Identification of phytochemical compounds to inhibit the matrix-like linker protein VP26 to block the assembles of white spot syndrome virus (WSSV) envelope and nucleocapsid protein of marine shrimp: In silico approach

Abstract

White spot syndrome virus (WSSV) is an enveloped pathogenic virus of cultured shrimp that has a mortality rate of up to 100 % in intensive aquaculture systems. The virulent pathogen causes an economic loss estimated at US$1 billion annually to global shrimp and prawn production. To date, no effective antiviral or vaccine has been progress that can reduce the economic losses caused by the pathogen. The complex genomic structure of the nucleocapsid of a virus, consisting of double-stranded DNA as genetic material surrounded by lipid envelope protein. It has been found that VP26, a major envelope protein interacts with the virus VP51 capsid and makes a bridge between the envelope and nucleocapsid protein resulting in mature virion of the virus. Blocking the interaction by targeting VP26 can hinder the mature virion production and non-infectivity of the virus. Therefore, in order to blocking the function of VP26, an in-silico drug design approach has been utilized to screen the potential antiviral compounds from the medicinal plant, Withania somnifera (WS) of Saudi Arabia. Isolated thirty-nine (39) phytochemicals compounds from the plant have initially been screened by molecular docking method. The best three compounds, namely, withanolide (CID: 118701104), Coagulin Q (CID: 10100411), and withanolide D (CID: 23266161) have been selected based on their docking score −8.2 kcal/mol, −8.1 kcal/mol and −7.9 kcal/mol, respectively, which have been further evaluated based on pharmacokinetics including ADME (Absorption, Distribution, Metabolism and Excretion) and toxicity approaches. Additionally, 100 ns molecular dynamics (MD) simulation methods confirmed the structural stability of the compounds to the binding sites of the VP26 protein. Therefore, the selected compounds can be utilized as an antiviral drug to fight against the WSSV virus, which will bring remarkable advancement in the aquaculture sector.