{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,11]],"date-time":"2026-04-11T22:41:15Z","timestamp":1775947275619,"version":"3.50.1"},"reference-count":44,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2022,3,15]],"date-time":"2022-03-15T00:00:00Z","timestamp":1647302400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"90th Anniversary of Chulalongkorn University Fund","award":["GCUGR1125633083M"],"award-info":[{"award-number":["GCUGR1125633083M"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Molecules"],"abstract":"<jats:p>Outbreaks of hand, foot, and mouth disease (HFMD) that occur worldwide are mainly caused by the Coxsackievirus-A16 (CV-A16) and Enterovirus-A71 (EV-A71). Unfortunately, neither an anti-HFMD drug nor a vaccine is currently available. Rupintrivir in phase II clinical trial candidate for rhinovirus showed highly potent antiviral activities against enteroviruses as an inhibitor for 3C protease (3Cpro). In the present study, we focused on designing 50 novel rupintrivir analogs against CV-A16 and EV-A71 3Cpro using computational tools. From their predicted binding affinities, the five compounds with functional group modifications at P1\u2032, P2, P3, and P4 sites, namely P1\u2032-1, P2-m3, P3-4, P4-5, and P4-19, could bind with both CV-A16 and EV-A71 3Cpro better than rupintrivir. Subsequently, these five analogs were studied by 500 ns molecular dynamics simulations. Among them, P2-m3, the derivative with meta-aminomethyl-benzyl group at the P2 site, showed the greatest potential to interact with the 3Cpro target by delivering the highest number of intermolecular hydrogen bonds and contact atoms. It formed the hydrogen bonds with L127 and K130 residues at the P2 site stronger than rupintrivir, supported by significantly lower MM\/PB(GB)SA binding free energies. Elucidation of designed rupintrivir analogs in our study provides the basis for developing compounds that can be candidate compounds for further HFMD treatment.<\/jats:p>","DOI":"10.3390\/molecules27061908","type":"journal-article","created":{"date-parts":[[2022,3,16]],"date-time":"2022-03-16T03:36:23Z","timestamp":1647401783000},"page":"1908","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Computational Screening of Newly Designed Compounds against Coxsackievirus A16 and Enterovirus A71"],"prefix":"10.3390","volume":"27","author":[{"given":"Amita","family":"Sripattaraphan","sequence":"first","affiliation":[{"name":"Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2605-5360","authenticated-orcid":false,"given":"Kamonpan","family":"Sanachai","sequence":"additional","affiliation":[{"name":"Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Warinthorn","family":"Chavasiri","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Siwaporn","family":"Boonyasuppayakorn","sequence":"additional","affiliation":[{"name":"Applied Medical Virology Research Unit, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0035-0070","authenticated-orcid":false,"given":"Phornphimon","family":"Maitarad","sequence":"additional","affiliation":[{"name":"Research Center of Nano Science and Technology, Shanghai University, Shanghai 200444, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thanyada","family":"Rungrotmongkol","sequence":"additional","affiliation":[{"name":"Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand"},{"name":"Ph.D. Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2022,3,15]]},"reference":[{"key":"ref_1","first-page":"1004","article-title":"Study on the association of hand, foot and mouth disease and enterovirus 71\/CA16 among children in Beijing, 2007","volume":"28","author":"Zhu","year":"2007","journal-title":"Zhonghua Liu Xing Bing Xue Za Zhi (Zhonghua Liuxingbingxue Zazhi)"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1140","DOI":"10.1111\/ped.12970","article-title":"Temporal and geographical clustering of Kawasaki disease in Japan: 2007\u20132012","volume":"58","author":"Sano","year":"2016","journal-title":"Pediatr. Int."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1080\/00365540701799359","article-title":"Enterovirus 71 in Taiwan, 2004\u20132006: Epidemiological and virological features","volume":"40","author":"Huang","year":"2008","journal-title":"Scand. J. Infect. Dis."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"78","DOI":"10.3201\/eid1301.020112","article-title":"Epidemic hand, foot and mouth disease caused by human enterovirus 71, Singapore","volume":"9","author":"Chan","year":"2003","journal-title":"Emerg. Infect. Dis."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"641","DOI":"10.3201\/eid1904.121666","article-title":"Hand, foot, and mouth disease caused by coxsackievirus A6, Thailand, 2012","volume":"19","author":"Puenpa","year":"2013","journal-title":"Emerg. Infect. Dis."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"165","DOI":"10.4103\/0378-6323.107631","article-title":"Hand, foot, and mouth disease: Current scenario and Indian perspective","volume":"79","author":"Sarma","year":"2013","journal-title":"Indian J. Dermatol. Venereol. Leprol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"748","DOI":"10.1128\/AAC.00841-08","article-title":"Real-time monitoring of human enterovirus (HEV)-infected cells and anti-HEV 3C protease potency by fluorescence resonance energy transfer","volume":"53","author":"Tsai","year":"2019","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1186\/s13104-016-1973-y","article-title":"A literature review and case report of hand, foot and mouth disease in an immunocompetent adult","volume":"9","year":"2016","journal-title":"BMC Res. Notes"},{"key":"ref_9","unstructured":"Guerra, A.M., Orille, E., and Waseem, M. (2021, October 24). Hand Foot and Mouth Disease, StatPearls, Available online: https:\/\/www.ncbi.nlm.nih.gov\/books\/NBK431082\/."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1016\/j.bsheal.2019.02.005","article-title":"Surveillance, epidemiology, and pathogen spectrum of hand, foot, and mouth disease in mainland of China from 2008 to 2017","volume":"1","author":"Ji","year":"2019","journal-title":"Biosafety Health"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"23444","DOI":"10.1038\/srep23444","article-title":"Neurological complications and risk factors of cardiopulmonary failure of EV-A71-related hand, foot and mouth disease","volume":"6","author":"Long","year":"2016","journal-title":"Sci. Rep."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"231","DOI":"10.3201\/eid0203.960312","article-title":"Role of enterovirus 71 in acute flaccid paralysis after the eradication of poliovirus in Brazil","volume":"2","author":"Winkler","year":"1996","journal-title":"Emerg. Infect. Dis."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"10319","DOI":"10.1128\/JVI.00787-11","article-title":"Enterovirus 71 and coxsackievirus A16 3C proteases: Binding to rupintrivir and their substrates and anti-hand, foot, and mouth disease virus drug design","volume":"85","author":"Lu","year":"2011","journal-title":"J. Virol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"10021","DOI":"10.1128\/JVI.05107-11","article-title":"Crystal structures of enterovirus 71 3C protease complexed with rupintrivir reveal the roles of catalytically important residues","volume":"85","author":"Wang","year":"2011","journal-title":"J. Virol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"7388","DOI":"10.1016\/j.bmc.2008.06.015","article-title":"Design, synthesis, and evaluation of 3C protease inhibitors as anti-enterovirus 71 agents","volume":"16","author":"Kuo","year":"2008","journal-title":"Bioorg. Med. Chem."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"2444","DOI":"10.1128\/AAC.43.10.2444","article-title":"In vitro antiviral activity of AG7088, a potent inhibitor of human rhinovirus 3C protease","volume":"43","author":"Patick","year":"1999","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1097","DOI":"10.1016\/S1474-4422(10)70209-X","article-title":"Clinical features, diagnosis, and management of enterovirus 71","volume":"9","author":"Ooi","year":"2010","journal-title":"Lancet Neurol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1016\/j.ab.2007.12.019","article-title":"A mammalian cell-based reverse two-hybrid system for functional analysis of 3C viral protease of human enterovirus 71","volume":"375","author":"Lee","year":"2008","journal-title":"Anal. Biochem."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1016\/j.antiviral.2012.12.029","article-title":"Rupintrivir is a promising candidate for treating severe cases of enterovirus-71 infection: Evaluation of antiviral efficacy in a murine infection model","volume":"97","author":"Zhang","year":"2013","journal-title":"Antivir. Res."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1128\/AAC.49.2.619-626.2005","article-title":"Conservation of amino acids in human rhinovirus 3C protease correlates with broad-spectrum antiviral activity of rupintrivir, a novel human rhinovirus 3C protease inhibitor","volume":"49","author":"Binford","year":"2005","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"11000","DOI":"10.1073\/pnas.96.20.11000","article-title":"Structure-assisted design of mechanism-based irreversible inhibitors of human rhinovirus 3C protease with potent antiviral activity against multiple rhinovirus serotypes","volume":"96","author":"Matthews","year":"1999","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"3907","DOI":"10.1128\/AAC.47.12.3907-3916.2003","article-title":"Phase II, randomized, double-blind, placebo-controlled studies of ruprintrivir nasal spray 2-percent suspension for prevention and treatment of experimentally induced rhinovirus colds in healthy volunteers","volume":"47","author":"Hayden","year":"2003","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"304","DOI":"10.1093\/infdis\/129.3.304","article-title":"An apparently new enterovirus isolated from patients with disease of the central nervous system","volume":"129","author":"Schmidt","year":"1974","journal-title":"J. Infect. Dis."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"7782","DOI":"10.1128\/AAC.01375-15","article-title":"Antiviral activity of broad-spectrum and enterovirus-specific inhibitors against clinical isolates of enterovirus D68","volume":"59","author":"Sun","year":"2015","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1213","DOI":"10.1021\/jm9805384","article-title":"Structure-based design, synthesis, and biological evaluation of irreversible human rhinovirus 3C protease inhibitors. 4. Incorporation of P1 lactam moieties as L-glutamine replacements","volume":"42","author":"Dragovich","year":"1999","journal-title":"J. Med. Chem."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"5814","DOI":"10.1128\/AAC.00534-15","article-title":"The enterovirus 3C protease inhibitor SG85 efficiently blocks rhinovirus replication and is not cross-resistant with rupintrivir","volume":"59","author":"Lacroix","year":"2015","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/j.bpc.2016.09.005","article-title":"Susceptibility of inhibitors against 3C protease of coxsackievirus A16 and enterovirus A71 causing hand, foot and mouth disease: A molecular dynamics study","volume":"219","author":"Jetsadawisut","year":"2016","journal-title":"Biophys. Chem."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"e00298-17","DOI":"10.1128\/AAC.00298-17","article-title":"Structure of the Enterovirus 71 3C Protease in Complex with NK-1.8 k and Indications for the Development of Antienterovirus Protease Inhibitor","volume":"61","author":"Wang","year":"2017","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"902","DOI":"10.1016\/j.tibs.2019.06.004","article-title":"Bringing molecular dynamics simulation data into view","volume":"44","author":"Hildebrand","year":"2019","journal-title":"Trends Biochem. Sci."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"20909","DOI":"10.1038\/s41598-020-77768-7","article-title":"Epidemical and etiological study on hand, foot and mouth disease following EV-A71 vaccination in Xiangyang, China","volume":"10","author":"Meng","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1021\/ct100578z","article-title":"PROPKA3: Consistent treatment of internal and surface residues in empirical pKa predictions","volume":"7","author":"Olsson","year":"2011","journal-title":"J. Chem. Theory Comput."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1021\/acs.jcim.7b00663","article-title":"Machine learning of partial charges derived from high-quality quantum-mechanical calculations","volume":"58","author":"Bleiziffer","year":"2018","journal-title":"J. Chem. Inf. Modeling"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1584","DOI":"10.1002\/jcc.20082","article-title":"Empirical force fields for biological macromolecules: Overview and issues","volume":"25","author":"MacKerell","year":"2004","journal-title":"J. Comput. Chem."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1668","DOI":"10.1002\/jcc.20290","article-title":"The Amber biomolecular simulation programs","volume":"26","author":"Case","year":"2005","journal-title":"J. Comput. Chem."},{"key":"ref_35","unstructured":"Frisch, M.J.E.A. (2021, July 16). Gaussian09. Available online: http:\/\/www.gaussian.com\/."},{"key":"ref_36","unstructured":"Case, D.A., Babin, V., Berryman, J.T., Betz, R.M., Cai, Q., Cerutti, D.S., Cheatham, T.E., Darden, I.T.A., Duke, R.E., and Gohlke, H. (2016). AMBER 16, University of California."},{"key":"ref_37","first-page":"1","article-title":"ACPYPE-Antechamber python parser interface","volume":"5","author":"Vranken","year":"2012","journal-title":"BMC Res. Notes"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"3696","DOI":"10.1021\/acs.jctc.5b00255","article-title":"ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB","volume":"11","author":"Maier","year":"2015","journal-title":"J. Chem. Theory Comput."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1157","DOI":"10.1002\/jcc.20035","article-title":"Development and testing of a general amber force field","volume":"25","author":"Wang","year":"2004","journal-title":"J. Comput. Chem."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1063\/1.445869","article-title":"Comparison of simple potential functions for simulating liquid water","volume":"79","author":"Jorgensen","year":"1983","journal-title":"J. Chem. Phys."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"867","DOI":"10.1529\/biophysj.104.046110","article-title":"Insights into saquinavir resistance in the G48V HIV-1 protease: Quantum calculations and molecular dynamic simulations","volume":"88","author":"Wittayanarakul","year":"2005","journal-title":"Biophys. J."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"4339","DOI":"10.1128\/JVI.01123-12","article-title":"3C protease of enterovirus 68: Structure-based design of Michael acceptor inhibitors and their broad-spectrum antiviral effects against picornaviruses","volume":"87","author":"Tan","year":"2013","journal-title":"J. Virol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"997","DOI":"10.1089\/cmb.2010.0237","article-title":"Is an intuitive convergence definition of molecular dynamics simulations solely based on the root mean square deviation possible?","volume":"18","author":"Knapp","year":"2011","journal-title":"J. Comput. Biol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"3084","DOI":"10.1021\/ct400341p","article-title":"PTRAJ and CPPTRAJ: Software for processing and analysis of molecular dynamics trajectory data","volume":"9","author":"Roe","year":"2013","journal-title":"J. Chem. Theory Comput."}],"container-title":["Molecules"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1420-3049\/27\/6\/1908\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T22:37:01Z","timestamp":1760135821000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1420-3049\/27\/6\/1908"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,3,15]]},"references-count":44,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2022,3]]}},"alternative-id":["molecules27061908"],"URL":"https:\/\/doi.org\/10.3390\/molecules27061908","relation":{},"ISSN":["1420-3049"],"issn-type":[{"value":"1420-3049","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,3,15]]}}}