1
|
Price NPJ, Jackson MA, Hartman TM, Bannantine JP, Naumann TA, Vermillion KE, Koch AA, Kennedy PD. Precursor-Directed Biosynthesis and Biological Testing of omega-Alicyclic- and neo-Branched Tunicamycin N-Acyl Variants. ACS Chem Biol 2023; 18:2267-2280. [PMID: 37788216 DOI: 10.1021/acschembio.3c00324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Tunicamycins (TUNs) are Streptomyces-derived natural products, widely used to block protein N-glycosylation in eukaryotes or cell wall biosynthesis in bacteria. Modified or synthetic TUN analogues that uncouple these activities have considerable potential as novel mode-of-action antibacterial agents. Chemically modified TUNs reported previously with attenuated activity on yeast have pinpointed eukaryotic-specific chemophores in the uridyl group and the N-acyl chain length and terminal branching pattern. A small molecule screen of fatty acid biosynthetic primers identified several novel alicyclic- and neo-branched TUN N-acyl variants, with primer incorporation at the terminal omega-acyl position. TUNs with unique 5- and 6-carbon ω-cycloalkane and ω-cycloalkene acyl chains are produced under fermentation and in yields comparable with the native TUN. The purification, structural assignments, and the comparable antimicrobial properties of 15 of these compounds are reported, greatly extending the structural diversity of this class of compounds for potential medicinal and agricultural applications.
Collapse
Affiliation(s)
- Neil P J Price
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Renewable Product Technology Research, 1815 N. University St., Peoria, Illinois 61604, United States
| | - Michael A Jackson
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Renewable Product Technology Research, 1815 N. University St., Peoria, Illinois 61604, United States
| | - Trina M Hartman
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Renewable Product Technology Research, 1815 N. University St., Peoria, Illinois 61604, United States
| | - John P Bannantine
- USDA, Agricultural Research Service, National Animal Disease Center, 1920 Dayton Ave., Ames, Iowa 50010, United States
| | - Todd A Naumann
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Renewable Product Technology Research, 1815 N. University St., Peoria, Illinois 61604, United States
| | - Karl E Vermillion
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Renewable Product Technology Research, 1815 N. University St., Peoria, Illinois 61604, United States
| | - Aaron A Koch
- Cayman Chemical, 1180 E. Ellsworth Rd., Ann Arbor, Michigan 48108, United States
| | - Paul D Kennedy
- Cayman Chemical, 1180 E. Ellsworth Rd., Ann Arbor, Michigan 48108, United States
| |
Collapse
|
2
|
Price NPJ, Jackson MA, Hartman TM, Brändén G, Ek M, Koch AA, Kennedy PD. Branched Chain Lipid Metabolism As a Determinant of the N-Acyl Variation of Streptomyces Natural Products. ACS Chem Biol 2021; 16:116-124. [PMID: 33411499 DOI: 10.1021/acschembio.0c00799] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Branched-chain fatty acids (BCFA) are encountered in Gram-positive bacteria, but less so in other organisms. The bacterial BCFA in membranes are typically saturated, with both odd- and even-numbered carbon chain lengths, and with methyl branches at either the ω-1 (iso) or ω-2 (anteiso) positions. The acylation with BCFA also contributes to the structural diversity of microbial natural products and potentially modulates biological activity. For the tunicamycin (TUN) family of natural products, the toxicity toward eukaryotes is highly dependent upon N-acylation with trans-2,3-unsaturated BCFA. The loss of the 2,3-unsaturation gives modified TUN with reduced eukaryotic toxicity but crucially with retention of the synergistic enhancement of the β-lactam group of antibiotics. Here, we infer from genomics, mass spectrometry, and deuterium labeling that the trans-2,3-unsaturated TUN variants and the saturated cellular lipids found in TUN-producing Streptomyces are derived from the same pool of BCFA metabolites. Moreover, non-natural primers of BCFA metabolism are selectively incorporated into the cellular lipids of TUN-producing Streptomyces and concomitantly produce structurally novel neo-branched TUN N-acyl variants.
Collapse
Affiliation(s)
- Neil P. J. Price
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, 1815 N. University St., Peoria, Illinois 61604, United States
| | - Michael A. Jackson
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, 1815 N. University St., Peoria, Illinois 61604, United States
| | - Trina M. Hartman
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, 1815 N. University St., Peoria, Illinois 61604, United States
| | - Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Margareta Ek
- Structure, Biophysics & FBLG, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Aaron A. Koch
- Cayman Chemical, 1180 E. Ellsworth Rd., Ann Arbor, Michigan 48108, United States
| | - Paul D. Kennedy
- Cayman Chemical, 1180 E. Ellsworth Rd., Ann Arbor, Michigan 48108, United States
| |
Collapse
|
3
|
Hering J, Dunevall E, Snijder A, Eriksson PO, Jackson MA, Hartman TM, Ting R, Chen H, Price NPJ, Brändén G, Ek M. Exploring the Active Site of the Antibacterial Target MraY by Modified Tunicamycins. ACS Chem Biol 2020; 15:2885-2895. [PMID: 33164499 DOI: 10.1021/acschembio.0c00423] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The alarming growth of antibiotic resistance that is currently ongoing is a serious threat to human health. One of the most promising novel antibiotic targets is MraY (phospho-MurNAc-pentapeptide-transferase), an essential enzyme in bacterial cell wall synthesis. Through recent advances in biochemical research, there is now structural information available for MraY, and for its human homologue GPT (GlcNAc-1-P-transferase), that opens up exciting possibilities for structure-based drug design. The antibiotic compound tunicamycin is a natural product inhibitor of MraY that is also toxic to eukaryotes through its binding to GPT. In this work, we have used tunicamycin and modified versions of tunicamycin as tool compounds to explore the active site of MraY and to gain further insight into what determines inhibitor potency. We have investigated tunicamycin variants where the following motifs have been modified: the length and branching of the tunicamycin fatty acyl chain, the saturation of the fatty acyl chain, the 6″-hydroxyl group of the GlcNAc ring, and the ring structure of the uracil motif. The compounds are analyzed in terms of how potently they bind to MraY, inhibit the activity of the enzyme, and affect the protein thermal stability. Finally, we rationalize these results in the context of the protein structures of MraY and GPT.
Collapse
Affiliation(s)
- Jenny Hering
- Structure, Biophysics and FBLG, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Elin Dunevall
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Arjan Snijder
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Per-Olof Eriksson
- Structure, Biophysics and FBLG, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Michael A. Jackson
- U.S. Department of Agriculture, National Center for Agricultural Utilization Research, Peoria, Illinois 61604, United States
| | - Trina M. Hartman
- U.S. Department of Agriculture, National Center for Agricultural Utilization Research, Peoria, Illinois 61604, United States
| | - Ran Ting
- Chemistry and Chemical Biology Centre, Bioland Laboratory, Guangzhou, China
| | - Hongming Chen
- Chemistry and Chemical Biology Centre, Bioland Laboratory, Guangzhou, China
| | - Neil P. J. Price
- U.S. Department of Agriculture, National Center for Agricultural Utilization Research, Peoria, Illinois 61604, United States
| | - Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Margareta Ek
- Structure, Biophysics and FBLG, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| |
Collapse
|
4
|
Price NPJ, Jackson MA, Vermillion KE, Blackburn JA, Hartman TM. Rhodium-catalyzed reductive modification of pyrimidine nucleosides, nucleotide phosphates, and sugar nucleotides. Carbohydr Res 2019; 488:107893. [PMID: 31884235 DOI: 10.1016/j.carres.2019.107893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 11/26/2019] [Accepted: 12/13/2019] [Indexed: 01/27/2023]
Abstract
Nucleosides and nucleotides are a group of small molecule effectors and substrates which include sugar nucleotides, purine and pyrimidine-based nucleotide phosphates, and diverse nucleotide antibiotics. We previously reported that hydrogenation of the nucleotide antibiotic tunicamycin leads to products with reduced toxicity on eukaryotic cells. We now report the hydrogenation of diverse sugar nucleosides, nucleotide phosphates, and pyrimidine nucleotides. UDP-sugars and other uridyl and thymidinyl nucleosides are quantitatively reduced to the corresponding 5,6-dihydro-nucleosides. Cytidyl pyrimidines are reduced, but the major products are the corresponding 5,6-dihydrouridyl nucleosides resulting from a deamination of the cytosine ring.
Collapse
Affiliation(s)
- Neil P J Price
- Agricultural Research Service, U.S. Department of Agriculture, National Center for Agricultural Utilization Research, Peoria, IL, USA.
| | - Michael A Jackson
- Agricultural Research Service, U.S. Department of Agriculture, National Center for Agricultural Utilization Research, Peoria, IL, USA
| | - Karl E Vermillion
- Agricultural Research Service, U.S. Department of Agriculture, National Center for Agricultural Utilization Research, Peoria, IL, USA
| | - Judith A Blackburn
- Agricultural Research Service, U.S. Department of Agriculture, National Center for Agricultural Utilization Research, Peoria, IL, USA
| | - Trina M Hartman
- Agricultural Research Service, U.S. Department of Agriculture, National Center for Agricultural Utilization Research, Peoria, IL, USA
| |
Collapse
|
5
|
Synergistic enhancement of beta-lactam antibiotics by modified tunicamycin analogs TunR1 and TunR2. J Antibiot (Tokyo) 2019; 72:807-815. [DOI: 10.1038/s41429-019-0220-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 06/26/2019] [Accepted: 07/08/2019] [Indexed: 01/15/2023]
|
6
|
Dong YY, Wang H, Pike ACW, Cochrane SA, Hamedzadeh S, Wyszyński FJ, Bushell SR, Royer SF, Widdick DA, Sajid A, Boshoff HI, Park Y, Lucas R, Liu WM, Lee SS, Machida T, Minall L, Mehmood S, Belaya K, Liu WW, Chu A, Shrestha L, Mukhopadhyay SMM, Strain-Damerell C, Chalk R, Burgess-Brown NA, Bibb MJ, Barry Iii CE, Robinson CV, Beeson D, Davis BG, Carpenter EP. Structures of DPAGT1 Explain Glycosylation Disease Mechanisms and Advance TB Antibiotic Design. Cell 2019; 175:1045-1058.e16. [PMID: 30388443 PMCID: PMC6218659 DOI: 10.1016/j.cell.2018.10.037] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 08/01/2018] [Accepted: 10/15/2018] [Indexed: 12/24/2022]
Abstract
Protein N-glycosylation is a widespread post-translational modification. The first committed step in this process is catalysed by dolichyl-phosphate N-acetylglucosamine-phosphotransferase DPAGT1 (GPT/E.C. 2.7.8.15). Missense DPAGT1 variants cause congenital myasthenic syndrome and disorders of glycosylation. In addition, naturally-occurring bactericidal nucleoside analogues such as tunicamycin are toxic to eukaryotes due to DPAGT1 inhibition, preventing their clinical use. Our structures of DPAGT1 with the substrate UDP-GlcNAc and tunicamycin reveal substrate binding modes, suggest a mechanism of catalysis, provide an understanding of how mutations modulate activity (thus causing disease) and allow design of non-toxic “lipid-altered” tunicamycins. The structure-tuned activity of these analogues against several bacterial targets allowed the design of potent antibiotics for Mycobacterium tuberculosis, enabling treatment in vitro, in cellulo and in vivo, providing a promising new class of antimicrobial drug. Structures of DPAGT1 with UDP-GlcNAc and tunicamycin reveal mechanisms of catalysis DPAGT1 mutations in patients with glycosylation disorders modulate DPAGT1 activity Structures, kinetics and biosynthesis reveal role of lipid in tunicamycin Lipid-altered, tunicamycin analogues give non-toxic antibiotics against TB
Collapse
Affiliation(s)
- Yin Yao Dong
- Structural Genomics Consortium, University of Oxford, Oxford, OX3 7DQ, UK
| | - Hua Wang
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Ashley C W Pike
- Structural Genomics Consortium, University of Oxford, Oxford, OX3 7DQ, UK
| | - Stephen A Cochrane
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK; School of Chemistry and Chemical Engineering, Queen's University, Belfast, UK
| | - Sadra Hamedzadeh
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Filip J Wyszyński
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Simon R Bushell
- Structural Genomics Consortium, University of Oxford, Oxford, OX3 7DQ, UK
| | - Sylvain F Royer
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - David A Widdick
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Andaleeb Sajid
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Helena I Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Yumi Park
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Ricardo Lucas
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Wei-Min Liu
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Seung Seo Lee
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Takuya Machida
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Leanne Minall
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | | | - Katsiaryna Belaya
- Neurosciences Group, Nuffield Department of Clinical Neuroscience, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Wei-Wei Liu
- Neurosciences Group, Nuffield Department of Clinical Neuroscience, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Amy Chu
- Structural Genomics Consortium, University of Oxford, Oxford, OX3 7DQ, UK
| | - Leela Shrestha
- Structural Genomics Consortium, University of Oxford, Oxford, OX3 7DQ, UK
| | | | | | - Rod Chalk
- Structural Genomics Consortium, University of Oxford, Oxford, OX3 7DQ, UK
| | | | - Mervyn J Bibb
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Clifton E Barry Iii
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | | | - David Beeson
- Neurosciences Group, Nuffield Department of Clinical Neuroscience, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Benjamin G Davis
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK.
| | | |
Collapse
|