Characterisation of plasmodial transketolases and identification of potential inhibitors: an in silico study

Abstract

Background Plasmodial transketolase (PTKT) enzyme is one of the novel pharmacological targets being explored as potential anti-malarial drug target due to its functional role and low sequence identity to the human enzyme. Despite this, features contributing to such have not been exploited for anti-malarial drug design. Additionally, there are no anti-malarial drugs targeting PTKTs whereas the broad activity of these inhibitors against PTKTs from other Plasmodium spp. is yet to be reported. This study characterises different PTKTs [Plasmodium falciparum (PfTKT), Plasmodium vivax (PvTKT), Plasmodium ovale (PoTKT), Plasmodium malariae (PmTKT) and Plasmodium knowlesi (PkTKT) and the human homolog (HsTKT)] to identify key sequence and structural based differences as well as the identification of selective potential inhibitors against PTKTs. Methods A sequence-based study was carried out using multiple sequence alignment, phylogenetic tree calculations and motif discovery analysis. Additionally, TKT models of PfTKT, PmTKT, PoTKT, PmTKT and PkTKT were modelled using the Saccharomyces cerevisiae TKT structure as template. Based on the modelled structures, molecular docking using 623 South African natural compounds was done. The stability, conformational changes and detailed interactions of selected compounds were accessed viz all-atom molecular dynamics (MD) simulations and binding free energy (BFE) calculations. Results Sequence alignment, evolutionary and motif analyses revealed key differences between plasmodial and the human TKTs. High quality homodimeric three-dimensional PTKTs structures were constructed. Molecular docking results identified three compounds (SANC00107, SANC00411 and SANC00620) which selectively bind in the active site of all PTKTs with the lowest (better) binding affinity ≤ − 8.5 kcal/mol. MD simulations of ligand-bound systems showed stable fluctuations upon ligand binding. In all systems, ligands bind stably throughout the simulation and form crucial interactions with key active site residues. Simulations of selected compounds in complex with human TKT showed that ligands exited their binding sites at different time steps. BFE of protein–ligand complexes showed key residues involved in binding. Conclusions This study highlights significant differences between plasmodial and human TKTs and may provide valuable information for the development of novel anti-malarial inhibitors. Identified compounds may provide a starting point in the rational design of PTKT inhibitors and analogues based on these scaffolds.

The mitochondrion of Plasmodium falciparum is required for cellular acetyl-CoA metabolism and protein acetylation

“…The thiamine antimetabolite oxythiamine kills blood-stage malaria parasites and dramatically reduces the ability of the parasites to incorporate carbon from glucose into acetyl-CoA ( 28 , 48 ). Although oxythiamine likely inhibits essential enzymes in isoprenoid biosynthesis ( 29 ) and the pentose phosphate pathway ( 73 ), its effect on acetyl-CoA synthesis can be explained through the inhibition of aPDH, mPDH, and KDH. The E3 subunit contains FAD cofactor ( 42 , 50 ) and should be required for the activity of both mPDH and KDH.…”

Global Analysis of Plasmodium falciparum Dihydropteroate Synthase Variants Associated with Sulfadoxine Resistance Reveals Variant Distribution and Mechanisms of Resistance: A Computational-Based Study

“…On the other hand, the slightly higher Rg exhibited by all mutants is indicative of increased protein unfolding. The noticeable bimodal conformational distribution for mutations A613S, A437G/A581G, and K450E/A581G and the multimodal distribution for mutant I431V might indicate a high degree of denaturation [44][45][46].…”

The mitochondrion of Plasmodium falciparum generates essential acetyl-CoA for protein acetylation

“…The thiamine antimetabolite oxythiamine kills blood-stage malaria parasites and dramatically reduces the ability of the parasites to incorporate carbon from glucose into acetyl-CoA 29, 49 . Although oxythiamine likely inhibits essential enzymes in isoprenoid biosynthesis 30 and the pentose phosphate pathway 75 , its effect on acetyl-CoA synthesis can be explained through the inhibition of aPDH, mPDH, and KDH. The cofactor lipoate is also required for the activity of PDH and KDH enzymes 35 .…”