A pyrazolo[1,5-a]pyrimidine scaffold small molecule DMH1 is an effective inhibitor of bone morphogenetic protein (BMP) type I receptor family kinase domains. It displays less potency to inhibit closely homologous TGF-β receptor kinases such as ALK5, and VEGF receptor type II kinase. In an effort to identify more potent lead compounds, we carried out a crystal structure-based DMH1 binding investigation across BMP, TGF-β and VEGF receptors by implementing <i>in situ</i> docking and free energy perturbation molecular dynamics simulations with explicit solvent.<br/><br/>We setup our absolute free energy calculations by treating different protein conformations from PBD x-ray database and distinct ligand orientation from docking as separated topologies. The calculated binding affinities are consistent with experimental data, which enable detailed analysis of the binding specificity. Our analysis revealed that the binding selectivity of DMH1 between ALK2 and ALK5 is tied to the ability of DMH1 to stabilize LYS on the β3 subunit, as well as the TYR on the P-loop in wilde type ALK2. The direct hydrogen bond between DMH1 and LYS235 in ALK2 distorts the salt bridge network in the activation loop. Our results also predict that DMH1 has no off-target effect on both VEGFR2 DFG-in and DFG-out conformation. In conclusion, ALK2 provides the most favorable binding environment for DMH1 among all the kinases examined. We observed critical residues at multiple locations of kinases that will guide us in designing new inhibitors.

Computational analysis of the binding specificity of DMH1 to Alk2, Alk5, and VEGFR2 kinases

249th National Meeting (2015)

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