1. Structure-based mapping of the histone-binding pocket of KDM4D using functionalized tetrazole and pyridine core compounds.
- Author
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Małecki PH, Fassauer GM, Rüger N, Schulig L, Link A, Krylova O, Heinemann U, and Weiss MS
- Subjects
- Humans, Binding Sites, Crystallography, X-Ray, Structure-Activity Relationship, Molecular Structure, Enzyme Inhibitors chemistry, Enzyme Inhibitors pharmacology, Enzyme Inhibitors chemical synthesis, Models, Molecular, Dose-Response Relationship, Drug, Jumonji Domain-Containing Histone Demethylases metabolism, Jumonji Domain-Containing Histone Demethylases antagonists & inhibitors, Jumonji Domain-Containing Histone Demethylases chemistry, Tetrazoles chemistry, Tetrazoles pharmacology, Tetrazoles metabolism, Tetrazoles chemical synthesis, Pyridines chemistry, Pyridines pharmacology, Pyridines metabolism, Pyridines chemical synthesis, Histones metabolism, Histones chemistry
- Abstract
KDM4 histone demethylases became an exciting target for inhibitor development as the evidence linking them directly to tumorigenesis mounts. In this study, we set out to better understand the binding cavity using an X-ray crystallographic approach to provide a detailed landscape of possible interactions within the under-investigated region of KDM4. Our design strategy was based on utilizing known KDM binding motifs, such as nicotinic acid and tetrazolylhydrazides, as core motifs that we decided to enrich with flexible tails to map the distal histone binding site. The resulting X-ray structures of the novel compounds bound to KDM4D, a representative of the KDM4 family, revealed the interaction pattern with distal residues in the histone-binding site. The most prominent protein rearrangement detected upon ligand binding is the loop movement that blocks the accessibility to the histone binding site. Apart from providing new sites that potential inhibitors can target, the novel compounds may prove helpful in exploring the capacity of ligands to bind in sites distal to the cofactor-binding site of other KDMs or 2-oxoglutarate (2OG)-dependent oxygenases. The case study proves that combining a strong small binding motif with flexible tails to probe the binding pocket will facilitate lead discovery in classical drug-discovery campaigns, given the ease of accessing X-ray quality crystals., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Masson SAS.. All rights reserved.)
- Published
- 2024
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