Aminoacyl tRNA Synthetases: Implications of Structural Biology in Drug Development against Trypanosomatid Parasites

Abstract

The ensemble of aminoacyl tRNA synthetases is regarded as a key component of the protein translation machinery. With the progressive increase in structure-based studies on tRNA synthetase-ligand complexes, the detailed picture of these enzymes is becoming clear. Having known their critical role in deciphering the genetic code in a living system, they have always been chosen as one of the important targets for development of antimicrobial drugs. Later on, the role of aminoacyl tRNA synthetases (aaRSs) on the survivability of trypanosomatids has also been validated. It became evident through several gene knockout studies that targeting even one of these enzymes affected parasitic growth drastically. Such successful studies have inspired researchers to search for inhibitors that could specifically target trypanosomal aaRSs, and their never-ending efforts have provided fruitful results. Taking all such studies into consideration, these macromolecules of prime importance deserve further investigation for the development of drugs that cure spectrum of infections caused by trypanosomatids. In this review, we have compiled advancements of over a decade that have taken place in the pursuit of devising drugs by using trypanosomatid aaRSs as a major target of interest. Several of these inhibitors work on an exemplary low concentration range without posing any threat to the mammalian cells which is a very critical aspect of the drug discovery process. Advancements have been made in terms of using structural biology as an important tool to analyze the architecture of the trypanosomatids aaRSs and concoction of inhibitors with augmented specificities toward their targets. Some of the inhibitors that have been tested on other parasites successfully but their efficacy has so far not been validated against these trypanosomatids have also been appended.

Figure 1

Global distribution of infections caused by trypanosomatids. Regions recognized for a particular trypanosomatid-related infection have been demarcated based on the technical health data published by WHO in the year 2018 for American trypanosomiasis and 2021 for leishmaniasis and human African trypanosomiasis. The green, red, and pink colors represent the localization of leishmaniasis, human African trypanosomiasis, and American trypanosomiasis, respectively. The orange color denotes regions where both leishmaniasis and human African trypanosomiasis are prevalent, while the blue color delineates regions where both leishmaniasis and American trypanosomiasis are found. The global map was generated using MapChart online server (https://www.mapchart.net/).

Figure 2

Evolution of drugs against trypanosomatid aaRSs in recent years. Target-specific inhibitor designing in order to attain enriched potency against trypanosomatid aaRSs has been mostly done for LeuRS, MetRS, and HisRS. Also, drugs like borrelidin and cladosporin which are well-known inhibitors of ThrRS and LysRS have shown promising results in the reduction of parasitic growth.

Figure 3

Schematic representation of a cell showing the process of aminoacylation. In the initial steps of aminoacylation, the tRNA synthetase is bound by ATP and its cognate amino acid that results in the formation of aminoacyl adenylate intermediate upon release of a pyrophosphate molecule. In the sequential steps, the cognate tRNA binds to this tRNA synthetase via its anticodon domain and the amino acid is transferred to its CCA arm resulting in the formation of adenylated tRNA (charged tRNA). On the release of charged tRNA as well as AMP, the tRNA synthetase is now ready for another cycle of aminoacylation.

Figure 4

Domain arrangement of trypanosomatid vs Homo sapiens LysRS. The trypanosomatid mitochondrial (mt) LysRS contain a C-terminal extension ranging between 90 and 115 amino acids, while the cytosolic (ct) ones have an N-terminal extension of nearly equal lengths.

Figure 5

Domain arrangement of cytosolic MetRS from trypanosomatid and human. Comparison of MetRS domains depicts the absence of the C-terminal dimerization domain in humans as well as trypanosmatids that is present elsewhere.

Figure 6

Domain arrangement of trypanosomatid vs human cytosolic TyrRS. All of the trypanosomatids TyrRS harbor an ELR motif which might play a role in chemotaxis.

Figure 7

Domain arrangement of cytosolic HisRS from trypanosomatid and human. The extensively lysine-rich N-terminal region is shown in the Pfam domains of trypanosomatids that is absent in the human form.

Figure 8

Domain arrangement of trypanosomatid vs Homo sapiens cytosolic ProRS. Pfam domain comparison shows the absence of Ybak/ProX domain at the N-terminus of human EPRS when compared to the trypanosomatid ProRS.

Figure 9

Surface view representation of TyrRS from human and L. donovani. (A) Human and (B) leishmanial TyrRS is compared to highlight the location of the extra pocket (EP) present in LdTyrRS. The residues of LdTyrRS EP are indicated in yellow color, while the ligand is displayed in white sticks.

Figure 10

Comparison between catalytic pockets of human and trypanosomatid aaRSs: the structural superimposition between the catalytic pockets of human and trypanosomatids has been shown for (A) AlaRS (corresponding RMSD of LdAlaRS and TbAlaRS from HsAlaRS is 0.28 and 0.35 Å), (B) HisRS (corresponding RMSD of LdHisRS and TbHisRS from HsHisRS is 1.05 and 1.08 Å, respectively), (C) LeuRS (corresponding RMSD of LdLeuRS and TbLeuRS from HsLeuRS is 0.22 and 0.56 Å, respectively), (D) MetRS (corresponding RMSD of LdMetRS and TbMetRS from HsMetRS is 1.1 and 0.82 Å, respectively), and (E) TyrRS (corresponding RMSD of LdMetRS and TbMetRS from HsMetRS is 0.39 and 0.35 Å, respectively). The residues of catalytic pockets are presented as sticks with black, green, and cyan for human, L. donovani, and T. brucei aaRSs, respectively.