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Elbaramawi SS, Eissa AG, Noureldin NA, Simons C. Exploring Proteus mirabilis Methionine tRNA Synthetase Active Site: Homology Model Construction, Molecular Dynamics, Pharmacophore and Docking Validation. Pharmaceuticals (Basel) 2023; 16:1263. [PMID: 37765071 PMCID: PMC10535265 DOI: 10.3390/ph16091263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/23/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
Currently, the treatment of Proteus mirabilis infections is considered to be complicated as the organism has become resistant to numerous antibiotic classes. Therefore, new inhibitors should be developed, targeting bacterial molecular functions. Methionine tRNA synthetase (MetRS), a member of the aminoacyl-tRNA synthetase family, is essential for protein biosynthesis offering a promising target for novel antibiotics discovery. In the context of computer-aided drug design (CADD), the current research presents the construction and analysis of a comparative homology model for P. mirabilis MetRS, enabling development of novel inhibitors with greater selectivity. Molecular Operating Environment (MOE) software was used to build a homology model for P. mirabilis MetRS using Escherichia coli MetRS as a template. The model was evaluated, and the active site of the target protein predicted from its sequence using conservation analysis. Molecular dynamic simulations were performed to evaluate the stability of the modeled protein structure. In order to evaluate the predicted active site interactions, methionine (the natural substrate of MetRS) and several inhibitors of bacterial MetRS were docked into the constructed model using MOE. After validation of the model, pharmacophore-based virtual screening for a systemically prepared dataset of compounds was performed to prove the feasibility of the proposed model, identifying possible parent compounds for further development of MetRS inhibitors against P. mirabilis.
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Affiliation(s)
- Samar S. Elbaramawi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt; (S.S.E.); (A.G.E.); (N.A.N.)
| | - Ahmed G. Eissa
- Department of Medicinal Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt; (S.S.E.); (A.G.E.); (N.A.N.)
| | - Nada A. Noureldin
- Department of Medicinal Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt; (S.S.E.); (A.G.E.); (N.A.N.)
| | - Claire Simons
- School of Pharmacy & Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, Cardiff CF10 3NB, UK
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Nasim F, Qureshi IA. Aminoacyl tRNA Synthetases: Implications of Structural Biology in Drug Development against Trypanosomatid Parasites. ACS OMEGA 2023; 8:14884-14899. [PMID: 37151504 PMCID: PMC10157851 DOI: 10.1021/acsomega.3c00826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 03/29/2023] [Indexed: 05/09/2023]
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.
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Gill J, Sharma A. Exploration of aminoacyl-tRNA synthetases from eukaryotic parasites for drug development. J Biol Chem 2022; 299:102860. [PMID: 36596362 PMCID: PMC9978631 DOI: 10.1016/j.jbc.2022.102860] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 01/01/2023] Open
Abstract
Parasitic diseases result in considerable human morbidity and mortality. The continuous emergence and spread of new drug-resistant parasite strains is an obstacle to controlling and eliminating many parasitic diseases. Aminoacyl-tRNA synthetases (aaRSs) are ubiquitous enzymes essential for protein synthesis. The design and development of diverse small molecule, drug-like inhibitors against parasite-encoded and expressed aaRSs have validated this enzyme family as druggable. In this work, we have compiled the progress to date towards establishing the druggability of aaRSs in terms of their biochemical characterization, validation as targets, inhibitor development, and structural interpretation from parasites responsible for malaria (Plasmodium), lymphatic filariasis (Brugia,Wuchereria bancrofti), giardiasis (Giardia), toxoplasmosis (Toxoplasma gondii), leishmaniasis (Leishmania), cryptosporidiosis (Cryptosporidium), and trypanosomiasis (Trypanosoma). This work thus provides a robust framework for the systematic dissection of aaRSs from these pathogens and will facilitate the cross-usage of potential inhibitors to jump-start anti-parasite drug development.
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Affiliation(s)
- Jasmita Gill
- ICMR-National Institute of Malaria Research, New Delhi, India
| | - Amit Sharma
- ICMR-National Institute of Malaria Research, New Delhi, India; Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
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Volynets GP, Gudzera OI, Usenko MO, Gorbatiuk OB, Yarmoluk SM, Tukalo MA. Probing interactions of aminoacyl-adenylate with Mycobacterium tuberculosis methionyl-tRNA synthetase through in silico site-directed mutagenesis and free energy calculation. J Biomol Struct Dyn 2022:1-9. [PMID: 35930324 DOI: 10.1080/07391102.2022.2107574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Methionyl-tRNA synthetase (MetRS) is an attractive molecular target for antibiotic discovery. Recently, we have developed several classes of small-molecular inhibitors of Mycobacterium tuberculosis MetRS possessing antibacterial activity. In this article, we performed in silico site-directed mutagenesis of aminoacyl-adenylate binding site of M. tuberculosis MetRS in order to identify crucial amino acid residues for substrate interaction. The umbrella sampling algorithm was used to calculate the binding free energy (ΔG) of these mutated forms with methionyl-adenylate analogue. According to the obtained results, the replacement of Glu24 and Leu293 by alanine leads to the most significant decrease in the binding free energy (ΔG) for adenylate analogue with methionyl-tRNA synthetase indicating increasing of the affinity, which in turn causes the loss of compounds inhibitory activity. Therefore, these amino acid residues can be proposed for further experimental site-directed mutagenesis to confirm binding mode of inhibitors and should be taken into account during chemical optimization to overcome resistance due to mutations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Galyna P Volynets
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics, the NAS of Ukraine, Kyiv, Ukraine
| | - Olga I Gudzera
- Department of Protein Synthesis Enzymology, Institute of Molecular Biology and Genetics, the NAS of Ukraine, Kyiv, Ukraine
| | - Mariia O Usenko
- Department of Cell Regulatory Mechanisms, Institute of Molecular Biology and Genetics, the NAS of Ukraine, Kyiv, Ukraine
| | - Oksana B Gorbatiuk
- Department of Cell Regulatory Mechanisms, Institute of Molecular Biology and Genetics, the NAS of Ukraine, Kyiv, Ukraine
| | - Sergiy M Yarmoluk
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics, the NAS of Ukraine, Kyiv, Ukraine
| | - Michael A Tukalo
- Department of Protein Synthesis Enzymology, Institute of Molecular Biology and Genetics, the NAS of Ukraine, Kyiv, Ukraine
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Sanz-Rodríguez CE, Hoffman B, Guyett PJ, Purmal A, Singh B, Pollastri MP, Mensa-Wilmot K. Physiologic Targets and Modes of Action for CBL0137, a Lead for Human African Trypanosomiasis Drug Development. Mol Pharmacol 2022; 102:1-16. [PMID: 35605992 PMCID: PMC9341264 DOI: 10.1124/molpharm.121.000430] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 04/20/2022] [Indexed: 08/15/2023] Open
Abstract
CBL0137 is a lead drug for human African trypanosomiasis, caused by Trypanosoma brucei Herein, we use a four-step strategy to 1) identify physiologic targets and 2) determine modes of molecular action of CBL0137 in the trypanosome. First, we identified fourteen CBL0137-binding proteins using affinity chromatography. Second, we developed hypotheses of molecular modes of action, using predicted functions of CBL0137-binding proteins as guides. Third, we documented effects of CBL0137 on molecular pathways in the trypanosome. Fourth, we identified physiologic targets of the drug by knocking down genes encoding CBL0137-binding proteins and comparing their molecular effects to those obtained when trypanosomes were treated with CBL0137. CBL0137-binding proteins included glycolysis enzymes (aldolase, glyceraldehyde-3-phosphate dehydrogenase, phosphofructokinase, phosphoglycerate kinase) and DNA-binding proteins [universal minicircle sequence binding protein 2, replication protein A1 (RPA1), replication protein A2 (RPA2)]. In chemical biology studies, CBL0137 did not reduce ATP level in the trypanosome, ruling out glycolysis enzymes as crucial targets for the drug. Thus, many CBL0137-binding proteins are not physiologic targets of the drug. CBL0137 inhibited 1) nucleus mitosis, 2) nuclear DNA replication, and 3) polypeptide synthesis as the first carbazole inhibitor of eukaryote translation. RNA interference (RNAi) against RPA1 inhibited both DNA synthesis and mitosis, whereas RPA2 knockdown inhibited mitosis, consistent with both proteins being physiologic targets of CBL0137. Principles used here to distinguish drug-binding proteins from physiologic targets of CBL0137 can be deployed with different drugs in other biologic systems. SIGNIFICANCE STATEMENT: To distinguish drug-binding proteins from physiologic targets in the African trypanosome, we devised and executed a multidisciplinary approach involving biochemical, genetic, cell, and chemical biology experiments. The strategy we employed can be used for drugs in other biological systems.
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Affiliation(s)
- Carlos E Sanz-Rodríguez
- Department of Cellular Biology, University of Georgia, Athens, Georgia (C.E.S.-R., B.H., P.J.G., K.M.-W.); Buffalo Biolabs Inc, Buffalo, New York (A.P.); Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts (B.S., M.P.); and Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, Georgia (K.M.-W.)
| | - Benjamin Hoffman
- Department of Cellular Biology, University of Georgia, Athens, Georgia (C.E.S.-R., B.H., P.J.G., K.M.-W.); Buffalo Biolabs Inc, Buffalo, New York (A.P.); Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts (B.S., M.P.); and Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, Georgia (K.M.-W.)
| | - Paul J Guyett
- Department of Cellular Biology, University of Georgia, Athens, Georgia (C.E.S.-R., B.H., P.J.G., K.M.-W.); Buffalo Biolabs Inc, Buffalo, New York (A.P.); Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts (B.S., M.P.); and Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, Georgia (K.M.-W.)
| | - Andrei Purmal
- Department of Cellular Biology, University of Georgia, Athens, Georgia (C.E.S.-R., B.H., P.J.G., K.M.-W.); Buffalo Biolabs Inc, Buffalo, New York (A.P.); Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts (B.S., M.P.); and Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, Georgia (K.M.-W.)
| | - Baljinder Singh
- Department of Cellular Biology, University of Georgia, Athens, Georgia (C.E.S.-R., B.H., P.J.G., K.M.-W.); Buffalo Biolabs Inc, Buffalo, New York (A.P.); Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts (B.S., M.P.); and Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, Georgia (K.M.-W.)
| | - Michael P Pollastri
- Department of Cellular Biology, University of Georgia, Athens, Georgia (C.E.S.-R., B.H., P.J.G., K.M.-W.); Buffalo Biolabs Inc, Buffalo, New York (A.P.); Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts (B.S., M.P.); and Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, Georgia (K.M.-W.)
| | - Kojo Mensa-Wilmot
- Department of Cellular Biology, University of Georgia, Athens, Georgia (C.E.S.-R., B.H., P.J.G., K.M.-W.); Buffalo Biolabs Inc, Buffalo, New York (A.P.); Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts (B.S., M.P.); and Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, Georgia (K.M.-W.)
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Yi J, Cai Z, Qiu H, Lu F, Luo Z, Chen B, Gu Q, Xu J, Zhou H. Fragment screening and structural analyses highlight the ATP-assisted ligand binding for inhibitor discovery against type 1 methionyl-tRNA synthetase. Nucleic Acids Res 2022; 50:4755-4768. [PMID: 35474479 PMCID: PMC9071491 DOI: 10.1093/nar/gkac285] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 04/05/2022] [Accepted: 04/13/2022] [Indexed: 12/24/2022] Open
Abstract
Methionyl-tRNA synthetase (MetRS) charges tRNAMet with l-methionine (L-Met) to decode the ATG codon for protein translation, making it indispensable for all cellular lives. Many gram-positive bacteria use a type 1 MetRS (MetRS1), which is considered a promising antimicrobial drug target due to its low sequence identity with human cytosolic MetRS (HcMetRS, which belongs to MetRS2). Here, we report crystal structures of a representative MetRS1 from Staphylococcus aureus (SaMetRS) in its apo and substrate-binding forms. The connecting peptide (CP) domain of SaMetRS differs from HcMetRS in structural organization and dynamic movement. We screened 1049 chemical fragments against SaMetRS preincubated with or without substrate ATP, and ten hits were identified. Four cocrystal structures revealed that the fragments bound to either the L-Met binding site or an auxiliary pocket near the tRNA CCA end binding site of SaMetRS. Interestingly, fragment binding was enhanced by ATP in most cases, suggesting a potential ATP-assisted ligand binding mechanism in MetRS1. Moreover, co-binding with ATP was also observed in our cocrystal structure of SaMetRS with a class of newly reported inhibitors that simultaneously occupied the auxiliary pocket, tRNA site and L-Met site. Our findings will inspire the development of new MetRS1 inhibitors for fighting microbial infections.
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Affiliation(s)
| | | | - Haipeng Qiu
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China,Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Feihu Lu
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China,Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhiteng Luo
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China,Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Bingyi Chen
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China,Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Qiong Gu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jun Xu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Huihao Zhou
- To whom correspondence should be addressed. Tel: +86 20 39943350;
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Parrot C, Moulinier L, Bernard F, Hashem Y, Dupuy D, Sissler M. Peculiarities of aminoacyl-tRNA synthetases from trypanosomatids. J Biol Chem 2021; 297:100913. [PMID: 34175310 PMCID: PMC8319005 DOI: 10.1016/j.jbc.2021.100913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/17/2021] [Accepted: 06/22/2021] [Indexed: 10/28/2022] Open
Abstract
Trypanosomatid parasites are responsible for various human diseases, such as sleeping sickness, animal trypanosomiasis, or cutaneous and visceral leishmaniases. The few available drugs to fight related parasitic infections are often toxic and present poor efficiency and specificity, and thus, finding new molecular targets is imperative. Aminoacyl-tRNA synthetases (aaRSs) are essential components of the translational machinery as they catalyze the specific attachment of an amino acid onto cognate tRNA(s). In trypanosomatids, one gene encodes both cytosolic- and mitochondrial-targeted aaRSs, with only three exceptions. We identify here a unique specific feature of aaRSs from trypanosomatids, which is that most of them harbor distinct insertion and/or extension sequences. Among the 26 identified aaRSs in the trypanosome Leishmania tarentolae, 14 contain an additional domain or a terminal extension, confirmed in mature mRNAs by direct cDNA nanopore sequencing. Moreover, these RNA-Seq data led us to address the question of aaRS dual localization and to determine splice-site locations and the 5'-UTR lengths for each mature aaRS-encoding mRNA. Altogether, our results provided evidence for at least one specific mechanism responsible for mitochondrial addressing of some L. tarentolae aaRSs. We propose that these newly identified features of trypanosomatid aaRSs could be developed as relevant drug targets to combat the diseases caused by these parasites.
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Affiliation(s)
- Camila Parrot
- ARNA - UMR5320 CNRS - U1212 INSERM, Université de Bordeaux, IECB, Pessac, France
| | - Luc Moulinier
- CSTB Complex Systems and Translational Bioinformatics, ICube laboratory and Strasbourg Federation of Translational Medicine (FMTS), CNRS, Université de Strasbourg, Strasbourg, France
| | - Florian Bernard
- ARNA - UMR5320 CNRS - U1212 INSERM, Université de Bordeaux, IECB, Pessac, France
| | - Yaser Hashem
- ARNA - UMR5320 CNRS - U1212 INSERM, Université de Bordeaux, IECB, Pessac, France
| | - Denis Dupuy
- ARNA - UMR5320 CNRS - U1212 INSERM, Université de Bordeaux, IECB, Pessac, France
| | - Marie Sissler
- ARNA - UMR5320 CNRS - U1212 INSERM, Université de Bordeaux, IECB, Pessac, France.
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Spontaneous Selection of Cryptosporidium Drug Resistance in a Calf Model of Infection. Antimicrob Agents Chemother 2021; 65:AAC.00023-21. [PMID: 33753338 DOI: 10.1128/aac.00023-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/17/2021] [Indexed: 01/20/2023] Open
Abstract
The intestinal protozoan Cryptosporidium is a leading cause of diarrheal disease and mortality in young children. There is currently no fully effective treatment for cryptosporidiosis, which has stimulated interest in anticryptosporidial development over the last ∼10 years, with numerous lead compounds identified, including several tRNA synthetase inhibitors. Here, we report the results of a dairy calf efficacy trial of the methionyl-tRNA (Cryptosporidium parvum MetRS [CpMetRS]) synthetase inhibitor 2093 and the spontaneous emergence of drug resistance. Dairy calves experimentally infected with Cryptosporidium parvum initially improved with 2093 treatment, but parasite shedding resumed in two of three calves on treatment day 5. Parasites shed by each recrudescent calf had different amino acid-altering mutations in the gene encoding CpMetRS (CpMetRS), yielding either an aspartate 243-to-glutamate (D243E) or a threonine 246-to-isoleucine (T246I) mutation. Transgenic parasites engineered to have either the D243E or T246I CpMetRS mutation using CRISPR/Cas9 grew normally but were highly 2093 resistant; the D243E and T246I mutant-expressing parasites, respectively, had 2093 half-maximal effective concentrations (EC50s) that were 613- and 128-fold that of transgenic parasites with wild-type CpMetRS. In studies using recombinant enzymes, the D243E and T246I mutations shifted the 2093 IC50 >170-fold. Structural modeling of CpMetRS based on an inhibitor-bound Trypanosoma brucei MetRS crystal structure suggested that the resistance mutations reposition nearby hydrophobic residues, interfering with compound binding while minimally impacting substrate binding. This is the first report of naturally emerging Cryptosporidium drug resistance, highlighting the need to address the potential for anticryptosporidial resistance and establish strategies to limit its occurrence.
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Pang L, Weeks SD, Van Aerschot A. Aminoacyl-tRNA Synthetases as Valuable Targets for Antimicrobial Drug Discovery. Int J Mol Sci 2021; 22:1750. [PMID: 33578647 PMCID: PMC7916415 DOI: 10.3390/ijms22041750] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/04/2021] [Accepted: 02/06/2021] [Indexed: 12/20/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) catalyze the esterification of tRNA with a cognate amino acid and are essential enzymes in all three kingdoms of life. Due to their important role in the translation of the genetic code, aaRSs have been recognized as suitable targets for the development of small molecule anti-infectives. In this review, following a concise discussion of aaRS catalytic and proof-reading activities, the various inhibitory mechanisms of reported natural and synthetic aaRS inhibitors are discussed. Using the expanding repository of ligand-bound X-ray crystal structures, we classified these compounds based on their binding sites, focusing on their ability to compete with the association of one, or more of the canonical aaRS substrates. In parallel, we examined the determinants of species-selectivity and discuss potential resistance mechanisms of some of the inhibitor classes. Combined, this structural perspective highlights the opportunities for further exploration of the aaRS enzyme family as antimicrobial targets.
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Affiliation(s)
- Luping Pang
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49–box 1041, 3000 Leuven, Belgium;
- KU Leuven, Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, Herestraat 49–box 822, 3000 Leuven, Belgium
| | | | - Arthur Van Aerschot
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49–box 1041, 3000 Leuven, Belgium;
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