Protein Translation Enzyme lysyl-tRNA Synthetase Presents a New Target for Drug Development against Causative Agents of Loiasis and Schistosomiasis

Abstract

Helminth parasites are an assemblage of two major phyla of nematodes (also known as roundworms) and platyhelminths (also called flatworms). These parasites are a major human health burden, and infections caused by helminths are considered under neglected tropical diseases (NTDs). These infections are typified by limited clinical treatment options and threat of drug resistance. Aminoacyl-tRNA synthetases (aaRSs) are vital enzymes that decode genetic information and enable protein translation. The specific inhibition of pathogen aaRSs bores well for development of next generation anti-parasitics. Here, we have identified and annotated aaRSs and accessory proteins from Loa loa (nematode) and Schistosoma mansoni (flatworm) to provide a glimpse of these protein translation enzymes within these parasites. Using purified parasitic lysyl-tRNA synthetases (KRSs), we developed series of assays that address KRS enzymatic activity, oligomeric states, crystal structure and inhibition profiles. We show that L. loa and S. mansoni KRSs are potently inhibited by the fungal metabolite cladosporin. Our co-crystal structure of Loa loa KRS-cladosporin complex reveals key interacting residues and provides a platform for structure-based drug development. This work hence provides a new direction for both novel target discovery and inhibitor development against eukaryotic pathogens that include L. loa and S. mansoni.

Side chain rotameric changes and backbone dynamics enable specific cladosporin binding in Plasmodium falciparum lysyl‐tRNA synthetase

“…Note that the amino acid residues in the CLD binding pocket of KRSs are highly conserved except at two positions near the ATP binding pocket and adjacent to the methyl moiety of the THP ring of CLD (Figure A—red box). The basis for the CLD selectivity has been ascribed to these two key selectivity residues that show clear divergence across species (Figure A) . In Pf KRS, Val and Ser occupy these two positions .…”

“…Cladosporin (CLD) and some of its stereoisomers are potent inhibitors of Plasmodium falciparum lysyl‐tRNA synthetase ( Pf KRS) and of other pathogen KRSs . CLD is synthesized by various fungi, for example, Aspergillus flavus and Cladosporium cladosporioides and its structure has been established as 3,4‐dihydro‐6,8‐dihydroxy‐3‐(6‐methyltetrahydropyran‐2‐ylmethyl) isocumarin.…”

“…The 6,8‐dihydroxylisocoumarin in CLD is joined to the methyltetrahydropyran (mTHP) group and constitutes the active scaffold of CLD that mimics an adenosine moiety (Figure A) . The discovery of CLD has opened new avenues to target a plethora of eukaryotic parasites . In addition to Pf KRS, CLD is a known inhibitor of KRSs from helminth parasites— Schistosoma mansoni ( Sm ) and Loa loa ( Ll ) .…”

“…The discovery of CLD has opened new avenues to target a plethora of eukaryotic parasites . In addition to Pf KRS, CLD is a known inhibitor of KRSs from helminth parasites— Schistosoma mansoni ( Sm ) and Loa loa ( Ll ) . The biochemical basis for CLD selectivity has been accredited to two key residues near the ATP binding pocket of KRSs, wherein the structurally smaller residues of Val 328 and Ser 344 (in Pf KRS) are CLD‐obliging whereas the bulkier corresponding residues (for instance) of Gln 321 and Thr 337 (in Hs KRS) impede CLD engagement .…”

“…The biochemical basis for CLD selectivity has been accredited to two key residues near the ATP binding pocket of KRSs, wherein the structurally smaller residues of Val 328 and Ser 344 (in Pf KRS) are CLD‐obliging whereas the bulkier corresponding residues (for instance) of Gln 321 and Thr 337 (in Hs KRS) impede CLD engagement . It has been proposed earlier that the selectivity residues of Val 328 and Ser 344 in Pf KRS are vital for CLD binding, and any side chain that is larger than either may cause steric clashes with the drug, thereby displaying poor potency …”