DOI: 10.3390/pharmaceutics14071461] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/05/2022] [Accepted: 07/10/2022] [Indexed: 02/05/2023] Open
Abstract
P38α mitogen-activated protein kinase (p38α MAPK), one of the p38 MAPK isoforms participating in a signaling cascade, has been identified for its pivotal role in the regulation of physiological processes such as cell proliferation, differentiation, survival, and death. Herein, by shedding light on docking- and 100-ns dynamic-based screening from 3210 FDA-approved drugs, we found that lomitapide (a lipid-lowering agent) and nilotinib (a Bcr-Abl fusion protein inhibitor) could alternatively inhibit phosphorylation of p38α MAPK at the allosteric site. All-atom molecular dynamics simulations and free energy calculations including end-point and QM-based ONIOM methods revealed that the binding affinity of the two screened drugs exhibited a comparable level as the known p38α MAPK inhibitor (BIRB796), suggesting the high potential of being a novel p38α MAPK inhibitor. In addition, noncovalent contacts and the number of hydrogen bonds were found to be corresponding with the great binding recognition. Key influential amino acids were mostly hydrophobic residues, while the two charged residues including E71 and D168 were considered crucial ones due to their ability to form very strong H-bonds with the focused drugs. Altogether, our contributions obtained here could be theoretical guidance for further conducting experimental-based preclinical studies necessary for developing therapeutic agents targeting p38α MAPK.
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Affiliation(s)
- Utid Suriya
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Panupong Mahalapbutr
- Department of Biochemistry, Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khan Kaen 40002, Thailand;
| | - Thanyada Rungrotmongkol
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Chulalongkorn University, Bangkok 10330, Thailand
- Ph.D. Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
- Correspondence:
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