In recent years, the availability of high resolution structures of enzyme-inhibitor complexes has led to an increased understanding of molecular interactions. Using this structural information, computer-based approaches help identify or design ligands that posses good steric and chemical complementarity to various sites on the enzyme. This process is referred to as """"""""structure-based molecular design"""""""". The long term objective of this work is to develop a method to computationally screen and evaluate ligands as potential lead compounds. We are seeking a method that is rapid and reasonably accurate. The DOCK suite of programs, developed by the Kuntz group, identifies and characterizes sites on a receptor or protein for inhibitor binding; orients (a database of) molecules; and evaluates these molecules for goodness of fit. We are applying the structure-based methodology to identify inhibitors of the enzyme inosine monophosphate dehydrogenase (impdh), which plays a key role in growth of several parasites. MidasPlus is used to examine different conformations and orientations of the ligand and enzyme. MidasPlus is also used to display and select site points (referred to as DOCK spheres) within the enzyme active site. A MidasPlus delegate, VIEWDOCK, has been particularly important in examining output of DOCK jobs and in selecting compounds for testing in the parasite project. We expect VIEWDOCK to continue to be useful in this manner in other similar projects examining DOCK output.
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