Molecular docking and structure-based virtual screening studies of potential drug target, CAAX prenyl proteases, of Leishmania donovani

Abstract

Targeting CAAX prenyl proteases of Leishmania donovani can be a good approach towards developing a drug molecule against Leishmaniasis. We have modeled the structure of CAAX prenyl protease I and II of L. donovani, using homology modeling approach. The structures were further validated using Ramachandran plot and ProSA. Active site prediction has shown difference in the amino acid residues present at the active site of CAAX prenyl protease I and CAAX prenyl protease II. The electrostatic potential surface of the CAAX prenyl protease I and II has revealed that CAAX prenyl protease I has more electropositive and electronegative potentials as compared CAAX prenyl protease II suggesting significant difference in their activity. Molecular docking with known bisubstrate analog inhibitors of protein farnesyl transferase and peptidyl (acyloxy) methyl ketones reveals significant binding of these molecules with CAAX prenyl protease I, but comparatively less binding with CAAX prenyl protease II. New and potent inhibitors were also found using structure-based virtual screening. The best docked compounds obtained from virtual screening were subjected to induced fit docking to get best docked configurations. Prediction of drug-like characteristics has revealed that the best docked compounds are in line with Lipinski’s rule. Moreover, best docked protein–ligand complexes of CAAX prenyl protease I and II are found to be stable throughout 20 ns simulation. Overall, the study has identified potent drug molecules targeting CAAX prenyl protease I and II of L. donovani whose drug candidature can be verified further using biochemical and cellular studies.

Keywords:

• CAAX prenyl proteases
• prenylation
• membrane protein
• molecular dynamics simulation
• docking

Acknowledgments

Infrastructural facilities and research fellowship to SS, RB by Indian Institute of Technology Guwahati is acknowledged. Financial support by Department of Biotechnology, Government of India in the form of research grant to VKD and SKS (Project No.: BT/502/NE/TBP/2013) is also acknowledged. Homology-modeled Structure of ornithione decarboxylase of L. donovani is submitted to Protein Model DataBase (https://bioinformatics.cineca.it/PMDB/). The PMBD IDs of the submission are PM0080313 and PM0080314 for CAAX preny protease I and CAAX preny protease II, respectively.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was supported by Department of Biotechnology, Ministry of Science and Technology [project number BT/502/NE/TBP/2013].