Investigation of Hot Spot Region in XIAP Inhibitor Binding Site by Fragment Molecular Orbital Method

Abstract

X-linked inhibitor of apoptosis protein (XIAP) is an important regulator of cancer cell survival whose BIR3 domain (XIAP-BIR3) recognizes the Smac N-terminal tetrapeptide sequence (AVPI), making it an attractive protein-protein interaction (PPI) target for cancer therapies. We used the fragment molecular orbital (FMO) method to study the binding modes and affinities between XIAP-BIR3 and a series of its inhibitors (<b>1</b>-<b>8)</b> that mimic the AVPI binding motif; the inhibitors had common interactions with key residues in a hot spot region of XIAP-BIR3 (P1-P4 subpockets) with increased binding affinity mainly attributed to specific interactions with the P1 and P4 subpockets. Based on the structural information from FMO results, we proposed a novel XIAP natural product inhibitor, neoeriocitrin <b>10</b>, which was derived from our preciously reported XIAP-BIR3 inhibitor <b>9</b>, can be used as a highly potent candidate for XIAP-BIR3 inhibition. We also performed pair interaction energy decomposition analysis to investigate the binding energies between specific binding residues and individual ligands, showing that the novel natural product neoeriocitrin <b>10</b> had a higher binding affinity than epicatechin gallate <b>9</b>. Molecular docking and dynamics simulations were performed to explore the mode of binding between <b>10</b> and XIAP-BIR3, demonstrating that <b>10</b> binds more strongly to the P1 and P4 pockets than <b>9</b>. Overall, we present a novel natural product, neoeriocitrin <b>10</b>, and demonstrate that the FMO method can be used to identify hot spots in PPIs and design new compounds for XIAP inhibition.