Design of ligands based on BPdC scaffold for binding to the hydrophobic pocket in the N-terminal domain of nucleoprotein of hRSV

Respiratory virus infections cause approximately four million deaths annually globally, with human Respiratory Syncytial Virus (hRSV) being a major cause of acute respiratory disease in newborns, infants, and elderly, often resulting in bronchiolitis and pneumonia. 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. In this context, studies revealed that the interaction of small ligands 1-benzyl-1H-pyrazole-3,5-dicarboxylate (BPdC) with the hydrophobic pocket of the nucleoprotein/phosphoprotein binding site in the N-terminal domain of the nucleocapsid protein N (N-NTD) of hRSV holds promise strategy for developing a new form to combat this virus. These small compounds (named M61, M68, and M81) inhibit the binding of the N protein to the phosphoprotein, hindering hRSV replication. The present study aimed to propose new small compounds based on the BPdC scaffold for binding to the hydrophobic pocket of N-NTD. For that, a set of computational tools such as molecular docking, molecular dynamics simulations, binding mapping via FTMap, and binding free energy calculation was employed. Modifications in the aromatic ring of BPdCs were proposed with organic probes mapped via FTMap, resulting in six new compounds formed by the original ligands M61, M68, and M81 with the probes ADY/DFO (acetaldehyde) and AMN (amino), which were selected based on physicochemical and pharmacological characteristics of the ADMET tests. Molecular dynamics simulations showed that the ligands modified with the ADY/DFO probe presented greater stability with the N/P binding site of the N-NTD when compared to the original BPdC compounds. Binding free energy calculations via MM-PBSA indicated that the new compounds have binding energy values slightly higher than those of the base ligands, with an increase in the number of hydrogen bonds. Therefore, the results of the present work can help in the understanding of N-NTD/ligands molecular interactions and the development of new strategies to combat hRSV infections.