5LGN

Thieno[3,2-b]pyrrole-5-carboxamides as Novel Reversible Inhibitors of Histone Lysine Demethylase KDM1A/LSD1: Compound 19


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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.

Sartori, L.Mercurio, C.Amigoni, F.Cappa, A.Faga, G.Fattori, R.Legnaghi, E.Ciossani, G.Mattevi, A.Meroni, G.Moretti, L.Cecatiello, V.Pasqualato, S.Romussi, A.Thaler, F.Trifiro, P.Villa, M.Vultaggio, S.Botrugno, O.A.Dessanti, P.Minucci, S.Zagarri, E.Carettoni, D.Iuzzolino, L.Varasi, M.Vianello, P.

(2017) J. Med. Chem. 60: 1673-1692

  • DOI: 10.1021/acs.jmedchem.6b01018

  • PubMed 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-resolv ...

    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 IC 50 , 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, IC 50 = 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 IC 50 (0.162 μM), capable of inhibiting the target in cells.


    Organizational Affiliation

    Genextra Group, DAC s.r.l. , Via Adamello 16, 20139 Milano, Italy.,IFOM- The FIRC Institute of Molecular Oncology Foundation , Via Adamello 16, 20139 Milano, Italy.,Department of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology , Via Adamello 16, 20139 Milano, Italy.,Department of Biology and Biotechnology, University of Pavia , Via Ferrata 1, 27100 Pavia, Italy.,Axxam , via A. Meucci 3, 20091 Bresso, Milano, Italy.,Crystallography Unit, Department of Experimental Oncology, European Institute of Oncology , Via Adamello 16, 20139 Milano, Italy.,Department of Biosciences, University of Milan , Via Celoria, 26, 20133 Milano, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific histone demethylase 1A
A
670Homo sapiensMutation(s): 0 
Gene Names: KDM1A (AOF2, KDM1, KIAA0601, LSD1)
EC: 1.-.-.-
Find proteins for O60341 (Homo sapiens)
Go to Gene View: KDM1A
Go to UniProtKB:  O60341
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
REST corepressor 1
B
133Homo sapiensMutation(s): 0 
Gene Names: RCOR1 (KIAA0071, RCOR)
Find proteins for Q9UKL0 (Homo sapiens)
Go to Gene View: RCOR1
Go to UniProtKB:  Q9UKL0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
6W0
Query on 6W0

Download SDF File 
Download CCD File 
A
~{N}-[3-(methoxymethyl)phenyl]-4-methyl-thieno[3,2-b]pyrrole-5-carboxamide
C16 H16 N2 O2 S
ZQZRVLFBPXQREF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.193 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 120.510α = 90.00
b = 180.440β = 90.00
c = 235.420γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
REFMACphasing
REFMACrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
AIRCItalyIG15208

Revision History 

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 1.1: 2017-03-22
    Type: Database references