Over the past decade one can observe a scientific revolution taking place resulting in an explosion of new biotechnologies. Moreover, with the end of the human genome project and following expansion of the extensive genetic research an unprecedented number of new biological targets useful in drug design have been identified. Simultaneously, new methods such as combinatorial synthesis have expanded the overall size of chemical libraries and high-throughtput technologies have enabled to screen more than one million compounds a day [43]. However, an increasing size of chemical libraries in a random fashion may not necessary increase a probability of success and the overall number of successfully identified leads. Thus, success of any drug discovery program depend heavily on the assumed selection criteria of appropriate molecules [58] which properties should maximize the chances of identifying ligands for any given target. Selection criteria used for compounds to generate diverse as well as focused chemical libraries are briefly discussed in the present overview. We describe the most important quality factors such as size, diversity and chemical tractability which should be always kept in mind during the design of chemical libraries. Chemical space is enormous and limited only by a chemist`s imagination. The number of possible drug-like molecules within chemical space has been estimated to be around 1060 [17]. In contrast the overall number of atoms in the observable Universe is approximately 1080. It is obvious that it is impossible to synthesize every possible molecule so one need to explore only those regions of chemical space which are enriched with molecules of appropriate structure and function. Recent strategies for the design of high-quality collections of structurally diverse sets of small molecules are discussed in the context of probing the chemical space in order to find new biologically active structures.
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