title: Thieno[3,2-b]pyrrole-5-carboxamides as New Reversible Inhibitors of Histone Lysine Demethylase KDM1A/LSD1. Part 1: High-Throughput Screening and Preliminary Exploration.
abstract: 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 N-phenyl-4H-thieno[3, 2-b]pyrrole-5-carboxamide for which we obtained X-ray structures of the most potent hit (compound 19, 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 90, which inhibited the enzyme with a submicromolar IC50(0.162 μM), capable of inhibiting the target in cells.
authors.affiliation: Department of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology , Via Adamello 16, 20139 Milano, Italy.
authors.forename: Luca
authors.initials: L
authors.lastname: Sartori
authors.affiliation: Department of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology , Via Adamello 16, 20139 Milano, Italy.|Genextra Group, DAC s.r.l. , Via Adamello 16, 20139 Milano, Italy.
authors.forename: Ciro
authors.initials: C
authors.lastname: Mercurio
authors.affiliation: Department of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology , Via Adamello 16, 20139 Milano, Italy.
authors.forename: Federica
authors.initials: F
authors.lastname: Amigoni
authors.affiliation: Department of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology , Via Adamello 16, 20139 Milano, Italy.
authors.forename: Anna
authors.initials: A
authors.lastname: Cappa
authors.affiliation: Department of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology , Via Adamello 16, 20139 Milano, Italy.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Fagá
authors.affiliation: Department of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology , Via Adamello 16, 20139 Milano, Italy.
authors.forename: Raimondo
authors.initials: R
authors.lastname: Fattori
authors.affiliation: Department of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology , Via Adamello 16, 20139 Milano, Italy.
authors.forename: Elena
authors.initials: E
authors.lastname: Legnaghi
authors.affiliation: Department of Biology and Biotechnology, University of Pavia , Via Ferrata 1, 27100 Pavia, Italy.
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Ciossani
authors.affiliation: Department of Biology and Biotechnology, University of Pavia , Via Ferrata 1, 27100 Pavia, Italy.
authors.forename: Andrea
authors.identifier: 0000-0002-9523-7128
authors.initials: A
authors.lastname: Mattevi
authors.affiliation: Department of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology , Via Adamello 16, 20139 Milano, Italy.
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Meroni
authors.affiliation: Department of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology , Via Adamello 16, 20139 Milano, Italy.
authors.forename: Loris
authors.identifier: 0000-0002-9851-2965
authors.initials: L
authors.lastname: Moretti
authors.affiliation: Crystallography Unit, Department of Experimental Oncology, European Institute of Oncology , Via Adamello 16, 20139 Milano, Italy.|IFOM- The FIRC Institute of Molecular Oncology Foundation , Via Adamello 16, 20139 Milano, Italy.
authors.forename: Valentina
authors.initials: V
authors.lastname: Cecatiello
authors.affiliation: Crystallography Unit, Department of Experimental Oncology, European Institute of Oncology , Via Adamello 16, 20139 Milano, Italy.
authors.forename: Sebastiano
authors.initials: S
authors.lastname: Pasqualato
authors.affiliation: Department of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology , Via Adamello 16, 20139 Milano, Italy.
authors.forename: Alessia
authors.initials: A
authors.lastname: Romussi
authors.affiliation: Department of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology , Via Adamello 16, 20139 Milano, Italy.
authors.forename: Florian
authors.initials: F
authors.lastname: Thaler
authors.affiliation: Department of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology , Via Adamello 16, 20139 Milano, Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Trifiró
authors.affiliation: Department of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology , Via Adamello 16, 20139 Milano, Italy.
authors.forename: Manuela
authors.initials: M
authors.lastname: Villa
authors.affiliation: Department of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology , Via Adamello 16, 20139 Milano, Italy.
authors.forename: Stefania
authors.initials: S
authors.lastname: Vultaggio
authors.affiliation: Department of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology , Via Adamello 16, 20139 Milano, Italy.
authors.forename: Oronza A
authors.initials: OA
authors.lastname: Botrugno
authors.affiliation: Department of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology , Via Adamello 16, 20139 Milano, Italy.
authors.forename: Paola
authors.initials: P
authors.lastname: Dessanti
authors.affiliation: Department of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology , Via Adamello 16, 20139 Milano, Italy.|Department of Biosciences, University of Milan , Via Celoria, 26, 20133 Milano, Italy.
authors.forename: Saverio
authors.initials: S
authors.lastname: Minucci
authors.affiliation: Department of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology , Via Adamello 16, 20139 Milano, Italy.
authors.forename: Elisa
authors.initials: E
authors.lastname: Zagarrí
authors.affiliation: Axxam , via A. Meucci 3, 20091 Bresso, Milano, Italy.
authors.forename: Daniele
authors.initials: D
authors.lastname: Carettoni
authors.affiliation: Axxam , via A. Meucci 3, 20091 Bresso, Milano, Italy.
authors.forename: Lucia
authors.initials: L
authors.lastname: Iuzzolino
authors.affiliation: Department of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology , Via Adamello 16, 20139 Milano, Italy.
authors.forename: Mario
authors.initials: M
authors.lastname: Varasi
authors.affiliation: Department of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology , Via Adamello 16, 20139 Milano, Italy.
authors.forename: Paola
authors.identifier: 0000-0001-9100-2711
authors.initials: P
authors.lastname: Vianello
mesh_terms: D045744:Cell Line, Tumor; D018360:Crystallography, X-Ray; D015195:Drug Design; D004791:Enzyme Inhibitors / Q000494:pharmacology*; D057166:High-Throughput Screening Assays; D056466:Histone Demethylases / Q000037:antagonists & inhibitors*; D006801:Humans; D066244:Proton Magnetic Resonance Spectroscopy; D011758:Pyrroles / Q000737:chemistry / Q000494:pharmacology*; D021241:Spectrometry, Mass, Electrospray Ionization; D013329:Structure-Activity Relationship
chemical_list: D004791:Enzyme Inhibitors; D011758:Pyrroles; D056466:Histone Demethylases; C495195:KDM1A protein, human