Albany 2001

category image Biomolecular
SUNY at Albany
June 19-23, 2001

Insights to subsite recognition in thiol protease inhibitor complexes: understanding specificity, the basis of differential inhibition.

This study explores the differential binding mode and interactional features of E-64 and its derivative E-64-C along with other inhibitors leupeptin and ZPACK to a series of thiol proteases e.g. papain, actinidin, caricain, chymopapain, calotropin DI and the recent x-ray structure of calotropinDII solved in our laboratory at 2.1? resolution. Knowledge based molecular docking of these inhibitors in the catalytic site of different cysteine proteases shows minute differences exploited in the catalytic pockets of various members of this family to manifest their specificities. An insight developed on the differential inhibition of proteases by the above inhibitors via crystallography and modelling indicated the interactional involvement of the chemically potent group of ligand to catalytic pocket which influences the inhibitory activity. Both the characteristics of the enzyme (e.g. subsites and hydrophobicity) as well as the nature of the inhibitor influence the selectivity of an inhibitor towards an enzyme. The difference accessible surface area (DASA) of each of the proteases with and without inhibitors revealed the subsite residues involved in the inhibition and subsequent calculation of the accessible surface area for each of the complexed structure has indicated the differential binding modes, tight enough to prevent the accessibility of solvent molecules to the active site zone of the different enzymes. The Sn-Pn (n=1~3) interactions of the inhibitors and their disposition with the main chains of the active site residues though look similar in the respective complexes, all the proteases in the papain superfamily are not exactly papain like and significant differences have been observed in the side chain interactions of S2-P2 and S3-P3 pairs due to the presence of different residues in the respective subsites for their different functional specificity. The observed subtle differences in the binding mode of the inhibitors to the receptors clarifies why there is differential inhibition, key to selective specificity, and in turn help in designing potential inhibitors for the protease system.

Asim K. Bera, Suparna Bhattacharya, Asok K. Pal, Sawan Sen, Sibani Chakraborty, Sreya Ghosh, Soumen Ghosh, U. Halder, B.P. Mukhopadhyay and Asok Banerjee.

Biophysics Department; Bose Institute, Calcutta 700 054, India
Phone: +91 33 3379544; Fax: +91 33 3343886; ashoke@bic.boseinst.ernet.in