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Commun Biol ; 5(1): 1188, 2022 Nov 05.
Article in English | MEDLINE | ID: covidwho-2106511


SARS-CoV-2 has evolved continuously and accumulated spike mutations with each variant having a different binding for the cellular ACE2 receptor. It is not known whether the interactions between such mutated spikes and ACE2 glycans are conserved among different variant lineages. Here, we focused on three ACE2 glycosylation sites (53, 90 and 322) that are geometrically close to spike binding sites and investigated the effect of their glycosylation pattern on spike affinity. These glycosylation deletions caused distinct site-specific changes in interactions with the spike and acted cooperatively. Of note, the particular interaction profiles were conserved between the SARS-CoV-2 parental virus and the variants of concern (VOCs) Delta and Omicron. Our study provides insights for a better understanding of the importance of ACE2 glycosylation on ACE2/SARS-CoV-2 spike interaction and guidance for further optimization of soluble ACE2 for therapeutic use.

COVID-19 , Spike Glycoprotein, Coronavirus , Humans , Spike Glycoprotein, Coronavirus/chemistry , Angiotensin-Converting Enzyme 2/genetics , SARS-CoV-2/genetics , Glycosylation , Peptidyl-Dipeptidase A , Protein Binding
Biophys Physicobiol ; 18: 215-222, 2021.
Article in English | MEDLINE | ID: covidwho-1993621


Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes the coronavirus disease 2019 (COVID-19), spread rapidly around the globe. The main protease encoded by SARS-CoV-2 is essential for processing of the polyproteins translated from the viral RNA genome, making this protein a potential drug target. A recently reported mutation in the protease, P108S, may be responsible for milder symptoms observed in COVID-19 patients in Tokyo. Starting from a crystal structure of the SARS-CoV-2 main protease in the dimeric form, we performed triplicate 5.0-µs molecular dynamics simulations of the wild-type and P108S mutant. Our computational results suggest a link between the mutation P108S and dynamics of the catalytic sites in the main protease: The catalytic dyad become considerably inaccessible to substrates in the P108S mutant. Our results also demonstrate the potential of molecular dynamics simulations to complement experimental techniques and other computational methods, such as protein design calculations, which predict effects of mutations based on static crystal structures. Further studies are certainly necessary to quantitively understand the relationships between the P108S mutation and physical properties of the main protease, but the results of our study will immediately inform development of new protease inhibitors.