Exploring HDAC8 and SARS-CoV-2 Mpro Inhibition for Drug Discovery

Abstract

This study presents innovative strategies for protein-targeted drug discovery, offering new avenues for therapeutic development. Initially, to address the pitfall of low selectivity in current high-throughput HDAC ligand screening platforms, we developed a mass spectrometry-based selection platform screening from a peptide library designed to target the structurally diverse peptide-binding clefts of HDACs. Employing a non-canonical amino acid, ketoK, as an anchor, we synthesized a six-mer peptide library. We validate this method with peptide N(KetoK)FFWE, exhibiting significant inhibitory potential.

Subsequently, we investigate the enhanced Mpro inhibitory efficacy of Zn(NO3)2 when coupled with S-substituted tropolones. Our computational modeling reinforces the proposed inhibition mechanism, revealing an increase in inhibitory efficiency upon Zn2+ coordination and emphasizing the crucial role of ligand spatial arrangement in modulating inhibition effectiveness.

In the final stage, we focus on the identification of potent inhibitors against Mpro, a critical SARS-CoV-2 target. We identified BRD4354, a potent in vitro Mpro inhibitor, showing superior performance despite its relatively small molecular weight. Mass spectrometry analysis and activity assay results underpin our proposed time-dependent, twostep inhibition mechanism.