Effect of Ph on Stability of Dimer Structure of the Main Protease of Coronavirus-2

25 Pages Posted: 21 Mar 2022

See all articles by Pornthep Sompornpisut

Pornthep Sompornpisut

Chulalongkorn University

Panisak Boonamnaj

Chulalongkorn University

R.B. Pandey

University of Southern Mississippi

Abstract

The viral main protease (M pro ) from a novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a key enzyme essential for viral replication and has becomes an attractive target for antiviral drug development. The M pro forms a functional dimer and exhibits a pH-dependent enzyme activity and dimerization. Here, we report a molecular dynamics (MD) investigation to gain insights into the structural stability of the enzyme dimer at pH 7 and 4. Our data shows larger changes in structure of the protein with the acidic pH than that with the neutral pH. Structural analysis of MD trajectories reveals a substantial increase in intersubunit separation, the loss of domain contacts, binding free energy and interaction energy of the dimer which implies the protein instability and tendency of dimer dissociation at pH 4. The loss in the interaction energy is mainly driven by electrostatic interactions. We have identified the intersubunit hydrogen-bonding residues involved in the decreased dimer stability. These findings may be helpful for rational drug design and target evaluation against COVID-19.

Keywords: pH effect, Mpro, coronavirus, main protease, dimer, molecular dynamics

Suggested Citation

Sompornpisut, Pornthep and Boonamnaj, Panisak and Pandey, R.B., Effect of Ph on Stability of Dimer Structure of the Main Protease of Coronavirus-2. Available at SSRN: https://ssrn.com/abstract=4060672 or http://dx.doi.org/10.2139/ssrn.4060672

Pornthep Sompornpisut (Contact Author)

Chulalongkorn University ( email )

Bangkok
Bangkok 10330
Thailand

Panisak Boonamnaj

Chulalongkorn University ( email )

R.B. Pandey

University of Southern Mississippi ( email )

Hattiesburg, MS 39406
United States

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