{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,2]],"date-time":"2025-11-02T08:19:35Z","timestamp":1762071575515,"version":"build-2065373602"},"reference-count":43,"publisher":"MDPI AG","issue":"20","license":[{"start":{"date-parts":[[2022,10,12]],"date-time":"2022-10-12T00:00:00Z","timestamp":1665532800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Science Foundation of China","doi-asserted-by":"publisher","award":["81803430","22003020","12074151","BE2019650","BK20191032","CJ20200045"],"award-info":[{"award-number":["81803430","22003020","12074151","BE2019650","BK20191032","CJ20200045"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Natural Science Foundation of Jiangsu Province","award":["81803430","22003020","12074151","BE2019650","BK20191032","CJ20200045"],"award-info":[{"award-number":["81803430","22003020","12074151","BE2019650","BK20191032","CJ20200045"]}]},{"name":"Changzhou Sci &amp; Tech Program","award":["81803430","22003020","12074151","BE2019650","BK20191032","CJ20200045"],"award-info":[{"award-number":["81803430","22003020","12074151","BE2019650","BK20191032","CJ20200045"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Molecules"],"abstract":"<jats:p>COVID-19 can cause different neurological symptoms in some people, including smell, inability to taste, dizziness, confusion, delirium, seizures, stroke, etc. Owing to the issue of vaccine effectiveness, update and coverage, we still need one or more diversified strategies as the backstop to manage illness. Characterizing the structural basis of ligand recognition in the main protease (Mpro) of SARS-CoV-2 will facilitate its rational design and development of potential drug candidates with high affinity and selectivity against COVID-19. Up to date, covalent-, non-covalent inhibitors and allosteric modulators have been reported to bind to different active sites of Mpro. In the present work, we applied the molecular dynamics (MD) simulations to systematically characterize the potential binding features of catalytic active site and allosteric binding sites in Mpro using a dataset of 163 3D structures of Mpro-inhibitor complexes, in which our results are consistent with the current studies. In addition, umbrella sampling (US) simulations were used to explore the dissociation processes of substrate pathway and allosteric pathway. All the information provided new insights into the protein features of Mpro and will facilitate its rational drug design for COVID-19.<\/jats:p>","DOI":"10.3390\/molecules27206823","type":"journal-article","created":{"date-parts":[[2022,10,12]],"date-time":"2022-10-12T05:31:18Z","timestamp":1665552678000},"page":"6823","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Elucidation of Binding Features and Dissociation Pathways of Inhibitors and Modulators in SARS-CoV-2 Main Protease by Multiple Molecular Dynamics Simulations"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4095-6539","authenticated-orcid":false,"given":"Lei","family":"Xu","sequence":"first","affiliation":[{"name":"Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou 213001, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Liangxu","family":"Xie","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou 213001, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dawei","family":"Zhang","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou 213001, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6380-698X","authenticated-orcid":false,"given":"Xiaojun","family":"Xu","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou 213001, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2022,10,12]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1038\/s41586-020-2550-z","article-title":"SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls","volume":"584","author":"Tan","year":"2020","journal-title":"Nature"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1038\/s41579-020-00459-7","article-title":"Characteristics of SARS-CoV-2 and COVID-19","volume":"19","author":"Hu","year":"2021","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"110476","DOI":"10.1016\/j.envres.2020.110476","article-title":"The Europe second wave of COVID-19 infection and the Italy \u201cstrange\u201d situation","volume":"193","author":"Bontempi","year":"2021","journal-title":"Environ. Res."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"177","DOI":"10.15585\/mmwr.mm6907a1","article-title":"Interim estimates of 2019\u201320 seasonal influenza vaccine effectiveness\u2014United States, February 2020","volume":"69","author":"Dawood","year":"2020","journal-title":"MMWR Morb. Mortal. Wkly. Rep."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"105252","DOI":"10.1016\/j.antiviral.2022.105252","article-title":"Remdesivir, Molnupiravir and Nirmatrelvir remain active against SARS-CoV-2 Omicron and other variants of concern","volume":"198","author":"Vangeel","year":"2022","journal-title":"Antiviral. Res."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"128629","DOI":"10.1016\/j.bmcl.2022.128629","article-title":"Main protease mutants of SARS-CoV-2 variants remain susceptible to nirmatrelvir","volume":"62","author":"Ullrich","year":"2022","journal-title":"Bioorg. Med. Chem. Lett."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1038\/s41392-021-00468-9","article-title":"Structural basis for the inhibition of the SARS-CoV-2 main protease by the anti-HCV drug narlaprevir","volume":"6","author":"Bai","year":"2021","journal-title":"Signal Transduct. Target. Ther."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"322","DOI":"10.1038\/s41422-022-00618-w","article-title":"SARS-CoV-2 Omicron variant is highly sensitive to molnupiravir, nirmatrelvir, and the combination","volume":"32","author":"Li","year":"2022","journal-title":"Cell Res."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1038\/s41586-020-2180-5","article-title":"Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor","volume":"581","author":"Lan","year":"2020","journal-title":"Nature"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1126\/science.abb3405","article-title":"Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved \u03b1-ketoamide inhibitors","volume":"368","author":"Zhang","year":"2020","journal-title":"Science"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"eabd4596","DOI":"10.1126\/sciadv.abd4596","article-title":"Activity profiling and crystal structures of inhibitor-bound SARS-CoV-2 papain-like protease: A framework for anti\u2013COVID-19 drug design","volume":"6","author":"Rut","year":"2020","journal-title":"Sci. Adv."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1499","DOI":"10.1126\/science.abc1560","article-title":"Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir","volume":"368","author":"Yin","year":"2020","journal-title":"Science"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1038\/s41586-020-2223-y","article-title":"Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors","volume":"582","author":"Jin","year":"2020","journal-title":"Nature"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"5047","DOI":"10.1038\/s41467-020-18709-w","article-title":"Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease","volume":"11","author":"Douangamath","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"3202","DOI":"10.1038\/s41467-020-16954-7","article-title":"Structural plasticity of SARS-CoV-2 3CL Mpro active site cavity revealed by room temperature X-ray crystallography","volume":"11","author":"Kneller","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"642","DOI":"10.1126\/science.abf7945","article-title":"X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease","volume":"372","author":"Reinke","year":"2021","journal-title":"Science"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"e2117142119","DOI":"10.1073\/pnas.2117142119","article-title":"Structural basis for replicase polyprotein cleavage and substrate specificity of main protease from SARS-CoV-2","volume":"119","author":"Zhao","year":"2022","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The protein data bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"946","DOI":"10.1093\/bib\/bbaa260","article-title":"MCCS: A novel recognition pattern-based method for fast track discovery of anti-SARS-CoV-2 drugs","volume":"22","author":"Feng","year":"2021","journal-title":"Brief. Bioinform."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"3333","DOI":"10.1021\/acschemneuro.0c00457","article-title":"Binding characterization of GPCRs-modulator by molecular complex characterizing system (MCCS)","volume":"11","author":"Feng","year":"2020","journal-title":"ACS Chem. Neurosci."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"bbaa239","DOI":"10.1093\/bib\/bbaa239","article-title":"MCCS, a novel characterization method for protein\u2013ligand complex","volume":"22","author":"Chen","year":"2021","journal-title":"Brief. Bioinform."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"10037","DOI":"10.1073\/pnas.181342398","article-title":"Electrostatics of nanosystems: Application to microtubules and the ribosome","volume":"98","author":"Baker","year":"2001","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"W665","DOI":"10.1093\/nar\/gkh381","article-title":"PDB2PQR: An automated pipeline for the setup of Poisson\u2013Boltzmann electrostatics calculations","volume":"32","author":"Dolinsky","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"ref_24","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_25","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_26","doi-asserted-by":"crossref","first-page":"10269","DOI":"10.1021\/j100142a004","article-title":"A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model","volume":"97","author":"Bayly","year":"1993","journal-title":"J. Phys. Chem."},{"key":"ref_27","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_28","doi-asserted-by":"crossref","first-page":"10089","DOI":"10.1063\/1.464397","article-title":"Particle mesh Ewald: An N\u00b7log (N) method for Ewald sums in large systems","volume":"98","author":"Darden","year":"1993","journal-title":"J. Chem. Phys."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"10163","DOI":"10.1039\/C6CP08232G","article-title":"Prediction of luciferase inhibitors by the high-performance MIEC-GBDT approach based on interaction energetic patterns","volume":"19","author":"Chen","year":"2017","journal-title":"Phys. Chem. Chem. Phys."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1201","DOI":"10.1016\/j.jmb.2007.12.054","article-title":"Characterization of domain\u2013peptide interaction interface: A case study on the amphiphysin-1 SH3 domain","volume":"376","author":"Hou","year":"2008","journal-title":"J. Mol. Biol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1074\/mcp.M800450-MCP200","article-title":"Characterization of Domain-Peptide Interaction Interface: A Generic Structure-based Model to Decipher the Binding Specificity of SH3 Domains* S","volume":"8","author":"Hou","year":"2009","journal-title":"Mol. Cell. Proteom."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1021\/ci100275a","article-title":"Assessing the performance of the MM\/PBSA and MM\/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations","volume":"51","author":"Hou","year":"2011","journal-title":"J. Chem. Inf. Model."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"866","DOI":"10.1002\/jcc.21666","article-title":"Assessing the performance of the molecular mechanics\/Poisson Boltzmann surface area and molecular mechanics\/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking","volume":"32","author":"Hou","year":"2011","journal-title":"J. Comput. Chem."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"8408","DOI":"10.1021\/jp404160y","article-title":"Assessing the performance of MM\/PBSA and MM\/GBSA methods. 3. The impact of force fields and ligand charge models","volume":"117","author":"Xu","year":"2013","journal-title":"J. Phys. Chem. B"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"22035","DOI":"10.1039\/C4CP03179B","article-title":"Assessing the performance of MM\/PBSA and MM\/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM\/GBSA and MM\/PBSA rescoring","volume":"16","author":"Sun","year":"2014","journal-title":"Phys. Chem. Chem. Phys."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"2376","DOI":"10.1021\/ci400188q","article-title":"Insight into crizotinib resistance mechanisms caused by three mutations in ALK tyrosine kinase using free energy calculation approaches","volume":"53","author":"Sun","year":"2013","journal-title":"J. Chem. Inf. Model."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"9478","DOI":"10.1021\/acs.chemrev.9b00055","article-title":"End-point binding free energy calculation with MM\/PBSA and MM\/GBSA: Strategies and applications in drug design","volume":"119","author":"Wang","year":"2019","journal-title":"Chem. Rev."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"W322","DOI":"10.1093\/nar\/gkz397","article-title":"HawkDock: A web server to predict and analyze the protein\u2013protein complex based on computational docking and MM\/GBSA","volume":"47","author":"Weng","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"2844","DOI":"10.1021\/acs.jcim.1c00091","article-title":"VAD-MM\/GBSA: A Variable Atomic Dielectric MM\/GBSA Model for Improved Accuracy in Protein\u2013Ligand Binding Free Energy Calculations","volume":"61","author":"Wang","year":"2021","journal-title":"J. Chem. Inf. Model."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1002\/prot.20033","article-title":"Exploring protein native states and large-scale conformational changes with a modified generalized born model","volume":"55","author":"Onufriev","year":"2004","journal-title":"Proteins"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1002\/(SICI)1096-987X(19990130)20:2<217::AID-JCC4>3.0.CO;2-A","article-title":"Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO)","volume":"20","author":"Weiser","year":"1999","journal-title":"J. Comput. Chem."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"882","DOI":"10.1093\/bib\/bbaa155","article-title":"Virus-CKB: An integrated bioinformatics platform and analysis resource for COVID-19 research","volume":"22","author":"Feng","year":"2021","journal-title":"Brief. Bioinform."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"115860","DOI":"10.1016\/j.bmc.2020.115860","article-title":"Protease targeted COVID-19 drug discovery and its challenges: Insight into viral main protease (Mpro) and papain-like protease (PLpro) inhibitors","volume":"29","author":"Amin","year":"2021","journal-title":"Bioorg. Med. Chem."}],"container-title":["Molecules"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1420-3049\/27\/20\/6823\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T00:50:25Z","timestamp":1760143825000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1420-3049\/27\/20\/6823"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,10,12]]},"references-count":43,"journal-issue":{"issue":"20","published-online":{"date-parts":[[2022,10]]}},"alternative-id":["molecules27206823"],"URL":"https:\/\/doi.org\/10.3390\/molecules27206823","relation":{},"ISSN":["1420-3049"],"issn-type":[{"type":"electronic","value":"1420-3049"}],"subject":[],"published":{"date-parts":[[2022,10,12]]}}}