Discovery of new promising USP14 inhibitors: computational evaluation of the thumb-palm pocket

Abstract

Ubiquitin-specific protease 14 (USP14) is a member of the deubiquitinating enzymes (DUBs) involved in disrupting the ubiquitin-proteasome regulation system, responsible for the degradation of impaired and misfolded proteins, which is an essential mechanism in eukaryotic cells. The involvement of USP14 in cancer progression and neurodegenerative disorders has been reported. Thereof USP14 is a prime therapeutic target; hence, designing efficacious inhibitors against USP14 is central in curbing these conditions. Herein, we relied on structural bioinformatics methods incorporating molecular docking, molecular mechanics generalized born surface area (MM-GBSA), molecular dynamics simulation (MD simulation), and ADME to identify potential allosteric USP14 inhibitors. A library of over 733 compounds from the PubChem repository with >90% match to the IU1 chemical structure was screened in a multi-step framework to attain prospective drug-like inhibitors. Two potential lead compounds (CID 43013232 and CID 112370349) were shown to record better binding affinity compared to IU1, but with subtle difference to IU1-47, a 10-fold potent compound when compared to IU1. The stability of the lead molecules complexed with USP14 was studied via MD simulation. The molecules were found to be stable within the binding site throughout the 50 ns simulation time. Moreover, the protein-ligand interactions across the simulation run time suggest Phe331, Tyr476, and Gln197 as crucial residues for USP14 inhibition. Furthermore, in-silico pharmacological evaluation revealed the lead compounds as pharmacological sound molecules. Overall, the methods deployed in this study revealed two novel candidates that may show selective inhibitory activity against USP14, which could be exploited to produce potent and harmless USP14 inhibitors.Communicated by Ramaswamy H. Sarma.