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Tye MA, Payne NC, Johansson C, Singh K, Santos SA, Fagbami L, Pant A, Sylvester K, Luth MR, Marques S, Whitman M, Mota MM, Winzeler EA, Lukens AK, Derbyshire ER, Oppermann U, Wirth DF, Mazitschek R. Elucidating the path to Plasmodium prolyl-tRNA synthetase inhibitors that overcome halofuginone resistance. Nat Commun 2022; 13:4976. [PMID: 36008486 PMCID: PMC9403976 DOI: 10.1038/s41467-022-32630-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 08/10/2022] [Indexed: 02/07/2023] Open
Abstract
The development of next-generation antimalarials that are efficacious against the human liver and asexual blood stages is recognized as one of the world's most pressing public health challenges. In recent years, aminoacyl-tRNA synthetases, including prolyl-tRNA synthetase, have emerged as attractive targets for malaria chemotherapy. We describe the development of a single-step biochemical assay for Plasmodium and human prolyl-tRNA synthetases that overcomes critical limitations of existing technologies and enables quantitative inhibitor profiling with high sensitivity and flexibility. Supported by this assay platform and co-crystal structures of representative inhibitor-target complexes, we develop a set of high-affinity prolyl-tRNA synthetase inhibitors, including previously elusive aminoacyl-tRNA synthetase triple-site ligands that simultaneously engage all three substrate-binding pockets. Several compounds exhibit potent dual-stage activity against Plasmodium parasites and display good cellular host selectivity. Our data inform the inhibitor requirements to overcome existing resistance mechanisms and establish a path for rational development of prolyl-tRNA synthetase-targeted anti-malarial therapies.
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Affiliation(s)
- Mark A Tye
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Graduate School of Arts and Sciences, Cambridge, MA, USA
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - N Connor Payne
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Catrine Johansson
- Botnar Research Centre, NIHR Oxford Biomedical Research Unit, University of Oxford, Oxford, UK
- Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Kritika Singh
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Sofia A Santos
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Lọla Fagbami
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Graduate School of Arts and Sciences, Cambridge, MA, USA
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Akansha Pant
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Madeline R Luth
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Sofia Marques
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Malcolm Whitman
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA, USA
| | - Maria M Mota
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Elizabeth A Winzeler
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | | | | | - Udo Oppermann
- Botnar Research Centre, NIHR Oxford Biomedical Research Unit, University of Oxford, Oxford, UK
- Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Dyann F Wirth
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ralph Mazitschek
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA.
- Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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2
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Bodman SE, Breen C, Kirkland S, Wheeler S, Robertson E, Plasser F, Butler SJ. Sterically demanding macrocyclic Eu(iii) complexes for selective recognition of phosphate and real-time monitoring of enzymatically generated adenosine monophosphate. Chem Sci 2022; 13:3386-3394. [PMID: 35432862 PMCID: PMC8943852 DOI: 10.1039/d1sc05377a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 02/10/2022] [Indexed: 12/15/2022] Open
Abstract
The design of molecular receptors that bind and sense anions in biologically relevant aqueous solutions is a key challenge in supramolecular chemistry. The recognition of inorganic phosphate is particularly challenging because of its high hydration energy and pH dependent speciation. Adenosine monophosphate (AMP) represents a valuable but elusive target for supramolecular detection because of its structural similarity to the more negatively charged anions, ATP and ADP. We report two new macrocyclic Eu(iii) receptors capable of selectively sensing inorganic phosphate and AMP in water. The receptors contain a sterically demanding 8-(benzyloxy)quinoline pendant arm that coordinates to the metal centre, creating a binding pocket suitable for phosphate and AMP, whilst excluding potentially interfering chelating anions, in particular ATP, bicarbonate and lactate. The sensing selectivity of our Eu(iii) receptors follows the order AMP > ADP > ATP, which represents a reversal of the order of selectivity observed for most reported nucleoside phosphate receptors. We have exploited the unique host–guest induced changes in emission intensity and lifetime for the detection of inorganic phosphate in human serum samples, and for monitoring the enzymatic production of AMP in real-time. We present two new europium-based anion receptors that selectively bind to inorganic phosphate and AMP in aqueous media. Their sensing selectivity follows the order AMP > ADP > ATP, representing a reversal of the selectivity order observed for most nucleoside phosphate receptors.![]()
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Affiliation(s)
- Samantha E. Bodman
- Department of Chemistry, Loughborough University, Epinal Way, Loughborough, LE11 3TU, UK
| | - Colum Breen
- Department of Chemistry, Loughborough University, Epinal Way, Loughborough, LE11 3TU, UK
| | - Sam Kirkland
- Department of Chemistry, Loughborough University, Epinal Way, Loughborough, LE11 3TU, UK
| | - Simon Wheeler
- Department of Chemistry, Loughborough University, Epinal Way, Loughborough, LE11 3TU, UK
| | - Erin Robertson
- Department of Chemistry, Loughborough University, Epinal Way, Loughborough, LE11 3TU, UK
| | - Felix Plasser
- Department of Chemistry, Loughborough University, Epinal Way, Loughborough, LE11 3TU, UK
| | - Stephen J. Butler
- Department of Chemistry, Loughborough University, Epinal Way, Loughborough, LE11 3TU, UK
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3
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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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4
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Itoh M, Dai H, Horike SI, Gonzalez J, Kitami Y, Meguro-Horike M, Kuki I, Shimakawa S, Yoshinaga H, Ota Y, Okazaki T, Maegaki Y, Nabatame S, Okazaki S, Kawawaki H, Ueno N, Goto YI, Kato Y. Biallelic KARS pathogenic variants cause an early-onset progressive leukodystrophy. Brain 2020; 142:560-573. [PMID: 30715177 DOI: 10.1093/brain/awz001] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 11/09/2018] [Accepted: 11/27/2018] [Indexed: 12/13/2022] Open
Abstract
The leukodystrophies cause severe neurodevelopmental defects from birth and follow an incurable and progressive course that often leads to premature death. It has recently been reported that abnormalities in aminoacyl t-RNA synthetase (ARS) genes are linked to various unique leukodystrophies and leukoencephalopathies. Aminoacyl t-RNA synthetase proteins are fundamentally known as the first enzymes of translation, catalysing the conjugation of amino acids to cognate tRNAs for protein synthesis. It is known that certain aminoacyl t-RNA synthetase have multiple non-canonical roles in both transcription and translation, and their disruption results in varied and complicated phenotypes. We clinically and genetically studied seven patients (six male and one female; aged 2 to 12 years) from five unrelated families who all showed the same phenotypes of severe developmental delay or arrest (7/7), hypotonia (6/7), deafness (7/7) and inability to speak (6/7). The subjects further developed intractable epilepsy (7/7) and nystagmus (6/6) with increasing age. They demonstrated characteristic laboratory data, including increased lactate and/or pyruvate levels (7/7), and imaging findings (7/7), including calcification and abnormal signals in the white matter and pathological involvement (2/2) of the corticospinal tracts. Through whole-exome sequencing, we discovered genetic abnormalities in lysyl-tRNA synthetase (KARS). All patients harboured the variant [c.1786C>T, p.Leu596Phe] KARS isoform 1 ([c.1702C>T, p.Leu568Phe] of KARS isoform 2) either in the homozygous state or compound heterozygous state with the following KARS variants, [c.879+1G>A; c.1786C>T, p.Glu252_Glu293del; p.Leu596Phe] ([c.795+1G>A; c.1702C>T, p.Glu224_Glu255del; p.Leu568Phe]) and [c.650G>A; c.1786C>T, p.Gly217Asp; p.Leu596Phe] ([c.566G>A; c.1702C>T, p.Gly189Asp; p.Leu568Phe]). Moreover, similarly disrupted lysyl-tRNA synthetase (LysRS) proteins showed reduced enzymatic activities and abnormal CNSs in Xenopus embryos. Additionally, LysRS acts as a non-canonical inducer of the immune response and has transcriptional activity. We speculated that the complex functions of the abnormal LysRS proteins led to the severe phenotypes in our patients. These KARS pathological variants are novel, including the variant [c.1786C>T; p.Leu596Phe] (c.1702C>T; p.Leu568Phe) shared by all patients in the homozygous or compound-heterozygous state. This common position may play an important role in the development of severe progressive leukodystrophy. Further research is warranted to further elucidate this relationship and to investigate how specific mutated LysRS proteins function to understand the broad spectrum of KARS-related diseases.
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Affiliation(s)
- Masayuki Itoh
- Department of Mental Retardation and Birth Defect Research, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Hongmei Dai
- Department of Mental Retardation and Birth Defect Research, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Shin-Ichi Horike
- Advanced Science Research Center, Kanazawa University, Kanazawa, Japan
| | - John Gonzalez
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL, USA
| | - Yoshikazu Kitami
- Department of Mental Retardation and Birth Defect Research, National Center of Neurology and Psychiatry, Kodaira, Japan
| | | | - Ichiro Kuki
- Department of Pediatric Neurology, Osaka City General Hospital, Osaka, Japan
| | | | - Harumi Yoshinaga
- Department of Child Neurology, Okayama University, Okayama, Japan
| | - Yoko Ota
- Department of Pathology and Experimental Medicine, Okayama University, Okayama, Japan
| | - Tetsuya Okazaki
- Department of Child Neurology, University of Tottori, Yonago, Japan
| | | | - Shin Nabatame
- Department of Pediatrics, Osaka University, Osaka, Japan
| | - Shin Okazaki
- Department of Pediatric Neurology, Osaka City General Hospital, Osaka, Japan
| | - Hisashi Kawawaki
- Department of Pediatric Neurology, Osaka City General Hospital, Osaka, Japan
| | - Naoto Ueno
- Department of Developmental Biology, National Institute for Basic Biology, Natural Institutes of Natural Sciences, Okazaki, Japan.,Department of Basic Biology, School of Life Science, the Graduate University of Advanced Studies (SOKENDAI), Hayama, Japan
| | - Yu-Ichi Goto
- Department of Mental Retardation and Birth Defect Research, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Yoichi Kato
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL, USA.,Department of Cell Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
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5
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Zhang P, Ma S. Recent development of leucyl-tRNA synthetase inhibitors as antimicrobial agents. MEDCHEMCOMM 2019; 10:1329-1341. [PMID: 31534653 PMCID: PMC6727470 DOI: 10.1039/c9md00139e] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 05/26/2019] [Indexed: 12/14/2022]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) widely exist in organisms and mediate protein synthesis. Inhibiting these synthetases can lead to the termination of protein synthesis and subsequently achieve antibacterial and antiparasitic purposes. Moreover, the structures of aaRSs found in eukaryotes have considerable structural differences compared to those in prokaryotes, based on which it is possible to develop highly selective inhibitors. Leucyl-tRNA synthetase (LeuRS) with unique synthesis and editing sites is one of 20 kinds of aaRSs. Many inhibitors targeting LeuRS have been designed and synthesized, some of which have entered clinical use. For example, the benzoxaborole compound AN2690 has been approved by the FDA for the treatment of onychomycosis. AN3365 is suspended in the phase II clinical trial due to the rapid development of AN3365 resistance, but it may be used in combination with other antibiotics. The aaRSs, especially LeuRS, are being considered as targets of new potential anti-infective drugs for the treatment of not only bacterial or fungal infections but also infections by trypanosomes and malaria parasites. This review mainly describes the development of LeuRS inhibitors, focusing on their mechanisms of action, structure-activity relationships (SARs), and in vitro and in vivo activities.
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Affiliation(s)
- Panpan Zhang
- Department of Medicinal Chemistry , Key Laboratory of Chemical Biology , Ministry of Education , School of Pharmaceutical Sciences , Shandong University , 44, West Culture Road , Jinan 250012 , P. R. China . E mail:
| | - Shutao Ma
- Department of Medicinal Chemistry , Key Laboratory of Chemical Biology , Ministry of Education , School of Pharmaceutical Sciences , Shandong University , 44, West Culture Road , Jinan 250012 , P. R. China . E mail:
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6
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Charlton MH, Aleksis R, Saint-Leger A, Gupta A, Loza E, Ribas de Pouplana L, Kaula I, Gustina D, Madre M, Lola D, Jaudzems K, Edmund G, Randall CP, Kime L, O’Neill AJ, Goessens W, Jirgensons A, Finn PW. N-Leucinyl Benzenesulfonamides as Structurally Simplified Leucyl-tRNA Synthetase Inhibitors. ACS Med Chem Lett 2018; 9:84-88. [PMID: 29456792 DOI: 10.1021/acsmedchemlett.7b00374] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 01/18/2018] [Indexed: 12/12/2022] Open
Abstract
N-Leucinyl benzenesulfonamides have been discovered as a novel class of potent inhibitors of E. coli leucyl-tRNA synthetase. The binding of inhibitors to the enzyme was measured by using isothermal titration calorimetry. This provided information on enthalpy and entropy contributions to binding, which, together with docking studies, were used for structure-activity relationship analysis. Enzymatic assays revealed that N-leucinyl benzenesulfonamides display remarkable selectivity for E. coli leucyl-tRNA synthetase compared to S. aureus and human orthologues. The simplest analogue of the series, N-leucinyl benzenesulfonamide (R = H), showed the highest affinity against E. coli leucyl-tRNA synthetase and also exhibited antibacterial activity against Gram-negative pathogens (the best MIC = 8 μg/mL, E. coli ATCC 25922), which renders it as a promising template for antibacterial drug discovery.
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Affiliation(s)
- Michael H. Charlton
- Oxford Drug Design Ltd., Oxford Centre for Innovation, New Road, Oxford, OX1 1BY. U.K
| | - Rihards Aleksis
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia
| | - Adélaïde Saint-Leger
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Catalonia, Spain
- ICREA, Pg. Lluís Company 23, 08010 Barcelona, Catalonia, Spain
| | - Arya Gupta
- Antimicrobial
Research Centre and School of Molecular and Cellular Biology, Faculty
of Biological Sciences, University of Leeds, Leeds, LS2 9JT, U.K
| | - Einars Loza
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Catalonia, Spain
- ICREA, Pg. Lluís Company 23, 08010 Barcelona, Catalonia, Spain
| | - Ilze Kaula
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia
| | - Daina Gustina
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia
| | - Marina Madre
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia
| | - Daina Lola
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia
| | - Kristaps Jaudzems
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia
| | - Grace Edmund
- Oxford Drug Design Ltd., Oxford Centre for Innovation, New Road, Oxford, OX1 1BY. U.K
| | - Christopher P. Randall
- Antimicrobial
Research Centre and School of Molecular and Cellular Biology, Faculty
of Biological Sciences, University of Leeds, Leeds, LS2 9JT, U.K
| | - Louise Kime
- Antimicrobial
Research Centre and School of Molecular and Cellular Biology, Faculty
of Biological Sciences, University of Leeds, Leeds, LS2 9JT, U.K
| | - Alex J. O’Neill
- Antimicrobial
Research Centre and School of Molecular and Cellular Biology, Faculty
of Biological Sciences, University of Leeds, Leeds, LS2 9JT, U.K
| | - Wil Goessens
- Erasmus University Medical Center Rotterdam, Department
of Medical Microbiology and Infectious Diseases, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Aigars Jirgensons
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia
| | - Paul W. Finn
- Oxford Drug Design Ltd., Oxford Centre for Innovation, New Road, Oxford, OX1 1BY. U.K
- Department
of Applied Computing, University of Buckingham, Hunter Street, Buckingham, MK18 1EG, U.K
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Grube CD, Roy H. A continuous assay for monitoring the synthetic and proofreading activities of multiple aminoacyl-tRNA synthetases for high-throughput drug discovery. RNA Biol 2017; 15:659-666. [PMID: 29168435 PMCID: PMC6103669 DOI: 10.1080/15476286.2017.1397262] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) catalyze the aminoacylation of tRNAs to produce the aminoacyl-tRNAs (aa-tRNAs) required by ribosomes for translation of the genetic message into proteins. To ensure the accuracy of tRNA aminoacylation, and consequently the fidelity of protein synthesis, some aaRSs exhibit a proofreading (editing) site, distinct from the aa-tRNA synthetic site. The aaRS editing site hydrolyzes misacylated products formed when a non-cognate amino acid is used during tRNA charging. Because aaRSs play a central role in protein biosynthesis and cellular life, these proteins represent longstanding targets for therapeutic drug development to combat infectious diseases. Most existing aaRS inhibitors target the synthetic site, and it is only recently that drugs targeting the proofreading site have been considered. In the present study, we developed a robust assay for the high-throughput screening of libraries of inhibitors targeting both the synthetic and the proofreading sites of up to four aaRSs simultaneously. Thus, this assay allows for screening of eight distinct enzyme active sites in a single experiment. aaRSs from several prominent human pathogens (i.e., Mycobacterium tuberculosis, Plasmodium falciparum, and Escherichia coli) were used for development of this assay.
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Affiliation(s)
- Christopher D Grube
- a Burnett School of Biomedical Sciences, College of Medicine , University of Central Florida , Orlando , Florida , United States of America
| | - Hervé Roy
- a Burnett School of Biomedical Sciences, College of Medicine , University of Central Florida , Orlando , Florida , United States of America
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