ISSN print edition: 0366-6352 ISSN electronic edition: 1336-9075 Registr. No.: MK SR 9/7 Published monthly

Potential antiviral peptides against the nucleoprotein of SARS-CoV-2

Iktedar Mahdi, Humyara Yeasmin, Imtiaz Hossain, Raina Masnoon Badhan, Md. Ackas Ali, Md. Abdul Kaium, Rajib Islam, Md. Abu Sufian, and Mohammad A. Halim

Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh

E-mail: mhalim1@kennesaw.edu

Received: 20 June 2022  Accepted: 21 September 2022

Abstract:

Nucleoprotein is a conserved structural protein of SARS-CoV-2, which is involved in several functions, including replication, packaging, and transcription. In this research, 21 antiviral peptides that are known to have inhibitory function against nucleoprotein in several other viruses, were screened computationally against the nucleoprotein of SARS-CoV-2. The complexes of five best performing peptides (AVP1142, AVP1145, AVP1148, AVP1150, AVP1155) with nucleoprotein were selected for subsequent screening via 5 ns molecular dynamics (MD) simulation. Two peptides, namely AVP1145 and AVP1155, came out as promising candidates and hence were selected for 200 ns MD simulation for further validation, incorporating a DMPC-based membrane environment. In the long MD simulation, both AVP1155 and AVP1145 utilized multiple residues—mainly aromatic, acidic, and nonpolar residues—as interacting points to remain in contact with the nucleoprotein and formed predominantly hydrogen bonds along with hydrophobic and electrostatic interactions. However, AVP1155 proved to be superior to AVP1145 when its complex with nucleoprotein was analyzed in terms of root-mean-square deviation, root-mean-square fluctuation, radius of gyration, solvent accessible surface area and free energy landscape. In a nutshell, the findings of this research may guide future studies in the development of selective peptide inhibitors of SARS-CoV-2 nucleoprotein.

Keywords: SARS-CoV-2; Nucleoprotein; Antiviral peptides; Molecular dynamics simulation; Interacting residues

Full paper is available at www.springerlink.com.

DOI: 10.1007/s11696-022-02514-4

Chemical Papers 77 (2) 813–823 (2023)