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In this study, molecular dynamics (MD) simulations, free energy calculations and free energy decomposition were used to explore the interaction profiles of MK5172 with the wild-type (WT) and four mutated (R155K, D168A, D168V and A156T) HCV NS3\/4A proteases. The binding free energies predicted by Molecular Mechanics\/Generalized Born Solvent Area (MM\/GBSA) are consistent with the trend of the experimental drug resistance data. The free energy decomposition analysis shows that the resistant mutants may change the protein\u2013MK5172 interaction profiles, resulting in the unbalanced energetic distribution amongst the catalytic triad, the strand 135\u2013139 and the strand 154\u2013160. Moreover, umbrella sampling (US) simulations were employed to elucidate the unbinding processes of MK5172 from the active pockets of the WT HCV NS3\/4A protease and the four mutants. The US simulations demonstrate that the dissociation pathways of MK5172 escaping from the binding pockets of the WT and mutants are quite different, and it is quite possible that MK5172 will be harder to get access to the correct binding sites of the mutated proteases, thereafter leading to drug resistance.<\/jats:p>\n                  <jats:p\/>","DOI":"10.1039\/c5mb00394f","type":"journal-article","created":{"date-parts":[[2015,7,21]],"date-time":"2015-07-21T09:00:45Z","timestamp":1437469245000},"page":"2568-2578","update-policy":"https:\/\/doi.org\/10.1039\/rsc_crossmark_policy","source":"Crossref","is-referenced-by-count":19,"title":["Exploring resistance mechanisms of HCV NS3\/4A protease mutations to MK5172: insight from molecular dynamics simulations and free energy calculations"],"prefix":"10.1093","volume":"11","author":[{"given":"Yan","family":"Guan","sequence":"first","affiliation":[{"name":"Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University b , Suzhou, Jiangsu 215123, China"},{"name":"College of Pharmaceutical Sciences, Zhejiang University a , Hangzhou, Zhejiang 310058, China \u00a0 tingjunhou@hotmail.com \u00a0 tingjunhou@zju.edu.cn \u00a0 lidancps@zju.edu.cn"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Huiyong","family":"Sun","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, Zhejiang University a , Hangzhou, Zhejiang 310058, China \u00a0 tingjunhou@hotmail.com \u00a0 tingjunhou@zju.edu.cn \u00a0 lidancps@zju.edu.cn"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peichen","family":"Pan","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, Zhejiang University a , Hangzhou, Zhejiang 310058, China \u00a0 tingjunhou@hotmail.com \u00a0 tingjunhou@zju.edu.cn \u00a0 lidancps@zju.edu.cn"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Youyong","family":"Li","sequence":"additional","affiliation":[{"name":"Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University b , Suzhou, Jiangsu 215123, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dan","family":"Li","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, Zhejiang University a , Hangzhou, Zhejiang 310058, China \u00a0 tingjunhou@hotmail.com \u00a0 tingjunhou@zju.edu.cn \u00a0 lidancps@zju.edu.cn"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tingjun","family":"Hou","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, Zhejiang University a , Hangzhou, Zhejiang 310058, China \u00a0 tingjunhou@hotmail.com \u00a0 tingjunhou@zju.edu.cn \u00a0 lidancps@zju.edu.cn"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,7,21]]},"reference":[{"key":"2026010815112726300_cit1"},{"key":"2026010815112726300_cit2","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1016\/j.coviro.2011.10.001","volume":"1","author":"Thompson","year":"2011","journal-title":"Curr. 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