Structural basis of phospholipase A₂ inhibition for the synthesis of Prostaglandins by the plant alkaloid aristolochic acid from a 1.7 Å crystal structure

Abstract

This is the first structural observation of a plant product showing high affinity for phospholipase A₂ and regulating the synthesis of arachidonic acid, an intermediate in the production of prostaglandins. The crystal structure of a complex formed between Vipera russelli phospholipase A₂ and a plant alkaloid aristolochic acid has been determined and refined to 1.7 Å resolution. The structure contains two crystallographically independent molecules of phospholipase A₂ in the form of an asymmetric dimer with one molecule of aristolochic acid bound to one of them specifically. The most significant differences introduced by asymmetric molecular association in the structures of two molecules pertain to the conformations of their calcium binding loops, B-wings, and the C-terminal regions. These differences are associated with a unique conformational behavior of Trp³¹. Trp³¹ is located at the entrance of the characteristic hydrophobic channel which works as a passage to the active site residues in the enzyme. In the case of molecule A, Trp³¹ is found at the interface of two molecules and it forms a number of hydrophobic interactions with the residues of molecule B. Consequently, it is pulled outwardly, leaving the mouth of the hydrophobic channel wide open. On the other hand, Trp³¹ in molecule B is exposed to the surface and moves inwardly due to the polar environment on the molecular surface, thus narrowing the opening of the hydrophobic channel. As a result, the aristolochic acid is bound to molecule A only while the binding site of molecule B is empty. It is noteworthy that the most critical interactions in the binding of aristolochic acid are provided by its OH group which forms two hydrogen bonds, one each with His⁴⁸ and Asp⁴⁹.