Bioactivity Databases

The current drug discovery paradigm allocates a short period of time (3–12 months) for the process of lead identification. Thus, medicinal chemists have a rather short amount of time to familiarize themselves with prior art i.e., background information related to the biological target and to chemotypes relevant on the intended, or related targets. Gathering such background information is enabled by chemical databases such as Chemical Abstracts via SciFinder, Beilstein and Spresi, by medicinal chemistry related patent databases such as the MDL Drug Data Report, (MDDR), the World Drug Index, (WDI), Current Patents Fast Alert, and by collections of bioactive compounds such as Comprehensive Medicinal Chemistry, and the Physician Desk Reference, (PDR). As pharmaceutical drug discovery relies on chemogenomics, the average end-user has learned to expect database systems with built-in search engines that seamlessly mine chemical and biological data within an information-rich, integrated resource. The integration process itself requires hierarchical classification schemes, such that knowledge related to target-focused chemical libraries and biological target families can be mined simultaneously. Such tools being under development, we address bioactivity databases in general with focus on bioinformatics and cheminformatics resources. Technical details are omitted for clarity. Readers are encouraged to consult the general references, as well as software documentation. The first section, “Databases and Management Systems”, introduces databases in general. The second part, “Bioactivity Databases: Some Design Guidelines” provides guiding principles for designing and maintaining bioactivity databases. The third section “Biological and Bioactivity Information Databases Examples”, provides a brief overview of currently available bioactivity databases.