Design of Specific Peptide Inhibitors of Phospholipase A2: Crystal Structures of two Complexes of Phospholipase A2 with Two Pentapeptides

Biophysics, All India Institute of Medical Sciences* Institute of Medical Biochemistry and Molecular Biology, University of Hamburg, c/o DESY, 22603, Hamburg, Germany**
â—‹Nagendra Singh* Rishi K. Somvanshi* Nagendra Singh* Sujata Sharma* Markus Perbandt** Christian Betzel** Sharmistha Dey* Tej P. Singh*

Phospholipase A2 (PLA2) is an important target for the design of anti - inflammatory drugs. The structure of PLA2 has shown that the substrate-binding channel contains inner hydrophobic face with Asp49 and His 48 at the end of the channel. In order to fit into such a substrate-binding channel, two new peptides Phe - Leu - Ser - Thr - Lys (FLSTK) and Phe - Leu - Ala - Tyr - Lys (FLAYK) were synthesized. The analysis of data obtained from the binding studies with Surface Plasmon Resonance gave dissociation constants (Kd) of 2.5 x 10-8 M and 1.4 x 10-8 M respectively. PLA2 was co-crystallized with both peptides. The X-ray intensity data were collected using synchrotron beamline to 1.2 A and 1.7 A respectively. The crystal structures were determined with molecular replacement method and refined to R factors of 19.2% and 17.5% respectively. The excellent qualities of electron densities were observed for the both peptides at the substrate-binding site. As per the design strategy in both complexes, the Lys residue formed ionic interactions with Asp 49. We also observed several solvent mediated hydrogen bonds and van der Waals interactions between PLA2 and the peptides. The overall conformations of peptides were similar except at residues 3 and 4 because these residues were different in two peptides. The protein residues of the substrate-binding site in the two complexes have similar conformations as observed in the native PLA2 structure. However, the side chains show considerable rotations about various bonds. Both peptides form tight complexes with PLA2 and block the enzyme activity. These and other peptides with high binding affinities provide important leads for developing useful anti-inflammatory agents.