Using Pharmabase to Perform Pharmacological Analyses of Cell Function

Abstract

In this post-genomic period of biological research, the emphasis in cell biology is returning to an understanding of cell function and dynamics, particularly with regard to protein composition and function. New technologies abound, offering methods to examine protein-dependent processes in living systems, frequently in real time. Experimentally, one popular tool for defining and manipulating such activities is the use of pharmacological compounds to alter the performance of proteins within the living cell. However, using these compounds can be a daunting process, particularly to the uninitiated. Locating the correct compound, understanding its target specificity, and even knowing how to handle and prepare it for use, are frequently in the domain of the specialist. Pharmabase sets out to overcome these barriers by providing simple protocols, guiding the user through a series of choices, to a database of compound records addressing the points above.Pharmabase is a database containing detailed information on the physicochemical properties of ∼1000 pharmacologically active small molecules and compounds. The compound data are linked to the target molecules, frequently proteins, organized to display their function within a cell. For example, the database is organized so that the user can navigate to known interactions between these small molecules and their receptors within the biological system of membrane transport. This unit describes how to search and access the information in Pharmabase. The different search routes presented are based broadly on subject and/or graphic navigation. Getting started with Pharmabase and performing simple searches via subject or compound is described in Basic Protocol 1. The main way to search Pharmabase is via Membrane Transport (Basic Protocol 2). This subject navigator allows the investigator to access compounds targeting membrane transporters of ions and molecules. Transporters, in the context of this database, encompass channels, pumps, and porters (symporters, uniporters, and antiporters). (Further material on the diversity of these mechanisms and links to gene sites can be found at http://www.tcdb.org and the role of these molecules in disease can be accessed through http://www.channelopathies.org.; also see Rose and Griggs, 2001.) Four other subject-based navigators, derived by subset organization, are described in Basic Protocol 3. These are: Metabolism, Intracellular Messengers, Cell Signaling, and Cell Area. The compound database is sorted according to these subsets and their constitutive components. These secondary navigation routes are in place to provide a cross-referencing structure to other indexing methods and all share the purpose of reducing the database to a smaller subset of compounds and targets, tailored to the user's interest. (These navigators will be further expanded and and additional search routines based around Diseases and Tissues, as well as Action Terms, e.g., "ionophore" or "reporter" are under construction). Basic Protocol 4 describes the most recent ...

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“…Chemical genetics is the use of small molecules to modulate protein function (Yeh and Crews, 2003;den Hertog, 2005). With the ever-increasing number of available compounds with known specificity (Smith and Remsen, 2006), loss-of-function analysis by drug inhibitor screening has become an excellent tool for the rapid and inexpensive identification of genes and gene families that participate in specific biological events. A powerful strategy first uses compounds with broad targeting, and then proceeds to more specific reagents when positive results are obtained in the chosen assay from a compound targeting a particular protein set.…”