1. Thieno[3,2-b]pyrrole-5-carboxamides as New Reversible Inhibitors of Histone Lysine Demethylase KDM1A/LSD1. Part 2: Structure-Based Drug Design and Structure-Activity Relationship.
- Author
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Vianello P, Sartori L, Amigoni F, Cappa A, Fagá G, Fattori R, Legnaghi E, Ciossani G, Mattevi A, Meroni G, Moretti L, Cecatiello V, Pasqualato S, Romussi A, Thaler F, Trifiró P, Villa M, Botrugno OA, Dessanti P, Minucci S, Vultaggio S, Zagarrí E, Varasi M, and Mercurio C
- Subjects
- Cell Line, Tumor, Crystallography, X-Ray, Drug Design, Enzyme Inhibitors chemistry, Fluorescence Resonance Energy Transfer, High-Throughput Screening Assays, Histone Demethylases, Humans, Inhibitory Concentration 50, Pyrroles chemistry, Structure-Activity Relationship, Enzyme Inhibitors pharmacology, Lysine chemistry, Pyrroles pharmacology
- Abstract
The balance of methylation levels at histone H3 lysine 4 (H3K4) is regulated by KDM1A (LSD1). KDM1A is overexpressed in several tumor types, thus representing an emerging target for the development of novel cancer therapeutics. We have previously described ( Part 1, DOI 10.1021.acs.jmedchem.6b01018 ) the identification of thieno[3,2-b]pyrrole-5-carboxamides as novel reversible inhibitors of KDM1A, whose preliminary exploration resulted in compound 2 with biochemical IC
50 = 160 nM. We now report the structure-guided optimization of this chemical series based on multiple ligand/KDM1A-CoRest cocrystal structures, which led to several extremely potent inhibitors. In particular, compounds 46, 49, and 50 showed single-digit nanomolar IC50 values for in vitro inhibition of KDM1A, with high selectivity in secondary assays. In THP-1 cells, these compounds transcriptionally affected the expression of genes regulated by KDM1A such as CD14, CD11b, and CD86. Moreover, 49 and 50 showed a remarkable anticlonogenic cell growth effect on MLL-AF9 human leukemia cells.- Published
- 2017
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