Structure-based discovery of novel non-competitive IDO1 inhibitors via conformational selection

Abstract

IDO1 has emerged as a compelling target for the development of novel therapies in diseases marked by immunosuppression, such as cancer. In recent years, growing evidence has also highlighted its involvement in non-immune signaling pathways, further enhancing its therapeutic potential. However, traditional drug design strategies focusing solely on targeting the active site of this enzyme exhibit limitations, leading to reduced selectivity and potential off-target effects. Consequently, alternative approaches, such as targeting allosteric pockets, are gaining attention driven by a growing understanding of protein dynamics, conformational flexibility, and their critical roles in regulating protein function. To address these challenges, we conducted an in-depth analysis of all available IDO1 crystal structures, which revealed an inactive conformation of the enzyme. Through this analysis, we identified an allosteric site unique to the inactive state of the protein, offering a novel opportunity to modulate its activity. Based on the population shift concept, we designed a ligand to selectively bind this druggable pocket, thereby stabilizing the inactive conformation of the enzyme. In vitro biological assays demonstrated that treatment with this compound effectively inhibits IDO1 activity, reduces tumor cell proliferation, and promotes dendritic cell maturation, as indicated by increased surface expression of CD86. Experimental validation of our conformationally driven inhibitor highlights the potential of a novel and innovative drug design strategy, introducing a new class of IDO1-targeting compounds. Our findings underscore the importance of understanding protein conformational dynamics and their influence on structure-function relationships as a foundation for the rational development of next-generation allosteric inhibitors.