Cosolvent MD on DPP4, DPP8 and DPP9
In this recent Journal of Chemical Information and Modeling paper by Olivier Beyens, our efforts in computational drug design against dipeptidyl peptidase 4 (DPP4), DPP8 and DPP9 are presented. Cosolvent molecular dynamics (MD) simulations have been applied to these three protein targets. The cosolvent molecular dynamics simulations reproduce key ligand binding features and known binding pockets, while also highlighting interesting fragment positions for future ligand optimization. The resulting fragment maps from the cosolvent molecular dynamics are freely available for use in future research (). Detailed instructions for easy visualization of the fragment maps are provided, ensuring that the results are usable by both computational and medicinal chemists. Additionally, we used the fragment maps to search for the binding pockets with significant potential using an algorithmic approach combining top fragment locations. To discover novel binding scaffolds, a limited pharmacophore screening was performed, where the pharmacophores were based on the analyses of the cosolvent simulations.