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

Abstract

Cladosporin (CLD) is a fungal metabolite that kills the malaria parasite via inhibiting its cytoplasmic lysyl‐tRNA synthetase (KRS) and abrogating protein translation. Here we provide structural and drug selectivity analyses on CLD interacting residues in apo and holo KRSs from Plasmodium falciparum, Homo sapiens, Cryptosporidium parvum, and Mycobacterium ulcerans. We show that both gross and subtle alterations in protein backbone and sidechains drive the active site structural plasticity that allows integration of CLD in KRSs. The ligand‐induced fit of CLD in PfKRS is marked by closure and stabilization of three disordered loops and one alpha helix. However, these structural rearragements are not evident in KRS‐CLD complexes from H. sapiens, C. parvum, or M. ulcerans. Strikingly, CLD fits into the MuKRS active site due to a remarkable rotameric alteration in its clash‐prone methionine residue that provides accommodation for the methyl moiety in CLD. Although the high concentrations of drugs used for Hs, Cp, and MuKRS‐CLD complexes in co‐crystallization studies enable elucidation of a structural framework for understanding drug binding in KRSs, we propose that these data should be concurrently assessed via biochemical studies of potency and drug selectivity given the poor cell‐based activity of CLD against human and bacterial cells. Our comprehensive analyses of KRS‐CLD interactions, therefore, highlight vital issues in structure‐based drug discovery studies.

Aminoacyl tRNA synthetases as potential drug targets of the Panthera pathogen Babesia

“…The Plasmodium KRS (for cladosporin, CLD) and PRS (for halofuginone) are currently being studied as potential drug targets [19, 24, 59–61]. We analysed CLD which, along with its analogs, is being investigated as an inhibitor of P. falciparum -KRS ( Pf -KRS) and of various other pathogen KRSs [21, 62]. Several amino acid residues in CLD binding pocket are highly conserved except at two positions near the ATP binding pocket and adjacent to CLD methyl moiety (Fig.…”

“…6b). It is noteworthy that biochemical analysis of recombinant KRSs has previously shown that CLD displays a nanomolar range potency of inhibition (IC50 ~ 40–90 nM) against Pf -KRS, which is ~ 500-fold higher when compared with Hs -KRS [20, 62, 63]. This suggests potential poor selectivity for P. tigris KRS due to the same bulkier residues (QT) at the CLD binding pocket in comparison to the smaller, more favourable residues (CS/VT) in Babesia spp.…”

Inhibition ofPlasmodium falciparumLysyl‐tRNA Synthetase via a Piperidine‐Ring Scaffold Inspired Cladosporin Analogues

“…It was noted that the isocoumarin moiety makes comparatively stronger H-bond with side chains of Glu325, Asn332 and Arg553 (Supporting Information Figure S4). [25,27] The THP moiety of cladosporin is stabilized by hydrophobic interactions with the side chains of Thr337, Glu494 and Asn497.…”

Conformational heterogeneity in apo and drug-bound structures of Toxoplasma gondii prolyl-tRNA synthetase

“…Additionally, we recently extended the r.m.s.d.-r.m.s.d. /res analyses to another set of aaRS structures bound to ATP at 2.3 Å resolution and cladosporin at 2.1 Å resolution (Chhibber-Goel & Sharma, 2019). R.m.s.d.s for ATP-bound Homo sapiens lysyl-tRNA synthetase (HsKRS) structures remain below $1 Å and the maximum r.m.s.d.…”