Aminoacyl-tRNA Synthetases as Targets for Structure Guided Drug Design (SGDD) Against Pathogenic Protozoa and Bacteria
Barros Alvarez, Ximena
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Tuberculosis (TB) and neglected tropical diseases (NTDs) caused by trypanosomatids are devastating diseases affecting millions of people around the globe. Mycobacterium tuberculosis causes TB, while the trypanosomatids Trypanosoma brucei, Trypanosoma cruzi and parasites of the genus Leishmania, cause sleeping sickness (or human African trypanosomiasis (HAT)), Chagas disease (or American trypanosomiasis) and the leishmaniases in tropical and subtropical areas of the world. Visceral leishmaniasis (VL), the deadliest form of the disease, is caused by L. infantum and L. donovani. For some of these diseases there is no vaccine or cure. For others, vaccine protection and treatment efficiency are limited. In some cases, development of resistance to available drugs has made useless otherwise successful treatments. New drugs as well as new drug targets are desperately needed. The essential aminoacyl-tRNA synthetase (aaRS) enzymes provide the charged tRNAs required for protein synthesis. AaRS have been previously pursued as drug targets in bacteria and fungi and have been validated as drug targets in protozoa. The structural work presented as part of this dissertation has been part of collaborative structure guided drug design (SGDD) projects among various research groups, most of them within University of Washington, for the discovery and iterative optimization of inhibitors targeting aaRSs of parasitic protozoa and bacteria. The selection of methionyl-tRNA synthetase (MetRS) and tyrosyl-tRNA synthetase (TyrRS) as drug targets was done based on their predicted feasibility of developing selective inhibitors. Crystal structures of M. tuberculosis and T. brucei MetRS (MtubMetRS and TbruMetRS) and L. donovani TyrRS (LdonTyrRS) were solved in the presence of different compounds to assist in the iterative SGDD development of drugs against TB, HAT and VL, respectively. Structural information contributed in different stages in the SGDD process, from the description of new protein structures of the essential pathogenic aaRSs to the assistance in the optimization and design of novel inhibitors. In an example of early steps in the SGDD process, the crystal structure of MtubMetRS in complex with the catalytic intermediate Met-AMP was solved at 2.6 Å resolution. Differences with other MetRSs including the human counterparts were revealed and could potentially be useful in the chemotherapeutic development against TB. The use of nanobodies as crystallization chaperones and of the tyrosyl adenylate analog TyrSA was crucial for obtaining well diffracting crystals that lead to solving the crystal structure of LdonTyrRS at 2.75 Å resolution. The presence of an extra pocket (EP) was revealed that is not present in the human counterparts, but is shared with other pathogens, and could be exploited in seeking for a cure for VL and other infectious diseases. As an example of the value of the contribution of structural information in later stages in the SGDD process, a total of 57 crystal structures obtained upon soaking of TbruMetRS with multiple compounds and inhibitors served as platform to assist in the discovery and optimization of new lead compounds against the causative agent of HAT. Promising compounds generated through the utilization of collaborative SGDD strategies as the described in this dissertation should eventually facilitate the development of inhibitors targeting homologous aaRS across the related protozoa and bacteria affecting the lives of the most underprivileged human populations worldwide.
- Biological chemistry