Abstract Description

Aminoacyl tRNA synthetases (aaRSs) play an important role in the protein synthesis cascade by coupling amino acids to their cognate tRNAs. We recently published an article reporting the potential allosteric effects of certain South African natural compounds (SANCDB) (PMID: 40367238) against Plasmodium falciparum isoleucyl-tRNA synthetase (PfIleRS). Building on these work, we hereby screened a curated library of analogues derived from natural products against PfIleRS which is a multistage antimalarial target. Through molecular docking, molecular dynamics simulations, binding free energy calculations, and dynamic residue analysis (DRN) we demonstrated that allosteric ligands could disrupt ATP binding affinity in the active site, leading to structural perturbations in PfIleRS. 14 potential allosteric compounds were elucidated based on their high preferential binding to PfIleRS over its human homolog and the satisfaction of ADMET drug-like properties. Three analogues (AN39, AN324, and SMI_354) caused major conformational shifts in PfIleRS compared to PfIleRS holo references during 200 ns molecular dynamics simulations. Free-energy landscapes showed that PfIleRS in complex with: AN39, AN324, AN592, and SMI_153 ligands sampled several conformations, which could suggest some level of instability, while the holo references were mainly in one stable energy basin. Active site analysis showed a persistent increase in the centre of mass distance between isoleucine and AMP substrates coupled with a reduction in AMP binding affinity in PfIleRS-AN39, PfIleRS-AN324, and PfIleRS-AN596 compared to the holo replicates. Network centrality metric betweenness centrality (BC) identified residues with high BC values that formed a potential allosteric path in the holo enzyme from the N-terminal Rossmann fold to the junctional domain. However, ligands: AN39, AN258, AN324, SMI_263, and SMI_467 in complex with PfIleRS interrupted this BC information flow. Furthermore, closeness centrality (CC) identified a cluster of residues in the active site and its vicinity that act as a linker between the catalytic Rossmann fold and the editing domains. These residues lost high CC values upon binding of ligands SMI_263, SMI_309, and SMI_354. Overall, analogues derived from SANCDB natural products showed potential to modulate both global and local PfIleRS protein motions, and therefore, a further in vitro investigation of the analogues’ effect on PfIleRS enzyme activity to validate their allosteric modulatory activities is needed.