Homology modeling and functional analysis of LPG2 protein of leishmania strains

Abstract

As drug resistance problem persists in case of Leishmaniasis, modeling and analysis of different essential proteins of Leishmania strains will help us further to discover novel lead compounds. Lipophosphoglycan 2 (LPG2) protein is required for the development of Leishmania throughout their life cycle, including for virulence to the mammalian host. LPG2 participates in a specialized virulence pathway, which may offer an attractive target for chemotherapy. Homology models of LPG2 of five Leishmania specieshave been constructed using the X-ray structures of different transporter proteinsas templates, by comparative protein modeling principles. The resulting model has the correct stereochemistry as gauged from the Ramachandran plot and good three-dimensional (3-D) structure compatibility as assessed by the Procheck and Profiles-3D scores. Functional assignment of LPG2 protein of Leishmania strains by SVM revealed that along with transporters activity it also performs several novel functions e.g. iron-binding, sodium-binding, copper binding. It also belongs to protein of major facilitator family (MFS) and type II (general) secretory pathway (IISP) family. Important functional motifs have been identified in LPG2 protein of different Leishmania strains using different programs. Potential Ligand Binding Sites (LBSs) in LPG2 protein of these strainshave been identified using Pocket Finder program. On the basis of structure of ligand binding sites, particular LPG2 inhibitors can be designed. The similarity in the molecular structure, function and differences in LBSs of LPG2of L. donovani, L. major, L. infantum, L. braziliensis and L. mexicana provide evidences for selective and specific LPG2 inhibitors. © 2009 Ganesh CS, et al.