title: 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.
authors.affiliation: a Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati , Assam 781039 , India.
authors.forename: Shalini
authors.initials: S
authors.lastname: Singh
authors.affiliation: b Computer Aided Drug Designing and Molecular Modeling Laboratory, Department of Bioinformatics , Alagappa University , Karaikudi , Tamil Nadu 630004 , India.
authors.forename: Sitrarasu
authors.initials: S
authors.lastname: Vijaya Prabhu
authors.affiliation: b Computer Aided Drug Designing and Molecular Modeling Laboratory, Department of Bioinformatics , Alagappa University , Karaikudi , Tamil Nadu 630004 , India.
authors.forename: Venkatesan
authors.initials: V
authors.lastname: Suryanarayanan
authors.affiliation: a Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati , Assam 781039 , India.
authors.forename: Ruchika
authors.initials: R
authors.lastname: Bhardwaj
authors.affiliation: b Computer Aided Drug Designing and Molecular Modeling Laboratory, Department of Bioinformatics , Alagappa University , Karaikudi , Tamil Nadu 630004 , India.
authors.forename: Sanjeev Kumar
authors.initials: SK
authors.lastname: Singh
authors.affiliation: a Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati , Assam 781039 , India.
authors.forename: Vikash Kumar
authors.initials: VK
authors.lastname: Dubey
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D055808:Drug Discovery; D015801:Helminth Proteins / Q000037:antagonists & inhibitors / Q000737:chemistry*; D007893:Leishmania donovani / Q000187:drug effects / Q000201:enzymology*; D008968:Molecular Conformation; D062105:Molecular Docking Simulation; D010447:Peptide Hydrolases / Q000737:chemistry*; D011480:Protease Inhibitors / Q000737:chemistry* / Q000494:pharmacology; D011485:Protein Binding; D013329:Structure-Activity Relationship
chemical_list: D015801:Helminth Proteins; D011480:Protease Inhibitors; D010447:Peptide Hydrolases
keywords: CAAX prenyl proteases; docking; membrane protein; molecular dynamics simulation; prenylation