All-Atom Perspective of the DENV-3 Methyltransferase Inhibition Mechanism

The Dengue virus (DENV) is an enveloped, single-stranded RNA virus with several antigenically distinct serotypes (DENV-1 to DENV-5). Dengue fever, as a major public health threat transmitted by mosquitoes, affects millions of people worldwide (especially in tropical and subtropical regions). Toward drug developments of DENV, the nonstructural protein 5 methyltransferase (MTase) serves as an attractive target. The MTase transforms S-adenosyl methionine to S-adenosyl homocysteine (SAH), which is thereby selected as the target with which external drugs compete with. In this work, using alanine scanning with generalized Born and interaction entropy (ASGB-IE), we provide an all-atom perspective of the protein–ligand interactions formed by DENV-3 MTase and SAH derivatives. Residues with consistently high contributions to stabilization are summarized, and the general DENV-3 MTase inhibition mechanism is elucidated. Additionally, the mutational impact on binding thermodynamics is found to be entropy-driven. We also highlight the advantage of the ASGB-IE method for affinity estimation compared to standard end-point protocols, which is highly related to the selection of interfacial residues in free energy estimation. Finally, we performed a thorough scan of the mutational space on critical sites (saturation mutagenesis) and identified 14 mutants causing resistance to the current inhibitors.