Research ArticleBIOCHEMISTRY

Polymyxins and quinazolines are LSD1/KDM1A inhibitors with unusual structural features

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Science Advances  09 Sep 2016:
Vol. 2, no. 9, e1601017
DOI: 10.1126/sciadv.1601017
  • Fig. 1 Polymyxins and quinazolines bind LSD1-CoREST.

    (A) Chemical structures of polymyxin B and polymyxin E (colistin). Highlighted in blue are the positively charged propanamine units. Both antibiotics bind LSD1-CoREST with high affinity, as observed by inhibition and binding assays. (B) Chemical structures of quinazoline-derived compounds binding to LSD1. The atom numbering of the quinazoline core ring is shown for compound E11 as a reference for the compound series. Fluorescence polarization (FP) signal was measured in millipolarization units (mP) and plotted against inhibitor concentration. n.d., not determined.

  • Fig. 2 Polymyxins B and E bind LSD1 in a similar conformation in the active site.

    (A and B) When bound, the antibiotics do not establish interactions with FAD (yellow sticks). Polymyxin B is depicted in blue sticks and polymyxin E is depicted in orange sticks. 2FoFc electron density maps (1.2σ level) are calculated before the inclusion of the ligand in the refinement. (C) LSD1-bound polymyxins establish interactions with a patch of negatively charged residues (highlighted in red on the protein surface).

  • Fig. 3 Noncovalent quinazoline-derived compound E11 obstructs the LSD1 active site in a unique multiple stacking assembly.

    (A) A stack of five inhibitor molecules (green sticks) binding the active site of LSD1-CoREST (white and wheat cartoon, respectively) at >5 Å from FAD (yellow sticks). (B) Side view of the LSD1-CoREST complex with E11 showing the inhibitors at the entrance of the binding site. 2FoFc electron density maps (1.2σ level) are calculated before the inclusion of the ligand in the refinement. I to V indicate each stacking inhibitor, with I being the most proximal to FAD, and V the most distal. (C) Simplified views of inhibitor molecules stacking in alternate flipped orientations at an intermolecular distance of 3.8 to 4.0 Å (side view). Red bars on the right indicate the position of the methoxy groups in each ligand. (D) Surface highlight (red) of negatively charged residues of LSD1 that represent the primary binding region for compound E11.

Supplementary Materials

  • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/2/9/e1601017/DC1

    Supplementary Materials and Methods

    fig. S1. Cellular characterization of LSD1 reversible inhibitors.

    fig. S2. Comparison of polymyxin B and polymyxin E conformations from multiple data sets.

    fig. S3. Characterization of the binding of E11 to LSD1-CoREST in solution by isothermal titration calorimetry.

    fig. S4. Noncovalent quinazoline-derived compound MC3767 binds the LSD1 active site in a multiple stacking assembly as E11.

    fig. S5. Workflow of the PDB search for multicopy stacking small-molecule inhibitors.

    fig. S6. Comparison of histone methyltransferase G9a-like protein (GLP) and histone demethylase LSD1 in complex with compound E11.

    fig. S7. LSD1 druggable space is expanded by the binding of noncovalent compounds.

    table S1. Diffraction, data collection, and refinement statistics.

    table S2. Diffraction, data collection, and refinement statistics for all data sets of polymyxins B and E.

    table S3. List of protein inhibitor structures displaying multiple stacking conformation identified from PDB search.

    table S4. List of published LSD1 PDB structures in complex with ligands.

    References (3755)

  • Supplementary Materials

    This PDF file includes:

    • Supplementary Materials and Methods
    • fig. S1. Cellular characterization of LSD1 reversible inhibitors.
    • fig. S2. Comparison of polymyxin B and polymyxin E conformations from multiple data sets.
    • fig. S3. Characterization of the binding of E11 to LSD1-CoREST in solution by isothermal titration calorimetry.
    • fig. S4. Noncovalent quinazoline-derived compound MC3767 binds the LSD1 active site in a multiple stacking assembly as E11.
    • fig. S5. Workflow of the PDB search for multicopy stacking small-molecule inhibitors.
    • fig. S6. Comparison of histone methyltransferase G9a-like protein (GLP) and histone demethylase LSD1 in complex with compound E11.
    • fig. S7. LSD1 druggable space is expanded by the binding of noncovalent compounds.
    • table S1. Diffraction, data collection, and refinement statistics.
    • table S2. Diffraction, data collection, and refinement statistics for all data sets of polymyxins B and E.
    • table S3. List of protein inhibitor structures displaying multiple stacking conformation identified from PDB search.
    • table S4. List of published LSD1 PDB structures in complex with ligands.
    • References (3755)

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