The qHTS data in PubChem is preliminary, and for
this reason and because of limited compound quantities, we do not supply probe
compounds to investigators other than those who originally submitted the
assay.
The data presented in PubChem
from the NCGC listed as “qHTS”
represents primary quantitative
high throughput screening data. Each sample is tested as a
titration series to provide a concentration-response output.
While the results accurately
describe the effect of the sample on the
assay endpoint, the “actives” are not
necessarily due to the perturbation of
the intended target (i.e., they may
be artifactual positives). Despite this, these primary data are provided to allow analysis by cheminformatic
algorithms, guide the selection of
compounds for subsequent chemistry
optimization, and to populate the ‘chemical genomics’ database of compound-activity
profiles. The value of this database should
increase as additional assays and compounds are added.
In interpreting and using
qHTS data the investigator should remain
cognizant of the following:
(1) The sample
tested is very limited in quantity,
so neither the NGCG nor the MLSCN repository
can supply screening samples upon request. Some samples
are commercially available and inexpensive, and can be purchased directly
from vendors. Compounds about which
more is known, designated as “probes” by the MLSCN, will be designated as such
in PubChem and arrangements for their broader availability to investigators will
be made by the MLSCN.
(2) The effect of the sample on the assay
described in PubChem may reflect artifacts that result from the
sample’s physical or spectroscopic
properties, such as its interference in the assay due to
aggregation in aqueous buffer,
or absorbance of emitted fluorescence
for signal detection. Flags indicating the propensity for interfering
phenomenon from samples in the library will be added to the data set as it is
determined.
(3) QC information is not necessarily
current. The results are determined from “samples”,
indicated as such, because the term
“compound” implies a single
chemical entity. Subsequent analysis by LC-MS and verification
of the activity will be performed for
a subset of the actives. This data will be entered into PubChem as it is
generated.
(4) The IC50/EC50s (referred to by the NCGC as AC50s)
determined from the
normalized titration-response data (n =1) are estimates. Curve fitting
artifacts can occur due to the high
throughput nature of the analysis. A flag indicating whether a curve fit has
been verified will be updated over time. In addition, the primary data is
available for interpretations by others.
|