Table 1
From the following article
Reporting data from high-throughput screening of small-molecule libraries
James Inglese, Caroline E Shamu & R Kiplin Guy
Nature Chemical Biology 3, 438 - 441 (2007)
doi:10.1038/nchembio0807-438
Table 1. Reporting parameters for small-molecule screening data
| Category | Parameters | Examples (see text for more detail) |
|---|---|---|
| Assay | Nature of the assay | Cell-free multicomponent assay, or mammalian cell-based imaging assay |
| Assay strategy | Detection of double-stranded DNA using intercalated fluorescence enhancement of fluorophore, or cellular cytosol-to-nuclear translocation of GFP-tagged nuclear hormone receptor | |
| Reagents and sources | Standard information | |
| Assay protocol | Key steps are outlined in Table 2 | |
| Library screened | Nature of the library | Rule of 5–compliant or stochastic clustering analysis gave 332 fingerprint diversity clusters, normalized to 17.1 clusters per 100 compounds (http://ccc.chem.pitt.edu/upcmld/Library_Diversity_Analysis.html) |
| Size of the library | 50,000 compounds arrayed in 384-well plates as single compounds at 10 mM in DMSO | |
| Source | University of Kansas Chemical Methodology and Library Development Center | |
| Details | An SD-format file of the UPCMLD library containing structure, ID, etc. is available at http://pubchem.ncbi.nlm.nih.gov/ (use PubChem compound UPCMLD) | |
| Quality control | All compounds assured by vendor as >90% pure with provided QC data; verified internally on 5% random sampling | |
| Concentration tested | Constant 10  M concentration, 0.1% DMSO, 1:1,000 dilution | |
| HTS process | Format | 96-well imaging plate (BD BioSciences) |
| Plate controls | Positive control: EC50 agonist (A1-D1); negative control: EC50 agonist + 10 IC50 antagonist (E1-H1); 12A-H: titration of agonist | |
| Plate number and duration | 150 96-well plates over 3 d | |
| Reagent and compound dispensing systems | Reagents and compounds delivered using a VPrep (Velocity11) | |
| Output, detector, analysis software | Fixed endpoint; imaging microscopy using ArrayScanVTi (Cellomics, Inc.); Molecular Translocation BioApplication (Cellomics, Inc.) | |
| Correction factors | B-score analysis and correction | |
| Normalization | % inhibition = 100 (corrected sample result - average of positive control)/(average of negative - average of positive control) | |
| Performance | Z and Z' plotted per plate for 100-plate screen. Interplate EC50 MSR = 2.5 | |
| Post-HTS analysis | Selection of actives | Actives were selected from the primary screen using a threshold based on statistical criteria |
| Retesting of initial actives | Original samples rearrayed and retested using screening assay; compounds with replicated activity tested in dose-response mode | |
| Structure confirmation | Compound structure verified by analytical chemistry methods | |
| Compound purification/resynthesis | Validated actives resynthesized or repurchased and retested | |
| Screen results | List of all screening positives | List of positives ranked by % activity at fixed concentration and defined selection cutoff threshold |
| List of validated compounds | Rank order of compounds, based on score in selection criteria | |
| Comments on active compound selection | Potency, cellular efficacy, pharmacological parameters and toxicity used to rank actives |
