Active site and structural analysis of sesquiterpene synthase towards synthesis of aromatic compounds related to agarwood formation in Aquilaria malaccensis

Abstract

Agarwood is a fragrant resinous wood that has been widely used in traditional medicines, incense and perfume. Formation of agarwood in branches and trunks of certain genera including Aquilaria and Gyrinops is due to activation of defence mechanism that causes by natural phenomena or microbial infection. The main fragrant compounds of agarwood are sesquiterpenes and phenylethyl chromone derivatives, and a great variety of sesquiterpenes are contained in high-quality agarwood. Their diverse cyclic and acyclic structures are known to be synthesized from farnesyl pyrophosphate (FPP) by sesquiterpene synthase catalytic action. Mechanisms of reaction control and structures of sesquiterpene synthases from Aquilaria sp are studied by many groups trying to clarify the structure-function relationship in these enzymes, however the molecular recognition between the catalytic residues of sesquiterpene synthases with FPP producing the aroma compound remains unclear. In this study, sesquiterpene synthases isolated from Aquilaria malaccensis (AGS3) was predicted for its structure and docking simulation has been performed to determine the affinity of active site residues of sesquiterpene synthases towards FPP molecules. To reveal the unique catalytic mechanism of AGS3, the molecular docking of AGS3 was carried out in two different sites involving active site entrance for initial catalysis and within substrate cavity for final step. It was found that the aspartate and glutamate rich regions interacts with metal complexes at the entrance of active site and aromatic residues was subsequently interact with farnesyl chain of FPP within the substrate binding pocket while the diphosphate moiety of FPP (ppi) detached the substrate. This model will serve to be a framework for exploring the roles of active site residues of AGS3 to explore the enzyme function of sesquiterpene synthase producing aromatic compound sesquiterpene of agarwood in A. malaccensis.