Discovery of a new binding site for the possible gain in neomorphic activity in R132H_IDH1

Abstract

In the Krebs cycle, the isocitrate dehydrogenase 1 (IDH1) catalyses the conversion of isocitrate (ICT) to α-ketoglutarate (α-KG), generating Nicotinamide Adenine Dinucleotide Phosphate (NADPH), which helps maintain redox balance, facilitates lipid biosynthesis, and provides protection against oxidative stress. The missense mutation at the R132 in IDH1, where the Arginine (R) is substituted by a Histidine (H), exhibits a neomorphic gain of function, catalyzing the aberrant production of D-2-hydroxyglutarate (D-2-HG), instead of the α-KG. The X-ray crystallographic and kinetic studies indicate that the mutation reshapes the binding and catalytic sites, leading to a shift in enzymatic activity that drives oncogenic metabolism in gliomas. Nevertheless, the in-depth mechanism of the molecular dynamics-based functioning of wild-type IDH1 (WT_IDH1) and the impact of mutation on its conformational dynamics remain unknown to date. Herein, we have performed molecular dynamics (MD) simulation of a gamut of systems, viz., the IDH1-apo form and the ICT, NADPH, and ICT_NADPH-bound complexes, respectively, with the monomer subunit of the mutated (R132H_IDH1) as well as the wild-type IDH1, under atomistic force fields. In this work, we report that the mutation (R132H) enhances the flexibility and induces disorder in various functionally relevant subdomains compared to their wild-type counterparts. Consequently, the disorderliness of regulatory segments and the loss of the hydrogen bonding network within the proximity of the mutant site result in the loss of binding affinity of ICT_NADPH at the active site, thereby altering the normal catalytic activity. Clustering of principal components using unsupervised machine learning (ML) methods uncovers distinct, thermodynamically stable conformations for mutant and wild-type IDH1. These findings support the earlier reported experimental studies. Nevertheless, from the comprehensive analyses of the trajectory of ICT_NADPH-bound R132H_IDH1, we discovered an alternative binding site, which is probably responsible for the gain in neomorphic activity that has not been detected and reported previously. Hence, we strongly believe that the findings may give therapeutic advances in the treatment of glioma.