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Batey SFD, Davie MJ, Hems ES, Liston JD, Scott TA, Alt S, Francklyn CS, Wilkinson B. The catechol moiety of obafluorin is essential for antibacterial activity. RSC Chem Biol 2023; 4:926-941. [PMID: 37920400 PMCID: PMC10619133 DOI: 10.1039/d3cb00127j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/11/2023] [Indexed: 11/04/2023] Open
Abstract
Obafluorin is a Pseudomonas fluorescens antibacterial natural product that inhibits threonyl-tRNA synthetase (ThrRS). It acts as a broad-spectrum antibiotic against a range of clinically relevant pathogens and comprises a strained β-lactone ring decorated with catechol and 4-nitro-benzyl moieties. The catechol moiety is widespread in nature and its role in the coordination of ferric iron has been well-characterised in siderophores and Trojan horse antibiotics. Here we use a combination of mutasynthesis, bioassays, enzyme assays and metal binding studies to delineate the role of the catechol moiety in the bioactivity of obafluorin. We use P. fluorescens biosynthetic mutants to generate obafluorin analogues with modified catechol moieties. We demonstrate that an intact catechol is required for both antibacterial activity and inhibition of the ThrRS molecular target. Although recent work showed that the obafluorin catechol coordinates Zn2+ in the ThrRS active site, we find that obafluorin is a weak Zn2+ binder in vitro, contrasting with a strong, specific 1 : 1 interaction with Fe3+. We use bioassays with siderophore transporter mutants to probe the role of the obafluorin catechol in Fe3+-mediated uptake. Surprisingly, obafluorin does not behave as a Trojan horse antibiotic but instead exhibits increased antibacterial activity in the presence of Fe3+. We further demonstrate that Fe3+ binding prevents the hydrolytic breakdown of the β-lactone ring, revealing a hitherto unreported function for the catechol moiety in natural product bioactivity.
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Affiliation(s)
- Sibyl F D Batey
- Department of Molecular Microbiology, John Innes Centre Norwich Research Park Norwich NR4 7UH UK
| | - Melissa J Davie
- Department of Molecular Microbiology, John Innes Centre Norwich Research Park Norwich NR4 7UH UK
| | - Edward S Hems
- Department of Molecular Microbiology, John Innes Centre Norwich Research Park Norwich NR4 7UH UK
| | - Jonathon D Liston
- Department of Molecular Microbiology, John Innes Centre Norwich Research Park Norwich NR4 7UH UK
| | - Thomas A Scott
- Department of Molecular Microbiology, John Innes Centre Norwich Research Park Norwich NR4 7UH UK
| | - Silke Alt
- Department of Molecular Microbiology, John Innes Centre Norwich Research Park Norwich NR4 7UH UK
| | - Christopher S Francklyn
- Department of Biochemistry, College of Medicine, University of Vermont, Burlington Vermont 05405 USA
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre Norwich Research Park Norwich NR4 7UH UK
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2
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Structural Basis of Cysteine Ligase MshC Inhibition by Cysteinyl-Sulfonamides. Int J Mol Sci 2022; 23:ijms232315095. [PMID: 36499418 PMCID: PMC9736012 DOI: 10.3390/ijms232315095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 11/25/2022] [Accepted: 11/26/2022] [Indexed: 12/03/2022] Open
Abstract
Mycothiol (MSH), the major cellular thiol in Mycobacterium tuberculosis (Mtb), plays an essential role in the resistance of Mtb to various antibiotics and oxidative stresses. MshC catalyzes the ATP-dependent ligation of 1-O-(2-amino-2-deoxy-α-d-glucopyranosyl)-d-myo-inositol (GlcN-Ins) with l-cysteine (l-Cys) to form l-Cys-GlcN-Ins, the penultimate step in MSH biosynthesis. The inhibition of MshC is lethal to Mtb. In the present study, five new cysteinyl-sulfonamides were synthesized, and their binding affinity with MshC was evaluated using a thermal shift assay. Two of them bind the target with EC50 values of 219 and 231 µM. Crystal structures of full-length MshC in complex with these two compounds showed that they were bound in the catalytic site of MshC, inducing dramatic conformational changes of the catalytic site compared to the apo form. In particular, the observed closure of the KMSKS loop was not detected in the published cysteinyl-sulfamoyl adenosine-bound structure, the latter likely due to trypsin treatment. Despite the confirmed binding to MshC, the compounds did not suppress Mtb culture growth, which might be explained by the lack of adequate cellular uptake. Taken together, these novel cysteinyl-sulfonamide MshC inhibitors and newly reported full-length apo and ligand-bound MshC structures provide a promising starting point for the further development of novel anti-tubercular drugs targeting MshC.
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Destruxin A Interacts with Aminoacyl tRNA Synthases in Bombyx mori. J Fungi (Basel) 2021; 7:jof7080593. [PMID: 34436132 PMCID: PMC8396844 DOI: 10.3390/jof7080593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 11/16/2022] Open
Abstract
Destruxin A (DA), a hexa-cyclodepsipeptidic mycotoxin produced by the entomopathogenic fungus Metarhizium anisopliae, exhibits insecticidal activities in a wide range of pests and is known as an innate immunity inhibitor. However, its mechanism of action requires further investigation. In this research, the interactions of DA with the six aminoacyl tRNA synthetases (ARSs) of Bombyx mori, BmAlaRS, BmCysRS, BmMetRS, BmValRS, BmIleRS, and BmGluProRS, were analyzed. The six ARSs were expressed and purified. The BLI (biolayer interferometry) results indicated that DA binds these ARSs with the affinity indices (KD) of 10−4 to 10−5 M. The molecular docking suggested a similar interaction mode of DA with ARSs, whereby DA settled into a pocket through hydrogen bonds with Asn, Arg, His, Lys, and Tyr of ARSs. Furthermore, DA treatments decreased the contents of soluble protein and free amino acids in Bm12 cells, which suggested that DA impedes protein synthesis. Lastly, the ARSs in Bm12 cells were all downregulated by DA stress. This study sheds light on exploring and answering the molecular target of DA against target insects.
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Travin DY, Severinov K, Dubiley S. Natural Trojan horse inhibitors of aminoacyl-tRNA synthetases. RSC Chem Biol 2021; 2:468-485. [PMID: 34382000 PMCID: PMC8323819 DOI: 10.1039/d0cb00208a] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/10/2021] [Indexed: 12/18/2022] Open
Abstract
For most antimicrobial compounds with intracellular targets, getting inside the cell is the major obstacle limiting their activity. To pass this barrier some antibiotics mimic the compounds of specific interest for the microbe (siderophores, peptides, carbohydrates, etc.) and hijack the transport systems involved in their active uptake followed by the release of a toxic warhead inside the cell. In this review, we summarize the information about the structures, biosynthesis, and transport of natural inhibitors of aminoacyl-tRNA synthetases (albomycin, microcin C-related compounds, and agrocin 84) that rely on such "Trojan horse" strategy to enter the cell. In addition, we provide new data on the composition and distribution of biosynthetic gene clusters reminiscent of those coding for known Trojan horse aminoacyl-tRNA synthetases inhibitors. The products of these clusters are likely new antimicrobials that warrant further investigation.
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Affiliation(s)
- Dmitrii Y Travin
- Center of Life Sciences, Skolkovo Institute of Science and Technology Moscow Russia
- Institute of Gene Biology, Russian Academy of Sciences Moscow Russia
| | - Konstantin Severinov
- Center of Life Sciences, Skolkovo Institute of Science and Technology Moscow Russia
- Institute of Gene Biology, Russian Academy of Sciences Moscow Russia
- Waksman Institute for Microbiology, Rutgers, Piscataway New Jersey USA
| | - Svetlana Dubiley
- Center of Life Sciences, Skolkovo Institute of Science and Technology Moscow Russia
- Institute of Gene Biology, Russian Academy of Sciences Moscow Russia
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Guo Z, Tang Y, Tang W, Chen Y. Heptose-containing bacterial natural products: structures, bioactivities, and biosyntheses. Nat Prod Rep 2021; 38:1887-1909. [PMID: 33704304 DOI: 10.1039/d0np00075b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: up to 2020Glycosylated natural products hold great potential as drugs for the treatment of human and animal diseases. Heptoses, known as seven-carbon-chain-containing sugars, are a group of saccharides that are rarely observed in natural products. Based on the structures of the heptoses, the heptose-containing natural products can be divided into four groups, characterized by heptofuranose, highly-reduced heptopyranose, d-heptopyranose, and l-heptopyranose. Many of them possess remarkable biological properties, including antibacterial, antifungal, antitumor, and pain relief activities, thereby attracting great interest in biosynthesis and chemical synthesis studies to understand their construction mechanisms and structure-activity relationships. In this review, we summarize the structural properties, biological activities, and recent progress in the biosynthesis of bacterial natural products featuring seven-carbon-chain-containing sugars. The biosynthetic origins of the heptose moieties are emphasized.
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Affiliation(s)
- Zhengyan Guo
- State Key Laboratory of Microbial Resources, CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China. and University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Yue Tang
- State Key Laboratory of Microbial Resources, CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China. and University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Wei Tang
- State Key Laboratory of Microbial Resources, CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China. and University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Yihua Chen
- State Key Laboratory of Microbial Resources, CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China. and University of Chinese Academy of Sciences, 100049 Beijing, China
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Li Z, Xin W, Wang Q, Zhu M, Zhou H. Design and synthesis of N-(3-sulfamoylphenyl)amides as Trypanosoma brucei leucyl-tRNA synthetase inhibitors. Eur J Med Chem 2021; 217:113319. [PMID: 33725631 DOI: 10.1016/j.ejmech.2021.113319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 02/17/2021] [Accepted: 02/17/2021] [Indexed: 11/26/2022]
Abstract
The protozoan parasite Trypanosoma brucei (T. brucei) causes human African trypanosomiasis (HAT), which is a fatal and neglected disease in the tropic areas, and new treatments are urgently needed. Leucyl-tRNA synthetase (LeuRS) is an attractive target for the development of antimicrobial agents. In this work, starting from the hit compound thiourea ZCL539, we designed and synthesized a series of amides as effective T. brucei LeuRS (TbLeuRS) synthetic site inhibitors. The most potent compounds 74 and 91 showed IC50 of 0.24 and 0.25 μM, which were about 700-fold more potent than the starting hit compound. The structure-activity relationship was also discussed. These compounds provided a new scaffold and lead compounds for further development of antitrypanosomal agents.
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Affiliation(s)
- Zezhong Li
- State Key Laboratory of Microbial Metabolism, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Weixiang Xin
- State Key Laboratory of Microbial Metabolism, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Qing Wang
- State Key Laboratory of Microbial Metabolism, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Mingyan Zhu
- State Key Laboratory of Microbial Metabolism, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Huchen Zhou
- State Key Laboratory of Microbial Metabolism, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
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Abstract
Aminoacyl-tRNA synthetases (AARSs) have been considered very attractive drug-targets for decades. This interest probably emerged with the identification of differences in AARSs between prokaryotic and eukaryotic species, which provided a rationale for the development of antimicrobials targeting bacterial AARSs with minimal effect on the homologous human AARSs. Today we know that AARSs are not only attractive, but also valid drug targets as they are housekeeping proteins that: (i) play a fundamental role in protein translation by charging the corresponding amino acid to its cognate tRNA and preventing mistranslation mistakes [1], a critical process during fast growing conditions of microbes; and (ii) present significant differences between microbes and humans that can be used for drug development [2]. Together with the vast amount of available data on both pathogenic and mammalian AARSs, it is expected that, in the future, the numerous reported inhibitors of AARSs will provide the basis to develop new therapeutics for the treatment of human diseases. In this chapter, a detailed summary on the state-of-the-art in drug discovery and drug development for each aminoacyl-tRNA synthetase will be presented.
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Affiliation(s)
- Maria Lukarska
- Institute for Advanced Biosciences (IAB), Structural Biology of Novel Drug Targets in Human Diseases, INSERM U1209, CNRS UMR 5309, University Grenoble Alpes, Grenoble, France
| | - Andrés Palencia
- Institute for Advanced Biosciences (IAB), Structural Biology of Novel Drug Targets in Human Diseases, INSERM U1209, CNRS UMR 5309, University Grenoble Alpes, Grenoble, France.
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Ushimaru R, Chen Z, Zhao H, Fan P, Liu H. Identification of the Enzymes Mediating the Maturation of the Seryl‐tRNA Synthetase Inhibitor SB‐217452 during the Biosynthesis of Albomycins. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Richiro Ushimaru
- Department of Chemistry, and Division of Chemical Biology and Medicinal ChemistryCollege of PharmacyUniversity of Texas at Austin Austin TX 78712 USA
| | - Zhang Chen
- Department of Chemistry, and Division of Chemical Biology and Medicinal ChemistryCollege of PharmacyUniversity of Texas at Austin Austin TX 78712 USA
| | - Houyuan Zhao
- Department of Chemistry, and Division of Chemical Biology and Medicinal ChemistryCollege of PharmacyUniversity of Texas at Austin Austin TX 78712 USA
| | - Po‐hsun Fan
- Department of Chemistry, and Division of Chemical Biology and Medicinal ChemistryCollege of PharmacyUniversity of Texas at Austin Austin TX 78712 USA
| | - Hung‐wen Liu
- Department of Chemistry, and Division of Chemical Biology and Medicinal ChemistryCollege of PharmacyUniversity of Texas at Austin Austin TX 78712 USA
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Abstract
Aminoacyl-tRNA synthetases (ARSs) are essential enzymes for protein synthesis with evolutionarily conserved enzymatic mechanisms. Despite their similarity across organisms, scientists have been able to generate effective anti-infective agents based on the structural differences in the catalytic clefts of ARSs from pathogens and humans. However, recent genomic, proteomic and functionomic advances have unveiled unexpected disease-associated mutations and altered expression, secretion and interactions in human ARSs, revealing hidden biological functions beyond their catalytic roles in protein synthesis. These studies have also brought to light their potential as a rich and unexplored source for new therapeutic targets and agents through multiple avenues, including direct targeting of the catalytic sites, controlling disease-associated protein-protein interactions and developing novel biologics from the secreted ARS proteins or their parts. This Review addresses the emerging biology and therapeutic applications of human ARSs in diseases including autoimmune and rare diseases, and cancer.
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Ushimaru R, Chen Z, Zhao H, Fan PH, Liu HW. Identification of the Enzymes Mediating the Maturation of the Seryl-tRNA Synthetase Inhibitor SB-217452 during the Biosynthesis of Albomycins. Angew Chem Int Ed Engl 2020; 59:3558-3562. [PMID: 31863717 DOI: 10.1002/anie.201915275] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 12/17/2019] [Indexed: 12/21/2022]
Abstract
Albomycin δ2 is a sulfur-containing sideromycin natural product that shows potent antibacterial activity against clinically important pathogens. The l-serine-thioheptose dipeptide partial structure, known as SB-217452, has been found to be the active seryl-tRNA synthetase inhibitor component of albomycin δ2 . Herein, it is demonstrated that AbmF catalyzes condensation between the 6'-amino-4'-thionucleoside with the d-ribo configuration and seryl-adenylate supplied by the serine adenylation activity of AbmK. Formation of the dipeptide is followed by C3'-epimerization to produce SB-217452 with the d-xylo configuration, which is catalyzed by the radical S-adenosyl-l-methionine enzyme AbmJ. Gene deletion suggests that AbmC is involved in peptide assembly linking SB-217452 with the siderophore moiety. This study establishes how the albomycin biosynthetic machinery generates its antimicrobial component SB-217452.
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Affiliation(s)
- Richiro Ushimaru
- Department of Chemistry, and Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX, 78712, USA
| | - Zhang Chen
- Department of Chemistry, and Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX, 78712, USA
| | - Houyuan Zhao
- Department of Chemistry, and Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX, 78712, USA
| | - Po-Hsun Fan
- Department of Chemistry, and Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX, 78712, USA
| | - Hung-Wen Liu
- Department of Chemistry, and Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX, 78712, USA
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11
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Xin W, Li Z, Wang Q, Du J, Zhu M, Zhou H. Design and synthesis of α-phenoxy-N-sulfonylphenyl acetamides as Trypanosoma brucei Leucyl-tRNA synthetase inhibitors. Eur J Med Chem 2020; 185:111827. [DOI: 10.1016/j.ejmech.2019.111827] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 10/21/2019] [Accepted: 10/26/2019] [Indexed: 11/17/2022]
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12
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Scott TA, Batey SFD, Wiencek P, Chandra G, Alt S, Francklyn CS, Wilkinson B. Immunity-Guided Identification of Threonyl-tRNA Synthetase as the Molecular Target of Obafluorin, a β-Lactone Antibiotic. ACS Chem Biol 2019; 14:2663-2671. [PMID: 31675206 DOI: 10.1021/acschembio.9b00590] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
To meet the ever-growing demands of antibiotic discovery, new chemical matter and antibiotic targets are urgently needed. Many potent natural product antibiotics which were previously discarded can also provide lead molecules and drug targets. One such example is the structurally unique β-lactone obafluorin, produced by Pseudomonas fluorescens ATCC 39502. Obafluorin is active against both Gram-positive and -negative pathogens; however, the biological target was unknown. We now report that obafluorin targets threonyl-tRNA synthetase, and we identify a homologue, ObaO, which confers immunity to the obafluorin producer. Disruption of obaO in P. fluorescens ATCC 39502 results in obafluorin sensitivity, whereas expression in sensitive E. coli strains confers resistance. Enzyme assays demonstrate that E. coli threonyl-tRNA synthetase is fully inhibited by obafluorin, whereas ObaO is only partly susceptible, exhibiting a very unusual partial inhibition mechanism. Altogether, our data highlight the utility of an immunity-guided approach for the identification of an antibiotic target de novo and will ultimately enable the generation of improved obafluorin variants.
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Affiliation(s)
- Thomas A. Scott
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Sibyl F. D. Batey
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Patrick Wiencek
- Department of Biochemistry, College of Medicine, University of Vermont, Burlington, Vermont 05405, United States
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Silke Alt
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Christopher S. Francklyn
- Department of Biochemistry, College of Medicine, University of Vermont, Burlington, Vermont 05405, United States
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
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Wang S, Dong G, Sheng C. Structural simplification: an efficient strategy in lead optimization. Acta Pharm Sin B 2019; 9:880-901. [PMID: 31649841 PMCID: PMC6804494 DOI: 10.1016/j.apsb.2019.05.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/04/2019] [Accepted: 05/15/2019] [Indexed: 02/06/2023] Open
Abstract
The trend toward designing large hydrophobic molecules for lead optimization is often associated with poor drug-likeness and high attrition rates in drug discovery and development. Structural simplification is a powerful strategy for improving the efficiency and success rate of drug design by avoiding “molecular obesity”. The structural simplification of large or complex lead compounds by truncating unnecessary groups can not only improve their synthetic accessibility but also improve their pharmacokinetic profiles, reduce side effects and so on. This review will summarize the application of structural simplification in lead optimization. Numerous case studies, particularly those involving successful examples leading to marketed drugs or drug-like candidates, will be introduced and analyzed to illustrate the design strategies and guidelines for structural simplification.
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Key Words
- 11β-HSD, 11β-hydroxysteroid dehydrogenase
- 3D, three-dimensional
- ADMET, absorption, distribution, metabolism, excretion and toxicity
- AM2, adrenomedullin-2 receptor
- BIOS, biology-oriented synthesis
- CCK, cholecystokinin receptor
- CGRP, calcitonin gene-related peptide
- Drug design
- Drug discovery
- GlyT1, glycine transport 1
- HBV, hepatitis B virus
- HDAC, histone deacetylase
- HLM, human liver microsome
- JAKs, Janus tyrosine kinases
- LE, ligand efficiency
- Lead optimization
- LeuRS, leucyl-tRNA synthetase
- MCRs, multicomponent reactions
- MDR-TB, multidrug-resistant tuberculosis
- MW, molecular weight
- NP, natural product
- NPM, nucleophosmin
- PD, pharmacodynamic
- PK, pharmacokinetic
- PKC, protein kinase C
- Pharmacophore-based simplification
- Reducing chiral centers
- Reducing rings number
- SAHA, vorinostat
- SAR, structure‒activity relationship
- SCONP, structural classification of natural product
- Structural simplification
- Structure-based simplification
- TSA, trichostatin A
- TbLeuRS, T. brucei LeuRS
- ThrRS, threonyl-tRNA synthetase
- VANGL1, van-Gogh-like receptor protein 1
- aa-AMP, aminoacyl-AMP
- aa-AMS, aminoacylsulfa-moyladenosine
- aaRSs, aminoacyl-tRNA synthetases
- hA3 AR, human A3 adenosine receptor
- mTORC1, mammalian target of rapamycin complex 1
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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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15
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Nautiyal M, De Graef S, Pang L, Gadakh B, Strelkov SV, Weeks SD, Van Aerschot A. Comparative analysis of pyrimidine substituted aminoacyl-sulfamoyl nucleosides as potential inhibitors targeting class I aminoacyl-tRNA synthetases. Eur J Med Chem 2019; 173:154-166. [PMID: 30995568 DOI: 10.1016/j.ejmech.2019.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/01/2019] [Accepted: 04/01/2019] [Indexed: 12/27/2022]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) catalyse the ATP-dependent coupling of an amino acid to its cognate tRNA. Being vital for protein translation aaRSs are considered a promising target for the development of novel antimicrobial agents. 5'-O-(N-aminoacyl)-sulfamoyl adenosine (aaSA) is a non-hydrolysable analogue of the aaRS reaction intermediate that has been shown to be a potent inhibitor of this enzyme family but is prone to chemical instability and enzymatic modification. In an attempt to improve the molecular properties of this scaffold we synthesized a series of base substituted aaSA analogues comprising cytosine, uracil and N3-methyluracil targeting leucyl-, tyrosyl- and isoleucyl-tRNA synthetases. In in vitro assays seven out of the nine inhibitors demonstrated Kiapp values in the low nanomolar range. To complement the biochemical studies, X-ray crystallographic structures of Neisseria gonorrhoeae leucyl-tRNA synthetase and Escherichia coli tyrosyl-tRNA synthetase in complex with the newly synthesized compounds were determined. These highlighted a subtle interplay between the base moiety and the target enzyme in defining relative inhibitory activity. Encouraged by this data we investigated if the pyrimidine congeners could escape a natural resistance mechanism, involving acetylation of the amine of the aminoacyl group by the bacterial N-acetyltransferases RimL and YhhY. With RimL the pyrimidine congeners were less susceptible to inactivation compared to the equivalent aaSA, whereas with YhhY the converse was true. Combined the various insights resulting from this study will pave the way for the further rational design of aaRS inhibitors.
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Affiliation(s)
- Manesh Nautiyal
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49 Box 1041, B-3000, Leuven, Belgium
| | - Steff De Graef
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 Box 822, B-3000, Leuven, Belgium
| | - Luping Pang
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49 Box 1041, B-3000, Leuven, Belgium; Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 Box 822, B-3000, Leuven, Belgium
| | - Bharat Gadakh
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49 Box 1041, B-3000, Leuven, Belgium
| | - Sergei V Strelkov
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 Box 822, B-3000, Leuven, Belgium
| | - Stephen D Weeks
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 Box 822, B-3000, Leuven, Belgium
| | - Arthur Van Aerschot
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49 Box 1041, B-3000, Leuven, Belgium.
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16
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Singh H, Kaur B, Kaur H, Singh P. A bisubstrate reagent orchestrating adenosine triphosphate and l-tyrosine and making tyrosyl adenylate: partial mimicking of tyrosyl-tRNA synthetase. Org Biomol Chem 2019; 16:9446-9453. [PMID: 30515504 DOI: 10.1039/c8ob02866d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We report the development of a bisubstrate reagent that, similar to tyrosyl t-RNA synthetase (TyrTS), provides a surface for ATP and l-Tyr to render a pseudo-intramolecular reaction forming 5'-tyrosyl adenylate (tyrAd). The presence of the reagent in solution with TyrTS marred the enzymatic reaction and, noticeably, tyrAd formed under the catalytic mode of the biomodel reagent was not picked up by TyrTS and hence was not transferred to tRNA. A potential application of this reagent, which doesn't allow the formation of tyrosyl tRNA, may lie in an emerging therapeutic targeting the translation machinery of cells without inhibiting the normal workings of enzymes.
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Affiliation(s)
- Harpreet Singh
- Department of Chemistry and Centre for Advanced Studies, University with Potential for Excellence - Guru Nanak Dev University, Amritsar-143005, India.
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17
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Rusch M, Thevenon A, Hoepfner D, Aust T, Studer C, Patoor M, Rollin P, Livendahl M, Ranieri B, Schmitt E, Spanka C, Gademann K, Bouchez LC. Design and Synthesis of Metabolically Stable tRNA Synthetase Inhibitors Derived from Cladosporin. Chembiochem 2019; 20:644-649. [DOI: 10.1002/cbic.201800587] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Marion Rusch
- NIBR–Novartis Institute for Biomedical Research Fabrikstrasse 22-1.051.17 4054 Basel Switzerland
| | - Arnaud Thevenon
- NIBR–Novartis Institute for Biomedical Research Fabrikstrasse 22-1.051.17 4054 Basel Switzerland
- Department of ChemistryImperial College London SW7 2AZ UK
| | - Dominic Hoepfner
- NIBR–Novartis Institute for Biomedical Research Fabrikstrasse 22-1.051.17 4054 Basel Switzerland
| | - Thomas Aust
- NIBR–Novartis Institute for Biomedical Research Fabrikstrasse 22-1.051.17 4054 Basel Switzerland
| | - Christian Studer
- NIBR–Novartis Institute for Biomedical Research Fabrikstrasse 22-1.051.17 4054 Basel Switzerland
| | - Maude Patoor
- NIBR–Novartis Institute for Biomedical Research Fabrikstrasse 22-1.051.17 4054 Basel Switzerland
| | - Patrick Rollin
- Institut de Chimie Organique et Analytique (ICOA)UMR7311Université d'Orléans 45100 Orléans France
| | - Madeleine Livendahl
- NIBR–Novartis Institute for Biomedical Research Fabrikstrasse 22-1.051.17 4054 Basel Switzerland
| | - Beatrice Ranieri
- NIBR–Novartis Institute for Biomedical Research Fabrikstrasse 22-1.051.17 4054 Basel Switzerland
| | - Esther Schmitt
- NIBR–Novartis Institute for Biomedical Research Fabrikstrasse 22-1.051.17 4054 Basel Switzerland
| | - Carsten Spanka
- NIBR–Novartis Institute for Biomedical Research Fabrikstrasse 22-1.051.17 4054 Basel Switzerland
| | - Karl Gademann
- University of ZürichDepartment of Chemistry Winterthurerstrasse 190 8057 Zürich Switzerland
| | - Laure C. Bouchez
- NIBR–Novartis Institute for Biomedical Research Fabrikstrasse 22-1.051.17 4054 Basel Switzerland
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18
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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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