Targeting tRNA-synthetase interactions towards novel therapeutic discovery against eukaryotic pathogens

Abstract

The development of chemotherapies against eukaryotic pathogens is especially challenging because of both the evolutionary conservation of drug targets between host and parasite, and the evolution of strain-dependent drug resistance. There is a strong need for new nontoxic drugs with broad-spectrum activity against trypanosome parasites such as Leishmania and Trypanosoma. A relatively untested approach is to target macromolecular interactions in parasites rather than small molecular interactions, under the hypothesis that the features specifying macromolecular interactions diverge more rapidly through coevolution. We computed tRNA Class-Informative Features in humans and independently in eight distinct clades of trypanosomes, identifying parasite-specific informative features, including base pairs and base mis-pairs, that are broadly conserved over approximately 250 million years of trypanosome evolution. Validating these observations, we demonstrated biochemically that tRNA:aminoacyl-tRNA synthetase (aaRS) interactions are a promising target for antitrypanosomal drug discovery. From a marine natural products extract library, we identified several fractions with inhibitory activity toward Leishmania major alanyl-tRNA synthetase (AlaRS) but no activity against the human homolog. These marine natural products extracts showed cross-reactivity towards Trypanosoma cruzi AlaRS indicating the broad-spectrum potential of our network predictions. We also identified Leishmania major threonyl-tRNA synthetase (ThrRS) inhibitors from the same library. We discuss why chemotherapies targeting multiple aaRSs should be less prone to the evolution of resistance than monotherapeutic or synergistic combination chemotherapies targeting only one aaRS.

Structural and Genetic Determinants of Convergence in the Drosophila tRNA Structure–Function Map

“…As described in Kelly et al ( 2020 ), we reimplemented our previously published algorithm to estimate structure-conditioned functional information statistics from Freyhult et al ( 2006 ) extending it to compute functional information for all sixteen possible base-pair or base mis-pair features occurring in any paired-sites of the consensus secondary structure of tRNAs. The program accepts as input a set of multiple alignments, one for each functional sub-family of any RNA or protein multigene family, all mutually structurally aligned, and computes as its output function logo visualizations and tables of statistics on CIFs and their evolution in one or more taxa.…”

“…Even though our tRNA structure–function maps are based on an information criterion rather than a conservation criterion, we recently showed that tRNA CIFs, including Class-Informative Base-Pairs (CIBPs) and Class-Informative Mis-Pairs (CIMPs), are highly conserved within trypanosomes and between trypanosomes and humans, even while showing evidence of co-evolutionary divergence (Kelly et al 2020 ). Furthermore, our tRNA CIF annotations could predict differential susceptibility to inhibition by chemical agents of homologous aminoacyl-tRNA synthetases (aaRSs) from trypanosomes and humans (Kelly et al 2020 ).…”

“…Even though our tRNA structure–function maps are based on an information criterion rather than a conservation criterion, we recently showed that tRNA CIFs, including Class-Informative Base-Pairs (CIBPs) and Class-Informative Mis-Pairs (CIMPs), are highly conserved within trypanosomes and between trypanosomes and humans, even while showing evidence of co-evolutionary divergence (Kelly et al 2020 ). Furthermore, our tRNA CIF annotations could predict differential susceptibility to inhibition by chemical agents of homologous aminoacyl-tRNA synthetases (aaRSs) from trypanosomes and humans (Kelly et al 2020 ). We also found that tRNA gene clusters are conserved in trypanosomes and show clear evidence of rapid evolution by duplication, deletion, and rearrangements (Kelly et al 2020 ) consistent with findings from genome comparisons of diverse eukaryotic groups (Bermudez-Santana et al 2010 ; Velandia-Huerto et al 2016 ).…”

“…Furthermore, our tRNA CIF annotations could predict differential susceptibility to inhibition by chemical agents of homologous aminoacyl-tRNA synthetases (aaRSs) from trypanosomes and humans (Kelly et al 2020 ). We also found that tRNA gene clusters are conserved in trypanosomes and show clear evidence of rapid evolution by duplication, deletion, and rearrangements (Kelly et al 2020 ) consistent with findings from genome comparisons of diverse eukaryotic groups (Bermudez-Santana et al 2010 ; Velandia-Huerto et al 2016 ).…”

Benzopyrazine-Based Small Molecule Inhibitors As Trypanocidal and Leishmanicidal Agents: Green Synthesis, In Vitro, and In Silico Evaluations

“…T. cruzi Histidyl-tRNA synthetase (PDB ID: 4YPF; Koh et al, 2015) and T. cruzi trans-sialidase (PDB ID: 1S0J; Amaya et al, 2004) are considered as two major biological drug targets for American trypanosomiasis whereas Leishmanial rRNA A-site (PDB ID: 4K32; Shalev et al, 2013) and Leishmania major N-myristoyltransferase (PDB ID: 6QDA; Bell et al, 2020) are considered as the major biomolecular drug targets for leishmaniasis (Kelly et al, 2020). As shown in Table 2, compound 1 showed comparable in vitro trypanocidal and leishmanicidal activities with two standard commercial drugs; therefore, we hypothesized the inhibition of the proteins as mentioned earlier with compound 1.…”