1
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Gong X, Zhou Y, Qin Q, Wang B, Wang L, Jin C, Fang W. Nitrate assimilation compensates for cell wall biosynthesis in the absence of Aspergillus fumigatus phosphoglucose isomerase. Appl Environ Microbiol 2024; 90:e0113824. [PMID: 39158312 PMCID: PMC11412302 DOI: 10.1128/aem.01138-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 07/20/2024] [Indexed: 08/20/2024] Open
Abstract
Phosphoglucose isomerase (PGI) links glycolysis, the pentose phosphate pathway (PPP), and the synthesis of cell wall precursors in fungi by facilitating the reversible conversion between glucose-6-phosphate (Glc6p) and fructose-6-phosphate (Fru6P). In a previous study, we established the essential role of PGI in cell wall biosynthesis in the opportunistic human fungal pathogen Aspergillus fumigatus, highlighting its potential as a therapeutic target. In this study, we conducted transcriptomic analysis and discovered that the Δpgi mutant exhibited enhanced glycolysis, reduced PPP, and an upregulation of cell wall precursor biosynthesis pathways. Phenotypic analysis revealed defective protein N-glycosylation in the mutant, notably the absence of glycosylated virulence factors DPP V and catalase 1. Interestingly, the cell wall defects in the mutant were not accompanied by activation of the MpkA-dependent cell wall integrity (CWI) signaling pathway. Instead, nitrate assimilation was activated in the Δpgi mutant, stimulating glutamine synthesis and providing amino donors for chitin precursor biosynthesis. Blocking the nitrate assimilation pathway severely impaired the growth of the Δpgi mutant, highlighting the crucial role of nitrate assimilation in rescuing cell wall defects. This study unveils the connection between nitrogen assimilation and cell wall compensation in A. fumigatus.IMPORTANCEAspergillus fumigatus is a common and serious human fungal pathogen that causes a variety of diseases. Given the limited availability of antifungal drugs and increasing drug resistance, it is imperative to understand the fungus' survival mechanisms for effective control of fungal infections. Our previous study highlighted the essential role of A. fumigatus PGI in maintaining cell wall integrity, phosphate sugar homeostasis, and virulence. The present study further illuminates the involvement of PGI in protein N-glycosylation. Furthermore, this research reveals that the nitrogen assimilation pathway, rather than the canonical MpkA-dependent CWI pathway, compensates for cell wall deficiencies in the mutant. These findings offer valuable insights into a novel adaptation mechanism of A. fumigatus to address cell wall defects, which could hold promise for the treatment of infections.
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Affiliation(s)
- Xiufang Gong
- Institute of
Biological Sciences and Technology, Guangxi Academy of
Sciences, Nanning,
Guangxi, China
- State Key Laboratory
of Mycology, Institute of Microbiology, Chinese Academy of
Sciences, Beijing,
China
| | - Yao Zhou
- Institute of
Biological Sciences and Technology, Guangxi Academy of
Sciences, Nanning,
Guangxi, China
| | - Qijian Qin
- Institute of
Biological Sciences and Technology, Guangxi Academy of
Sciences, Nanning,
Guangxi, China
| | - Bin Wang
- Institute of
Biological Sciences and Technology, Guangxi Academy of
Sciences, Nanning,
Guangxi, China
| | - Linqi Wang
- State Key Laboratory
of Mycology, Institute of Microbiology, Chinese Academy of
Sciences, Beijing,
China
| | - Cheng Jin
- Institute of
Biological Sciences and Technology, Guangxi Academy of
Sciences, Nanning,
Guangxi, China
- State Key Laboratory
of Mycology, Institute of Microbiology, Chinese Academy of
Sciences, Beijing,
China
| | - Wenxia Fang
- Institute of
Biological Sciences and Technology, Guangxi Academy of
Sciences, Nanning,
Guangxi, China
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2
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Lu Q, Zhou Y, Ding Y, Cui Y, Li W, Liu T. Structure and Inhibition of Insect UDP- N-acetylglucosamine Pyrophosphorylase: A Key Enzyme in the Hexosamine Biosynthesis Pathway. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:19286-19294. [PMID: 39039661 DOI: 10.1021/acs.jafc.4c03834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
UDP-N-acetylglucosamine pyrophosphorylase (UAP) catalyzes the last step in the hexosamine biosynthesis pathway to directly produce UDP-N-acetylglucosamine (UDP-GlcNAc). Because UAPs play important physiological and pathological roles in organisms, they are considered potential targets for drug and pesticide development. However, the lack of efficient and selective inhibitors is a bottleneck that must be overcome. This study reports the first crystal structure of the insect UAP from Spodoptera frugiperda (SfUAP) in complex with UDP-GlcNAc. SfUAP has two insect-specific structural characteristics in the active pocket, namely, a free Cys (Cys334) and a Mg2+ binding site, which differentiate it from human UAP (HsAGX1) and fungal UAP (AfUAP) in terms of substrate and inhibitor binding. N-(4-Nitrophenyl)maleimide (pNPMI) and myricetin are discovered as potent covalent and noncovalent inhibitors of SfUAP, respectively. Moreover, myricetin can significantly reduce the level of cellular O-GlcNAcylation by inhibiting both UAP and O-GlcNAc transferase. These findings provide novel insights into the development of UAP-based drugs and pesticides.
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Affiliation(s)
- Qiong Lu
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Yong Zhou
- School of Software, Dalian University of Technology, Dalian 116024, China
| | - Yi Ding
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Yuntian Cui
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Wenda Li
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Tian Liu
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian 116024, China
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3
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Asogwa FC, Izuchukwu UD, Louis H, Eze CC, Ekeleme CM, Ezugwu JA, Benjamin I, Attah SI, Agwamba EC, Ekoh OC, Adeyinka AS. Synthesis, Characterization and Theoretical Investigations on the Molecular Structure, Electronic Property and anti-Trypanosomal Activity of Benzenesulphonamide-Based Carboxamide and Its Derivatives. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2150653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Fredrick C. Asogwa
- Department of Pure and Applied Chemistry, University of Calabar, Calabar, Cross River State, Nigeria
| | - Ugwu D. Izuchukwu
- Department of Pure & Industrial Chemistry, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Hitler Louis
- Department of Pure and Applied Chemistry, University of Calabar, Calabar, Cross River State, Nigeria
| | - Cosmas C. Eze
- Department of Pure & Industrial Chemistry, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Chinedu M. Ekeleme
- Department of Biochemistry, College of Basic Medical Sciences, University of Calabar, Calabar, Nigeria
| | - James A. Ezugwu
- Department of Pure & Industrial Chemistry, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Innocent Benjamin
- Department of Pure and Applied Chemistry, University of Calabar, Calabar, Cross River State, Nigeria
| | - Solomon I. Attah
- Department of Pure & Industrial Chemistry, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Ernest C. Agwamba
- Department of Chemical Sciences, Clifford University, Owerrinta, Nigeria
| | - Ogechi C. Ekoh
- Department of Chemistry, Evangel University, Akaeze, Nigeria
| | - Adedapo S. Adeyinka
- Department of Chemical Sciences, University of Johannesburg, Johannesburg, South Africa
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4
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Das J, Kumar R, Shah V, Sharma AK. Functional characterization of chitin synthesis pathway genes, HaAGM and HaUAP, reveal their crucial roles in ecdysis and survival of Helicoverpa armigera (Hübner). PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2022; 188:105273. [PMID: 36464378 DOI: 10.1016/j.pestbp.2022.105273] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/26/2022] [Accepted: 10/23/2022] [Indexed: 06/17/2023]
Abstract
The chitin metabolic pathway is one of the most lucrative targets for designing pest management regimes. Inhibition of the chitin synthesis pathway causes detrimental effects on the normal growth and development of insects. Phospho-N-acetylglucosamine mutase (AGM) and UDP-N-acetylglucosamine pyrophosphorylase (UAP) are two key chitin biosynthesis enzymes in insects including Helicoverpa armigera, a pest of global significance. In the present study, we have identified, cloned and recombinantly expressed AGM and UAP from H. armigera (HaAGM and HaUAP). Biochemical characterization of recombinant HaAGM and HaUAP exhibited high affinities for their natural substrates N-acetyl glucosamine-6-phosphate (Km 38.72 ± 2.41) and N-acetyl glucosamine-1-phosphate (Km 3.66 ± 0.13), respectively. In the coupled enzyme-catalytic assay, HaAGM and HaUAP yielded the end-products, inorganic pyrophosphate and UDP-GlcNAc, confirming their active participation in the chitin synthesis pathway of H. armigera. Gene expression profiling revealed that HaAGM and HaUAP genes were expressed in all developmental stages and key tissues. These genes also showed substantial responses towards the moulting hormone 20-hydroxyecdysone and chitin biosynthesis inhibitor, novaluron. Remarkably, the RNAi-mediated knockdown of either HaAGM or HaUAP led to severe developmental deformities and significant mortality ranging from 65.61 to 72.54%. Overall findings suggest that HaAGM and HaUAP play crucial roles in the ecdysis and survival of H. armigera. Further, these genes could serve as potential targets for designing pest management strategies for H. armigera.
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Affiliation(s)
- Joy Das
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India; ICAR-Central Institute for Cotton Research, Nagpur, Maharashtra, India
| | - Rakesh Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India; ICAR-Central Institute for Cotton Research, Nagpur, Maharashtra, India
| | - Vivek Shah
- ICAR-Central Institute for Cotton Research, Nagpur, Maharashtra, India
| | - Ashwani Kumar Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India.
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5
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Bandini G, Damerow S, Sempaio Guther ML, Guo H, Mehlert A, Paredes Franco JC, Beverley S, Ferguson MAJ. An essential, kinetoplastid-specific GDP-Fuc: β-D-Gal α-1,2-fucosyltransferase is located in the mitochondrion of Trypanosoma brucei. eLife 2021; 10:e70272. [PMID: 34410224 PMCID: PMC8439653 DOI: 10.7554/elife.70272] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 08/15/2021] [Indexed: 02/06/2023] Open
Abstract
Fucose is a common component of eukaryotic cell-surface glycoconjugates, generally added by Golgi-resident fucosyltransferases. Whereas fucosylated glycoconjugates are rare in kinetoplastids, the biosynthesis of the nucleotide sugar GDP-Fuc has been shown to be essential in Trypanosoma brucei. Here we show that the single identifiable T. brucei fucosyltransferase (TbFUT1) is a GDP-Fuc: β-D-galactose α-1,2-fucosyltransferase with an apparent preference for a Galβ1,3GlcNAcβ1-O-R acceptor motif. Conditional null mutants of TbFUT1 demonstrated that it is essential for both the mammalian-infective bloodstream form and the insect vector-dwelling procyclic form. Unexpectedly, TbFUT1 was localized in the mitochondrion of T. brucei and found to be required for mitochondrial function in bloodstream form trypanosomes. Finally, the TbFUT1 gene was able to complement a Leishmania major mutant lacking the homologous fucosyltransferase gene (Guo et al., 2021). Together these results suggest that kinetoplastids possess an unusual, conserved and essential mitochondrial fucosyltransferase activity that may have therapeutic potential across trypanosomatids.
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Affiliation(s)
- Giulia Bandini
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Sebastian Damerow
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Maria Lucia Sempaio Guther
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Hongjie Guo
- Department of Molecular Microbiology, Washington University School of MedicineSt. LouisUnited States
| | - Angela Mehlert
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Jose Carlos Paredes Franco
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Stephen Beverley
- Department of Molecular Microbiology, Washington University School of MedicineSt. LouisUnited States
| | - Michael AJ Ferguson
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of DundeeDundeeUnited Kingdom
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6
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Zhang Y, Fang W, Raimi OG, Lockhart DEA, Ferenbach AT, Lu L, van Aalten DMF. Genetic and structural validation of phosphomannomutase as a cell wall target in Aspergillus fumigatus. Mol Microbiol 2021; 116:245-259. [PMID: 33629421 DOI: 10.1111/mmi.14706] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 02/03/2021] [Accepted: 02/15/2021] [Indexed: 11/29/2022]
Abstract
Aspergillus fumigatus is an opportunistic mold responsible for severe life-threatening fungal infections in immunocompromised patients. The cell wall, an essential structure composed of glucan, chitin, and galactomannan, is considered to be a target for the development of antifungal drugs. The nucleotide sugar donor GDP-mannose (GDP-Man) is required for the biosynthesis of galactomannan, glycosylphosphatidylinositol (GPI) anchors, glycolipid, and protein glycosylation. Starting from fructose-6-phosphate, GDP-Man is produced by the sequential action of the enzymes phosphomannose isomerase, phosphomannomutase (Pmm), and GDP-mannose pyrophosphorylase. Here, using heterokaryon rescue and gene knockdown approaches we demonstrate that the phosphomannomutase encoding gene in A. fumigatus (pmmA) is essential for survival. Reduced expression of pmmA is associated with significant morphological defects including retarded germination, growth, reduced conidiation, and abnormal polarity. Moreover, the knockdown strain exhibited an altered cell wall organization and sensitivity toward cell wall perturbing agents. By solving the first crystal structure of A. fumigatus phosphomannomutase (AfPmmA) we identified non-conservative substitutions near the active site when compared to the human orthologues. Taken together, this work provides a genetic and structural foundation for the exploitation of AfPmmA as a potential antifungal target.
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Affiliation(s)
- Yuanwei Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Centre for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China.,School of Life Sciences, University of Dundee, Dundee, UK
| | - Wenxia Fang
- School of Life Sciences, University of Dundee, Dundee, UK.,National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, China
| | | | | | | | - Ling Lu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Centre for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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7
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Sampaio Guther ML, Prescott AR, Kuettel S, Tinti M, Ferguson MAJ. Nucleotide sugar biosynthesis occurs in the glycosomes of procyclic and bloodstream form Trypanosoma brucei. PLoS Negl Trop Dis 2021; 15:e0009132. [PMID: 33592041 PMCID: PMC7909634 DOI: 10.1371/journal.pntd.0009132] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 02/26/2021] [Accepted: 01/12/2021] [Indexed: 11/19/2022] Open
Abstract
In Trypanosoma brucei, there are fourteen enzymatic biotransformations that collectively convert glucose into five essential nucleotide sugars: UDP-Glc, UDP-Gal, UDP-GlcNAc, GDP-Man and GDP-Fuc. These biotransformations are catalyzed by thirteen discrete enzymes, five of which possess putative peroxisome targeting sequences. Published experimental analyses using immunofluorescence microscopy and/or digitonin latency and/or subcellular fractionation and/or organelle proteomics have localized eight and six of these enzymes to the glycosomes of bloodstream form and procyclic form T. brucei, respectively. Here we increase these glycosome localizations to eleven in both lifecycle stages while noting that one, phospho-N-acetylglucosamine mutase, also localizes to the cytoplasm. In the course of these studies, the heterogeneity of glycosome contents was also noted. These data suggest that, unlike other eukaryotes, all of nucleotide sugar biosynthesis in T. brucei is compartmentalized to the glycosomes in both lifecycle stages. The implications are discussed.
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Affiliation(s)
- Maria Lucia Sampaio Guther
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Alan R. Prescott
- Dundee Imaging Facility, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Sabine Kuettel
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Michele Tinti
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Michael A. J. Ferguson
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
- * E-mail:
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8
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Chen X, Raimi OG, Ferenbach AT, van Aalten DM. A missense mutation in a patient with developmental delay affects the activity and structure of the hexosamine biosynthetic pathway enzyme AGX1. FEBS Lett 2021; 595:110-122. [PMID: 33098688 PMCID: PMC7839538 DOI: 10.1002/1873-3468.13968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 09/23/2020] [Accepted: 10/15/2020] [Indexed: 11/21/2022]
Abstract
O-GlcNAcylation is a post-translational modification catalysed by O-GlcNAc transferase (OGT). Missense mutations in OGT have been associated with developmental disorders, OGT-linked congenital disorder of glycosylation (OGT-CDG), which are characterized by intellectual disability. OGT relies on the hexosamine biosynthetic pathway (HBP) for provision of its UDP-GlcNAc donor. We considered whether mutations in UDP-N-acetylhexosamine pyrophosphorylase (UAP1), which catalyses the final step in the HBP, would phenocopy OGT-CDG mutations. A de novo mutation in UAP1 (NM_001324114:c.G685A:p.A229T) was reported in a patient with intellectual disability. We show that this mutation is pathogenic and decreases the stability and activity of the UAP1 isoform AGX1 in vitro. X-ray crystallography reveals a structural shift proximal to the mutation, leading to a conformational change of the N-terminal domain. These data suggest that the UAP1A229T missense mutation could be a contributory factor to the patient phenotype.
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Affiliation(s)
- Xiping Chen
- Division of Gene Regulation and ExpressionSchool of Life SciencesUniversity of DundeeDundeeUK
| | - Olawale G. Raimi
- Division of Gene Regulation and ExpressionSchool of Life SciencesUniversity of DundeeDundeeUK
| | - Andrew T. Ferenbach
- Division of Gene Regulation and ExpressionSchool of Life SciencesUniversity of DundeeDundeeUK
| | - Daan M.F. van Aalten
- Division of Gene Regulation and ExpressionSchool of Life SciencesUniversity of DundeeDundeeUK
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9
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Raimi OG, Hurtado-Guerrero R, Borodkin V, Ferenbach A, Urbaniak MD, Ferguson MAJ, van Aalten DMF. A mechanism-inspired UDP- N-acetylglucosamine pyrophosphorylase inhibitor. RSC Chem Biol 2020; 1:13-25. [PMID: 34458745 PMCID: PMC8386105 DOI: 10.1039/c9cb00017h] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 02/13/2020] [Indexed: 11/21/2022] Open
Abstract
UDP-N-acetylglucosamine pyrophosphorylase (UAP1) catalyses the last step in eukaryotic biosynthesis of uridine diphosphate-N-acetylglucosamine (UDP-GlcNAc), converting UTP and GlcNAc-1P to the sugar nucleotide. Gene disruption studies have shown that this gene is essential in eukaryotes and a possible antifungal target, yet no inhibitors of fungal UAP1 have so far been reported. Here we describe the crystal structures of substrate/product complexes of UAP1 from Aspergillus fumigatus that together provide snapshots of catalysis. A structure with UDP-GlcNAc, pyrophosphate and Mg2+ provides the first Michaelis complex trapped for this class of enzyme, revealing the structural basis of the previously reported Mg2+ dependence and direct observation of pyrophosphorolysis. We also show that a highly conserved lysine mimics the role of a second metal observed in structures of bacterial orthologues. A mechanism-inspired UTP α,β-methylenebisphosphonate analogue (meUTP) was designed and synthesized and was shown to be a micromolar inhibitor of the enzyme. The mechanistic insights and inhibitor described here will facilitate future studies towards the discovery of small molecule inhibitors of this currently unexploited potential antifungal drug target. UDP-N-acetylglucosamine pyrophosphorylase (UAP1) catalyses the last step in eukaryotic biosynthesis of uridine diphosphate-N-acetylglucosamine (UDP-GlcNAc), converting UTP and GlcNAc-1P to the sugar nucleotide.![]()
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Affiliation(s)
- Olawale G Raimi
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee Dow Street DD1 5EH Dundee UK
| | - Ramon Hurtado-Guerrero
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee Dow Street DD1 5EH Dundee UK
| | - Vladimir Borodkin
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee Dow Street DD1 5EH Dundee UK
| | - Andrew Ferenbach
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee Dow Street DD1 5EH Dundee UK
| | - Michael D Urbaniak
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee Dow Street DD1 5EH Dundee UK
| | - Michael A J Ferguson
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee Dow Street DD1 5EH Dundee UK
| | - Daan M F van Aalten
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee Dow Street DD1 5EH Dundee UK
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10
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Palaka BK, Velmurugan Ilavarasi A, Sapam TD, Kotapati KV, Nallala VS, Khan MB, Ampasala DR. Molecular cloning, gene expression analysis, and in silico characterization of UDP-N-acetylglucosamine pyrophosphorylase from Bombyx mori. Biotechnol Appl Biochem 2019; 66:880-899. [PMID: 31397000 DOI: 10.1002/bab.1802] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 08/07/2019] [Indexed: 12/16/2022]
Abstract
The present study was aimed to explore the molecular and structural features of UDP-N-acetylglucosamine pyrophosphorylase of Bombyx mori (BmUAP), an essential enzyme for chitin synthesis in insects. The BmUAP cDNA sequence was cloned and expression profiles were monitored during the molting and feeding stages of silkworm larvae. The effect of 20-hydroxyecdysone (20E) on BmUAP expression, and on silkworm molting was studied, which revealed that 20E regulates its expression. Multiple sequence alignment of various pyrophosphorylases revealed that the residues N223, G290, N327, and K407 of human UAP (PDB ID: 1JV1) were found to be highly conserved in BmUAP and all other eukaryotic UAPs considered for the study. Phylogenetic analysis inferred that the UAPs possess discrete variations in primary structure among different insect Orders while sharing good identity between species of the Order. The structure of BmUAP was predicted and its interactions with uridine triphosphate, N-acetylglucosamine-1-phosphate, and UDP-N-acetylglucosamine were analyzed. Virtual screening with a library of natural compounds resulted in five potential hits with good binding affinities. On further analysis, these five hits were found to be mimicking substrate and product, in inducing conformational changes in the active site. This work provides crucial information on molecular interactions and structural dynamics of insect UAPs.
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Affiliation(s)
- Bhagath Kumar Palaka
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | | | - Tuleshwori Devi Sapam
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Kasi Viswanath Kotapati
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Venkata Satyanarayana Nallala
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Mohd Babu Khan
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Dinakara Rao Ampasala
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
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11
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Identification of Leishmania major UDP-Sugar Pyrophosphorylase Inhibitors Using Biosensor-Based Small Molecule Fragment Library Screening. Molecules 2019; 24:molecules24050996. [PMID: 30871023 PMCID: PMC6429087 DOI: 10.3390/molecules24050996] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/04/2019] [Accepted: 03/07/2019] [Indexed: 11/29/2022] Open
Abstract
Leishmaniasis is a neglected disease that is caused by different species of the protozoan parasite Leishmania, and it currently affects 12 million people worldwide. The antileishmanial therapeutic arsenal remains very limited in number and efficacy, and there is no vaccine for this parasitic disease. One pathway that has been genetically validated as an antileishmanial drug target is the biosynthesis of uridine diphosphate-glucose (UDP-Glc), and its direct derivative UDP-galactose (UDP-Gal). De novo biosynthesis of these two nucleotide sugars is controlled by the specific UDP-glucose pyrophosphorylase (UGP). Leishmania parasites additionally express a UDP-sugar pyrophosphorylase (USP) responsible for monosaccharides salvage that is able to generate both UDP-Gal and UDP-Glc. The inactivation of the two parasite pyrophosphorylases UGP and USP, results in parasite death. The present study reports on the identification of structurally diverse scaffolds for the development of USP inhibitors by fragment library screening. Based on this screening, we selected a small set of commercially available compounds, and identified molecules that inhibit both Leishmania major USP and UGP, with a half-maximal inhibitory concentration in the 100 µM range. The inhibitors were predicted to bind at allosteric regulation sites, which were validated by mutagenesis studies. This study sets the stage for the development of potent USP inhibitors.
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12
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Decker D, Kleczkowski LA. UDP-Sugar Producing Pyrophosphorylases: Distinct and Essential Enzymes With Overlapping Substrate Specificities, Providing de novo Precursors for Glycosylation Reactions. FRONTIERS IN PLANT SCIENCE 2019; 9:1822. [PMID: 30662444 PMCID: PMC6329318 DOI: 10.3389/fpls.2018.01822] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 11/23/2018] [Indexed: 05/02/2023]
Abstract
Nucleotide sugars are the key precursors for all glycosylation reactions and are required both for oligo- and polysaccharides synthesis and protein and lipid glycosylation. Among all nucleotide sugars, UDP-sugars are the most important precursors for biomass production in nature (e.g., synthesis of cellulose, hemicellulose, and pectins for cell wall production). Several recent studies have already suggested a potential role for UDP-Glc in plant growth and development, and UDP-Glc has also been suggested as a signaling molecule, in addition to its precursor function. In this review, we will cover primary mechanisms of formation of UDP-sugars, by focusing on UDP-sugar metabolizing pyrophosphorylases. The pyrophosphorylases can be divided into three families: UDP-Glc pyrophosphorylase (UGPase), UDP-sugar pyrophosphorylase (USPase), and UDP-N-acetyl glucosamine pyrophosphorylase (UAGPase), which can be distinguished both by their amino acid sequences and by differences in substrate specificity. Substrate specificities of these enzymes are discussed, along with structure-function relationships, based on their crystal structures and homology modeling. Earlier studies with transgenic plants have revealed that each of the pyrophosphorylases is essential for plant survival, and their loss or a decrease in activity results in reproductive impairment. This constitutes a problem when studying exact in vivo roles of the enzymes using classical reverse genetics approaches. Thus, strategies involving the use of specific inhibitors (reverse chemical genetics) are also discussed. Further characterization of the properties/roles of pyrophosphorylases should address fundamental questions dealing with mechanisms and control of carbohydrate synthesis and may allow to identify targets for manipulation of biomass production in plants.
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Affiliation(s)
| | - Leszek A. Kleczkowski
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
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Decker D, Kleczkowski LA. Substrate Specificity and Inhibitor Sensitivity of Plant UDP-Sugar Producing Pyrophosphorylases. FRONTIERS IN PLANT SCIENCE 2017; 8:1610. [PMID: 28970843 PMCID: PMC5609113 DOI: 10.3389/fpls.2017.01610] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 09/04/2017] [Indexed: 05/08/2023]
Abstract
UDP-sugars are essential precursors for glycosylation reactions producing cell wall polysaccharides, sucrose, glycoproteins, glycolipids, etc. Primary mechanisms of UDP sugar formation involve the action of at least three distinct pyrophosphorylases using UTP and sugar-1-P as substrates. Here, substrate specificities of barley and Arabidopsis (two isozymes) UDP-glucose pyrophosphorylases (UGPase), Arabidopsis UDP-sugar pyrophosphorylase (USPase) and Arabidopsis UDP-N-acetyl glucosamine pyrophosphorylase2 (UAGPase2) were investigated using a range of sugar-1-phosphates and nucleoside-triphosphates as substrates. Whereas all the enzymes preferentially used UTP as nucleotide donor, they differed in their specificity for sugar-1-P. UGPases had high activity with D-Glc-1-P, but could also react with Fru-1-P and Fru-2-P (Km values over 10 mM). Contrary to an earlier report, their activity with Gal-1-P was extremely low. USPase reacted with a range of sugar-1-phosphates, including D-Glc-1-P, D-Gal-1-P, D-GalA-1-P (Km of 1.3 mM), β-L-Ara-1-P and α-D-Fuc-1-P (Km of 3.4 mM), but not β-L-Fuc-1-P. In contrast, UAGPase2 reacted only with D-GlcNAc-1-P, D-GalNAc-1-P (Km of 1 mM) and, to some extent, D-Glc-1-P (Km of 3.2 mM). Generally, different conformations/substituents at C2, C4, and C5 of the pyranose ring of a sugar were crucial determinants of substrate specificity of a given pyrophosphorylase. Homology models of UDP-sugar binding to UGPase, USPase and UAGPase2 revealed more common amino acids for UDP binding than for sugar binding, reflecting differences in substrate specificity of these proteins. UAGPase2 was inhibited by a salicylate derivative that was earlier shown to affect UGPase and USPase activities, consistent with a common structural architecture of the three pyrophosphorylases. The results are discussed with respect to the role of the pyrophosphorylases in sugar activation for glycosylated end-products.
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Ogungbe IV, Setzer WN. The Potential of Secondary Metabolites from Plants as Drugs or Leads against Protozoan Neglected Diseases-Part III: In-Silico Molecular Docking Investigations. Molecules 2016; 21:E1389. [PMID: 27775577 PMCID: PMC6274513 DOI: 10.3390/molecules21101389] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 10/06/2016] [Accepted: 10/12/2016] [Indexed: 12/11/2022] Open
Abstract
Malaria, leishmaniasis, Chagas disease, and human African trypanosomiasis continue to cause considerable suffering and death in developing countries. Current treatment options for these parasitic protozoal diseases generally have severe side effects, may be ineffective or unavailable, and resistance is emerging. There is a constant need to discover new chemotherapeutic agents for these parasitic infections, and natural products continue to serve as a potential source. This review presents molecular docking studies of potential phytochemicals that target key protein targets in Leishmania spp., Trypanosoma spp., and Plasmodium spp.
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Affiliation(s)
- Ifedayo Victor Ogungbe
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS 39217, USA.
| | - William N Setzer
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA.
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Wang Q, Heizer E, Rosa BA, Wildman SA, Janetka JW, Mitreva M. Characterization of parasite-specific indels and their proposed relevance for selective anthelminthic drug targeting. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2016; 39:201-211. [PMID: 26829384 PMCID: PMC4789095 DOI: 10.1016/j.meegid.2016.01.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 12/29/2015] [Accepted: 01/28/2016] [Indexed: 01/18/2023]
Abstract
Insertions and deletions (indels) are important sequence variants that are considered as phylogenetic markers that reflect evolutionary adaptations in different species. In an effort to systematically study indels specific to the phylum Nematoda and their structural impact on the proteins bearing them, we examined over 340,000 polypeptides from 21 nematode species spanning the phylum, compared them to non-nematodes and identified indels unique to nematode proteins in more than 3000 protein families. Examination of the amino acid composition revealed uneven usage of amino acids for insertions and deletions. The amino acid composition and cost, along with the secondary structure constitution of the indels, were analyzed in the context of their biological pathway associations. Species-specific indels could enable indel-based targeting for drug design in pathogens/parasites. Therefore, we screened the spatial locations of the indels in the parasite's protein 3D structures, determined the location of the indel and identified potential unique drug targeting sites. These indels could be confirmed by RNA-Seq data. Examples are presented illustrating the close proximity of some indels to established small-molecule binding pockets that can potentially facilitate selective targeting to the parasites and bypassing their host, thus reducing or eliminating the toxicity of the potential drugs. This study presents an approach for understanding the adaptation of pathogens/parasites at a molecular level, and outlines a strategy to identify such nematode-selective targets that remain essential to the organism. With further experimental characterization and validation, it opens a possible channel for the development of novel treatments with high target specificity, addressing both host toxicity and resistance concerns.
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Affiliation(s)
- Qi Wang
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | - Esley Heizer
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | - Bruce A Rosa
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | - Scott A Wildman
- Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
| | - James W Janetka
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Ave., St. Louis, MO, USA
| | - Makedonka Mitreva
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA; Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
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Watson AK, Williams TA, Williams BAP, Moore KA, Hirt RP, Embley TM. Transcriptomic profiling of host-parasite interactions in the microsporidian Trachipleistophora hominis. BMC Genomics 2015; 16:983. [PMID: 26589282 PMCID: PMC4654818 DOI: 10.1186/s12864-015-1989-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 10/06/2015] [Indexed: 12/28/2022] Open
Abstract
Background Trachipleistophora hominis was isolated from an HIV/AIDS patient and is a member of a highly successful group of obligate intracellular parasites. Methods Here we have investigated the evolution of the parasite and the interplay between host and parasite gene expression using transcriptomics of T. hominis-infected rabbit kidney cells. Results T. hominis has about 30 % more genes than small-genome microsporidians. Highly expressed genes include those involved in growth, replication, defence against oxidative stress, and a large fraction of uncharacterised genes. Chaperones are also highly expressed and may buffer the deleterious effects of the large number of non-synonymous mutations observed in essential T. hominis genes. Host expression suggests a general cellular shutdown upon infection, but ATP, amino sugar and nucleotide sugar production appear enhanced, potentially providing the parasite with substrates it cannot make itself. Expression divergence of duplicated genes, including transporters used to acquire host metabolites, demonstrates ongoing functional diversification during microsporidian evolution. We identified overlapping transcription at more than 100 loci in the sparse T. hominis genome, demonstrating that this feature is not caused by genome compaction. The detection of additional transposons of insect origin strongly suggests that the natural host for T. hominis is an insect. Conclusions Our results reveal that the evolution of contemporary microsporidian genomes is highly dynamic and innovative. Moreover, highly expressed T. hominis genes of unknown function include a cohort that are shared among all microsporidians, indicating that some strongly conserved features of the biology of these enormously successful parasites remain uncharacterised. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1989-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrew K Watson
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
| | - Tom A Williams
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
| | - Bryony A P Williams
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Devon, UK.
| | - Karen A Moore
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Devon, UK.
| | - Robert P Hirt
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
| | - T Martin Embley
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
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Eixelsberger T, Weber H, Nidetzky B. Probing of the reaction pathway of human UDP-xylose synthase with site-directed mutagenesis. Carbohydr Res 2015; 416:1-6. [PMID: 26342152 DOI: 10.1016/j.carres.2015.08.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 08/11/2015] [Accepted: 08/12/2015] [Indexed: 11/28/2022]
Abstract
Uridine 5'-diphosphate (UDP)-xylose (UDP-Xyl) synthase (UXS) catalyzes the oxidative decarboxylation of UDP-glucuronic acid (UDP-GlcUA) to UDP-Xyl. The closely related UDP-glucuronic acid 4-epimerase (UGAE) interconverts UDP-GlcUA and UDP-galacturonic acid (UDP-GalUA) in a highly similar manner via the intermediate UDP-xylo-hexopyranos-4-uluronic acid (UDP-4-keto-GlcUA). Unlike UXS, however, UGAE prevents the decarboxylation. Human UXS (hUXS) and UGAE from Arabidopsis thaliana exhibit high structural similarity in the active site, but two catalytically important residues in hUXS (Glu(120) and Arg(277)) are replaced by Ser and Thr in the UGAE group. Additionally, Asn(176), which participates in substrate binding, is changed to Thr. We therefore analyzed single, double and triple mutants of hUXS carrying these substitutions to evaluate their significance for product specificity. All mutants showed considerably lower activities than wild-type hUXS (>1000-fold reduction). NMR spectroscopic analysis of the reaction products showed that UDP-β-L-threo-pentopyranos-4-ulose (UDP-4-keto-Xyl), UDP-Xyl or both, but no UDP-GalUA or UDP-4-keto-GlcUA were formed. Correlation of product characteristics, such as deuterium incorporation, with the amino acid replacements gave insights into structure-function relationships in UXS, suggesting that interaction between active site and overall enzyme structure rather than distinct conserved residues are decisive for product formation.
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Affiliation(s)
- Thomas Eixelsberger
- Institute of Biotechnology and Biochemical Engineering, NAWI Graz, Graz University of Technology, Petersgasse 12/I, A-8010 Graz, Austria
| | - Hansjörg Weber
- Institute of Organic Chemistry, NAWI Graz, Graz University of Technology, Stremayrgasse 9, A-8010 Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, NAWI Graz, Graz University of Technology, Petersgasse 12/I, A-8010 Graz, Austria; Austrian Centre of Industrial Biotechnology, Petersgasse 14, A-8010 Graz, Austria.
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Soni V, Upadhayay S, Suryadevara P, Samla G, Singh A, Yogeeswari P, Sriram D, Nandicoori VK. Depletion of M. tuberculosis GlmU from Infected Murine Lungs Effects the Clearance of the Pathogen. PLoS Pathog 2015; 11:e1005235. [PMID: 26489015 PMCID: PMC4619583 DOI: 10.1371/journal.ppat.1005235] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 09/27/2015] [Indexed: 01/06/2023] Open
Abstract
M. tuberculosis N-acetyl-glucosamine-1-phosphate uridyltransferase (GlmUMtb) is a bi-functional enzyme engaged in the synthesis of two metabolic intermediates N-acetylglucosamine-1-phosphate (GlcNAc-1-P) and UDP-GlcNAc, catalyzed by the C- and N-terminal domains respectively. UDP-GlcNAc is a key metabolite essential for the synthesis of peptidoglycan, disaccharide linker, arabinogalactan and mycothiols. While glmUMtb was predicted to be an essential gene, till date the role of GlmUMtb in modulating the in vitro growth of Mtb or its role in survival of pathogen ex vivo / in vivo have not been deciphered. Here we present the results of a comprehensive study dissecting the role of GlmUMtb in arbitrating the survival of the pathogen both in vitro and in vivo. We find that absence of GlmUMtb leads to extensive perturbation of bacterial morphology and substantial reduction in cell wall thickness under normoxic as well as hypoxic conditions. Complementation studies show that the acetyl- and uridyl- transferase activities of GlmUMtb are independently essential for bacterial survival in vitro, and GlmUMtb is also found to be essential for mycobacterial survival in THP-1 cells as well as in guinea pigs. Depletion of GlmUMtb from infected murine lungs, four weeks post infection, led to significant reduction in the bacillary load. The administration of Oxa33, a novel oxazolidine derivative that specifically inhibits GlmUMtb, to infected mice resulted in significant decrease in the bacillary load. Thus our study establishes GlmUMtb as a strong candidate for intervention measures against established tuberculosis infections. The synthesis of the Mtb cell wall involves a cascade of reactions catalyzed by cytosolic and cell membrane-bound enzymes. The reaction catalyzed by GlmUMtb (an enzyme with acetyltransferase and uridyltransferase activities) generates UDP-GlcNAc, a central nucleotide-sugar building block of the cell wall. Apart from cell wall synthesis UDP-GlcNAc is an essential metabolite participating in other cellular processes including disaccharide linker and mycothiol biosynthesis. GlmUMtb shares very little sequence similarity with eukaryotic acetyltransferase and uridyltransferase enzymes. Many pathogens have alternative pathway(s) for foraging GlcNAc from the host. The present study was undertaken to see the effects of depleting GlmUMtb on pathogen survival in the host animal. We have generated a conditional gene replacement mutant of glmUMtb and find that depletion of GlmUMtb at any stage of bacterial growth or in mice infected with Mtb including a well-established infection, results in irreversible bacterial death due to perturbation of cell wall synthesis. We have developed a novel anti-GlmUMtb inhibitor (Oxa33), identified its binding site on GlmUMtb, and shown its specificity for GlmUMtb. The study demonstrates that GlmUMtb is a promising target for therapeutic intervention and Oxa33 can be pursued as a lead molecule.
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Affiliation(s)
- Vijay Soni
- National Institute of Immunology, New Delhi, India
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Hyderabad, India
| | | | - Priyanka Suryadevara
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Hyderabad, India
| | - Ganesh Samla
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Hyderabad, India
| | - Archana Singh
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Perumal Yogeeswari
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Hyderabad, India
| | - Dharmarajan Sriram
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Hyderabad, India
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Perna AM, Rodrigues T, Schmidt TP, Böhm M, Stutz K, Reker D, Pfeiffer B, Altmann KH, Backert S, Wessler S, Schneider G. Fragment-Based De Novo Design Reveals a Small-Molecule Inhibitor ofHelicobacter PyloriHtrA. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201504035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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20
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Perna AM, Rodrigues T, Schmidt TP, Böhm M, Stutz K, Reker D, Pfeiffer B, Altmann KH, Backert S, Wessler S, Schneider G. Fragment-Based De Novo Design Reveals a Small-Molecule Inhibitor of Helicobacter Pylori HtrA. Angew Chem Int Ed Engl 2015; 54:10244-8. [PMID: 26069090 DOI: 10.1002/anie.201504035] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Indexed: 01/22/2023]
Abstract
Sustained identification of innovative chemical entities is key for the success of chemical biology and drug discovery. We report the fragment-based, computer-assisted de novo design of a small molecule inhibiting Helicobacter pylori HtrA protease. Molecular binding of the designed compound to HtrA was confirmed through biophysical methods, supporting its functional activity in vitro. Hit expansion led to the identification of the currently best-in-class HtrA inhibitor. The results obtained reinforce the validity of ligand-based de novo design and binding-kinetics-guided optimization for the efficient discovery of pioneering lead structures and prototyping drug-like chemical probes with tailored bioactivity.
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Affiliation(s)
- Anna M Perna
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland)
| | - Tiago Rodrigues
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland)
| | | | - Manja Böhm
- Department of Biology, Universität Erlangen-Nürnberg (Germany)
| | - Katharina Stutz
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland)
| | - Daniel Reker
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland)
| | - Bernhard Pfeiffer
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland)
| | - Karl-Heinz Altmann
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland)
| | - Steffen Backert
- Department of Biology, Universität Erlangen-Nürnberg (Germany)
| | - Silja Wessler
- Department of Molecular Biology, Universität Salzburg (Austria)
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland).
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Tran AT, Wen D, West NP, Baker EN, Britton WJ, Payne RJ. Inhibition studies on Mycobacterium tuberculosis N-acetylglucosamine-1-phosphate uridyltransferase (GlmU). Org Biomol Chem 2014; 11:8113-26. [PMID: 24158720 DOI: 10.1039/c3ob41896k] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Peptidoglycan is an essential component of the cell wall of bacteria, including Mycobacterium tuberculosis, that provides structural strength and rigidity to enable internal osmotic pressure to be withstood. The first committed step in the biosynthesis of peptidoglycan involves the formation of uridine diphosphate-N-acetylglucosamine (UDP-GlcNAc) from uridine triphosphate (UTP) and GlcNAc-1-phosphate. This reaction is catalysed by N-acetylglucosamine-1-phosphate uridyltransferase (GlmU), a bifunctional enzyme with two independent active sites that possess acetyltransferase and uridyltransferase activities. Herein, we report the first inhibition study targeted against the uridyltransferase activity of M. tuberculosis GlmU. A number of potential inhibitors were initially prepared leading to the discovery of active aminoquinazoline-based compounds. The most potent inhibitor in this series exhibited an IC50 of 74 μM against GlmU uridyltransferase activity and serves as a promising starting point for the discovery of more potent inhibitors.
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Affiliation(s)
- Anh Thu Tran
- School of Chemistry, Building F11. and The University of Sydney, Camperdown, NSW 2006, Australia.
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Abstract
Allostery is the most direct and efficient way for regulation of biological macromolecule function, ranging from the control of metabolic mechanisms to signal transduction pathways. Allosteric modulators target to allosteric sites, offering distinct advantages compared to orthosteric ligands that target to active sites, such as greater specificity, reduced side effects, and lower toxicity. Allosteric modulators have therefore drawn increasing attention as potential therapeutic drugs in the design and development of new drugs. In recent years, advancements in our understanding of the fundamental principles underlying allostery, coupled with the exploitation of powerful techniques and methods in the field of allostery, provide unprecedented opportunities to discover allosteric proteins, detect and characterize allosteric sites, design and develop novel efficient allosteric drugs, and recapitulate the universal features of allosteric proteins and allosteric modulators. In the present review, we summarize the recent advances in the repertoire of allostery, with a particular focus on the aforementioned allosteric compounds.
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Affiliation(s)
- Shaoyong Lu
- Department of Pathophysiology, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai, China
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