Insilico Alpha-Helical Structural Recognition of Temporin Antimicrobial Peptides and Its Interactions with Middle East Respiratory Syndrome-Coronavirus

Abstract

Many antimicrobial peptides (AMPs) have multiple antimicrobial immunity effects. One such class of peptides is temporins. Temporins are the smallest (AMPs) found in nature and are highly active against gram-positive bacteria. Nowadays, there was a rapid increase in the availability of the 3D structure of proteins in PDB (protein data bank). The conserved residues and 3D structural conformations of temporins (AMPs) were still unknown. The present study explores the sequence analysis, alpha-helical structural conformations of temporins. The sequence of temporins was deracinated from APD3 database, the three-dimensional structure was constructed by homology modeling studies. The sequence analysis results show that the conserved residues among the peptide sequences, the maximum of the sequences are 70% alike to each other. The secondary structure prediction results revealed that 99% of temporin (AMPs) exhibited in alpha-helical form. The 3D structure speculated using RAMPAGE exposes the alpha-helical conformation in all temporins (AMPs). The phylogenetic analysis reveals the evolutionary relationships of temporins (AMPs), which are branched into seven clusters. As a result, we identified a list of potential temporin AMPs which docked to the antiviral protein (MERS-CoV), it shows good protein-peptide binding. This computational approach may serve as a good model for the rationale design of temporin based antibiotics.

Antimicrobial Peptides: Classification, Design, Application and Research Progress in Multiple Fields

“…According to recent research, the lipopeptide EK1C4, derived from EK1 (SLDQINVTFLDLEYEMKKLEEAIKKLEESYIDLKEL), is the most effective fusion inhibitor against COVID-19 S protein-mediated membrane fusion ( Xia et al, 2020 ). Homology modeling and protein-peptide docking showed that temporin has potential therapeutic applications against MERS-CoV ( Marimuthu et al, 2019 ). Two AMPs from the non-structural protein nsp10 of SARS-CoV, K12, and K29, can inhibit SARS-CoV replication ( Ke et al, 2012 ).…”

In Silico Discovery of Antimicrobial Peptides as an Alternative to Control SARS-CoV-2

“…However, no previous studies have reported the interaction of AMPs with SARS-CoV-2 target proteins. In this respect, some studies have previously evaluated the activity of natural and synthetic peptides, including defensins, plectasins, temporins and cathelicidins, against multiple respiratory viruses, such as influenza A virus H5N1, H1N1, MERS-CoV, and SARS-CoV [ 27 , 28 , 29 , 39 , 40 , 57 ]. Similar to this study, in silico analyses showed the potent antiviral effects of AMPs against Betacoronavirus [ 27 , 39 ].…”

“…In this respect, some studies have previously evaluated the activity of natural and synthetic peptides, including defensins, plectasins, temporins and cathelicidins, against multiple respiratory viruses, such as influenza A virus H5N1, H1N1, MERS-CoV, and SARS-CoV [ 27 , 28 , 29 , 39 , 40 , 57 ]. Similar to this study, in silico analyses showed the potent antiviral effects of AMPs against Betacoronavirus [ 27 , 39 ]. According to our results, the AMPs are attractive candidates as alternative to conventional antiviral drugs to control SARS-CoV-2 infection, because they offer several potential advantages, including specific anti-CoV effects, high selectivity, and do not be associated with severe adverse effects according to in vitro and in vivo assays [ 58 , 59 , 60 ].…”

“…Recently, several in silico studies have been performed to investigate the interactions between drug compounds and target proteins of SARS-CoV-2 [ 12 , 38 ], but there is no available information on the interactions of AMPs against structural proteins of this virus. However, computational approaches for structural information and protein–peptide interactions of AMPs against MERS-CoV and SARS-CoV, showed significant interactions with the Sgp [ 27 , 39 , 40 ].…”

Peptides and Dendrimers: How to Combat Viral and Bacterial Infections

“…The six amino acid residues N-myristoylated-peptide, from larval hemolymph of the tobacco budworm Heliothis virescens , is active against HIV-1 and HSV-1 [ 62 ]. An homology modeling study demonstrated that temporins may provide therapeutic applications against MERS-CoV [ 63 ]. The antiviral activity of defensins has been widely demonstrated against several viruses, including HIV, influenza virus, human adenovirus, severe acute respiratory syndrome coronavirus (SARSC), papillomavirus (HPV), respiratory syncytial virus (RSV), and herpes simplex virus (HSV) [ 64 ].…”