Wang P,Â Li Y,Â Shao Q,Â Zhou W,Â Wang K., JÂ DrugÂ Target., 2014 Sep 19:1-7. [Epub ahead of print]
Phospholipase A2 (PLA2) is potentially an important target for anti-inflammatory therapeutics. Here, we described a systematic scheme that integrated protein docking andÂ peptideÂ redocking, molecular dynamics simulation, and binding affinity analysis to rationally design PLA2 inhibitory peptidesÂ based on a solved PLA2 crystal structure. The scheme employed protein docking to sample the interaction modes of PLA2 with its natural inhibitor Clara cell protein, from which a number ofÂ peptideÂ fragments, including a pentapeptide LLLGS, were cut off and redocked to serve as the lead entities of PLA2 inhibitoryÂ peptides. In addition, a systematic mutation energy map that characterized the binding free energy changes Î”G upon mutations of each position of the putative pentapeptide to 20 amino acids was also profiled, which was subsequently used to guideÂ peptideÂ structure optimization. In order to solidify the computational findings, we performed kinetic and inhibition studies of few designedÂ peptidesÂ against human secretory PLA2. Consequently, eightÂ peptidesÂ were successfully identified to have potent inhibition potency, in which the LLAYK and AVFRS were found to suppress enzymatic activity significantly (Kiâ€‰=â€‰0.75â€‰Â±â€‰0.06 and 4.2â€‰Â±â€‰0.3â€‰Î¼M, respectively). A further structure examination revealed that the designedÂ peptidesÂ can form intensive nonpolar networks of van der Waals contacts and hydrophobic interactions at their complex interfaces with PLA2, conferring considerable stability and affinity for the formed complex systems.