Combinatorial libraries structure-based design

TABLE 15.1 Specialized Computational Technologies for Target Structure-Based Design of Combinatorial Libraries... 

Tondi D, Costi MR Enhancing the drug discovery process by integration of structure-based design and combinatorial synthesis. In Viswanadhan AK, Chose VN, editors. Combinatorial library design and evaluation. New York Marcel Dekker, 2001. p. 563-604. 

The integration of combinatorial chemistry, structure-based library design and virtual screening [268, 269] also resulted in successful applications [270, 271]. It ultimately should result in broader SAR information about directionality and physicochemical requirements of acceptable building blocks. This concept is based on feasible scaffolds for exploring protein subsites using parallel or combinatorial synthesis. 

Eksterowicz, J. E., Evensen, E., Lemmen, C., et al. (2002) Coupling structure-based design with combinatorial chemistry application of active site derived pharmacophores with informative library design. J. Mol. Graph. Model. 20, 469-477. 

When used for relative similarity and diversity, only potential pharmacophores that contain the defined special centre-type are used. The frame of reference for similarity/diversity studies is thus changed to one that is focused on the feature of interest distances are now measured relative to this special centre. For example, the special centre could be the centroid of a substructure [10] such as biphenyl tetrazole or diphenylmethane, enabling the calculation and comparison of all 3D pharmacophoric shapes that contain this substructure the substructure is said to be privileged . For structure-based design, the potential pharmacophores in a site can be restricted to those that contain a specific site point (e.g. in a pocket, or at the entrance to a pocket). In the context of combinatorial library design, the relative measure can be those pharmacophoric shapes that contain a special site-point that represents where the attachment point for a reagent would be. In figure 1, the special point would be centre-type number 3, which can be reserved for this purpose. 

When structure-based strategies are used to help choose reactants for a combinatorial library, the strengths of both approaches complement each other. Although the structure-based design is not accurate, it statistically enhances and focuses the combinatorial library. Billions of possible library compounds can be generated on the computer in a virtual library and evaluated. From this, a smaller set of the order of thousands can be chosen... 

Sun, Y., Ewing, T.J.A., Skillman, A.G. and Kuntz, I.D. Combinatorial DOCK Structure-based Combinatorial Docking and Library Design, J. Comput.-AidedMol. Des., 1998, in press. 

Profile This privately held company was founded in 1993 to integrate advanced technologies in structure-based design, combinatorial chemistry, and chemi-informatics for the cost-effective discovery of orally active pharmaceuticals. The company has developed a system capable of generating new drugs through computer-controlled robotic synthesis and analysis of chemical libraries. Current drug discovery efforts are focused on cardiovascular disease and cancer. 

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