{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T14:58:55Z","timestamp":1768489135290,"version":"3.49.0"},"posted":{"date-parts":[[2020,7,1]]},"group-title":"Biophysics","reference-count":39,"publisher":"openRxiv","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2020,7,1]]},"abstract":"<jats:p>\n                  Broad-spectrum antiviral drugs are urgently needed to stop the COVID-19 pandemic and prevent future ones. The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is related to SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV), which have caused the previous outbreaks. The papain-like protease (PLpro) is an attractive drug target due to its essential roles in the viral life cycle. As a cysteine protease, PLpro is rich in cysteines and histidines and their protonation\/deprotonation modulates catalysis and conformational plasticity. Here we report the pK\n                  <jats:sub>a<\/jats:sub>\n                  calculations and assessment of the proton-coupled conformational dynamics of SARS-CoV-2 in comparison to SARS-CoV and MERS-CoV PLpros using a newly developed GPU-accelerated implicit-solvent continuous constant pH molecular dynamics method with an asynchronous replica-exchange scheme. The calculated pK\n                  <jats:sub>a<\/jats:sub>\n                  \u2019s support the catalytic roles of the Cys-His-Asp triad. We also found that several residues can switch protonation states at physiological pH, among which is C270\/271 located on the flexible blocking loop 2 (BL2) of SARS-CoV-2\/CoV PLpro. Simulations revealed that the BL2 conformational dynamics is coupled to the titration of C271\/270, in agreement with the crystal structures of SARS-CoV-2 PLpro. Simulations also revealed that BL2 in MERS-CoV PLpro is very flexible, sampling both open and closed states despite the lack of an analogous cysteine. Our work provides a starting point for more detailed mechanistic studies to assist structure-based design of broad-spectrum inhibitors against CoV PLpros.\n                <\/jats:p>","DOI":"10.1101\/2020.06.30.181305","type":"posted-content","created":{"date-parts":[[2020,7,1]],"date-time":"2020-07-01T08:55:12Z","timestamp":1593593712000},"source":"Crossref","is-referenced-by-count":2,"title":["Assessment of Proton-Coupled Conformational Dynamics of SARS and MERS Coronavirus Papain-like Proteases: Implication for Designing Broad-Spectrum Antiviral Inhibitors"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6675-7944","authenticated-orcid":false,"given":"Jack A.","family":"Henderson","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Neha","family":"Verma","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3234-0769","authenticated-orcid":false,"given":"Jana","family":"Shen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"key":"2020070310143028000_2020.06.30.181305v1.1","doi-asserted-by":"crossref","first-page":"4562","DOI":"10.1021\/acs.jmedchem.9b01828","article-title":"\u03b1-Ketoamides as Broad-Spectrum Inhibitors of Coronavirus and Enterovirus Replication: Structure-Based Design, Synthesis, and Activity Assessment","volume":"63","year":"2020","journal-title":"J. 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