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Document 21 Structure-Based Combinatorial Ligand Design Amedeo Caflisch University of Zürich, Zürich, Switzerland Claus Ehrhardt Novartis Pharma Inc., *Basel, Switzerland I. Introduction Page 541 Structure-based ligand design is fascinating and challenging. Whenever it is possible to determine the three-dimensional structure of a pharmacologically relevant enzyme or receptor, computational approaches can be used to design novel high-affinity ligands. These methods can complement the broad screening efforts, which represent traditional lead discovery. In this chapter we focus on our approach to computer-aided ligand design. It is based on the docking of a diverse set of molecular fragments into the active site of a macromolecular target and on the use of a combinatorial strategy to connect them to form candidate ligands. The methodology is illustrated by an application to human thrombin, a trypsin-like serine protease fulfilling a central role in both hemostasis and thrombosis. The selective inhibition of thrombin is expected to prevent thrombotic diseases. Ligand-design programs are being developed at an ever increasing rate and some are related to various aspects of our ligand design approach. The LEGO software tool is based on the combination of multiple fragment docking, automatic connection by small linker units (one to four atom chains), and searching of three-dimensional databases for complementary molecules [1,2]. It has been implemented within the MOLOC molecular modeling system [3], which allows the visualization of the functionality maps and interactive model building of the growing ligands. Another related approach is that embodied in the program LUDI [4–8]. It makes use of statistical data from small-molecule * Formerly Sandoz Pharma Ltd. http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_541.html [4/9/2004 12:51:01 AM]
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