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pH profiles of 3-chymotrypsin-like protease (3CLpro) from SARS-CoV-2 elucidate its catalytic mechanism and a histidine residue critical for activity.
Al Adem, Kenana; Ferreira, Juliana C; Fadl, Samar; Rabeh, Wael M.
  • Al Adem K; Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.
  • Ferreira JC; Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.
  • Fadl S; Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.
  • Rabeh WM; Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates. Electronic address: wael.rabeh@nyu.edu.
J Biol Chem ; 299(2): 102790, 2023 02.
Article in English | MEDLINE | ID: covidwho-2238444
ABSTRACT
3-Chymotrypsin-like protease (3CLpro) is a promising drug target for coronavirus disease 2019 and related coronavirus diseases because of the essential role of this protease in processing viral polyproteins after infection. Understanding the detailed catalytic mechanism of 3CLpro is essential for designing effective inhibitors of infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Molecular dynamics studies have suggested pH-dependent conformational changes of 3CLpro, but experimental pH profiles of SARS-CoV-2 3CLpro and analyses of the conserved active-site histidine residues have not been reported. In this work, pH-dependence studies of the kinetic parameters of SARS-CoV-2 3CLpro revealed a bell-shaped pH profile with 2 pKa values (6.9 ± 0.1 and 9.4 ± 0.1) attributable to ionization of the catalytic dyad His41 and Cys145, respectively. Our investigation of the roles of conserved active-site histidines showed that different amino acid substitutions of His163 produced inactive enzymes, indicating a key role of His163 in maintaining catalytically active SARS-CoV-2 3CLpro. By contrast, the H164A and H172A mutants retained 75% and 26% of the activity of WT, respectively. The alternative amino acid substitutions H172K and H172R did not recover the enzymatic activity, whereas H172Y restored activity to a level similar to that of the WT enzyme. The pH profiles of H164A, H172A, and H172Y were similar to those of the WT enzyme, with comparable pKa values for the catalytic dyad. Taken together, the experimental data support a general base mechanism of SARS-CoV-2 3CLpro and indicate that the neutral states of the catalytic dyad and active-site histidine residues are required for maximum enzyme activity.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Biocatalysis / Coronavirus 3C Proteases / SARS-CoV-2 / Histidine Limits: Humans Language: English Journal: J Biol Chem Year: 2023 Document Type: Article Affiliation country: J.jbc.2022.102790

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Biocatalysis / Coronavirus 3C Proteases / SARS-CoV-2 / Histidine Limits: Humans Language: English Journal: J Biol Chem Year: 2023 Document Type: Article Affiliation country: J.jbc.2022.102790