Molecular modeling, simulation and virtual screening of ribosomal phosphoprotein P1 from Plasmodium falciparum

Abstract

Ribosomal phosphoprotein P1 (RPP1) is acidic phosphoprotein which in association with neutral phosphoprotein P0 and acidic phosphoprotein P2 forms ribosomal P protein complex as (P1)2-P0-(P2)2. P protein is known to be immunogenic and has important role in protein translation. 3D structure of P1 is not known. We have built an ab-initio model of RPP1 of Plasmodium falciparum using I-TASSER. Stereochemical stability of structure was checked using PROCHECK and the normality of the local environment of amino acids was checked using WHATIF. Comparison between known protein structures in PDB database and model protein was done using Dali server. Molecular dynamic simulation study and virtual screening of RPP1 was carried out. Three dimensional model structure of RPP1 was generated and model validation studies proved the model to be steriochemically significant. RPP1 structure was found to be stable at room temperature in water environment demonstrated by 30 ns molecular dynamic simulation study. Dali superimposition showed 69% superimposition to known 3D structures in PDB. Further virtual screening and docking studies promoted good interaction of ligands Ecgonine, Prazepam and Ethyl loflazepate with RPP1. The work provides insight for molecular understanding of RPP1 of P. falciparum and can be used for development of antimalarial drugs.

Keywords: Antimalarial drug; Dockblaster; Molecular dynamics; RPP1.