Thieno[3,2‑<i>b</i>]pyrrole-5-carboxamides as New Reversible Inhibitors of Histone Lysine Demethylase KDM1A/LSD1. Part 2: Structure-Based Drug Design and Structure–Activity Relationship

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-<i>b</i>]­pyrrole-5-carboxamides as novel reversible inhibitors of KDM1A, whose preliminary exploration resulted in compound <b>2</b> with biochemical IC₅₀ = 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 <b>46</b>, <b>49</b>, and <b>50</b> 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, <b>49</b> and <b>50</b> showed a remarkable anticlonogenic cell growth effect on MLL-AF9 human leukemia cells

Thieno[3,2‑<i>b</i>]pyrrole-5-carboxamides as New Reversible Inhibitors of Histone Lysine Demethylase KDM1A/LSD1. Part 1: High-Throughput Screening and Preliminary Exploration

Lysine specific demethylase 1 KDM1A (LSD1) regulates histone methylation and it is increasingly recognized as a potential therapeutic target in oncology. We report on a high-throughput screening campaign performed on KDM1A/CoREST, using a time-resolved fluorescence resonance energy transfer (TR-FRET) technology, to identify reversible inhibitors. The screening led to 115 hits for which we determined biochemical IC₅₀, thus identifying four chemical series. After data analysis, we have prioritized the chemical series of <i>N</i>-phenyl-4<i>H</i>-thieno­[3, 2-<i>b</i>]­pyrrole-5-carboxamide for which we obtained X-ray structures of the most potent hit (compound <b>19</b>, IC₅₀ = 2.9 μM) in complex with the enzyme. Initial expansion of this chemical class, both modifying core structure and decorating benzamide moiety, was directed toward the definition of the moieties responsible for the interaction with the enzyme. Preliminary optimization led to compound <b>90</b>, which inhibited the enzyme with a submicromolar IC₅₀ (0.162 μM), capable of inhibiting the target in cells