Chemogenomics criteria

The aim of EUbOPEN is to assemble a highly annotated chemogenomics library (CGL) of approximately 5000 compounds covering 1000 targets. There are two sets of criteria which are peer reviewed by an external committee:

  1. General criteria applying to all CGL compounds
  2. Protein family specific guidance for selectivity

General criteria applying to all CGL compounds

  • Freedom to operate: available for research use and distribution by partners without IP issues
  • HPLC purity ≥ 95% (AUC), identity confirmed by ESI-MS
  • Up to five different ligand chemotypes per protein target with complementary selectivity profiles, preferably different modes of action/binding sites
  • Set of compounds for one target has appropriate selectivity (with family specific guidance); more stringent selectivity applies for targets with only one/few available ligand chemotypes, less stringent when many (five) chemotypes are available
  • Toxicity data determined by multiplex assay1 at appropriate concentration for later use
  • Activity data in liability panel available at appropriate concentration for later use
  • Compounds are manually rated by medicinal chemistry experts to flag unstable compounds/undesired structures (e.g. polyols, peroxides, quinones; predicted properties), activity in liability panel assays, and cell toxicity

1 E.g. Cell death/lysis after two hours or significant morphological changes after two hours. However, this excludes toxicity from on-target inhibition.

Protein family specific guidance for selectivity

Stringent selectivity applies for targets with only one/few available ligand chemotypes, less stringent when many (five) chemotypes are available.

Kinases

  • In vitro IC50 or Kd ≤ 100 nM or cellular IC50 ≤ 1 µM
  • Selectivity: desirable – screened across >100 kinases with S (>90% inhibition)1 ≤ 0.025 or gini score2 ≥ 0.6, each at 1 µM, and < 10 kinases outside the subfamily with cellular activity < 1 µM profiling within EUbOPEN/from literature

Nuclear Receptors

  • EC50 or IC50 in cellular reporter gene assay ≤ 10 µM
  • No unspecific effect on reporter activity in VP16-control assay at 10 µM
  • selectivity considering agonism and antagonism: up to 5 off-targets (> 5-fold activation, > 2-fold activation for constitutively active receptors) or S ≤ 0.1, each at 10 µM
  • Agonist and antagonist/inverse agonist considered as different “target”- profiling within EUbOPEN/from literature

1 S: (off-targets/untested targets), S=0.025 from an assay panel of 400 targets is equivalent to 10 off-targets with >90% inhibition

2 Gini score, example: JNK-IN-8 with approx. 10 off-targets has gini score of 0.69, ERK1/2 selective inhibitor SCH772984 has 0.66 and “dirty” compound OTSSP167 has 0.24.

GPCRs

  • In vitro IC50 or Ki ≤ 100 nM or cellular EC50 ≤ 0.2 µM (for the majority of chemogenomic compounds, these criteria apply. Exceptions will be presented to and agreed upon with the chemogenomics JMC, on a case by case basis)
  • Selectivity: Closely related isoforms plus up to 3 more off-targets allowed, 30-fold within same target family – profiling within EUbOPEN/from literature

Epigenetic proteins

  • In vitro IC50 or Kd ≤ 0.5 µM and cellular IC50 ≤ 5 µM
  • Selectivity: Closely related isoforms plus up to 3 more off-targets allowed, 30-fold within same target family – profiling within EUbOPEN/from literature

Enzymes (CYP enzymes, PDEs, proteases, etc.)

  • In vitro IC50 or Kd ≤ 0.5 µM or cellular IC50 ≤ 10 µM
  • Compounds for selected families profiled within EUbOPEN/from literature

SLCs, ion channels

  • In vitro IC50 or Kd ≤ 200 nM or cellular IC50 ≤ 10 µM selectivity over sequence-related targets in the same family >30

Other Proteins (Singletons)

  • In vitro IC50 or Kd ≤ 0.5 µM or cellular IC50 ≤ 10 µM