tetano
Editor, Senior Moderator
Elife
. 2026 Oct 26:15:RP109956.
doi: 10.7554/eLife.109956.
Chengxi Liu # 1 2 , Qinyu Jia # 1 2 , Chang Zhao # 1 2 , Zhong-Ping Yao 1 2
Affiliations Expand
The SARS-CoV-2 main protease (Mpro) is a key antiviral target that equilibrates between an active dimer and inactive monomer, making the dimerization interface a promising therapeutic vulnerability. This study investigates Mpro monomer-dimer equilibrium and conformational changes induced by inhibitor binding using 13C labeling with native mass spectrometry and hydrogen/deuterium exchange mass spectrometry (HDX-MS). We evaluated how peptidomimetic inhibitors (PF-07321332, PF-00835231, GC376, boceprevir) and non-peptidomimetic inhibitors (carmofur, ebselen, MR6-31-2, AT7519, pelitinib) influence Mpro dimerization and subunit exchange. Key findings revealed divergent mechanisms: peptidomimetic inhibitors significantly shifted the equilibrium towards the dimeric state, suppressing subunit exchange dynamics and rigidifying the dimer interface; in contrast, ebselen impaired dimer formation and increased interface flexibility. Notably, tandem mass spectrometry identified a novel covalent binding site for ebselen at C300. Molecular dynamics simulations and mutational analyses demonstrated that this C300 modification allosterically alters the hydrogen bond network of the dimer interface, directly contributing to ebselen-mediated dimer disruption and enzymatic inhibition. Overall, this study clarifies distinct inhibitory modes between peptidomimetics and ebselen, highlighting the therapeutic potential of targeting allosteric sites at the dimer interface for designing next-generation Mpro inhibitors.
Keywords: SARS-CoV-2 main protease; biochemistry; chemical biology; dimerization; ebselen; hydrogen/deuterium exchange mass spectrometry; native mass spectrometry; none; peptidomimetic inhibitors.
. 2026 Oct 26:15:RP109956.
doi: 10.7554/eLife.109956.
SARS-CoV-2 main protease inhibition through dimerization promotion by peptidomimetic inhibitors and disruption by ebselen
Chengxi Liu # 1 2 , Qinyu Jia # 1 2 , Chang Zhao # 1 2 , Zhong-Ping Yao 1 2
Affiliations Expand
- PMID: 42930075
- DOI: 10.7554/eLife.109956
Abstract
The SARS-CoV-2 main protease (Mpro) is a key antiviral target that equilibrates between an active dimer and inactive monomer, making the dimerization interface a promising therapeutic vulnerability. This study investigates Mpro monomer-dimer equilibrium and conformational changes induced by inhibitor binding using 13C labeling with native mass spectrometry and hydrogen/deuterium exchange mass spectrometry (HDX-MS). We evaluated how peptidomimetic inhibitors (PF-07321332, PF-00835231, GC376, boceprevir) and non-peptidomimetic inhibitors (carmofur, ebselen, MR6-31-2, AT7519, pelitinib) influence Mpro dimerization and subunit exchange. Key findings revealed divergent mechanisms: peptidomimetic inhibitors significantly shifted the equilibrium towards the dimeric state, suppressing subunit exchange dynamics and rigidifying the dimer interface; in contrast, ebselen impaired dimer formation and increased interface flexibility. Notably, tandem mass spectrometry identified a novel covalent binding site for ebselen at C300. Molecular dynamics simulations and mutational analyses demonstrated that this C300 modification allosterically alters the hydrogen bond network of the dimer interface, directly contributing to ebselen-mediated dimer disruption and enzymatic inhibition. Overall, this study clarifies distinct inhibitory modes between peptidomimetics and ebselen, highlighting the therapeutic potential of targeting allosteric sites at the dimer interface for designing next-generation Mpro inhibitors.
Keywords: SARS-CoV-2 main protease; biochemistry; chemical biology; dimerization; ebselen; hydrogen/deuterium exchange mass spectrometry; native mass spectrometry; none; peptidomimetic inhibitors.