The Asian subcontinents, especially India, are habitat to a large population of shrimp and other crustacean-infecting White Spot Syndrome Virus (WSSV). Shrimp aquaculture has suffered a major financial loss due to the virus. It is a highly transmissible disease that, can result in total mortality 3–10 days after an outbreak. About 300 kb of the WSSV genome codes for several infection-mediating proteins. The infection process and the interface with host cells are significantly influenced by the envelope proteins commonly VP28, VP26, and VP24. In this study, we have used the Immediate early structural proteins VP28, VP91, and VP108 to see the in-silico impact of antiviral compounds extracted from Halomonas salifodinae bacterium ethyl acetate extract. In the previous study, the compound’s antiviral activity has already been confirmed in shrimp (Fenneropenaeus indicus) in vivo. Molecular dynamics and simulation studies validate the impact of ligand binding on proteins. Combined, these in silico methods show how well the ligand inhibits the trimers’ ability to perform physiological functions. Consequently, employing Perfluorotributylamine as an antiviral and deciphering the intricate relationship between VP28, VP91, VP108, and Perfluorotributylamine can pave the way for the development of antivirals against white spot disease.