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The majority of clinical drugs achieve their effect by binding to a cavity and regulating the cavity, of its protein targets [1]. In general, drugs act on four main types of regulatory proteins that mediate the actions of hormones, neurotransmitters, and autacoids. These four types of regulatory proteins are carriers, proteins, ion channels, and receptors [2]. Certain characteristics are expected for therapeutic targets [3].

A potential target needs only not to be druggable but also linked to disease, most preferably playing critical and inimitable roles in disease state. Binding sites are to have certain structural and physiochemical properties to accommodate high-affinity site-specific binding and subsequent regulation of protein activity by drugs. They are not significantly involved in other important biological processes to avoid potential side effects. Useful information about these targets may be investigated by analysing their sequence properties, protein families, structural folds, biochemical classes, similarity proteins, gene location in the human genome, and associated pathways [4]. This information can be potentially useful in derivation of rule and developing predictive tools in the search for druggable and potential targets [4].

The number of molecular targets acted on by current drug therapy is still in dispute. In 1996, Drews and Ryser identified a total of 483 drug targets addressed by drug therapy [5, 6]. Approximately 45% are cell membrane receptors, 28% are enzymes, and the remaining classes comprise hormones (11%), ion channels (5%), nuclear receptors (2%), and DNA (2%). About 7% of the targets are not known biochemically. Later, Hopkins and Groom challenged this figure and suggested that ��rule-of-five�� compliant drugs acted primarily through only 120 underlying molecular targets [3, 7]. However, the statistical analysis of disease genes and related proteins suggested that the total number of the estimated potential targets in the human genome ranges from 600 to 1,500 [3].

In the meantime, another Cilengitide report showed the estimated total number of distinct targets is in the range of 1,700�C3,000 [8]. Chen et al. reported targets collected in the Therapeutic Target Database [9] is 997 distinct proteins, 1,494 distinct protein subtypes, and 41 nucleic acids, which are only targeted by at least one marketed drug and 1,267 research targets, which are only targeted by investigational agents that are not approved for clinical use at present [4].