The molecular dynamics simulation of coronavirus- based compound (6OHW structure) interaction with interferon beta-1a protein at different temperatures and pressures: Virus destruction process

Abstract

The Interferon beta-1a protein is a cytokine in the Interferon family that is used to treat a variety of ailments. Molecular Dynamics simulation was used to characterize the atomic disintegration of 6OHW structure of a corona virus-based compound with Interferon beta-1a protein in this computational study. Molecular Dynamics simulation results on the atomic evolution of the 6OHW structure were presented with estimating physical variables. Physically, our simulations showed the attraction forces between the virus and the atomic protein in the presence of H2O molecules, resulting in viral annihilation after t = 10 ns. The molecular dynamics package's initial pressure and temperature (Temp) changes were important for virus-protein system evolution. Numerically, increasing primary T and P from 300 K and 1 bar to 350 K and 5 bar reduced the atomic distance between virus and protein structures from 10 & Aring; to 2.71 & Aring; and 2.45 & Aring;. Bonding energy was another reported physical quantity in our Molecular Dynamics simulation work. The atomic parameter ranged from 152.57 kcal/mol to 148.54 kcal/mol due to changes in initial Temp and pressure. Ultimately, the diffusion coefficient of protein being simulated inside the atomic virus changed from 0.48 mu m2/s to 0.59 mu m2/s. This calculation demonstrated the suitable conduct of simulated protein throughout virus destruction process.