Developing C2-Aroyl Indoles as Novel Inhibitors of IDO1 and Understanding Their Mechanism of Inhibition via Mass Spectroscopy, QM/MM Calculations and Molecular Dynamics Simulation.

Jyoti Chauhan,Kshatresh Dutta Dubey,Srinivas R Maddi,Subhabrata Sen

doi:10.3389/fchem.2021.691319

Abstract

Indoleamine-2,3-dioxygenase (IDO1) and tryptophan dioxygenases are two heme based metalloenzymes that catalyze the tryptophan oxidation reaction by inserting molecular dioxygen to cleave the pyrrole ring. The mechanism of such ring cleavage reaction is of carcinogenic importance as the malignant tumors recruit this mechanism for immune invasion. In the presence study, we have synthesized a Novel C2 aroyl indoles inhibitor, 8d, which shows significant inhibition of 180 nM at IC50 scale. The binding and conformational changes that transpire after inhibitor binding were thoroughly studied by molecular docking and MD simulations. The subsequent QM/MM (Quantum Mechanical/Molecular Mechanical) calculations were used to proposed the mechanism of inhibition. The QM/MM calculations show that the reaction proceeds via multistep processes where the dioxygen insertion to the substrate 8a is the rate determining process. Theoretical mechanism is further supported by mass spectroscopy, and drug metabolism/pharmacokinetics study (DMPK) and metabolic stability of compound 8d was investigated in rat and human liver microsomes.

Highlights

The transformation of L-tryptophan (L-tryp) to kynurenine is an essential chemical reaction which is im-plicated in various biological process and in turn can be exploited as a therapeutic options in cancer, neurodegeneration, aging and immunity (Dunn et al, 2004; Munn and Mellor, 2007; Kershaw et al, 2014; Sas et al, 2018)
In we have investigated the mechanism of inhibition of C2aroyl indoles, a novel class of molecules against IDO1 through UV-Vis spectroscopy, molecular dynamic (MD) simulation and Quantum mechanics/molecular mechanics (QM/MM) calculations
UV absorption spectroscopy demonstrated that under the erobic reaction condition the heme binding ligands like 8a, d and e stabilizes the ferric IDO1 more than the deoxy ferrous IDO1. Based on this and from the literature reports of L-tryptophan degradation by IDO a probable reaction mechanism was proposed that involved epoxidation of 8d by IDO1 in presence of single oxygen, leading to either an ultimate ring opening of the indole moiety to provide the o-aminoacetophenone derivative D9 or intramolecular cyclization of the exocyclic amine to afford the hexahydropyrrolo [2, 3-b]indole E

Summary

Introduction

The transformation of L-tryptophan (L-tryp) to kynurenine is an essential chemical reaction which is im-plicated in various biological process and in turn can be exploited as a therapeutic options in cancer, neurodegeneration, aging and immunity (Dunn et al, 2004; Munn and Mellor, 2007; Kershaw et al, 2014; Sas et al, 2018). Despite exhibiting potential as a therapeutic target in myriad diseases, IDO1 is mainly implicated in cancer (Okamoto et al, 2005; Zou, 2005; Sugimoto et al, 2006; Mazarei and Leavitt, 2015; Song et al, 2018). Various bioactive small molecules belonging to different classes of heterocycles have been reported as IDO1 inhibitors (Dolusicand Frédérick, 2013; Muller et al, 2005). Among these plethora of reported IDO1 inhibitors only few have hitherto entered clinical trials.

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Results

Conclusion