Identifying epitopes for cluster of differentiation and design of new peptides inhibitors against human SARS-CoV-2 spike RBD by an in-silico approach

Jihane Akachar; El Mehdi Bouricha; Mohammed Hakmi; Lahcen Belyamani; Rachid El Jaoudi; Azeddine Ibrahimi

doi:10.1016/j.heliyon.2020.e05739

Identifying epitopes for cluster of differentiation and design of new peptides inhibitors against human SARS-CoV-2 spike RBD by an in-silico approach

Heliyon. 2020 Dec 14;6(12):e05739. doi: 10.1016/j.heliyon.2020.e05739. eCollection 2020 Dec.

Authors

Jihane Akachar¹, El Mehdi Bouricha¹, Mohammed Hakmi¹, Lahcen Belyamani², Rachid El Jaoudi¹, Azeddine Ibrahimi¹

Affiliations

¹ Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Morocco.
² Emergency Department, Military Hospital Mohammed V, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Morocco.

Abstract

The coronavirus disease 19 (COVID-19) is a highly contagious and rapidly spreading infection caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In some cases, the disease can be fatal which resulted in more than one million deaths worldwide according the WHO. Currently, there is no effective vaccine or treatment for COVID-19, however many small-molecule inhibitors have shown potent antiviral activity against SARS-CoV-2 and some of them are now under clinical trials. Despite their promising activities, the development of these small molecules for the clinical use can be limited by many factors like the off-target effect, the poor stability, and the low bioavailability. The clusters of differentiation CD147, CD209, CD299 have been identified as essential entry co-receptors for SARS-CoV-2 species specificity to humans, although the underlying mechanisms are yet to be fully elucidated. In this paper, protein-protein docking was utilized for identifying the critical epitopes in CD147, CD209 and CD299 which are involved in the binding with SARS-CoV-2 Spike receptor binding domain (RBD). The results of binding free energies showed a high affinity of SARS-CoV-2 RBD to CD299 receptor which was used as a reference to derive hypothetical peptide sequences with specific binding activities to SARS-CoV-2 RBD. Molecular docking and molecular dynamics simulations of the newly designed peptides showed favorable binding features and stability with SARS-CoV-2 RBD and therefore can be further considered as potential candidates in future anti-SARS CoV-2 drug discovery studies.

Keywords: Biological sciences; Chemistry; Cluster of differentiation; Computer science; Coronavirus 19; Engineering; Molecular docking; Molecular dynamics; Peptide-based drugs; Physics; Spike protein.