Data collections are useful to those involved in drug discovery, allowing them to benchmark the results of their own experiments, validate the accuracy of predictive models, or build new models
Bio-Rad Laboratories has released eight new databases that contain measured Adme/Tox properties including bioavailability, blood-brain barrier permeability, carcinogenic potency, toxicity, carcinogenicity of water disinfection by-products, estrogen receptor binding, mutagenicity, and water solubility for a broad range of chemical compounds.
These databases are the result of internal literature research and external collaboration with various scientific groups.
Michelle D'Souza, medicinal chemistry software product manager, remarked, "We are pleased to continually expand our offerings to make the KnowItAll system the most complete environment for in silico Adme/Tox on the market".
These new Adme/Tox data collections are useful to those involved in drug discovery, allowing them to benchmark the results of their own experiments against this data, validate the accuracy of predictive Adme/Tox models, or build new models using this experimental data as a training set for their models.
Bioavailability database - 232 structures.
This database includes experimental measurements for bioavailability as well as a range of the values.
In addition to these values, each database entry contains name, structure, formula, molecular weight, and pKa when available.
Blood-brain barrier permeability database - 87 structures.
This database includes experimental blood-brain barrier permeability values, which measure the partitioning of a compound across the blood-brain barrier and are used to assess whether or not a compound is likely to permeate this barrier.
In addition to these values, each database entry contains name, structure, formula, and molecular weight.
Carcinogenic Potency database - 1389 structures.
The tumour target site incidence and TD50 potencies for 1354 chemical substances tested in rats and mice, 80 chemical substances tested in hamsters, five chemicals tested in dogs, and 27 chemical substances tested in non-human primates are reported.
This database from the EPA summarises the results for experiments on 1370 substances in the Carcinogenic Potency Database (CPDB).
The CPDB, which continues to be expanded, includes detailed results and analyses of more than 5000 chronic, long term carcinogenesis bioassays reported in over 1200 papers in the general literature and more than 400 technical reports of the National Cancer Institute/National Toxicology Program.
EPA Fathead minnow acute toxicity database - 614 structures.
The acute toxicities of chemicals tested in common assay, with mode-of-action assessments and confirmatory measures are reported.
The EPA Fathead minnow acute toxicity database was generated by the US EPA Mid-Continental Ecology Division for the purpose of developing an expert system to predict acute toxicity from chemical structure based on mode of action considerations.
Hence, an important and unusual characteristic of this toxicity database is that the 617 tested industrial organic chemicals were expressly chosen to serve as a useful training set for development of predictive quantitative structure-activity relationships (Qsars).
EPA water disinfection by-products with carcinogenicity estimates - 209 structures.
The carcinogenicity estimates (high, moderate, or low concern) are reported by EPA experts using a mechanism-based analogue SAR approach on a set of water disinfection by-products, mostly small halogenated organics.
This database contains predicted estimates of carcinogenic potential for 209 chemicals detected in finished drinking water samples having undergone water disinfection treatment.
Since little or no health effects data exists for these disinfection by-product chemicals (DBPs), the goal of this database was for EPA scientists to provide informed estimates of carcinogenic potential to be used as one factor in ranking and prioritising future monitoring, testing, and research needs in the drinking water area.
Oestrogen receptor binding database - 232 structures.
These oestrogen receptor relative binding affinities were tested in a common in vitro assay and listed with chemical class-based structure activity features.
This database from the EPA consists of 232 chemicals (131 active and 101 inactive) selected a priori based on structural characteristics and tested in a well-validated and standardised in vitro rat uterine cytosol ER competitive-binding assay.
The database is a structurally diverse set of natural, synthetic, and environmental estrogens covering most known estrogenic classes and spanning a wide range of biological activity.
It represents the largest published ER binding database of same-assay results generated in a single laboratory.
Mutagenicity database-S9 - 334 structures.
This database includes experimental measurements for mutagenicity, an effect that occurs when cellular DNA is altered as a result of its interaction with a chemical entity.
In addition to these values, each database entry contains name, structure, formula, and molecular weight.
Water solubility database - 113 structures.
Water solubility is an important measurement in the absorption profile of potential drug compounds.
This database was built by incorporating structures and water solubility values obtained from John Dearden of Liverpool John Moores University.
It contains 113 diverse organic compounds.
The intrinsic water solubility values are in log(M) and mg/ml units.
In addition to these values, each database entry contains name, structure, formula, and molecular weight These databases are part of Bio-Rad's KnowItAll informatics system.
This system offers a complete suite of tools for the computer-based prediction of a potential drug's Adme/Tox profile, including the one of the largest collections of global predictive models, applications to build and validate models, experimental Adme/Tox data, and integrated tools for chemical structure handling, data management, and reporting.
