1st International and 10th National Iranian Conference on Bioinformatics
Home Accepted Papers
The potential of antimicrobial peptides as Covid-19 therapeutics using computational methods
Paper ID : 1387-ICB10
Authors:
Sara Mortezaali *1, Mahboobeh Zarrabi2
1دانشگاه الزهرا (س)
2گروه بیوفیزیک، دانشکده علوم زیستی، دانشگاه الزهرا، تهران، ایران
Abstract:
Background: A new type of coronavirus was first detected in December 2019 at Wuhan city, China.[1] The pneumonia-like disease caused by the virus is globally known as COVID-19. Apart from China, COVID-19 has spread to 213 countries and killed over 5,735,179 people in total as of today (7 February 2022).[2] With the case count and death toll rising each day, there is an urgent need for antiviral drugs against SARS-CoV-2.
Antimicrobial peptides (AMPs) have been widely regarded as a promising solution to combat harmful microorganisms. They are biologically active molecules produced by different organisms as an essential component of their innate immune response against invading pathogens.[3]
Materials and Methods: 110 antimicrobial peptides with a length of 5 to 50 amino acids have been chosen from DBAASP and the third structure of proteins have modeled by pepfold3 server. Then peptides have been refined by MODELLER. The structure of SARS_CoV_2 spike protein has been obtained from protein data bank (PDBID:6lzg). Spike’s ligand has been deleted by Chimera and non-polar hydrogens have been merged by autodock tools.
Finally, peptide files and receptor files have been loaded on pyrx, and docking was carried out for the spike protein with the grid box set to center x-, y-, z-axis values of −40.34, 30.85, 6.61 with a dimension of 35 Å x 50 Å x 30 Å.[4]
Result: For binding affinity, the best result was the 15288-spike complex with -11.5 Kj/mol. Then this complex was subsequently analyzed by MD simulation. RMSD, RMSF, and potential energy analysis were performed by gromacs.
Conclusion: Our results and studies show that a number of peptides in this library have the ability to bind to the spike protein. This interaction has the potential to disturb the function of the virus and these peptides can be used as a therapeutic agent.
Keywords:
Molecular Dynamic; Docking; Antimicrobial peptide; Coronavirus; Spike protein
Status : Paper Accepted (Poster Presentation)