Sialic acid analog as inhibitor for human coronavirus OC43-a study by molecular dynamics simulations

Abstract

Human coronavirus OC43 (HCoV-OC43) causes severe respiratory tract illness in humans. In the present study, we carried out 100 ns molecular dynamics (MD) simulations to investigate the conformational dynamics of HCoV-OC43 spike (S) glycoprotein complexes with sialic acid (SIA) analogs. The binding affinity between the HCoV-OC43 S and SIA analogs is analyzed using NAMD and MM-PBSA binding free energy calculation. It is concluded from the results of NAMD and MM/PBSA that the order of binding specificity toward HCoV-OC43 S is 9-O-Ac-Sia > SIA > Neu5Gc > zanamivir > Neu5Ac2en.

Graphical Abstract

Keywords:

• Coronavirus
• HCoV-OC43
• molecular dynamics simulations
• sialic acid analog
• spike glycoprotein

Acknowledgments

We thank the Department of Biotechnology and the Indian Institute of Technology Madras for their computational facilities.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

The work is partially supported by the Department of Biotechnology (DBT), New Delhi, Government of India for partial financial support to KV and MMG (Sanction order No.: BT/PR13410/BID/7/536/2015 and BT/PR12267/BID/7/506/2014).