1
|
Vacariu CM, Tanner ME. Recent Advances in the Synthesis and Biological Applications of Peptidoglycan Fragments. Chemistry 2022; 28:e202200788. [PMID: 35560956 DOI: 10.1002/chem.202200788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Indexed: 11/09/2022]
Abstract
The biosynthesis, breakdown, and modification of peptidoglycan (PG) play vital roles in both bacterial viability and in the response of human physiology to bacterial infection. Studies on PG biochemistry are hampered by the fact that PG is an inhomogeneous insoluble macromolecule. Chemical synthesis is therefore an important means to obtain PG fragments that may serve as enzyme substrates and elicitors of the human immune response. This review outlines the recent advances in the synthesis and biochemical studies of PG fragments, PG biosynthetic intermediates (such as Park's nucleotides and PG lipids), and PG breakdown products (such as muramyl dipeptides and anhydro-muramic acid-containing fragments). A rich variety of synthetic approaches has been applied to preparing such compounds since carbohydrate, peptide, and phospholipid chemical methodologies must all be applied.
Collapse
Affiliation(s)
- Condurache M Vacariu
- Department of Chemistry, University of British Columbia, V6T 1Z1, Vancouver, British Columbia, Canada
| | - Martin E Tanner
- Department of Chemistry, University of British Columbia, V6T 1Z1, Vancouver, British Columbia, Canada
| |
Collapse
|
2
|
Cai B, Panek JS, Amar S. Convergent Synthesis of Novel Muramyl Dipeptide Analogues: Inhibition of Porphyromonas gingivalis-Induced Pro-inflammatory Effects by High Doses of Muramyl Dipeptide. J Med Chem 2016; 59:6878-90. [PMID: 27353235 DOI: 10.1021/acs.jmedchem.6b00681] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Porphyromonas gingivalis (P.g.)-induced TNF-α can be affected by muramyl dipeptide (MDP) in a biphasic concentration-dependent manner. We found that in P.g.-exposed macrophages, treatment with 10 μg/mL of MDP (MDP-low) up-regulated TNF-α by 29%, while 100 μg/mL or higher (MDP-high) significantly decreased it (16% to 38%). MDP-high was found to affect the ubiquitin-editing enzyme A20 and activator protein 1 (AP1). An AP1 binding site was found in the promoter region of A20. A20 promoter activity was up-regulated after transfection of AP1 cDNA in cells. Four analogues of MDP (3-6) were prepared through a convergent strategy involving the synthesis of two unique carbohydrate fragments, 7a and 7b, using the peptide coupling reagents, EDCI and HOAt. Analogue 4 improved MDP function and P.g.-induced activities. We propose a new signaling pathway for TNF-α induction activated after exposing macrophages to both P.g. and MDP-high or analogue 4.
Collapse
Affiliation(s)
- Bin Cai
- Department of Chemistry, Boston University, Metcalf Center for Science and Engineering , 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - James S Panek
- Department of Chemistry, Boston University, Metcalf Center for Science and Engineering , 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Salomon Amar
- Center for Anti-Inflammatory Therapeutics, Department of Molecular & Cell Biology, Boston University Goldman School of Dental Medicine , 650 Albany Street, Suite 343, Boston, Massachusetts 02118, United States
| |
Collapse
|
3
|
Xing S, Gleason JL. A robust synthesis of N-glycolyl muramyl dipeptide via azidonitration/reduction. Org Biomol Chem 2015; 13:1515-20. [PMID: 25476476 DOI: 10.1039/c4ob02147a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A novel synthetic route leading to N-glycolyl muramyl dipeptide (MDP), a bacterial glycopeptide of particular interest in studies of nucleotide-binding oligomerization domain-containing protein 2 (NOD2), is described. The synthetic strategy hinges on the alkylation of benzylidene-protected glucal with 2-bromopropionic acid and thus circumvents a challenging and non-reproducible SN2 step at the C-3 position of glucosamine derivatives. The subsequent sequence includes an azidonitration and an unusual azide reduction/acylation step via an aza ylide/oxaphospholidine intermediate. This approach generates a protected N-glycolyl MDP that can be either subjected to a one-step global deprotection or differentially deprotected to obtain further derivatives.
Collapse
Affiliation(s)
- Shuo Xing
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, Quebec, Canada H3A 0B8.
| | | |
Collapse
|
4
|
Kovačević M, Rapić V, Lukač I, Molčanov K, Kodrin I, Barišić L. Novel fully protected muramic acid: A facile synthesis and structural study. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.06.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
5
|
Duong-Ly KC, Woo HN, Dunn CA, Xu W, Babič A, Bessman MJ, Amzel LM, Gabelli SB. A UDP-X diphosphatase from Streptococcus pneumoniae hydrolyzes precursors of peptidoglycan biosynthesis. PLoS One 2013; 8:e64241. [PMID: 23691178 PMCID: PMC3655063 DOI: 10.1371/journal.pone.0064241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 03/29/2013] [Indexed: 01/09/2023] Open
Abstract
The gene for a Nudix enzyme (SP_1669) was found to code for a UDP-X diphosphatase. The SP_1669 gene is localized among genes encoding proteins that participate in cell division in Streptococcus pneumoniae. One of these genes, MurF, encodes an enzyme that catalyzes the last step of the Mur pathway of peptidoglycan biosynthesis. Mur pathway substrates are all derived from UDP-glucosamine and all are potential Nudix substrates. We showed that UDP-X diphosphatase can hydrolyze the Mur pathway substrates UDP-N-acetylmuramic acid and UDP-N-acetylmuramoyl-L-alanine. The 1.39 Å resolution crystal structure of this enzyme shows that it folds as an asymmetric homodimer with two distinct active sites, each containing elements of the conserved Nudix box sequence. In addition to its Nudix catalytic activity, the enzyme has a 3'5' RNA exonuclease activity. We propose that the structural asymmetry in UDP-X diphosphatase facilitates the recognition of these two distinct classes of substrates, Nudix substrates and RNA. UDP-X diphosphatase is a prototype of a new family of Nudix enzymes with unique structural characteristics: two monomers, each consisting of an N-terminal helix bundle domain and a C-terminal Nudix domain, form an asymmetric dimer with two distinct active sites. These enzymes function to hydrolyze bacterial cell wall precursors and degrade RNA.
Collapse
Affiliation(s)
- Krisna C. Duong-Ly
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Hyun Nyun Woo
- Department of Biology and McCollum-Pratt Institute, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Christopher A. Dunn
- Department of Biology and McCollum-Pratt Institute, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - WenLian Xu
- Department of Biology and McCollum-Pratt Institute, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Andrej Babič
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Maurice J. Bessman
- Department of Biology and McCollum-Pratt Institute, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - L. Mario Amzel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail: (LMA); (SBG)
| | - Sandra B. Gabelli
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail: (LMA); (SBG)
| |
Collapse
|
6
|
Tedaldi LM, Pierce M, Wagner GK. Optimised chemical synthesis of 5-substituted UDP-sugars and their evaluation as glycosyltransferase inhibitors. Carbohydr Res 2012; 364:22-7. [PMID: 23147042 DOI: 10.1016/j.carres.2012.10.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 10/09/2012] [Accepted: 10/11/2012] [Indexed: 10/27/2022]
Abstract
We have investigated the applicability of different chemical methods for pyrophosphate bond formation to the synthesis of 5-substituted UDP-galactose and UDP-N-acetylglucosamine derivatives. The use of phosphoromorpholidate chemistry, in conjunction with N-methyl imidazolium chloride as the promoter, was identified as the most reliable synthetic protocol for the preparation of these non-natural sugar-nucleotides. Under these conditions, the primary synthetic targets 5-iodo UDP-galactose and 5-iodo UDP-N-acetylglucosamine were consistently obtained in isolated yields of 40-43%. Both 5-iodo UDP-sugars were used successfully as substrates in the Suzuki-Miyaura cross-coupling with 5-formylthien-2-ylboronic acid under aqueous conditions. Importantly, 5-iodo UDP-GlcNAc and 5-(5-formylthien-2-yl) UDP-GlcNAc showed moderate inhibitory activity against the GlcNAc transferase GnT-V, providing the first examples for the inhibition of a GlcNAc transferase by a base-modified donor analogue.
Collapse
Affiliation(s)
- Lauren M Tedaldi
- King's College London, School of Biomedical Sciences, Institute of Pharmaceutical Science & Department of Chemistry, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
| | | | | |
Collapse
|
7
|
Förster C, Kovačević M, Barišić L, Rapić V, Heinze K. Ferrocenyl-Labeled Sugar Amino Acids: Conformation and Properties. Organometallics 2012. [DOI: 10.1021/om300174p] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christoph Förster
- Institute
of Inorganic and Analytical
Chemistry, Johannes Gutenberg-University of Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Monika Kovačević
- Department of Chemistry and
Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, HR-10000 Zagreb,
Croatia
| | - Lidija Barišić
- Department of Chemistry and
Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, HR-10000 Zagreb,
Croatia
| | - Vladimir Rapić
- Department of Chemistry and
Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, HR-10000 Zagreb,
Croatia
| | - Katja Heinze
- Institute
of Inorganic and Analytical
Chemistry, Johannes Gutenberg-University of Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| |
Collapse
|
8
|
Yamaguchi T, Blázquez B, Hesek D, Lee M, Llarrull LI, Boggess B, Oliver AG, Fisher JF, Mobashery S. Inhibitors for Bacterial Cell-Wall Recycling. ACS Med Chem Lett 2012; 3:238-242. [PMID: 22844551 PMCID: PMC3404464 DOI: 10.1021/ml2002746] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2011] [Accepted: 01/19/2012] [Indexed: 11/28/2022] Open
Abstract
Gram-negative bacteria have evolved an elaborate process for the recycling of their cell wall, which is initiated in the periplasmic space by the action of lytic transglycosylases. The product of this reaction, β-D-N-acetylglucosamine-(1→4)-1,6-anhydro-β-D-N-acetylmuramyl-L-Ala-γ-D-Glu-meso-DAP-D-Ala-D-Ala (compound 1), is internalized to begin the recycling events within the cytoplasm. The first step in the cytoplasmic recycling is catalyzed by the NagZ glycosylase, which cleaves in a hydrolytic reaction the N-acetylglucosamine glycosidic bond of metabolite 1. The reactions catalyzed by both the lytic glycosylases and NagZ are believed to involve oxocarbenium transition species. We describe herein the synthesis and evaluation of four iminosaccharides as possible mimetics of the oxocarbenium species, and disclose one as a potent (compound 3, K(i) = 300 ± 15 nM) competitive inhibitor of NagZ.
Collapse
Affiliation(s)
- Takao Yamaguchi
- Department
Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556,
United States
| | - Blas Blázquez
- Department
Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556,
United States
| | - Dusan Hesek
- Department
Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556,
United States
| | - Mijoon Lee
- Department
Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556,
United States
| | - Leticia I. Llarrull
- Department
Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556,
United States
| | - Bill Boggess
- Department
Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556,
United States
| | - Allen G. Oliver
- Department
Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556,
United States
| | - Jed F. Fisher
- Department
Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556,
United States
| | - Shahriar Mobashery
- Department
Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556,
United States
| |
Collapse
|
9
|
Fang YQ, Bio MM, Hansen KB, Potter MS, Clausen A. Magnesium Coordination-Directed N-Selective Stereospecific Alkylation of 2-Pyridones, Carbamates, and Amides Using α-Halocarboxylic Acids. J Am Chem Soc 2010; 132:15525-7. [DOI: 10.1021/ja107709w] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Yuan-Qing Fang
- Department of Chemical Process Research & Development, Department of Analytical Research & Development, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142
| | - Matthew M. Bio
- Department of Chemical Process Research & Development, Department of Analytical Research & Development, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142
| | - Karl B. Hansen
- Department of Chemical Process Research & Development, Department of Analytical Research & Development, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142
| | - Matthew S. Potter
- Department of Chemical Process Research & Development, Department of Analytical Research & Development, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142
| | - Andrew Clausen
- Department of Chemical Process Research & Development, Department of Analytical Research & Development, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142
| |
Collapse
|
10
|
Yamaguchi T, Hesek D, Lee M, Oliver AG, Mobashery S. Sulfonylation-induced N- to O-acetyl migration in 2-acetamidoethanol derivatives. J Org Chem 2010; 75:3515-7. [PMID: 20361802 DOI: 10.1021/jo100456z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The first example of sulfonylation-induced N- to O-acetyl migration of 2-acetamidoethanol derivatives is described. This type of reaction could happen with any 2-acetamidoethanol derivatives under typical sulfonylation conditions (TsCl or MsCl, pyridine) and might be a common side reaction of significance. Furthermore, the results reveal that 2-acetamidoethanol derivatives with a sterically encumbered hydroxyl group result in the migration products in high yields. The mechanism of the migration reaction is discussed.
Collapse
Affiliation(s)
- Takao Yamaguchi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | | | | | | | | |
Collapse
|