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Kaushik S, Yadav J, Das S, Singh S, Jyoti A, Srivastava VK, Sharma V, Kumar S, Kumar S. Deciphering the Role of S-adenosyl Homocysteine Nucleosidase in Quorum
Sensing Mediated Biofilm Formation. Curr Protein Pept Sci 2022; 23:211-225. [DOI: 10.2174/1389203723666220519152507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/21/2022] [Accepted: 03/11/2022] [Indexed: 11/22/2022]
Abstract
Abstract:
S-adenosylhomocysteine nucleosidase (MTAN) is a protein that plays a crucial role in several
pathways of bacteria that are essential for its survival and pathogenesis. In addition to the role of
MTAN in methyl-transfer reactions, methionine biosynthesis, and polyamine synthesis, MTAN is also
involved in bacterial quorum sensing (QS). In QS, chemical signaling autoinducer (AI) secreted by
bacteria assists cell to cell communication and is regulated in a cell density-dependent manner. They
play a significant role in the formation of bacterial biofilm. MTAN plays a major role in the synthesis
of these autoinducers. Signaling molecules secreted by bacteria, i.e., AI-1 are recognized as acylated
homoserine lactones (AHL) that function as signaling molecules within bacteria. QS enables bacteria
to establish physical interactions leading to biofilm formation. The formation of biofilm is a primary
reason for the development of multidrug-resistant properties in pathogenic bacteria like Enterococcus
faecalis (E. faecalis). In this regard, inhibition of E. faecalis MTAN (EfMTAN) will block the QS and
alter the bacterial biofilm formation. In addition to this, it will also block methionine biosynthesis and
many other critical metabolic processes. It should also be noted that inhibition of EfMTAN will not
have any effect on human beings as this enzyme is not present in humans. This review provides a comprehensive
overview of the structural-functional relationship of MTAN. We have also highlighted the
current status, enigmas that warrant further studies, and the prospects for identifying potential inhibitors
of EfMTAN for the treatment of E. faecalis infections. In addition to this, we have also reported
structural studies of EfMTAN using homology modeling and highlighted the putative binding sites of
the protein.
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Affiliation(s)
- Sanket Kaushik
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Jyoti Yadav
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Satyajeet Das
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
- Structural Biology Lab, CSIR-Institute of Microbial Technology, Chandigarh-160036, India
| | - Suraj Singh
- Centre for Bioseparation Technology, VIT University, Vellore-632014, Tamil Nadu, India
| | - Anupam Jyoti
- Department of Biotechnology, University Institute of Biotechnology, Chandigarh University, Chandigarh, India
| | | | - Vinay Sharma
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Sanjit Kumar
- Centre for Bioseparation Technology, VIT University, Vellore-632014, Tamil Nadu, India
| | - Sujeet Kumar
- Centre for Proteomics and Drug Discovery, Amity Institute of Biotechnology, Amity University, Maharashtra, India
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2
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Yu K, Yue ME, Xu J, Jiang TF. Screening of 5′-Methylthioadenosine Nucleosidase Enzyme Inhibitors from Traditional Chinese Medicine and Small Molecular Compounds by Capillary Electrophoresis After Enzymatic Reaction at Capillary Inlet. Chromatographia 2020. [DOI: 10.1007/s10337-020-03873-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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3
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Zhang D, Burdette BE, Wang Z, Karn K, Li HY, Schramm VL, Tyler PC, Evans GB, Wang S. Transition State Analogues Enhanced by Fragment-Based Structural Analysis: Bacterial Methylthioadenosine Nucleosidases. Biochemistry 2020; 59:831-835. [PMID: 32022543 PMCID: PMC10644263 DOI: 10.1021/acs.biochem.9b01092] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transition state analogue inhibitor design (TSID) and fragment-based drug design (FBDD) are drug design approaches typically used independently. Methylthio-DADMe-Immucillin-A (MTDIA) is a tight-binding transition state analogue of bacterial 5'-methylthioadenosine nucleosidases (MTANs). Previously, Salmonella enterica MTAN structures were found to bind MTDIA and ethylene glycol fragments, but MTDIA modified to contain similar fragments did not enhance affinity. Seventy-five published MTAN structures were analyzed, and co-crystallization fragments were found that might enhance the binding of MTDIA to other bacterial MTANs through contacts external to MTDIA binding. The fragment-modified MTDIAs were tested with Helicobacter pylori MTAN and Staphylococcus aureus MTANs (HpMTAN and SaMTAN) as test cases to explore inhibitor optimization by potential contacts beyond the transition state contacts. Replacement of a methyl group with a 2'-ethoxyethanol group in MTDIA improved the dissociation constant 14-fold (0.09 nM vs 1.25 nM) for HpMTAN and 81-fold for SaMTAN (0.096 nM vs 7.8 nM). TSID combined with FBDD can be useful in enhancing already powerful inhibitors.
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Affiliation(s)
- Di Zhang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China; Department of Chemistry, University of Arkansas at Little Rock, Little Rock, Arkansas 72204, United States
| | - Brandon E. Burdette
- Department of Chemistry, University of Arkansas at Little Rock, Little Rock, Arkansas 72204, United States
| | - Zhengyu Wang
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Science, Little Rock, Arkansas 72205, United States
| | - Kumari Karn
- Department of Chemistry, University of Arkansas at Little Rock, Little Rock, Arkansas 72204, United States
| | - Hong-yu Li
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Science, Little Rock, Arkansas 72205, United States
| | - Vern L. Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, New York, New York 10461, United States
| | - Peter C. Tyler
- Ferrier Research Institute, Victoria University of Wellington, Wellington 5040, New Zealand
| | - Gary B. Evans
- Ferrier Research Institute, Victoria University of Wellington, Wellington 5040, New Zealand
| | - Shanzhi Wang
- Department of Chemistry, University of Arkansas at Little Rock, Little Rock, Arkansas 72204, United States
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4
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Cornell KA, Knippel RJ, Cortright GR, Fonken M, Guerrero C, Hall AR, Mitchell KA, Thurston JH, Erstad P, Tao A, Xu D, Parveen N. Characterization of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidases from Borrelia burgdorferi: Antibiotic targets for Lyme disease. Biochim Biophys Acta Gen Subj 2019; 1864:129455. [PMID: 31669585 DOI: 10.1016/j.bbagen.2019.129455] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 09/23/2019] [Accepted: 10/03/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Borrelia burgdorferi causes Lyme disease, the most common tick-borne illness in the United States. The Center for Disease Control and Prevention estimates that the occurrence of Lyme disease in the U.S. has now reached approximately 300,000 cases annually. Early stage Borrelia burgdorferi infections are generally treatable with oral antibiotics, but late stage disease is more difficult to treat and more likely to lead to post-treatment Lyme disease syndrome. METHODS Here we examine three unique 5'-methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidases (MTNs or MTANs, EC 3.2.2.9) responsible for salvage of adenine and methionine in B. burgdorferi and explore their potential as antibiotic targets to treat Lyme disease. Recombinant Borrelia MTNs were expressed and purified from E. coli. The enzymes were extensively characterized for activity, specificity, and inhibition using a UV spectrophotometric assay. In vitro antibiotic activities of MTN inhibitors were assessed using a bioluminescent BacTiter-Glo™ assay. RESULTS The three Borrelia MTNs showed unique activities against the native substrates MTA, SAH, and 5'-deoxyadenosine. Analysis of substrate analogs revealed that specific activity rapidly dropped as the length of the 5'-alkylthio substitution increased. Non-hydrolysable nucleoside transition state analogs demonstrated sub-nanomolar enzyme inhibition constants. Lastly, two late stage transition state analogs exerted in vitro IC50 values of 0.3-0.4 μg/mL against cultured B. burgdorferi cells. CONCLUSION B. burgdorferi is unusual in that it expresses three distinct MTNs (cytoplasmic, membrane bound, and secreted) that are effectively inactivated by nucleoside analogs. GENERAL SIGNIFICANCE The Borrelia MTNs appear to be promising targets for developing new antibiotics to treat Lyme disease.
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Affiliation(s)
- Kenneth A Cornell
- Department of Chemistry & Biochemistry, Boise State University, Boise, ID, USA; Biomolecular Research Center, Boise State University, Boise, ID, USA.
| | - Reece J Knippel
- Department of Chemistry & Biochemistry, Boise State University, Boise, ID, USA
| | - Gerald R Cortright
- Department of Chemistry & Biochemistry, Boise State University, Boise, ID, USA
| | - Meghan Fonken
- Department of Chemistry & Biochemistry, Boise State University, Boise, ID, USA
| | - Christian Guerrero
- Department of Chemistry & Biochemistry, Boise State University, Boise, ID, USA
| | - Amy R Hall
- Department of Chemistry & Biochemistry, Boise State University, Boise, ID, USA
| | - Kristen A Mitchell
- Biomolecular Research Center, Boise State University, Boise, ID, USA; Department of Biological Sciences, Boise State University, Boise, ID, USA
| | - John H Thurston
- Department of Chemistry, The College of Idaho, Caldwell, ID, USA
| | - Patrick Erstad
- Department of Chemistry, The College of Idaho, Caldwell, ID, USA; Department of Biomedical & Pharmaceutical Sciences, Idaho State University, Meridian, ID, USA
| | - Aoxiang Tao
- Department of Biomedical & Pharmaceutical Sciences, Idaho State University, Meridian, ID, USA
| | - Dong Xu
- Department of Biomedical & Pharmaceutical Sciences, Idaho State University, Meridian, ID, USA
| | - Nikhat Parveen
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA
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5
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Harijan RK, Hoff O, Ducati RG, Firestone RS, Hirsch BM, Evans GB, Schramm VL, Tyler PC. Selective Inhibitors of Helicobacter pylori Methylthioadenosine Nucleosidase and Human Methylthioadenosine Phosphorylase. J Med Chem 2019; 62:3286-3296. [PMID: 30860833 PMCID: PMC6635953 DOI: 10.1021/acs.jmedchem.8b01642] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacterial 5'-methylthioadenosine/ S-adenosylhomocysteine nucleosidase (MTAN) hydrolyzes adenine from its substrates to form S-methyl-5-thioribose and S-ribosyl-l-homocysteine. MTANs are involved in quorum sensing, menaquinone synthesis, and 5'-methylthioadenosine recycling to S-adenosylmethionine. Helicobacter pylori uses MTAN in its unusual menaquinone pathway, making H. pylori MTAN a target for antibiotic development. Human 5'-methylthioadenosine phosphorylase (MTAP), a reported anticancer target, catalyzes phosphorolysis of 5'-methylthioadenosine to salvage S-adenosylmethionine. Transition-state analogues designed for HpMTAN and MTAP show significant overlap in specificity. Fifteen unique transition-state analogues are described here and are used to explore inhibitor specificity. Several analogues of HpMTAN bind in the picomolar range while inhibiting human MTAP with orders of magnitude weaker affinity. Structural analysis of HpMTAN shows inhibitors extending through a hydrophobic channel to the protein surface. The more enclosed catalytic sites of human MTAP require the inhibitors to adopt a folded structure, displacing the phosphate nucleophile from the catalytic site.
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Affiliation(s)
- Rajesh K. Harijan
- Department of Biochemistry, Albert Einstein College
of Medicine, New York 10461, New York, United States
| | - Oskar Hoff
- Ferrier Research Institute, Victoria University of
Wellington, Wellington 5040, New Zealand
| | - Rodrigo G. Ducati
- Department of Biochemistry, Albert Einstein College
of Medicine, New York 10461, New York, United States
| | - Ross S. Firestone
- Department of Biochemistry, Albert Einstein College
of Medicine, New York 10461, New York, United States
| | - Brett M. Hirsch
- Department of Biochemistry, Albert Einstein College
of Medicine, New York 10461, New York, United States
| | - Gary B. Evans
- Ferrier Research Institute, Victoria University of
Wellington, Wellington 5040, New Zealand
| | - Vern L. Schramm
- Department of Biochemistry, Albert Einstein College
of Medicine, New York 10461, New York, United States
| | - Peter C. Tyler
- Ferrier Research Institute, Victoria University of
Wellington, Wellington 5040, New Zealand
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6
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Fleitas Martínez O, Rigueiras PO, Pires ÁDS, Porto WF, Silva ON, de la Fuente-Nunez C, Franco OL. Interference With Quorum-Sensing Signal Biosynthesis as a Promising Therapeutic Strategy Against Multidrug-Resistant Pathogens. Front Cell Infect Microbiol 2019; 8:444. [PMID: 30805311 PMCID: PMC6371041 DOI: 10.3389/fcimb.2018.00444] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 12/12/2018] [Indexed: 12/11/2022] Open
Abstract
Faced with the global health threat of increasing resistance to antibiotics, researchers are exploring interventions that target bacterial virulence factors. Quorum sensing is a particularly attractive target because several bacterial virulence factors are controlled by this mechanism. Furthermore, attacking the quorum-sensing signaling network is less likely to select for resistant strains than using conventional antibiotics. Strategies that focus on the inhibition of quorum-sensing signal production are especially attractive because the enzymes involved are expressed in bacterial cells but are not present in their mammalian counterparts. We review here various approaches that are being taken to interfere with quorum-sensing signal production via the inhibition of autoinducer-2 synthesis, PQS synthesis, peptide autoinducer synthesis, and N-acyl-homoserine lactone synthesis. We expect these approaches will lead to the discovery of new quorum-sensing inhibitors that can help to stem the tide of antibiotic resistance.
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Affiliation(s)
- Osmel Fleitas Martínez
- Programa de Pós-Graduação em Patologia Molecular, Universidade de Brasília, Brasília, Brazil.,Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, Brazil
| | - Pietra Orlandi Rigueiras
- Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, Brazil
| | - Állan da Silva Pires
- Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, Brazil
| | - William Farias Porto
- Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, Brazil.,S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil.,Porto Reports, Brasília, Brazil
| | - Osmar Nascimento Silva
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
| | - Cesar de la Fuente-Nunez
- Synthetic Biology Group, MIT Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, United States.,Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, United States.,Department of Biological Engineering, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, United States.,Broad Institute of MIT and Harvard, Cambridge, MA, United States.,The Center for Microbiome Informatics and Therapeutics, Cambridge, MA, United States
| | - Octavio Luiz Franco
- Programa de Pós-Graduação em Patologia Molecular, Universidade de Brasília, Brasília, Brazil.,Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, Brazil.,S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
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7
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Mutreja I, Warring SL, Lim KS, Swadi T, Clinch K, Mason JM, Sheen CR, Thompson DR, Ducati RG, Chambers ST, Evans GB, Gerth ML, Miller AG, Woodfield TBF. Biofilm Inhibition via Delivery of Novel Methylthioadenosine Nucleosidase Inhibitors from PVA-Tyramine Hydrogels while Supporting Mesenchymal Stromal Cell Viability. ACS Biomater Sci Eng 2019; 5:748-758. [PMID: 33405836 DOI: 10.1021/acsbiomaterials.8b01141] [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] [Indexed: 01/16/2023]
Abstract
The rise of antibiotic resistance, coupled with increased expectations for mobility in later life, is creating a need for biofilm inhibitors and delivery systems that will reduce surgical implant infection. A limitation of some of these existing delivery approaches is toxicity exhibited toward host cells. Here, we report the application of a novel inhibitor of the enzyme, methylthioadenosine nucleosidase (MTAN), a key enzyme in bacterial metabolic pathways, which include S-adenosylmethionine catabolism and purine nucleotide recycling, in combination with a poly(vinyl alcohol)-tyramine-based (PVA-Tyr) hydrogel delivery system. We demonstrate that a lead MTAN inhibitor, selected from a screened library of 34 candidates, (2S)-2-(4-amino-5H-pyrrolo3,2-dpyrimidin-7-ylmethyl)aminoundecan-1-ol (31), showed a minimum biofilm inhibitory concentration of 2.2 ± 0.4 μM against a clinical staphylococcal species isolated from an infected implant. We observed that extracellular DNA, a key constituent of biofilms, is significantly reduced when treated with 10 μM compound 31, along with a decrease in biofilm thickness. Compound 31 was incorporated into a hydrolytically degradable photo-cross-linked PVA-Tyr hydrogel and the release profile was evaluated by HPLC studies. Compound 31 released from the PVA-hydrogel system significantly reduced biofilm formation (77.2 ± 8.4% biofilm inhibition). Finally, compound 31 released from PVA-Tyr showed no negative impact on human bone marrow stromal cell (MSC) viability, proliferation, or morphology. The results demonstrate the potential utility of MTAN inhibitors in treating infections caused by Gram-positive bacteria, and the development of a nontoxic release system that has potential for tunability for time scale of delivery.
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Affiliation(s)
- Isha Mutreja
- Christchurch Regenerative Medicine and Tissue Engineering (CReaTE) Group, Department of Orthopaedic Surgery and Musculoskeletal Medicine, Centre for Bioengineering & Nanomedicine, University of Otago Christchurch, Christchurch 8140, New Zealand.,Medical Technologies Centre of Research Excellence, Auckland 1010, New Zealand
| | - Suzanne L Warring
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
| | - Khoon S Lim
- Christchurch Regenerative Medicine and Tissue Engineering (CReaTE) Group, Department of Orthopaedic Surgery and Musculoskeletal Medicine, Centre for Bioengineering & Nanomedicine, University of Otago Christchurch, Christchurch 8140, New Zealand.,Medical Technologies Centre of Research Excellence, Auckland 1010, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1010, New Zealand
| | - Tara Swadi
- Department of Pathology, University of Otago Christchurch Christchurch 8140, New Zealand
| | - Keith Clinch
- Ferrier Research Institute, Victoria University of Wellington, Lower Hutt 5046, New Zealand
| | - Jennifer M Mason
- Ferrier Research Institute, Victoria University of Wellington, Lower Hutt 5046, New Zealand
| | - Campbell R Sheen
- Protein Science and Engineering, Callaghan Innovation, c/- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Dion R Thompson
- Protein Science and Engineering, Callaghan Innovation, c/- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Rodrigo G Ducati
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Stephen T Chambers
- Department of Pathology, University of Otago Christchurch Christchurch 8140, New Zealand
| | - Gary B Evans
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1010, New Zealand.,Ferrier Research Institute, Victoria University of Wellington, Lower Hutt 5046, New Zealand
| | - Monica L Gerth
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1010, New Zealand
| | - Antonia G Miller
- Protein Science and Engineering, Callaghan Innovation, c/- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Tim B F Woodfield
- Christchurch Regenerative Medicine and Tissue Engineering (CReaTE) Group, Department of Orthopaedic Surgery and Musculoskeletal Medicine, Centre for Bioengineering & Nanomedicine, University of Otago Christchurch, Christchurch 8140, New Zealand.,Medical Technologies Centre of Research Excellence, Auckland 1010, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1010, New Zealand
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8
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Ducati RG, Harijan RK, Cameron SA, Tyler PC, Evans GB, Schramm VL. Transition-State Analogues of Campylobacter jejuni 5'-Methylthioadenosine Nucleosidase. ACS Chem Biol 2018; 13:3173-3183. [PMID: 30339406 DOI: 10.1021/acschembio.8b00781] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Campylobacter jejuni is a Gram-negative bacterium responsible for food-borne gastroenteritis and associated with Guillain-Barré, Reiter, and irritable bowel syndromes. Antibiotic resistance in C. jejuni is common, creating a need for antibiotics with novel mechanisms of action. Menaquinone biosynthesis in C. jejuni uses the rare futalosine pathway, where 5'-methylthioadenosine nucleosidase ( CjMTAN) is proposed to catalyze the essential hydrolysis of adenine from 6-amino-6-deoxyfutalosine to form dehypoxanthinylfutalosine, a menaquinone precursor. The substrate specificity of CjMTAN is demonstrated to include 6-amino-6-deoxyfutalosine, 5'-methylthioadenosine, S-adenosylhomocysteine, adenosine, and 5'-deoxyadenosine. These activities span the catalytic specificities for the role of bacterial MTANs in menaquinone synthesis, quorum sensing, and S-adenosylmethionine recycling. We determined inhibition constants for potential transition-state analogues of CjMTAN. The best of these compounds have picomolar dissociation constants and were slow-onset tight-binding inhibitors. The most potent CjMTAN transition-state analogue inhibitors inhibited C. jejuni growth in culture at low micromolar concentrations, similar to gentamicin. The crystal structure of apoenzyme C. jejuni MTAN was solved at 1.25 Å, and five CjMTAN complexes with transition-state analogues were solved at 1.42 to 1.95 Å resolution. Inhibitor binding induces a loop movement to create a closed catalytic site with Asp196 and Ile152 providing purine leaving group activation and Arg192 and Glu12 activating the water nucleophile. With inhibitors bound, the interactions of the 4'-alkylthio or 4'-alkyl groups of this inhibitor family differ from the Escherichia coli MTAN structure by altered protein interactions near the hydrophobic pocket that stabilizes 4'-substituents of transition-state analogues. These CjMTAN inhibitors have potential as specific antibiotic candidates against C. jejuni.
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Affiliation(s)
- Rodrigo G. Ducati
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Rajesh K. Harijan
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Scott A. Cameron
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Peter C. Tyler
- The Ferrier Research Institute, Victoria University of Wellington, 69 Gracefield Rd, Lower Hutt, 5010, New Zealand
| | - Gary B. Evans
- The Ferrier Research Institute, Victoria University of Wellington, 69 Gracefield Rd, Lower Hutt, 5010, New Zealand
- The Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
| | - Vern L. Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
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9
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Namanja-Magliano HA, Evans GB, Harijan RK, Tyler PC, Schramm VL. Transition State Analogue Inhibitors of 5'-Deoxyadenosine/5'-Methylthioadenosine Nucleosidase from Mycobacterium tuberculosis. Biochemistry 2017; 56:5090-5098. [PMID: 28836767 DOI: 10.1021/acs.biochem.7b00576] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Mycobacterium tuberculosis 5'-deoxyadenosine/5'-methylthioadenosine nucleosidase (Rv0091) catalyzes the N-riboside hydrolysis of its substrates 5'-methylthioadenosine (MTA) and 5'-deoxyadenosine (5'-dAdo). 5'-dAdo is the preferred substrate, a product of radical S-adenosylmethionine-dependent enzyme reactions. Rv0091 is characterized by a ribocation-like transition state, with low N-ribosidic bond order, an N7-protonated adenine leaving group, and an activated but weakly bonded water nucleophile. DADMe-Immucillins incorporating 5'-substituents of the substrates 5'-dAdo and MTA were synthesized and characterized as inhibitors of Rv0091. 5'-Deoxy-DADMe-Immucillin-A was the most potent among the 5'-dAdo transition state analogues with a dissociation constant of 640 pM. Among the 5'-thio substituents, hexylthio-DADMe-Immucillin-A was the best inhibitor at 87 pM. The specificity of Rv0091 for the Immucillin transition state analogues differs from those of other bacterial homologues because of an altered hydrophobic tunnel accepting the 5'-substituents. Inhibitors of Rv0091 had weak cell growth effects on M. tuberculosis or Mycobacterium smegmatis but were lethal toward Helicobacter pylori, where the 5'-methylthioadenosine nucleosidase is essential in menaquinone biosynthesis. We propose that Rv0091 plays a role in 5'-deoxyadenosine recycling but is not essential for growth in these Mycobacteria.
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Affiliation(s)
- Hilda A Namanja-Magliano
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Gary B Evans
- The Ferrier Research Institute, Victoria University of Wellington , Lower Hutt, Wellington 5040, New Zealand.,The Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland , Auckland, New Zealand
| | - Rajesh K Harijan
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Peter C Tyler
- The Ferrier Research Institute, Victoria University of Wellington , Lower Hutt, Wellington 5040, New Zealand
| | - Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
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10
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Namanja-Magliano HA, Stratton CF, Schramm VL. Transition State Structure and Inhibition of Rv0091, a 5'-Deoxyadenosine/5'-methylthioadenosine Nucleosidase from Mycobacterium tuberculosis. ACS Chem Biol 2016; 11:1669-76. [PMID: 27019223 DOI: 10.1021/acschembio.6b00144] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
5'-Methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) is a bacterial enzyme that catalyzes the hydrolysis of the N-ribosidic bond in 5'-methylthioadenosine (MTA) and S-adenosylhomocysteine (SAH). MTAN activity has been linked to quorum sensing pathways, polyamine biosynthesis, and adenine salvage. Previously, the coding sequence of Rv0091 was annotated as a putative MTAN in Mycobacterium tuberculosis. Rv0091 was expressed in Escherichia coli, purified to homogeneity, and shown to be a homodimer, consistent with MTANs from other microorganisms. Substrate specificity for Rv0091 gave a preference for 5'-deoxyadenosine relative to MTA or SAH. Intrinsic kinetic isotope effects (KIEs) for the hydrolysis of [1'-(3)H], [1'-(14)C], [5'-(3)H2], [9-(15)N], and [7-(15)N]MTA were determined to be 1.207, 1.038, 0.998, 1.021, and 0.998, respectively. A model for the transition state structure of Rv0091 was determined by matching KIE values predicted via quantum chemical calculations to the intrinsic KIEs. The transition state shows a substantial loss of C1'-N9 bond order, well-developed oxocarbenium character of the ribosyl ring, and weak participation of the water nucleophile. Electrostatic potential surface maps for the Rv0091 transition state structure show similarity to DADMe-immucillin transition state analogues. DADMe-immucillin transition state analogues showed strong inhibition of Rv0091, with the most potent inhibitor (5'-hexylthio-DADMe-immucillinA) displaying a Ki value of 87 pM.
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Affiliation(s)
- Hilda A. Namanja-Magliano
- Department
of Biochemistry, Albert Einstein College of Medicine, 1300 Morris
Park Avenue, Bronx, New York 10461, United States
| | - Christopher F. Stratton
- Department
of Biochemistry, Albert Einstein College of Medicine, 1300 Morris
Park Avenue, Bronx, New York 10461, United States
| | - Vern L. Schramm
- Department
of Biochemistry, Albert Einstein College of Medicine, 1300 Morris
Park Avenue, Bronx, New York 10461, United States
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11
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Wang S, Cameron SA, Clinch K, Evans GB, Wu Z, Schramm VL, Tyler PC. New Antibiotic Candidates against Helicobacter pylori. J Am Chem Soc 2015; 137:14275-80. [PMID: 26494017 PMCID: PMC6709534 DOI: 10.1021/jacs.5b06110] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Helicobacter pylori is a Gram-negative bacterium that colonizes the gut of over 50% of the world's population. It is responsible for most peptic ulcers and is an important risk factor for gastric cancer. Antibiotic treatment for H. pylori infections is challenging as drug resistance has developed to antibiotics with traditional mechanisms of action. H. pylori uses an unusual pathway for menaquinone biosynthesis with 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) catalyzing an essential step. We validated MTAN as a target with a transition-state analogue of the enzyme [Wang, S.; Haapalainen, A. M.; Yan, F.; et al. Biochemistry 2012, 51, 6892-6894]. MTAN inhibitors will only be useful drug candidates if they can both include tight binding to the MTAN target and have the ability to penetrate the complex cell membrane found in Gram-negative H. pylori. Here we explore structural scaffolds for MTAN inhibition and for growth inhibition of cultured H. pylori. Sixteen analogues reported here are transition-state analogues of H. pylori MTAN with dissociation constants of 50 pM or below. Ten of these prevent growth of the H. pylori with IC90 values below 0.01 μg/mL. These remarkable compounds meet the criteria for potent inhibition and cell penetration. As a consequence, 10 new H. pylori antibiotic candidates are identified, all of which prevent H. pylori growth at concentrations 16-2000-fold lower than the five antibiotics, amoxicillin, metronidazole, levofloxacin, tetracyclin, and clarithromycin, commonly used to treat H. pylori infections. X-ray crystal structures of MTAN cocrystallized with several inhibitors show them to bind in the active site making interactions consistent with transition-state analogues.
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Affiliation(s)
- Shanzhi Wang
- Department of Biochemistry, Albert Einstein College of Medicine, New York, New York, 10461, United States
| | - Scott A. Cameron
- Department of Biochemistry, Albert Einstein College of Medicine, New York, New York, 10461, United States
| | - Keith Clinch
- The Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, Wellington 5040, New Zealand
| | - Gary B. Evans
- The Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, Wellington 5040, New Zealand
| | - Zhimeng Wu
- The Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, Wellington 5040, New Zealand
| | - Vern L. Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, New York, New York, 10461, United States
| | - Peter C. Tyler
- The Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, Wellington 5040, New Zealand
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12
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Molecular dynamics study of the effect of active site protonation on Helicobacter pylori 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidase. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2015; 44:685-96. [DOI: 10.1007/s00249-015-1067-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 06/26/2015] [Accepted: 07/29/2015] [Indexed: 10/23/2022]
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13
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Barta ML, Thomas K, Yuan H, Lovell S, Battaile KP, Schramm VL, Hefty PS. Structural and biochemical characterization of Chlamydia trachomatis hypothetical protein CT263 supports that menaquinone synthesis occurs through the futalosine pathway. J Biol Chem 2014; 289:32214-32229. [PMID: 25253688 DOI: 10.1074/jbc.m114.594325] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The obligate intracellular human pathogen Chlamydia trachomatis is the etiological agent of blinding trachoma and sexually transmitted disease. Genomic sequencing of Chlamydia indicated this medically important bacterium was not exclusively dependent on the host cell for energy. In order for the electron transport chain to function, electron shuttling between membrane-embedded complexes requires lipid-soluble quinones (e.g. menaquionone or ubiquinone). The sources or biosynthetic pathways required to obtain these electron carriers within C. trachomatis are poorly understood. The 1.58Å crystal structure of C. trachomatis hypothetical protein CT263 presented here supports a role in quinone biosynthesis. Although CT263 lacks sequence-based functional annotation, the crystal structure of CT263 displays striking structural similarity to 5'-methylthioadenosine nucleosidase (MTAN) enzymes. Although CT263 lacks the active site-associated dimer interface found in prototypical MTANs, co-crystal structures with product (adenine) or substrate (5'-methylthioadenosine) indicate that the canonical active site residues are conserved. Enzymatic characterization of CT263 indicates that the futalosine pathway intermediate 6-amino-6-deoxyfutalosine (kcat/Km = 1.8 × 10(3) M(-1) s(-1)), but not the prototypical MTAN substrates (e.g. S-adenosylhomocysteine and 5'-methylthioadenosine), is hydrolyzed. Bioinformatic analyses of the chlamydial proteome also support the futalosine pathway toward the synthesis of menaquinone in Chlamydiaceae. This report provides the first experimental support for quinone synthesis in Chlamydia. Menaquinone synthesis provides another target for agents to combat C. trachomatis infection.
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Affiliation(s)
- Michael L Barta
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045
| | - Keisha Thomas
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461
| | - Hongling Yuan
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461
| | - Scott Lovell
- Protein Structure Laboratory, Del Shankel Structural Biology Center, University of Kansas, Lawrence, Kansas 66047, and
| | - Kevin P Battaile
- Industrial Macromolecular Crystallography Association-Collaborative Access Team, Hauptman-Woodward Medical Research Institute, Argonne, Illinois 60439
| | - Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461
| | - P Scott Hefty
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045,.
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14
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Wang S, Thomas K, Schramm VL. Catalytic site cooperativity in dimeric methylthioadenosine nucleosidase. Biochemistry 2014; 53:1527-35. [PMID: 24502544 PMCID: PMC3977580 DOI: 10.1021/bi401589n] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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5′-Methylthioadenosine/S-adenosylhomocysteine
nucleosidases (MTANs) are bacterial enzymes that catalyze hydrolysis
of the N-ribosidic bonds of 5′-methylthioadenosine
(MTA) and S-adenosylhomocysteine (SAH) to form adenine
and 5-thioribosyl groups. MTANs are involved in AI-1 and AI-2 bacterial
quorum sensing and the unusual futalosine-based menaquinone synthetic
pathway in Streptomyces,Helicobacter, and Campylobacter species. Crystal structures show MTANs to be homodimers with two
catalytic sites near the dimer interface. Here, we explore the cooperative
ligand interactions in the homodimer of Staphylococcus
aureus MTAN (SaMTAN). Kinetic analysis
indicated negative catalytic cooperativity. Titration of SaMTAN with the transition-state analogue MT-DADMe-ImmA gave unequal
catalytic site binding, consistent with negative binding cooperativity.
Thermodynamics of MT-DADMe-ImmA binding also gave negative cooperativity,
where the first site had different enthalpic and entropic properties
than the second site. Cysteine reactivity in a single-cysteine catalytic
site loop construct of SaMTAN is reactive in native
enzyme, less reactive when inhibitor is bound to one subunit, and
nonreactive upon saturation with inhibitor. A fusion peptide heterodimer
construct with one inactive subunit (E173Q) and one native subunit
gave 25% of native SaMTAN activity, similar to native SaMTAN with MT-DADMe-ImmA at one catalytic site. Pre-steady-state
kinetics showed fast chemistry at one catalytic site, consistent with
slow adenine release before catalysis occurs at the second catalytic
site. The results support the two catalytic sites acting sequentially,
with negative cooperativity and product release being linked to motion
of a catalytic site loop contributed by the neighboring subunit.
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Affiliation(s)
- Shanzhi Wang
- Department of Biochemistry, Albert Einstein College of Medicine, Yeshiva University , 1300 Morris Park Avenue, Bronx, New York 10461, United States
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15
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Kai K, Fujii H, Ikenaka R, Akagawa M, Hayashi H. An acyl-SAM analog as an affinity ligand for identifying quorum sensing signal synthases. Chem Commun (Camb) 2014; 50:8586-9. [DOI: 10.1039/c4cc03094j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We here report the affinity purification of N-acylhomoserine lactone synthases using beads conjugated with an enzyme inhibitor, which was designed based on the catalytic intermediate acyl-SAM.
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Affiliation(s)
- Kenji Kai
- Graduate School of Life and Environmental Sciences
- Osaka Prefecture University
- Sakai, Japan
| | - Hiroki Fujii
- Graduate School of Life and Environmental Sciences
- Osaka Prefecture University
- Sakai, Japan
| | - Rui Ikenaka
- Graduate School of Life and Environmental Sciences
- Osaka Prefecture University
- Sakai, Japan
| | - Mitsugu Akagawa
- Graduate School of Life and Environmental Sciences
- Osaka Prefecture University
- Sakai, Japan
| | - Hideo Hayashi
- Graduate School of Life and Environmental Sciences
- Osaka Prefecture University
- Sakai, Japan
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