Targeting the dengue virus NS5-Methyltransferase SAM binding site with limonoids: Molecular docking, dynamics...

Dengue virus (DENV) infects over 100 million people annually, yet no approved antiviral therapies are available. The DENV genome is a positive-sense single-stranded RNA (+) ssRNA) encoding ten proteins: three structural (capsid, membrane, and envelope) and seven non-structural (NS1-NS5). Among these, the NS5 methyltransferase (NS5-MTase) is essential for viral replication and is a promising drug target due to the absence of approved inhibitors. NS5-MTase has two binding sites: one for S-adenosyl-L-methionine (SAM) and another for RNA. The RNA-binding site is shallow and solvent-exposed, making the SAM-binding site a more suitable target for small-molecule inhibitors. Phytocompounds, particularly limonoids-a class of tetraterpenoids with known pharmacological activities are promising candidates in antiviral drug discovery. In this study, 500 limonoids were screened through molecular docking against the SAM-binding site of DENV NS5-MTase. This is the first large-scale in silico virtual screening of limonoids targeting this site. Three top compounds were identified: 7-deacetyl-21-hydroxyneotrichilenonelide (DHC), demethyl-3-detigloyl-iso-swietenine (DDIS), and demethyl-iso-swietenolide (DIS). The docking scores of the three compounds were -9.4, -9.5, and -9.9 kcal/mol, respectively. These three compounds were further evaluated using molecular dynamics (MD) simulations to assess the stability and interaction profiles of the protein-ligand complexes. DIS exhibited the most stable binding conformation (forming 3-4 H-bond/ns and maintaining a RMSD below 0.15 nm) and a more favorable interaction profile compared to the other compounds during MD simulations. Additionally, binding free energy (MM-PBSA), in silico ADMET analysis, and DFT calculations, also indicate that DIS is the most promising candidate against DENV.