Computational studies on the interaction of flavanones with the nucleoprotein/phosphoprotein binding site in the N-terminal domain of the hRSV nucleocapsid protein

The human Respiratory Syncytial Virus (hRSV) is a negative-sense single-stranded RNA virus that causes severe respiratory infections, especially in children. Despite recent advances in vaccines for the elderly and pregnant women, the only licensed treatment against hRSV is the monoclonal antibody palivizumab, which targets the virus's fusion protein. Thus, the search for antivirals against hRSV remains an important strategy. Among 11 hRSV proteins, the nucleoprotein N and the phosphoprotein P stand out as essential for viral replication. They interact with each other, specifically the N-terminal domain of N protein (N-NTD) with the C-terminal domain of phosphoprotein. In this context, studies revealed that the interaction of small ligands 1-benzyl-1H-pyrazole-3,5-dicarboxylate (BPdC) and flavanone hesperetin with the hydrophobic pocket of the nucleoprotein/phosphoprotein binding site in the N-NTD of hRSV holds promise strategy for developing a new form to combat this virus. This study aimed to perform a virtual screening of flavanones against the N-NTD of hRSV using the molecular docking program DOCK6 (UCSF), followed by energy refinement with the AMBER force field. To automate this process, a script was developed, allowing the protocol to be applied to hundreds of molecules targeting the hydrophobic pocket in the N-NTD. Out of the 340 flavanones tested, the 10 with the best energy values (most negative) according to the AMBER score were selected. Within these 10, it can stand out the first three: 7,4'-dibenzyloxy-5-hydroxy-flavanone (score –37.88), 5,7,4'-tri-(methoxymethoxy)-8,3'-di-(3-methyl-2-butenyl)flavanone (score –37.57), and 6,8-bis(p-methoxybenzyl)-3',4'-dimethoxy-5,7-dihydroxy-flavanone (score –37.02). The next step of this study will be to perform molecular dynamics simulations of the modeled N-NTD/flavanones complexes to evaluate structural stability and then perform binding free energy calculations via MM-GBSA to det