AI-ACCELERATED DRUG DISCOVERY
Novel inhibitors of BRD4 and SIRT1
Targeting cancer-related epigenetic factors

Background

BRD4
SITR1
  • Human Silent Mating Type Information Regulation 2 Homolog 1 (SIRT1) deacetylates histones and various other proteins, which are involved in multiple signalling pathways in cells.
  • Human Bromodomain-containing protein 4 (BRD4) a transcription factor that plays an important role in cancer development.
  • BRD4 is member of a family of at least four proteins sharing the same structural motif.

Methodology

  • Enamine stock collection of 3.2M compounds was subject to virtual screening.
  • 1000 top-ranked candidate compounds were selected.
  • 100 compounds were used for experimental validation for both targets.
  • The two-stage virtual screening workflow implemented in the Receptor.AI drug discovery platform was used.
  • In the first stage, the ligand-based and structure-based drug-target interaction AI models were used for initial screening.
  • After that, the most relevant ADMET endpoints were evaluated, and the proteome-wide selectivity profiles were computed for the top compounds.
  • In the stage of secondary screening, molecular docking with AI rescoring, which predicts the activity based on the docking poses, is performed for the molecules shortlisted during the initial screening.

Results

  • SITR1
    • 94 compounds have been tested in DSF against SIRT1.
    • Primary hits were subjected to counter-screening for selectivity against BRD4, CA, and Abl SH2.
    • The acceptable values of quality control indicate the robustness of the screening process.
    • With the selection criteria '|ΔTm SIRT1| > 3*ΔTm RSD DMSO SIRT1', 4 compounds demonstrated a significant binding effect on SIRT1 Tm.
    • 1 compound showed a selective effect on the target protein, following the selection criteria 
'|ΔTmDAbl SH2, CA, BRD4| > 3*TmD RSDDMSO Abl SH2, CA, BRD4'.
  • BRD4
    • 100 best-ranked hit candidates were passed for experimental validation to our partners.
    • 17 of them have shown affinity to BRD4.
    • These compounds are currently subject to in-depth experimental validation.
    • 7 best compounds were picked for further activity evaluation.
    • 3 compounds have shown notable biological activity:
        • RAIBD40009 470 nM,
        • RAIBD40062 730 nM,
        • RAIBD40067 4.8  uM.
    • 100 compounds have been tested in DSF (Differential Scanning Fluorimetry) against BRD4.
    • The acceptable values of quality control indicate the robustness of the performed screen.
    • Following the selection criteria | dTmDBRD4-ligand |** > 3*TmDRSD DMSO BRD4 ***, 17 compounds demonstrate significant binding effect on BRD4.8 of them belong to known classes of BRD4 inhibitors.
    • There are 9 entirely new BRD4 hits, belonging to 8 diverse chemical classes.
  • Discovered SIRT1 inhibitors (RAIST10058)
    • This compound has shown outstanding nanomolar activity (IC50 = 90 nM) measured by a functional assay based on the release of the fluorophore probe from acetylated p53-AFC, which makes it de facto a lead compound.
  • Discovered BRD4 inhibitors (RAIBD40009)
    • This compound, belonging to the previously unknown class of BRD4 inhibitors, has shown the best activity in experiments (470 nM).