Exploring the interaction of inhibitor ‘YM-1’ with Plasmodium falciparum HSP70s through in silico methods

YM-1 belongs to the rhodacyanine class of the 70kDa heat shock protein (Hsp70) inhibitors. It antagonizes nucleotide exchange factor (NEF) ‘BAG3’ to block the critical ATPase cycle of HSP70 chaperones thereby disabling them. The anti-cancer potential of this small molecule derivative of MKT-077 is attributed to its improved solubility and stability over its parent. In the current study, we have used bioinformatics tools including molecular docking to study the binding strength of YM-1 for Plasmodium falciparum (Pf) HSP70s. Of the four PfHSP70 homologs, the mitochondrial counterpart was predicted to bind most efficiently with YM-1 at a previously reported inhibitor binding site. The interaction of YM-1 with mitochondrial PfHSP70 was significantly better than with any of the other Pf homologs. Further analysis of this PfHSP70-YM-1 complex helped us to predict not just the types of interactions, but also specific residues of the protein involved in inhibitor engagement. Information reported in this article is important from the standpoint of design and development of newer rhodacyanine based drugs against malaria.