Showing papers by "Martin J. Scanlon published in 2000"

Conformational selection of inhibitors and substrates by proteolytic enzymes: implications for drug design and polypeptide processing.

Abstract: Inhibitors of proteolytic enzymes (proteases) are emerging as prospective treatments for diseases such as AIDS and viral infections, cancers, inflammatory disorders, and Alzheimer's disease. Generic approaches to the design of protease inhibitors are limited by the unpredictability of interactions between, and structural changes to, inhibitor and protease during binding. A computer analysis of superimposed crystal structures for 266 small molecule inhibitors bound to 48 proteases (16 aspartic, 17 serine, 8 cysteine, and 7 metallo) provides the first conclusive proof that inhibitors, including substrate analogues, commonly bind in an extended beta-strand conformation at the active sites of all these proteases. Representative superimposed structures are shown for (a) multiple inhibitors bound to a protease of each class, (b) single inhibitors each bound to multiple proteases, and (c) conformationally constrained inhibitors bound to proteases. Thus inhibitor/substrate conformation, rather than sequence/composition alone, influences protease recognition, and this has profound implications for inhibitor design. This conclusion is supported by NMR, CD, and binding studies for HIV-1 protease inhibitors/ substrates which, when preorganized in an extended conformation, have significantly higher protease affinity. Recognition is dependent upon conformational equilibria since helical and turn peptide conformations are not processed by proteases. Conformational selection explains the resistance of folded/structured regions of proteins to proteolytic degradation, the susceptibility of denatured proteins to processing, and the higher affinity of conformationally constrained 'extended' inhibitors/substrates for proteases. Other approaches to extended inhibitor conformations should similarly lead to high-affinity binding to a protease.

Pharmaceutical Applications of NMR

Abstract: Publisher Summary Nuclear magnetic resonance (NMR) spectroscopy plays an important role in the pharmaceutical sciences. This chapter focuses on the pharmaceutical applications of NMR. Some of the NMR methods used in the drug design and selected applications to specific classes of bioactive molecules are described in the chapter. Applications of NMR to drug design had the determination of structures and conformations of biologically important organic molecules. The development of methodology for assigning and determining the structures of peptides and proteins by two-dimensional (2D) NMR has enabled a wide range of new applications in the field of drug design. NMR instruments examine samples ranging in complexity from solutions of drug molecules, to their receptor proteins, to intact organs and animals. Three classes of NMR experiments can be identified-small-molecule NMR, macromolecular NMR, and in vivo NMR. Small-molecule NMR contributes both as an analytical tool for the verification of the structure of synthesized molecules and at the drug design stage. Macromolecular NMR assist in receptor-based drug design by providing the structures of key protein targets, and is also extremely valuable at the in vitro testing stage. NMR techniques used in drug design are drug conformations, protein structure determination, and protein–ligand complexes. NMR studies are important in characterizing the dynamic nature of insulin in solution, and consequently have provided some insight into receptor binding.