Identification of a novel and potent inhibitor of phospholipase A₂ in a medicinal plant: crystal structure at 1.93 Å and surface plasmon resonance analysis of phospholipase A₂ complexed with berberine

Abstract

Crystal of Russell Viper venom phospholipase A₂ complexed with an isoquinoline alkaloid, berberine from a herbaceous plant Cardiospermum halicacabum, was prepared and its structure was solved by X-ray crystallography. The crystal diffracted up to 1.93 Å and the structure solution clearly located the position of berberine in the active site of the enzyme. Two hydrogen bonds, one direct and the other water mediated, were formed between berberine and the enzyme. Gly 30 and His 48 made these two hydrogen bonds. Additionally, the hydrophobic surface of berberine made a number of hydrophobic contacts with side chains of neighboring amino acids. Surface Plasmon Resonance studies revealed strong binding affinity between berberine and phospholipase A₂. Enzyme inhibition studies proved that berberine is a competitive inhibitor of phospholipase A₂. It was inferred that the isoquinoline alkaloid, berberine, is a potent natural inhibitor of phospholipaseA₂.