Discovery of a New-Generation S-Adenosylmethionine-Noncompetitive Covalent Inhibitor Targeting the Lysine Methyltransferase Enhancer of Zeste Homologue 2

Abstract

The first-generation enhancer of zeste homologue 2 (EZH2) inhibitors suffer from several limitations, such as high dosage, cofactor S-adenosylmethionine (SAM) competition, and acquired drug resistance. Development of covalent EZH2 inhibitors that are noncompetitive with cofactor SAM offers an opportunity to overcome these disadvantages. The structure-based design of compound 16 (BBDDL2059) as a highly potent and selective covalent inhibitor of EZH2 is presented in this context. 16 inhibits EZH2 enzymatic activity at sub-nanomolar concentrations and achieves low nanomolar potencies in cell growth inhibition. The kinetic assay revealed that 16 is noncompetitive with the cofactor SAM, providing the basis for its superior activity over noncovalent and positive controls by reducing competition with cofactor SAM and offering a preliminary proof for its covalent inhibition nature. Mass spectrometric analysis and washout experiments firmly establish its covalent inhibition mechanism. This study demonstrates that covalent inhibition of EZH2 can offer a new opportunity for the development of promising new-generation drug candidates.

Discovery of a Highly Potent Lysine Methyltransferases G9a/NSD2 Dual Inhibitor to Treat Solid Tumors

“…The selectivity profiles of compound 16 were evaluated according to our previously reported protocols. , …”

Discovery of the First-in-Class RORγ Covalent Inhibitors for Treatment of Castration-Resistant Prostate Cancer

“…Compared to reversible noncovalent inhibitors, covalent inhibitors provide various potential advantages, including improved pharmacological potency and selectivity, prolonged duration of action, and reduced propensity for acquiring resistance. − Interestingly, Cys320 is identified in the binding site of reported RORγ reversible inhibitors as evidenced by the co-crystal structures of RORγ in complex with compounds 3 , 5 , and 6 (Figure ), which is suitable for the design of RORγ covalent inhibitors. In this regard, we performed a structure-based drug design approach to facilitate the development of the first-in-class RORγ covalent inhibitors.…”

Landscape of In Silico Tools for Modeling Covalent Modification of Proteins: A Review on Computational Covalent Drug Discovery

“…Allosteric covalent inhibitors bind to a site different from the active site of the enzyme to bring a substantial structural changes on the active site accounting for either partial or full inhibition. , One of the examples is the discovery of a first-in-class covalent allosteric inhibitor of a SUMO (small ubiquitin-like modifier) E1 activating enzyme that has shown promise in preclinical models of colorectal cancer . Another research project on the discovery of S -adenosylmethionine noncompetitive covalent inhibitors targeting lysine methyltransferase enhancer of EZH2 (zeste homologue 2) is a prime example of how covalent modifiers can successfully be used as noncompetitive inhibitors …”