(General overview of Antimicrobial Peptides (AMPs) and their effect over severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)

Abstract

Antimicrobial peptides (AMP) are structurally diverse substances that are produced naturally by almost all known organisms to counteract invading organisms. Even though AMPs adopt diverse sequences and structures, they show antimicrobial activity with different spectra of activity, affecting bacteria, viruses and fungi. Many of the natural AMPs have a cytotoxic effect on human cells, especially red blood cells, causing a haemolytic side effect. Thus, the chemical modification of natural AMPs or the use of fully synthesized peptides that designed through the in silico platform can be done to reduce cytotoxicity and preferably enhance the potency. The physiochemical properties of AMPs include sequence length, secondary structure and helicity, charge, hydrophobicity and amphipathiticity; these are overlapping parameters that can affect the potency, spectrum of activity, selectivity and stability of AMPs. Currently, communities all over the world are suffering from the COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), to which there is no direct antiviral or approved effective vaccine. SARS-CoV-2 depends fundamentally on the spike (S) protein surrounding its envelope to bind angiotensin-converting enzyme 2 (ACE2) receptors located on the surface of host cellular membrane to undergo conformational shift forming fusion core that facilitate fusion and subsequent cell entry. In fact, AMPs can form peptide- protein interactions, binding the components of the S protein and inhibiting viral entry, thus removing the virus’s capability to infect affected cells. In this dissertation, AMPs’ classification, their physiochemical properties and the mechanism of action by which they exert their antibacterial and antiviral activities are described. In addition, SARS-CoV-2 and its correlation with other coronaviruses as well as its pathogenesis, virology and genomic description use discussed, specifically focusing on its S protein as a target to develop potential peptides against it.