Inhibition Binding Mechanism Simulation of Horseshoe Crab Peptides for Sars-Cov-2 Main Protease
Disciplines
Amino Acids, Peptides, and Proteins | Biochemistry | Molecular Biology
Abstract (300 words maximum)
Horseshoe crabs were essential for the creation and testing of the coronavirus vaccines. The Sars-Cov-2 main protease is an essential tool for coronavirus’s propagation through the body and its structure is distinct from human proteases making it a prime target for inhibition. Sars-Cov-2 protease is however catalytically similar to HIV, providing a potential ground for comparison. In this study for the CHEM 3512 lab, the three horseshoe crab anti-HIV oligopeptides from the Antimicrobial Peptide database were analyzed by simulating their binding interactions with Sar-Cov-2 main protease. The models were created in Hdock and then imported into Pymol in order to analyze similarities in structure and binding interactions. All three oligopeptides studied were predicted by Hdock to bind to the protease’s catalytic site with the highest confidence scores for each at .7050, .7627, and .6411. The Hdock results as well as structural highlights shown in Pymol are discussed. Further study of these peptides’ inhibitory potential is suggested, particularly AP00212 which showed especially promising results in the Hdock simulation.
Academic department under which the project should be listed
CSM - Chemistry and Biochemistry
Primary Investigator (PI) Name
Rajnish Singh
Inhibition Binding Mechanism Simulation of Horseshoe Crab Peptides for Sars-Cov-2 Main Protease
Horseshoe crabs were essential for the creation and testing of the coronavirus vaccines. The Sars-Cov-2 main protease is an essential tool for coronavirus’s propagation through the body and its structure is distinct from human proteases making it a prime target for inhibition. Sars-Cov-2 protease is however catalytically similar to HIV, providing a potential ground for comparison. In this study for the CHEM 3512 lab, the three horseshoe crab anti-HIV oligopeptides from the Antimicrobial Peptide database were analyzed by simulating their binding interactions with Sar-Cov-2 main protease. The models were created in Hdock and then imported into Pymol in order to analyze similarities in structure and binding interactions. All three oligopeptides studied were predicted by Hdock to bind to the protease’s catalytic site with the highest confidence scores for each at .7050, .7627, and .6411. The Hdock results as well as structural highlights shown in Pymol are discussed. Further study of these peptides’ inhibitory potential is suggested, particularly AP00212 which showed especially promising results in the Hdock simulation.