Why is the Omicron main protease of SARS-CoV-2 less stable than its wild-type counterpart?A crystallographic,biophysical,and theoretical study  

作　　者：Mohamed Ibrahim Xinyuanyuan Sun Vinicius Martins de Oliveira Ruibin Liu Joseph Clayton Haifa El Kilani Jana Shen Rolf Hilgenfeld 

机构地区：[1]Institute of Molecular Medicine,University of Lübeck,23562 Lübeck,Germany [2]Department of Pharmaceutical Sciences,University of Maryland School of Pharmacy,Baltimore,MD 21201,USA [3]Division of Applied Regulatory Science,Office of Clinical Pharmacology,Office of Translational Sciences,Center for Drug Evaluation and Research,United States Food and Drug Administration,Silver Spring,MD 20993,USA [4]German Center for Infection Research(DZIF),Hamburg-Lübeck-Borstel-Riems Site,University of Lübeck,23562 Lübeck,Germany

出　　处：《hLife》2024年第8期419-433,共15页健康科学（英文）

基　　金：Financial support from the German Center for Infection Research(DZIF;project FF 01.905,to R.H.);the National Institutes of Health(R35GM148261 to J.S.)is gratefully acknowledged.R.H.is also supported by the Government of Schleswig-Holstein through its Structure;Excellence Fund as well as by a close partnership between the Possehl Foundation(Lübeck)and the University of Lübeck.

摘　　要：During the continuing evolution of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the Omicron variant of concern emerged in the second half of 2021 and has been dominant since November of that year.Along with its sublineages,it has maintained a prominent role ever since.The Nsp5 main protease(Mpro)of the Omicron virus is characterized by a single dominant mutation,P132H.Here we determined the X-ray crystal structures of the P132H mutant(or O-Mpro)as a free enzyme and in complex with the Mpro inhibitor,the alpha-ketoamide 13b-K,and we conducted enzymological,biophysical,as well as theoretical studies to characterize the O-Mpro.We found that O-Mpro has a similar overall structure and binding with 13b-K;however,it displays lower enzymatic activity and lower thermal stability compared to the WT-Mpro(with“WT”referring to the prototype strain).Intriguingly,the imidazole ring of His132 and the carboxylate plane of Glu240 are in a stacked configuration in the X-ray structures determined here.Empirical folding free energy calculations suggest that the O-Mpro dimer is destabilized relative to the WT-Mpro due to less favorable van der Waals interactions and backbone conformations in the individual protomers.All-atom continuous constant-pH molecular dynamics(MD)simulations reveal that His132 and Glu240 display coupled titration.At pH 7,His132 is predominantly neutral and in a stacked configuration with respect to Glu240 which is charged.In order to examine whether the Omicron mutation eases the emergence of further Mpro mutations,we also analyzed the P132H+T169S double mutant,which is characteristic of the BA.1.1.2 lineage.However,we found little evidence of a correlation between the two mutation sites.

关 键 词：severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) main protease Omicron molecular dynamics Pro>His mutant double mutant 

分 类 号：R563.1[医药卫生—呼吸系统]