Sequence analysis, multiple templates structure prediction and binding site identification of bromelain from ananas comosus

Bromelain is a proteolytic enzyme derived from pineapples and categorized as a cysteine protease. This enzyme is widely used as an anti-inflammatory agent in therapeutic applications. In this study, the molecular interactions of bromelain against phospholipase A2 (Pla2), a target protein in inflammatory diseases, were investigated. The knowledge of the structural properties and mechanism of bromelain is limited because of the unavailability of its structural information. Therefore, a comparative modelling study was conducted using MODELLER 9v14 to predict the three-dimensional (3D) model of stem bromelain and to investigate its structural properties. The 3D model of bromelain was successfully predicted through Homology modelling approach. Pocket detection was conducted, functionally and structurally important residues of the bromelain model were identified, and its cleft and ligand binding site were determined. Protein-protein docking was performed to predict all possible binding modes between bromelain and Pla2. Amino acids involved in the interactions between bromelain and Pla2 were identified. A few functional conserved residues located in the largest cleft of the model were involved in bromelain-Pla2 binding interactions.