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Uridyl Peptide Antibiotics: Developments in Biosynthesis and Medicinal Chemistry

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Abstract

The Uridyl-Peptide Antibiotics (UPAs) are a diverse group of bacterial metabolites that are characterized by a uridyl moiety linked to a peptidic residue. Included in this group are the pacidamycins, liposidomycins, capuramycins, and muraymycins. Most of these antibiotics are produced by Streptomyces species and are naturally found as complexes of closely related congeners. The compounds all bear some resemblance to intermediates involved in cell wall biosynthesis in bacteria and exert their antibacterial action through inhibition of the membrane-bound translocase I. Caprazamycin was the first of the UPAs for which a biosynthetic gene cluster was identified and cloned, which quickly led to the discovery of several others. Preliminary experiments have been reported in which biosynthetic insights were applied to the production of analogs for evaluation of antimicrobial activity. Synthetic chemistry has provided evidence for the core features necessary for target inhibition and antibacterial efficacy. Although many of the UPAs have shown potent antibacterial activity, and are effective in inhibiting a highly selective bacterial target, none have progressed to become commercially viable agents. In this chapter, we will explore recent findings that have clarified the promise and limitations of this class of antibiotics.

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References

  • Anderson MS, Eveland SS, Price NP (2000) Conserved cytoplasmic motifs that distinguish sub-groups of the polyprenol phosphate:N-acetylhexosamine-1-phosphate transferase family. FEMS Microb Lett 191:169–175

    Article  CAS  Google Scholar 

  • Bogatcheva E, Dubuisson T, Protopopova M, Einck L, Nacy CA, Reddy VM (2011) Chemical modification of capuramycins to enhance antibacterial activity. J Antimicrob Chemother 66:578–587

    Article  PubMed  CAS  Google Scholar 

  • Bouhss A, Trunkfield AE, Bugg TD, Mengin-Lecreulx D (2008) The biosynthesis of peptidoglycan lipid-linked intermediates. FEMS Microbiol Rev 32:208–233

    Article  PubMed  CAS  Google Scholar 

  • Brandish PE, Kimura KI, Inukai M, Southgate R, Lonsdale JT, Bugg TD (1996) Modes of action of tunicamycin, liposidomycin B, and mureidomycin A: inhibition of phospho-N-acetylmuramyl-pentapeptide translocase from Escherichia coli. Antimicrob Agents Chemother 40:1640–1644

    PubMed  CAS  Google Scholar 

  • Bugg TD, Braddick D, Dowson CG, Roper DI (2011) Bacterial cell wall assembly: still an attractive antibacterial target. Trends Biotechnol 29:167–173

    Article  PubMed  CAS  Google Scholar 

  • Chatterjee S, Nadkarni SR, Vijayakumar EK, Patel MV, Ganguli BN, Fehlhaber HW, Vertesy L (1994) Napsamycins, new Pseudomonas active antibiotics of the mureidomycin family from Streptomyces sp. HIL Y-82,11372. J Antibiot (Tokyo) 47:595–598

    Article  CAS  Google Scholar 

  • Chen RH, Buko AM, Whittern DN, McAlpine JB (1989) Pacidamycins, a novel series of antibiotics with anti-Pseudomonas aeruginosa activity. II. Isolation and structural elucidation. J Antibiot 42:512–520

    Article  PubMed  CAS  Google Scholar 

  • Deb Roy A, Gruschow S, Cairns N, Goss RJ (2010) Gene expression enabling synthetic diversification of natural products: chemogenetic generation of pacidamycin analogs. J Am Chem Soc 132:12243–12245

    Article  PubMed  Google Scholar 

  • Dini C, Collette P, Drochon N, Guillot JC, Lemoine G, Mauvais P, Aszodi J (2000) Synthesis of the nucleoside moiety of liposidomycins: elucidation of the pharmacophore of this family of MraY inhibitors. Bioorg Med Chem Lett 10:1839–1843

    Article  PubMed  CAS  Google Scholar 

  • Dini C, Didier-Laurent S, Drochon N, Feteanu S, Guillot JC, Monti F, Uridat E, Zhang J, Aszodi J (2002) Synthesis of sub-micromolar inhibitors of MraY by exploring the region originally occupied by the diazepanone ring in the liposidomycin structure. Bioorg Med Chem Lett 12:1209–1213

    Article  PubMed  CAS  Google Scholar 

  • Dubuisson T, Bogatcheva E, Krishnan MY, Collins MT, Einck L, Nacy CA, Reddy VM (2010) In vitro antimicrobial activities of capuramycin analogues against non-tuberculous mycobacteria. J Antimicrob Chemother 65:2590–2597

    Article  PubMed  CAS  Google Scholar 

  • Fujita Y, Kizuka M, Funabashi M, Ogawa Y, Ishikawa T, Nonaka K, Takatsu T (2011) A-90289 A and B, new inhibitors of bacterial translocase I, produced by Streptomyces sp. SANK 60405. J Antibiot 64:495–501

    Article  PubMed  CAS  Google Scholar 

  • Fujita Y, Murakami R, Muramatsu Y, Miyakoshi S, Takatsu T (2008) A-94964, novel inhibitor of bacterial translocase I, produced by Streptomyces sp. SANK 60404. II. Physico-chemical properties and structure elucidation. J Antibiot 61:545–549

    Article  PubMed  CAS  Google Scholar 

  • Gruschow S, Rackham EJ, Elkins B, Newill PL, Hill LM, Goss RJ (2009) New pacidamycin antibiotics through precursor-directed biosynthesis. ChemBioChem 10:355–360

    Article  PubMed  CAS  Google Scholar 

  • Grüschow S, Rackham EJ, Goss RJM (2011) Diversity in natural product families is governed by more than enzyme promiscuity alone: establishing control of the pacidamycin portfolio. Chem Sci 2:2182–2186

    Article  Google Scholar 

  • Hotoda H, Daigo M, Furukawa M, Murayama K, Hasegawa CA, Kaneko M, Muramatsu Y, Ishii MM, Miyakoshi S, Takatsu T, Inukai M, Kakuta M, Abe T, Fukuoka T, Utsui Y, Ohya S (2003a) Synthesis and antimycobacterial activity of capuramycin analogs. Part 2: acylated derivatives of capuramycin-related compounds. Bioor Med Chem Lett 13:2833–2836

    Google Scholar 

  • Hotoda H, Furukawa M, Daigo M, Murayama K, Kaneko M, Muramatsu Y, Ishii MM, Miyakoshi S, Takatsu T, Inukai M, Kakuta M, Abe T, Harasaki T, Fukuoka T, Utsui Y, Ohya S (2003b) Synthesis and antimycobacterial activity of capuramycin analogs. Part 1: substitution of the azepan-2-one moiety of capuramycin. Bioor Med Chem Lett 13:2829–2832

    Google Scholar 

  • Ii K, Ichikawa S, Al-Dabbagh B, Bouhss A, Matsuda A (2010) Function-oriented synthesis of simplified saprazamycins: discovery of oxazolidine-containing uridine derivatives as antibacterial agents against drug-resistant bacteria. J Med Chem 53:3793–3813

    Article  PubMed  CAS  Google Scholar 

  • Inukai M, Isono F, Takahashi S, Enokita R, Sakaida Y, Haneishi T (1989) Mureidomycins A-D, novel peptidylnucleoside antibiotics with spheroplast forming activity. I. Taxonomy, fermentation, isolation and physico-chemical properties. J Antibiot 42:662–666

    Article  PubMed  CAS  Google Scholar 

  • Inukai M, Isono F, Takatsuki A (1993) Selective inhibition of the bacterial translocase reaction in peptidoglycan synthesis by mureidomycins. Antimicrob Agents Chemother 37:980–983

    Article  PubMed  CAS  Google Scholar 

  • Isono F, Inukai M (1991) Mureidomycin A, a new inhibitor of bacterial peptidoglycan synthesis. Antimicrob Agents Chemother 35:234–236

    Article  PubMed  CAS  Google Scholar 

  • Isono K, Uramoto M, Kusakabe H, Kimura K, Isaki K, Nelson CC, McCloskey JA (1985) Liposidomycins: novel nucleoside antibiotics which inhibit bacterial peptidoglycan synthesis. J Antibiot 38:1617–1621

    Article  PubMed  CAS  Google Scholar 

  • Kaysser L, Eitel K, Tanino T, Siebenberg S, Matsuda A, Ichikawa S, Gust B (2010a) A new arylsulfate sulfotransferase involved in liponucleoside antibiotic biosynthesis in streptomycetes. J Biol Chem 285:12684–12694

    Article  PubMed  CAS  Google Scholar 

  • Kaysser L, Lutsch L, Siebenberg S, Wemakor E, Kammerer B, Gust B (2009) Identification and manipulation of the caprazamycin gene cluster lead to new simplified liponucleoside antibiotics and give insights into the biosynthetic pathway. J Biol Chem 284:14987–14996

    Article  PubMed  CAS  Google Scholar 

  • Kaysser L, Tang X, Wemakor E, Sedding K, Hennig S, Siebenberg S, Gust B (2011) Identification of a napsamycin biosynthesis gene cluster by genome mining. ChemBioChem 12:477–487

    Article  PubMed  CAS  Google Scholar 

  • Kaysser L, Wemakor E, Siebenberg S, Salas JA, Sohng JK, Kammerer B, Gust B (2010b) Formation and attachment of the deoxysugar moiety and assembly of the gene cluster for caprazamycin biosynthesis. Appl Environ Microbiol 76:4008–4018

    Article  PubMed  CAS  Google Scholar 

  • Koga T, Fukuoka T, Doi N, Harasaki T, Inoue H, Hotoda H, Kakuta M, Muramatsu Y, Yamamura N, Hoshi M, Hirota T (2004) Activity of capuramycin analogues against Mycobacterium tuberculosis, Mycobacterium avium and Mycobacterium intracellulare in vitro and in vivo. J Antimicrob Chemother 54:755–760

    Google Scholar 

  • Le Corre L, Gravier-Pelletier C, Le Merrer Y (2007) Towards new MraY inhibitors: a serine template for uracil and 5-amino-5-deoxyribosyl scaffolding. Eur J Org Chemistry 32:5386–5394

    Article  Google Scholar 

  • Li Y-B, Xie Y-Y, Du N-N, Lu Y, Xu H-Z, Wang B, Yu Y, Liu Y-X, Song D-Q, Chen R-X (2011) Synthesis and in vitro antitubercular evaluation of novel sansanmycin derivatives. Bioorg Med Chem Lett 21:6804–6807

    Article  PubMed  CAS  Google Scholar 

  • Lin YI, Li Z, Francisco GD, McDonald LA, Davis RA, Singh G, Yang Y, Mansour TS (2002) Muraymycins, novel peptidoglycan biosynthesis inhibitors: semisynthesis and SAR of their derivatives. Bioorg Med Chem Lett 12:2341–2344

    Article  PubMed  CAS  Google Scholar 

  • McDonald LA, Barbieri LR, Carter GT, Kruppa G, Feng X, Lotvin JA, Siegel MM (2003) FTMS structure elucidation of natural products: application to muraymycin antibiotics using ESI multi-CHEF SORI-CID FTMS(n), the top-down/bottom-up approach, and HPLC ESI capillary-skimmer CID FTMS. Anal Chem 75:2730–2739

    Article  PubMed  CAS  Google Scholar 

  • McDonald LA, Barbieri LR, Carter GT, Lenoy E, Lotvin J, Petersen PJ, Siegel MM, Singh G, Williamson RT (2002) Structures of the muraymycins, novel peptidoglycan biosynthesis inhibitors. J Am Chem Soc 124:10260–10261

    Article  PubMed  CAS  Google Scholar 

  • Murakami R, Fujita Y, Kizuka M, Kagawa T, Muramatsu Y, Miyakoshi S, Takatsu T, Inukai M (2007) A-102395, a new inhibitor of bacterial translocase I, produced by Amycolatopsis sp. SANK 60206. J Antibiot (Tokyo) 60:690–695

    Article  CAS  Google Scholar 

  • Murakami R, Fujita Y, Kizuka M, Kagawa T, Muramatsu Y, Miyakoshi S, Takatsu T, Inukai M (2008) A-94964, a novel inhibitor of bacterial translocase I, produced by Streptomyces sp. SANK 60404. I. Taxonomy, isolation and biological activity. J Antibiot (Tokyo) 61:537–544

    Article  CAS  Google Scholar 

  • Nikonenko BV, Reddy VM, Protopopova M, Bogatcheva E, Einck L, Nacy CA (2009) Activity of SQ641, a capuramycin analog, in a murine model of tuberculosis. Antimicrob Agents Chemother 53:3138–3139

    Article  PubMed  CAS  Google Scholar 

  • Price NP, Momany FA (2005) Modeling bacterial UDP-HexNAc: polyprenol-P HexNAc 1-P transferases. Glycobiology 15:29R–42R

    Article  PubMed  CAS  Google Scholar 

  • Rackham EJ, Gruschow S, Ragab AE, Dickens S, Goss RJ (2010) Pacidamycin biosynthesis: identification and heterologous expression of the first uridyl peptide antibiotic gene cluster. ChemBioChem 11:1700–1709

    Article  PubMed  CAS  Google Scholar 

  • Reddy VM, Einck L, Nacy CA (2008) In vitro antimycobacterial activities of capuramycin analogues. Antimicrob Agents Chemother 52:719–721

    Article  PubMed  CAS  Google Scholar 

  • Siebenberg S, Kaysser L, Wemakor E, Heide L, Gust B, Kammerer B (2011) Identification and structural elucidation of new caprazamycins from Streptomyces sp. MK730-62F2 by liquid chromatography/electrospray ionization tandem mass spectrometry. Rapid Commun Mass Spectrom 25:495–502

    Article  PubMed  CAS  Google Scholar 

  • Spork AP, Wiegmann D, Granitzka M, Stalke D, Ducho C (2011) Stereoselective synthesis of uridine-derived nucleosyl amino acids. J Org Chem 76:10083–10098

    Article  PubMed  CAS  Google Scholar 

  • Stachyra T, Dini C, Ferrari P, Bouhss A, van Heijenoort J, Mengin-Lecreulx D, Blanot D, Biton J, Le Beller D (2004) Fluorescence detection-based functional assay for high-throughput screening for MraY. Antimicrob Agents Chemother 48:897–902

    Article  PubMed  CAS  Google Scholar 

  • Tanino T, Al-Dabbagh B, Mengin-Lecreulx D, Bouhss A, Oyama H, Ichikawa S, Matsuda A (2011) Mechanistic analysis of muraymycin analogues: a guide to the design of MraY inhibitors. J Med Chem 54:8421–8439

    Article  PubMed  CAS  Google Scholar 

  • Tanino T, Ichikawa S, Al-Dabbagh B, Bouhss A, Oyama H, Matsuda A (2010a) Synthesis and biological evaluation of muraymycin analogues active against anti-drug resistant bacteria. ACS Med Chem Lett 1:258–262

    Article  CAS  Google Scholar 

  • Tanino T, Ichikawa S, Shiro M, Matsuda A (2010b) Total synthesis of (-)-muraymycin D2 and its epimer. J Org Chem 75:1366–1377

    Article  PubMed  CAS  Google Scholar 

  • Walsh CT, Zhang W (2011) Chemical logic and enzymatic machinery for biological assembly of peptidyl nucleoside antibiotics. ACS Chem Biol 6:1000–1007

    Article  PubMed  CAS  Google Scholar 

  • Winn M, Goss RJ, Kimura K, Bugg TD (2010) Antimicrobial nucleoside antibiotics targeting cell wall assembly: recent advances in structure-function studies and nucleoside biosynthesis. Nat Prod Rep 27:279–304

    Article  PubMed  CAS  Google Scholar 

  • Xie Y, Chen R, Si S, Sun C, Xu H (2007) A new nucleosidyl-peptide antibiotic, sansanmycin. J Antibiot 60:158–161

    Article  PubMed  CAS  Google Scholar 

  • Yamaguchi H, Sato S, Yoshida S, Takada K, Itoh M, Seto H, Otake N (1986) Capuramycin, a new nucleoside antibiotic. Taxonomy, fermentation, isolation and characterization. J Antibiot (Tokyo) 39:1047–1053

    Article  CAS  Google Scholar 

  • Yamashita A, Norton E, Petersen PJ, Rasmussen BA, Singh G, Yang Y, Mansour TS, Ho DM (2003) Muraymycins, novel peptidoglycan biosynthesis inhibitors: synthesis and SAR of their analogues. Bioorg Med Chem Lett 13:3345–3350

    Article  PubMed  CAS  Google Scholar 

  • Zhang W, Ntai I, Bolla ML, Malcolmson SJ, Kahne D, Kelleher NL, Walsh CT (2011a) Nine enzymes are required for assembly of the pacidamycin group of peptidyl nucleoside antibiotics. J Am Chem Soc 133:5240–5243

    Article  PubMed  CAS  Google Scholar 

  • Zhang W, Ntai I, Neil LK, Christopher TW (2011b) tRNA-dependent peptide bond formation by the transferase PacB in biosynthesis of the pacidamycin group of pentapeptidyl nucleoside antibiotics. PNAS 108:12249–12253

    Google Scholar 

  • Zhang W, Ostash B, Christopher TW (2010) Identification of the biosynthetic gene cluster for the pacidamycin group of peptidyl nucleoside antibiotics. PNAS 107:16828–16833

    Google Scholar 

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Correspondence to Guy T. Carter .

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Carter, G.T., McDonald, L.A. (2014). Uridyl Peptide Antibiotics: Developments in Biosynthesis and Medicinal Chemistry. In: Marinelli, F., Genilloud, O. (eds) Antimicrobials. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-39968-8_9

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