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Document Figure 2 Some heuristic rules frequently used in structure-based drug design. The positions of “bound” water molecules are key indicators for lead modification sites. outlined below, both the scaffold modification and structural recombination strategies are key components of an integrated drug discovery technology that combines structure-based design and combinatorial chemistry. III. Combinatorial Chemistry Page 528 Combinatorial chemical technology enables the parallel synthesis of organic compounds through the systematic addition of defined chemical components using highly reliable chemical reactions and robotic instrumentation [8–11]. Large libraries of compounds result from the combination of all possible reactions that can be done at one site with all the possible reactions that can be done at a second, third, or greater number of sites. Combinatorial chemical methods can potentially generate tens to hundreds of millions of new chemical compounds as mixtures, attached to a solid support, or as individual compounds. The first combinatorial libraries with millions of members were oligopeptide and oligonucleotide libraries for which reliable and versatile chemical reactions already existed [10,12,13]. However, these libraries were not generally useful as a source of leads for small-molecule pharmaceuticals due to the relatively high molecular weight of the resulting leads and other limitations of oligonucleotides and oligopeptides as drugs. More recently, “drug-like” libraries have been produced that offer much greater utility as a source of drug leads (Figure 3). However, practical limitations of the versatility and reliability of the chemical reactions used to make these libraries have resulted in somewhat smaller sets of compounds [14–18]. http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_528.html (1 of 2) [4/9/2004 12:48:37 AM]
Document Figure 3 Generation of combinatorial libraries. Traditional combinatorial libraries based on polypeptides or polynucleotides were built up by oligomer condensation and achieved a high level of diversity through conformational flexibility. Small-molecule libraries of drug-like molecules can be built up using a variety of strategies that focus on maximizing chemical diversity while (generally) minimizing conformational flexibility. Page 529 From the drug discovery perspective, large combinatorial libraries have the same utility as conventional pharmaceutical or natural-product compound libraries, i.e., as a source of leads for new drugs. The design of large combinatorial libraries is driven by the requirement that individual reactions be highly reliable and versatile, while producing libraries with the highest possible degree of chemical diversity. Individual steps must be optimized, the compatibility of building blocks must be examined thoroughly and the synthesis must be automated. As a consequence, a significant investment in time and resources must be made before a library can actually be produced. Designed and used in this way, large combinatorial libraries provide a new source of screening leads. However, libraries with maximum diversity, which may be used for “blind” lead discovery, do not address the principle rate-limiting step in drug discovery, the elaboration of a suitable SAR around the lead compound after an active lead has been discovered. http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_529.html (1 of 2) [4/9/2004 12:49:08 AM]
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