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Bobrovs R, Bolsakova J, Buitrago JAR, Varaceva L, Skvorcova M, Kanepe I, Rudnickiha A, Parisini E, Jirgensons A. Structure-based identification of salicylic acid derivatives as malarial threonyl tRNA-synthetase inhibitors. PLoS One 2024; 19:e0296995. [PMID: 38558084 PMCID: PMC10984466 DOI: 10.1371/journal.pone.0296995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/21/2023] [Indexed: 04/04/2024] Open
Abstract
Emerging resistance to existing antimalarial drugs drives the search for new antimalarials, and protein translation is a promising pathway to target. Threonyl t-RNA synthetase (ThrRS) is one of the enzymes involved in this pathway, and it has been validated as an anti-malarial drug target. Here, we present 9 structurally diverse low micromolar Plasmodium falciparum ThrRS inhibitors that were identified using high-throughput virtual screening (HTVS) and were verified in a FRET enzymatic assay. Salicylic acid-based compound (LE = 0.34) was selected as a most perspective hit and was subjected to hit-to-lead optimisation. A total of 146 hit analogues were synthesised or obtained from commercial vendors and were tested. Structure-activity relationship study was supported by the crystal structure of the complex of a salicylic acid analogue with a close homologue of the plasmodium target, E. coli ThrRS (EcThrRS). Despite the availability of structural information, the hit identified via virtual screening remained one of the most potent PfThrRS inhibitors within this series. However, the compounds presented herein provide novel scaffolds for ThrRS inhibitors, which could serve as starting points for further medicinal chemistry projects targeting ThrRSs or structurally similar enzymes.
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Affiliation(s)
| | | | | | | | | | - Iveta Kanepe
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | | | - Emilio Parisini
- Latvian Institute of Organic Synthesis, Riga, Latvia
- Department of Chemistry “G. Ciamician”, University of Bologna, Bologna, Italy
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2
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Bolsakova J, Bobrovs R, Varacheva L, Rudnickiha A, Kanepe I, Parisini E, Jirgensons A. Discovery of Malarial Threonyl tRNA Synthetase Inhibitors by Screening of a Focused Fragment Library. ACS Med Chem Lett 2024; 15:76-80. [PMID: 38229753 PMCID: PMC10789136 DOI: 10.1021/acsmedchemlett.3c00403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 12/10/2023] [Accepted: 12/13/2023] [Indexed: 01/18/2024] Open
Abstract
While Plasmodium falciparum threonyl tRNA synthetase (PfThrRS) has clearly been validated as a prospective antimalarial drug target, the number of known inhbitors of this enzyme is still limited. In order to expand the chemotypes acting as inhibitors of PfThrRS, a set of fragments were designed which incorporated bioisosteres of the N-acylphosphate moiety of the aminoacyladenylate as an intermediate of an enzymatic reaction. N-Acyl sulfamate- and N-acyl benzenethiazolsulfonamide-based fragments 9a and 9k were identified as inhibitors of the PfThrRSby biochemical assay at 100 μM concentration. These fragments were then developed into potent PfThrRS inhibitors (10a,b and 11) by linking them with an amino pyrimidine as a bioisostere of adenine in the enzymatic reaction intermediate.
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Affiliation(s)
| | - Raitis Bobrovs
- Latvian
Institute of Organic Synthesis, Riga LV-1006, Latvia
| | | | | | - Iveta Kanepe
- Latvian
Institute of Organic Synthesis, Riga LV-1006, Latvia
| | - Emilio Parisini
- Latvian
Institute of Organic Synthesis, Riga LV-1006, Latvia
- Department
of Chemistry “G. Ciamician”, University of Bologna, 40126 Bologna, Italy
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3
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Peck Y, Pickering D, Mobli M, Liddell MJ, Wilson DT, Ruscher R, Ryan S, Buitrago G, McHugh C, Love NC, Pinlac T, Haertlein M, Kron MA, Loukas A, Daly NL. Solution structure of the N-terminal extension domain of a Schistosoma japonicum asparaginyl-tRNA synthetase. J Biomol Struct Dyn 2023:1-11. [PMID: 37572327 DOI: 10.1080/07391102.2023.2241918] [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: 01/11/2023] [Accepted: 07/24/2023] [Indexed: 08/14/2023]
Abstract
Several secreted proteins from helminths (parasitic worms) have been shown to have immunomodulatory activities. Asparaginyl-tRNA synthetases are abundantly secreted in the filarial nematode Brugia malayi (BmAsnRS) and the parasitic flatworm Schistosoma japonicum (SjAsnRS), indicating a possible immune function. The suggestion is supported by BmAsnRS alleviating disease symptoms in a T-cell transfer mouse model of colitis. This immunomodulatory function is potentially related to an N-terminal extension domain present in eukaryotic AsnRS proteins but few structure/function studies have been done on this domain. Here we have determined the three-dimensional solution structure of the N-terminal extension domain of SjAsnRS. A protein containing the 114 N-terminal amino acids of SjAsnRS was recombinantly expressed with isotopic labelling to allow structure determination using 3D NMR spectroscopy, and analysis of dynamics using NMR relaxation experiments. Structural comparisons of the N-terminal extension domain of SjAsnRS with filarial and human homologues highlight a high degree of variability in the β-hairpin region of these eukaryotic N-AsnRS proteins, but similarities in the disorder of the C-terminal regions. Limitations in PrDOS-based intrinsically disordered region (IDR) model predictions were also evident in this comparison. Empirical structural data such as that presented in our study for N-SjAsnRS will enhance the prediction of sequence-homology based structure modelling and prediction of IDRs in the future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yoshimi Peck
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Darren Pickering
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Mehdi Mobli
- Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD, Australia
| | - Michael J Liddell
- College of Science and Engineering, James Cook University, Cairns, QLD, Australia
| | - David T Wilson
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Roland Ruscher
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Stephanie Ryan
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Geraldine Buitrago
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Connor McHugh
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | | | - Theresa Pinlac
- Department of Biochemistry, University of the Philippines, Manila, Philippines
| | | | - Michael A Kron
- Department of Medicine, Division of Infectious Diseases, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Alex Loukas
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Norelle L Daly
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
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4
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Buitrago JAR, Leitis G, Kaņepe-Lapsa I, Rudnickiha A, Parisini E, Jirgensons A. Synthesis and evaluation of an agrocin 84 toxic moiety (TM84) analogue as a malarial threonyl tRNA synthetase inhibitor. Org Biomol Chem 2023. [PMID: 37335076 DOI: 10.1039/d3ob00670k] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
An analogue of a toxic moiety (TM84) of natural product agrocin 84 containing threonine amide instead of 2,3-dihydroxy-4-methylpentanamide was prepared and evaluated as a putative Plasmodium falciparum threonyl t-RNA synthetase (PfThrRS) inhibitor. This TM84 analogue features submicromolar inhibitory potency (IC50 = 440 nM) comparable to that of borrelidin (IC50 = 43 nM) and therefore complements chemotypes known to inhibit malarial PfThrRS, which are currently limited to borrelidin and its analogues. The crystal structure of the inhibitor in complex with the E. coli homologue enzyme (EcThrRS) was obtained, revealing crucial ligand-protein interactions that will pave the way for the design of novel ThrRS inhibitors.
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Affiliation(s)
| | - Gundars Leitis
- Latvian Institute of Organic Synthesis, Riga LV-1006, Latvia
| | | | | | - Emilio Parisini
- Latvian Institute of Organic Synthesis, Riga LV-1006, Latvia
- Department of Chemistry "G. Ciamician", University of Bologna, 40126, Bologna, Italy.
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Ansari A, Seth A, Dutta M, Qamar T, Katiyar S, Jaiswal AK, Rani A, Majhi S, Kumar M, Bhatta RS, Guha R, Mitra K, Sashidhara KV, Kar S. Discovery, SAR and mechanistic studies of quinazolinone-based acetamide derivatives in experimental visceral leishmaniasis. Eur J Med Chem 2023; 257:115524. [PMID: 37290183 DOI: 10.1016/j.ejmech.2023.115524] [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: 04/17/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/10/2023]
Abstract
Towards identification of novel therapeutic candidates, a series of quinazolinone-based acetamide derivatives were synthesized and assessed for their anti-leishmanial efficacy. Amongst synthesized derivatives, compounds F12, F27 and F30 demonstrated remarkable activity towards intracellular L. donovani amastigotes in vitro, with IC50 values of 5.76 ± 0.84 μM, 3.39 ± 0.85 μM and 8.26 ± 1.23 μM against promastigotes, and 6.02 μM ± 0.52, 3.55 ± 0.22 μM and 6.23 ± 0.13 μM against amastigotes, respectively. Oral administration of compounds F12 and F27 entailed >85% reduction in organ parasite burden in L. donovani-infected BALB/c mice and hamsters, by promoting host-protective Th1 cytokine response. In host J774 macrophages, mechanistic studies revealed inhibition of PI3K/Akt/CREB axis, resulting in a decrease of IL-10 versus IL-12 release upon F27 treatment. In silico docking studies conducted with lead compound, F27 demonstrated plausible inhibition of Leishmania prolyl-tRNA synthetase, which was validated via detection of decreased proline levels in parasites and induction of amino acid starvation, leading to G1 cell cycle arrest and autophagy-mediated programmed cell death of L. donovani promastigotes. Structure-activity analysis and study of pharmacokinetic and physicochemical parameters suggest oral availability and underscore F27 as a promising lead for anti-leishmanial drug development.
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Affiliation(s)
- Alisha Ansari
- Medicinal and Process Chemistry Division, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Anuradha Seth
- Molecular Microbiology & Immunology Division, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Mukul Dutta
- Molecular Microbiology & Immunology Division, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Tooba Qamar
- Molecular Microbiology & Immunology Division, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India
| | - Sarita Katiyar
- Medicinal and Process Chemistry Division, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Arvind K Jaiswal
- Medicinal and Process Chemistry Division, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India
| | - Ankita Rani
- Molecular Microbiology & Immunology Division, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Swetapadma Majhi
- Electron Microscopy Unit, Sophisticated Analytical Instrument Facility Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Mukesh Kumar
- Pharmacokinetics and Metabolism Division, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India
| | - Rabi S Bhatta
- Pharmacokinetics and Metabolism Division, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Rajdeep Guha
- Laboratory Animal Facility Division, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India
| | - Kalyan Mitra
- Electron Microscopy Unit, Sophisticated Analytical Instrument Facility Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Koneni V Sashidhara
- Medicinal and Process Chemistry Division, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India.
| | - Susanta Kar
- Molecular Microbiology & Immunology Division, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India.
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6
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Liu Y, Zhang T, Chen SB, Cui YB, Wang SQ, Zhang HW, Shen HM, Chen JH. Retrospective analysis of Plasmodium vivax genomes from a pre-elimination China inland population in the 2010s. Front Microbiol 2023; 14:1071689. [PMID: 36846776 PMCID: PMC9948256 DOI: 10.3389/fmicb.2023.1071689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 01/04/2023] [Indexed: 02/11/2023] Open
Abstract
Introduction In malaria-free countries, imported cases are challenging because interconnections with neighboring countries with higher transmission rates increase the risk of parasite reintroduction. Establishing a genetic database for rapidly identifying malaria importation or reintroduction is crucial in addressing these challenges. This study aimed to examine genomic epidemiology during the pre-elimination stage by retrospectively reporting whole-genome sequence variation of 10 Plasmodium vivax isolates from inland China. Methods The samples were collected during the last few inland outbreaks from 2011 to 2012 when China implemented a malaria control plan. After next-generation sequencing, we completed a genetic analysis of the population, explored the geographic specificity of the samples, and examined clustering of selection pressures. We also scanned genes for signals of positive selection. Results China's inland populations were highly structured compared to the surrounding area, with a single potential ancestor. Additionally, we identified genes under selection and evaluated the selection pressure on drug-resistance genes. In the inland population, positive selection was detected in some critical gene families, including sera, msp3, and vir. Meanwhile, we identified selection signatures in drug resistance, such as ugt, krs1, and crt, and noticed that the ratio of wild-type dhps and dhfr-ts increased after China banned sulfadoxine-pyrimethamine (SP) for decades. Discussion Our data provides an opportunity to investigate the molecular epidemiology of pre-elimination inland malaria populations, which exhibited lower selection pressure on invasion and immune evasion genes than neighbouring areas, but increased drug resistance in low transmission settings. Our results revealed that the inland population was severely fragmented with low relatedness among infections, despite a higher incidence of multiclonal infections, suggesting that superinfection or co-transmission events are rare in low-endemic circumstances. We identified selective signatures of resistance and found that the proportion of susceptible isolates fluctuated in response to the prohibition of specific drugs. This finding is consistent with the alterations in medication strategies during the malaria elimination campaign in inland China. Such findings could provide a genetic basis for future population studies, assessing changes in other pre-elimination countries.
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Affiliation(s)
- Ying Liu
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China,National Health Commission of the People’s Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, Shanghai, China,World Health Organization (WHO) Collaborating Center for Tropical Diseases, Shanghai, China,National Center for International Research on Tropical Diseases, Shanghai, China,Henan Provincial Center for Disease Control and Prevention, Zhengzhou, China
| | - Tao Zhang
- Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Shen-Bo Chen
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China,National Health Commission of the People’s Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, Shanghai, China,World Health Organization (WHO) Collaborating Center for Tropical Diseases, Shanghai, China,National Center for International Research on Tropical Diseases, Shanghai, China
| | - Yan-Bing Cui
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China,National Health Commission of the People’s Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, Shanghai, China,World Health Organization (WHO) Collaborating Center for Tropical Diseases, Shanghai, China,National Center for International Research on Tropical Diseases, Shanghai, China
| | - Shu-Qi Wang
- Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Hong-Wei Zhang
- Henan Provincial Center for Disease Control and Prevention, Zhengzhou, China
| | - Hai-Mo Shen
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China,National Health Commission of the People’s Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, Shanghai, China,World Health Organization (WHO) Collaborating Center for Tropical Diseases, Shanghai, China,National Center for International Research on Tropical Diseases, Shanghai, China,Hai-Mo Shen, ✉
| | - Jun-Hu Chen
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China,National Health Commission of the People’s Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, Shanghai, China,World Health Organization (WHO) Collaborating Center for Tropical Diseases, Shanghai, China,National Center for International Research on Tropical Diseases, Shanghai, China,School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China,*Correspondence: Jun-Hu Chen, ✉
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7
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Zhang S, Cai J, Xie Y, Zhang X, Yang X, Lin S, Xiang W, Zhang J. Anti-Phytophthora Activity of Halofuginone and the Corresponding Mode of Action. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:12364-12371. [PMID: 36126316 DOI: 10.1021/acs.jafc.2c04266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Febrifugine, a natural alkaloid, exhibits specific anti-phytophthora activity; however, its mode of action is unclear. In this study, halofuginone, a synthetic derivative of febrifugine, showed significantly higher anti-phytophthora activities than those of febrifugine and the commercial drug metalaxyl against Phytophthora sojae, Phytophthora capsici, and Phytophthora infestans with effective concentration for 50% inhibition (EC50) values of 0.665, 0.673, and 0.178 μg/mL, respectively. Proline could alleviate the growth inhibition of halofuginone on P. capsici, implying that halofuginone might target prolyl-tRNA synthetase (PcPRS). The anti-phytophthora mechanism of halofuginone was then investigated by molecular docking, fluorescence titration, and enzymatic inhibition assays. The results revealed that halofuginone could bind to PcPRS and shared a similar binding site with the substrate proline. Point mutations at Glu316 and Arg345 led to 24.5 and 16.1% decreases in the enzymatic activity of PcPRS but 816.742- and 459.557-fold increases in the resistance to halofuginone, respectively. The results further confirmed that halofuginone was a competitive inhibitor of proline against PcPRS, and Glu316 and Arg345 played important roles in the binding of halofuginone and proline. Taken together, the results indicated that halofuginone is an alternative anti-phytophthora drug candidate and that PcPRS represents a potential target for the development of new pesticides.
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Affiliation(s)
- Saisai Zhang
- School of Life Science, Northeast Agricultural University, Harbin150030, China
| | - Jialing Cai
- School of Life Science, Northeast Agricultural University, Harbin150030, China
| | - Yimeng Xie
- School of Life Science, Northeast Agricultural University, Harbin150030, China
| | - Xinyu Zhang
- Department of Critical Care Medicine, Harbin Medical University Cancer Hospital, Harbin150081, China
| | - Xilang Yang
- School of Life Science, Northeast Agricultural University, Harbin150030, China
| | - Shenyuan Lin
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang110866, China
| | - Wensheng Xiang
- School of Life Science, Northeast Agricultural University, Harbin150030, China
| | - Ji Zhang
- School of Life Science, Northeast Agricultural University, Harbin150030, China
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8
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Functional characterization of 5' UTR cis-acting sequence elements that modulate translational efficiency in Plasmodium falciparum and humans. Malar J 2022; 21:15. [PMID: 34991611 PMCID: PMC8739713 DOI: 10.1186/s12936-021-04024-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/14/2021] [Indexed: 11/10/2022] Open
Abstract
Background The eukaryotic parasite Plasmodium falciparum causes millions of malarial infections annually while drug resistance to common anti-malarials is further confounding eradication efforts. Translation is an attractive therapeutic target that will benefit from a deeper mechanistic understanding. As the rate limiting step of translation, initiation is a primary driver of translational efficiency. It is a complex process regulated by both cis and trans acting factors, providing numerous potential targets. Relative to model organisms and humans, P. falciparum mRNAs feature unusual 5′ untranslated regions suggesting cis-acting sequence complexity in this parasite may act to tune levels of protein synthesis through their effects on translational efficiency. Methods Here, in vitro translation is deployed to compare the role of cis-acting regulatory sequences in P. falciparum and humans. Using parasite mRNAs with high or low translational efficiency, the presence, position, and termination status of upstream “AUG”s, in addition to the base composition of the 5′ untranslated regions, were characterized. Results The density of upstream “AUG”s differed significantly among the most and least efficiently translated genes in P. falciparum, as did the average “GC” content of the 5′ untranslated regions. Using exemplars from highly translated and poorly translated mRNAs, multiple putative upstream elements were interrogated for impact on translational efficiency. Upstream “AUG”s were found to repress translation to varying degrees, depending on their position and context, while combinations of upstream “AUG”s had non-additive effects. The base composition of the 5′ untranslated regions also impacted translation, but to a lesser degree. Surprisingly, the effects of cis-acting sequences were remarkably conserved between P. falciparum and humans. Conclusions While translational regulation is inherently complex, this work contributes toward a more comprehensive understanding of parasite and human translational regulation by examining the impact of discrete cis-acting features, acting alone or in context. Supplementary Information The online version contains supplementary material available at 10.1186/s12936-021-04024-2.
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9
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Rybak M, Gudzera OI, Gorbatiuk OB, Usenko MO, Yarmoluk SM, Tukalo MA, Volynets GP. Rational Design of Hit Compounds Targeting Staphylococcus aureus Threonyl-tRNA Synthetase. ACS OMEGA 2021; 6:24910-24918. [PMID: 34604672 PMCID: PMC8482496 DOI: 10.1021/acsomega.1c03789] [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: 07/16/2021] [Indexed: 06/13/2023]
Abstract
Staphylococcus aureus is one of the most dangerous nosocomial pathogens which cause a wide variety of hospital-acquired infectious diseases. S. aureus is considered as a superbug due to the development of multidrug resistance to all current therapeutic regimens. Therefore, the discovery of antibiotics with novel mechanisms of action to combat staphylococcal infections is of high priority for modern medicinal chemistry. Nowadays, aminoacyl-tRNA synthetases are considered as promising molecular targets for antibiotic development. In the present study, we used for the first time S. aureus threonyl-tRNA synthetase (ThrRS) as a molecular target. Recombinant S. aureus ThrRS was obtained in the soluble form in a sufficient amount for inhibitor screening assay. Using the molecular docking approach, we selected 180 compounds for investigation of inhibitory activity toward ThrRS. Among the tested compounds, we identified five inhibitors from different chemical classes decreasing the activity of ThrRS by more than 70% at a concentration of 100 μM. The most active compound 2,4-dibromo-6-{[4-(4-nitro-phenyl)-thiazol-2-yl]-hydrazonomethyl}-phenol has an IC50 value of 56.5 ± 3.5 μM. These compounds are not cytotoxic toward eukaryotic cells HEK293 (EC50 > 100 μM) and can be useful for further optimization and biological research.
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Affiliation(s)
- Mariia
Yu. Rybak
- Department
of Protein Synthesis Enzymology, Institute
of Molecular Biology and Genetics National Academy of Sciences of
Ukraine, 150 Zabolotnogo Street, Kyiv 03143, Ukraine
| | - Olga I. Gudzera
- Department
of Protein Synthesis Enzymology, Institute
of Molecular Biology and Genetics National Academy of Sciences of
Ukraine, 150 Zabolotnogo Street, Kyiv 03143, Ukraine
| | - Oksana B. Gorbatiuk
- Department
of Cell Regulatory Mechanisms, Institute
of Molecular Biology and Genetics National Academy of Sciences of
Ukraine, 150 Zabolotnogo Street, Kyiv 03143, Ukraine
| | - Mariia O. Usenko
- Department
of Cell Regulatory Mechanisms, Institute
of Molecular Biology and Genetics National Academy of Sciences of
Ukraine, 150 Zabolotnogo Street, Kyiv 03143, Ukraine
| | - Sergiy M. Yarmoluk
- Department
of Medicinal Chemistry, Institute of Molecular
Biology and Genetics National Academy of Sciences of Ukraine, 150 Zabolotnogo Street, Kyiv 03143, Ukraine
| | - Michael A. Tukalo
- Department
of Protein Synthesis Enzymology, Institute
of Molecular Biology and Genetics National Academy of Sciences of
Ukraine, 150 Zabolotnogo Street, Kyiv 03143, Ukraine
| | - Galyna P. Volynets
- Department
of Medicinal Chemistry, Institute of Molecular
Biology and Genetics National Academy of Sciences of Ukraine, 150 Zabolotnogo Street, Kyiv 03143, Ukraine
- The
Scientific-Services Company “OTAVA”, 150 Zabolotnogo Street, Kyiv 03143, Ukraine
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10
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Chhibber-Goel J, Yogavel M, Sharma A. Structural analyses of the malaria parasite aminoacyl-tRNA synthetases provide new avenues for antimalarial drug discovery. Protein Sci 2021; 30:1793-1803. [PMID: 34184352 DOI: 10.1002/pro.4148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/12/2021] [Accepted: 06/22/2021] [Indexed: 11/10/2022]
Abstract
Malaria is a parasitic illness caused by the genus Plasmodium from the apicomplexan phylum. Five plasmodial species of P. falciparum (Pf), P. knowlesi, P. malariae, P. ovale, and P. vivax (Pv) are responsible for causing malaria in humans. According to the World Malaria Report 2020, there were 229 million cases and ~ 0.04 million deaths of which 67% were in children below 5 years of age. While more than 3 billion people are at risk of malaria infection globally, antimalarial drugs are their only option for treatment. Antimalarial drug resistance keeps arising periodically and thus threatens the main line of malaria treatment, emphasizing the need to find new alternatives. The availability of whole genomes of P. falciparum and P. vivax has allowed targeting their unexplored plasmodial enzymes for inhibitor development with a focus on multistage targets that are crucial for parasite viability in both the blood and liver stages. Over the past decades, aminoacyl-tRNA synthetases (aaRSs) have been explored as anti-bacterial and anti-fungal drug targets, and more recently (since 2009) aaRSs are also the focus of antimalarial drug targeting. Here, we dissect the structure-based knowledge of the most advanced three aaRSs-lysyl- (KRS), prolyl- (PRS), and phenylalanyl- (FRS) synthetases in terms of development of antimalarial drugs. These examples showcase the promising potential of this family of enzymes to provide druggable targets that stall protein synthesis upon inhibition and thereby kill malaria parasites selectively.
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Affiliation(s)
- Jyoti Chhibber-Goel
- Structural Parasitology Group, Molecular Medicine, International Center for Genetic Engineering and Biotechnology, New Delhi, India
| | - Manickam Yogavel
- Structural Parasitology Group, Molecular Medicine, International Center for Genetic Engineering and Biotechnology, New Delhi, India
| | - Amit Sharma
- Structural Parasitology Group, Molecular Medicine, International Center for Genetic Engineering and Biotechnology, New Delhi, India.,ICMR-National Institute of Malaria Research, New Delhi, India
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Nyamai DW, Tastan Bishop Ö. Aminoacyl tRNA synthetases as malarial drug targets: a comparative bioinformatics study. Malar J 2019; 18:34. [PMID: 30728021 PMCID: PMC6366043 DOI: 10.1186/s12936-019-2665-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 01/27/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Treatment of parasitic diseases has been challenging due to evolution of drug resistant parasites, and thus there is need to identify new class of drugs and drug targets. Protein translation is important for survival of malarial parasite, Plasmodium, and the pathway is present in all of its life cycle stages. Aminoacyl tRNA synthetases are primary enzymes in protein translation as they catalyse amino acid addition to the cognate tRNA. This study sought to understand differences between Plasmodium and human aminoacyl tRNA synthetases through bioinformatics analysis. METHODS Plasmodium berghei, Plasmodium falciparum, Plasmodium fragile, Plasmodium knowlesi, Plasmodium malariae, Plasmodium ovale, Plasmodium vivax, Plasmodium yoelii and human aminoacyl tRNA synthetase sequences were retrieved from UniProt database and grouped into 20 families based on amino acid specificity. These families were further divided into two classes. Both families and classes were analysed. Motif discovery was carried out using the MEME software, sequence identity calculation was done using an in-house Python script, multiple sequence alignments were performed using PROMALS3D and TCOFFEE tools, and phylogenetic tree calculations were performed using MEGA vs 7.0 tool. Possible alternative binding sites were predicted using FTMap webserver and SiteMap tool. RESULTS Motif discovery revealed Plasmodium-specific motifs while phylogenetic tree calculations showed that Plasmodium proteins have different evolutionary history to the human homologues. Human aaRSs sequences showed low sequence identity (below 40%) compared to Plasmodium sequences. Prediction of alternative binding sites revealed potential druggable sites in PfArgRS, PfMetRS and PfProRS at regions that are weakly conserved when compared to the human homologues. Multiple sequence analysis, motif discovery, pairwise sequence identity calculations and phylogenetic tree analysis showed significant differences between parasite and human aaRSs proteins despite functional and structural conservation. These differences may provide a basis for further exploration of Plasmodium aminoacyl tRNA synthetases as potential drug targets. CONCLUSION This study showed that, despite, functional and structural conservation, Plasmodium aaRSs have key differences from the human homologues. These differences in Plasmodium aaRSs can be targeted to develop anti-malarial drugs with less toxicity to the host.
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Affiliation(s)
- Dorothy Wavinya Nyamai
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa.
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12
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Francklyn CS, Mullen P. Progress and challenges in aminoacyl-tRNA synthetase-based therapeutics. J Biol Chem 2019; 294:5365-5385. [PMID: 30670594 DOI: 10.1074/jbc.rev118.002956] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aminoacyl-tRNA synthetases (ARSs) are universal enzymes that catalyze the attachment of amino acids to the 3' ends of their cognate tRNAs. The resulting aminoacylated tRNAs are escorted to the ribosome where they enter protein synthesis. By specifically matching amino acids to defined anticodon sequences in tRNAs, ARSs are essential to the physical interpretation of the genetic code. In addition to their canonical role in protein synthesis, ARSs are also involved in RNA splicing, transcriptional regulation, translation, and other aspects of cellular homeostasis. Likewise, aminoacylated tRNAs serve as amino acid donors for biosynthetic processes distinct from protein synthesis, including lipid modification and antibiotic biosynthesis. Thanks to the wealth of details on ARS structures and functions and the growing appreciation of their additional roles regulating cellular homeostasis, opportunities for the development of clinically useful ARS inhibitors are emerging to manage microbial and parasite infections. Exploitation of these opportunities has been stimulated by the discovery of new inhibitor frameworks, the use of semi-synthetic approaches combining chemistry and genome engineering, and more powerful techniques for identifying leads from the screening of large chemical libraries. Here, we review the inhibition of ARSs by small molecules, including the various families of natural products, as well as inhibitors developed by either rational design or high-throughput screening as antibiotics and anti-parasitic therapeutics.
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Affiliation(s)
- Christopher S Francklyn
- From the Department of Biochemistry, College of Medicine, University of Vermont, Burlington, Vermont 05405
| | - Patrick Mullen
- From the Department of Biochemistry, College of Medicine, University of Vermont, Burlington, Vermont 05405
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Cela M, Paulus C, Santos MAS, Moura GR, Frugier M, Rudinger-Thirion J. Plasmodium apicoplast tyrosyl-tRNA synthetase recognizes an unusual, simplified identity set in cognate tRNATyr. PLoS One 2018; 13:e0209805. [PMID: 30592748 PMCID: PMC6310243 DOI: 10.1371/journal.pone.0209805] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 12/11/2018] [Indexed: 11/18/2022] Open
Abstract
The life cycle of Plasmodium falciparum, the agent responsible for malaria, depends on both cytosolic and apicoplast translation fidelity. Apicoplast aminoacyl-tRNA synthetases (aaRS) are bacterial-like enzymes devoted to organellar tRNA aminoacylation. They are all encoded by the nuclear genome and are translocated into the apicoplast only after cytosolic biosynthesis. Apicoplast aaRSs contain numerous idiosyncratic sequence insertions: An understanding of the roles of these insertions has remained elusive and they hinder efforts to heterologously overexpress these proteins. Moreover, the A/T rich content of the Plasmodium genome leads to A/U rich apicoplast tRNA substrates that display structural plasticity. Here, we focus on the P. falciparum apicoplast tyrosyl-tRNA synthetase (Pf-apiTyrRS) and its cognate tRNATyr substrate (Pf-apitRNATyr). Cloning and expression strategies used to obtain an active and functional recombinant Pf-apiTyrRS are reported. Functional analyses established that only three weak identity elements in the apitRNATyr promote specific recognition by the cognate Pf-apiTyrRS and that positive identity elements usually found in the tRNATyr acceptor stem are excluded from this set. This finding brings to light an unusual behavior for a tRNATyr aminoacylation system and suggests that Pf-apiTyrRS uses primarily negative recognition elements to direct tyrosylation specificity.
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Affiliation(s)
- Marta Cela
- UPR 9002 Architecture et Réactivité de l’ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg Cedex, France
| | - Caroline Paulus
- UPR 9002 Architecture et Réactivité de l’ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg Cedex, France
| | - Manuel A. S. Santos
- Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - Gabriela R. Moura
- Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - Magali Frugier
- UPR 9002 Architecture et Réactivité de l’ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg Cedex, France
- * E-mail:
| | - Joëlle Rudinger-Thirion
- UPR 9002 Architecture et Réactivité de l’ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg Cedex, France
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Manickam Y, Chaturvedi R, Babbar P, Malhotra N, Jain V, Sharma A. Drug targeting of one or more aminoacyl-tRNA synthetase in the malaria parasite Plasmodium falciparum. Drug Discov Today 2018; 23:1233-1240. [PMID: 29408369 DOI: 10.1016/j.drudis.2018.01.050] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/02/2018] [Accepted: 01/29/2018] [Indexed: 11/28/2022]
Abstract
Malaria remains a major infectious disease and, despite incidence reduction, it threatens resurgence in drug-resistant forms. Antimalarial drugs remain the mainstay of therapeutic options and hence there is a constant need to identify and validate new druggable targets. Plasmodium falciparum aminoacyl-tRNA synthetases (Pf-aaRSs) drive protein translation and are potent targets for development of next-generation antimalarials. Here, we detail advances made in structural-biology-based investigations in Pf-aaRSs and discuss their distribution of druggable pockets. This review establishes a platform for systematic experimental dissection of malarial parasite aaRSs as a new focus for sustained drug development efforts against malaria.
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Affiliation(s)
- Yogavel Manickam
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi 110067, India
| | - Rini Chaturvedi
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi 110067, India
| | - Palak Babbar
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi 110067, India
| | - Nipun Malhotra
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi 110067, India
| | - Vitul Jain
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi 110067, India; Present address: Division of Structural Biology, Wellcome Trust Centre for Human Genetics, The Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Amit Sharma
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi 110067, India.
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Torrie LS, Brand S, Robinson DA, Ko EJ, Stojanovski L, Simeons FRC, Wyllie S, Thomas J, Ellis L, Osuna-Cabello M, Epemolu O, Nühs A, Riley J, MacLean L, Manthri S, Read KD, Gilbert IH, Fairlamb AH, De Rycker M. Chemical Validation of Methionyl-tRNA Synthetase as a Druggable Target in Leishmania donovani. ACS Infect Dis 2017; 3:718-727. [PMID: 28967262 PMCID: PMC5663395 DOI: 10.1021/acsinfecdis.7b00047] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
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Methionyl-tRNA synthetase
(MetRS) has been chemically validated as a drug target in the kinetoplastid
parasite Trypanosoma brucei. In the present study,
we investigate the validity of this target in the related trypanosomatid Leishmania donovani. Following development of a robust high-throughput
compatible biochemical assay, a compound screen identified DDD806905
as a highly potent inhibitor of LdMetRS (Ki of 18 nM). Crystallography revealed this compound
binds to the methionine pocket of MetRS with enzymatic studies confirming
DDD806905 displays competitive inhibition with respect to methionine
and mixed inhibition with respect to ATP binding. DDD806905 showed
activity, albeit with different levels of potency, in various Leishmania cell-based viability assays, with on-target activity
observed in both Leishmania promastigote cell assays
and a Leishmania tarentolae in vitro translation
assay. Unfortunately, this compound failed to show efficacy in an
animal model of leishmaniasis. We investigated the potential causes
for the discrepancies in activity observed in different Leishmania cell assays and the lack of efficacy in the animal model and found
that high protein binding as well as sequestration of this dibasic
compound into acidic compartments may play a role. Despite medicinal
chemistry efforts to address the dibasic nature of DDD806905 and analogues,
no progress could be achieved with the current chemical series. Although
DDD806905 is not a developable antileishmanial compound, MetRS remains
an attractive antileishmanial drug target.
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Affiliation(s)
- Leah S. Torrie
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Stephen Brand
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - David A. Robinson
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Eun Jung Ko
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Laste Stojanovski
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Frederick R. C. Simeons
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Susan Wyllie
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - John Thomas
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Lucy Ellis
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Maria Osuna-Cabello
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Ola Epemolu
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Andrea Nühs
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Jennifer Riley
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Lorna MacLean
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Sujatha Manthri
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Kevin D. Read
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Ian H. Gilbert
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Alan H. Fairlamb
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Manu De Rycker
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
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16
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Rayevsky AV, Sharifi M, Tukalo MA. Molecular modeling and molecular dynamics simulation study of archaeal leucyl-tRNA synthetase in complex with different mischarged tRNA in editing conformation. J Mol Graph Model 2017; 76:289-295. [PMID: 28743072 DOI: 10.1016/j.jmgm.2017.06.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 06/07/2017] [Accepted: 06/23/2017] [Indexed: 12/20/2022]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) play important roles in maintaining the accuracy of protein synthesis. Some aaRSs accomplish this via editing mechanisms, among which leucyl-tRNA synthetase (LeuRS) edits non-cognate amino acid norvaline mainly by post-transfer editing. However, the molecular basis for this pathway for eukaryotic and archaeal LeuRS remain unclear. In this study, a complex of archaeal P. horikoshii LeuRS (PhLeuRS) with misacylated tRNALeu was modeled wherever tRNA's acceptor stem was oriented directly into the editing site. To understand the distinctive features of organization we reconstructed a complex of PhLeuRS with tRNA and visualize post-transfer editing interactions mode by performing molecular dynamics (MD) simulation studies. To study molecular basis for substrate selectivity by PhLeuRS's editing site we utilized MD simulation of the entire LeuRS complexes using a diverse charged form of tRNAs, namely norvalyl-tRNALeu and isoleucyl-tRNALeu. In general, the editing site organization of LeuRS from P.horikoshii has much in common with bacterial LeuRS. The MD simulation results revealed that the post-transfer editing substrate norvalyl-A76, binds more strongly than isoleucyl-A76. Moreover, the branched side chain of isoleucine prevents water molecules from being closer and hence the hydrolysis reaction slows significantly. To investigate a possible mechanism of the post-transfer editing reaction, by PhLeuRS we have determined that two water molecules (the attacking and assisting water molecules) are localized near the carbonyl group of the amino acid to be cleaved off. These water molecules approach the substrate from the opposite side to that observed for Thermus thermophilus LeuRS (TtLeuRS). Based on the results obtained, it was suggested that the post-transfer editing mechanism of PhLeuRS differs from that of prokaryotic TtLeuRS.
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Affiliation(s)
- A V Rayevsky
- Institute of Molecular Biology and Genetics, NAS of Ukraine, 150 Academician Zabolotny Str., Kyiv 03680, Ukraine.
| | - M Sharifi
- Medway School of Pharmacy, Universities of Kent and Greenwich, Kent ME4 4TB, UK
| | - M A Tukalo
- Institute of Molecular Biology and Genetics, NAS of Ukraine, 150 Academician Zabolotny Str., Kyiv 03680, Ukraine.
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Saint-Léger A, Ribas de Pouplana L. A new set of assays for the discovery of aminoacyl-tRNA synthetase inhibitors. Methods 2016; 113:34-45. [PMID: 27989759 DOI: 10.1016/j.ymeth.2016.10.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/21/2016] [Accepted: 10/24/2016] [Indexed: 01/08/2023] Open
Abstract
Current biochemical methods available to monitor the activity of aminoacyl-tRNA synthetases (ARS) are ill-suited to high-throughput screening approaches for the identification of small-molecule inhibitors of these enzymes. In an attempt to improve the limitations of current assays we have developed a suite of new methods designed to streamline the discovery of new ARS antagonists. This set of assays includes approaches to monitor ARS activity in vitro, in human cells, and in bacteria. They are applicable to several ARSs from any given organism, can be easily adapted to very high-throughput set-ups, and allow for a multi-factorial selection of drug candidates.
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Affiliation(s)
- Adélaïde Saint-Léger
- Omnia Molecular S.L., c/ Baldiri Reixac 15-21, 08028 Barcelona, Catalonia, Spain
| | - Lluís Ribas de Pouplana
- Omnia Molecular S.L., c/ Baldiri Reixac 15-21, 08028 Barcelona, Catalonia, Spain; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, c/ Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluis Companys 23, 08010 Barcelona, Catalonia, Spain.
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