{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T11:20:55Z","timestamp":1785410455490,"version":"3.56.0"},"reference-count":34,"publisher":"American Society for Microbiology","issue":"10","license":[{"start":{"date-parts":[[2025,10,23]],"date-time":"2025-10-23T00:00:00Z","timestamp":1761177600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,10,23]],"date-time":"2025-10-23T00:00:00Z","timestamp":1761177600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Virol"],"published-print":{"date-parts":[[2025,10,23]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Proteases are versatile therapeutic targets for a wide variety of human diseases, including cancer, cardiovascular diseases, and infections by viruses, bacteria, and parasites. The main protease (M\n                      <jats:sup>pro<\/jats:sup>\n                      ) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19), has been one of the major drug targets for the treatment of COVID-19. In this study, a small-molecule covalent inhibitor,\n                      <jats:bold>H102<\/jats:bold>\n                      , of SARS-CoV-2 M\n                      <jats:sup>pro<\/jats:sup>\n                      was developed from serial structural modifications on a compound previously reported by us to have anti-SARS-CoV-2 activity.\n                      <jats:bold>H102<\/jats:bold>\n                      exhibited very high potency in SARS-CoV-2 M\n                      <jats:sup>pro<\/jats:sup>\n                      inhibition with IC\n                      <jats:sub>50<\/jats:sub>\n                      of 8.8 nM and strongly prevented SARS-CoV-2 replication in VeroE6 cells. The co-crystal structure of\n                      <jats:bold>H102<\/jats:bold>\n                      bound to M\n                      <jats:sup>pro<\/jats:sup>\n                      determined at 1.50 \u00c5 resolution provided a structural mechanism of\n                      <jats:bold>H102<\/jats:bold>\n                      \u2019s action and revealed an unusual distortion of the catalytic dyad of the viral enzyme which was caused by the benzyl ring of P2 position of\n                      <jats:bold>H102<\/jats:bold>\n                      interacting with the side chain of catalytic dyad His41 residue of M\n                      <jats:sup>pro<\/jats:sup>\n                      and pulling His41 side chain away from the other catalytic dyad Cys145 residue. This structural mechanism of\n                      <jats:bold>H102<\/jats:bold>\n                      is very different from that of other reported covalent M\n                      <jats:sup>pro<\/jats:sup>\n                      inhibitors for which His41 side chain orientation and its close proximity to Cys145 remain unchanged with the binding of a covalent inhibitor. As such,\n                      <jats:bold>H102<\/jats:bold>\n                      may serve as a biochemical probe for investigating further an unusual mechanism of the viral enzyme\u2019s catalytic dyad disruption and inhibition, and as a prototype distinct from other reported covalent inhibitors for the development of novel antiviral agents.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>\n                        A nanomolar potent small-molecule inhibitor,\n                        <jats:bold>H102<\/jats:bold>\n                        , of SARS-CoV-2 M\n                        <jats:sup>pro<\/jats:sup>\n                        was developed and exhibited strong anti-SARS-CoV-2 infection activity in cells. Co-crystal structure determination of its complex with M\n                        <jats:sup>pro<\/jats:sup>\n                        provided a structural mechanism of\n                        <jats:bold>H102<\/jats:bold>\n                        \u2019s action and revealed an interesting structural feature: the benzyl ring at the P2 position of\n                        <jats:bold>H102<\/jats:bold>\n                        interacts with the reorientated His41 side chain, accompanied by a significant increase of the distance between the catalytic dyad Cys145-His41 residues, which is uncommon in reported covalent inhibitors. Compound\n                        <jats:bold>H102<\/jats:bold>\n                        may be used as a biochemical probe to further investigate mechanisms of M\n                        <jats:sup>pro<\/jats:sup>\n                        inhibition and potentially different type of lead for developing antiviral agents for treating disease caused by novel coronavirus SARS-CoV-2.\n                      <\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/jvi.00658-25","type":"journal-article","created":{"date-parts":[[2025,9,15]],"date-time":"2025-09-15T13:01:23Z","timestamp":1757941283000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":3,"title":["Discovery of a potent covalent inhibitor that unusually distorts the catalytic dyad of SARS-CoV-2 main protease"],"prefix":"10.1128","volume":"99","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-7530-1274","authenticated-orcid":false,"given":"Juan","family":"Wang","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03cve4549","id-type":"ROR","asserted-by":"publisher"}],"name":"School of Life Sciences, Tsinghua University","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-6561-2254","authenticated-orcid":true,"given":"Xiaohong","family":"Sang","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02d5ks197","id-type":"ROR","asserted-by":"publisher"}],"name":"Ciechanover Institute of Precision and Regenerative Medicine, School of Medicine, The Chinese University of Hong Kong","place":["Shenzhen, 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