Abstract
Natural products continue to be a predominant source for new anti-infective agents. Research at the Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) and the Helmholtz Centre for Infection Research (HZI) is dedicated to the development of new lead structures against infectious diseases and, in particular, new antibiotics against hard-to-treat and multidrug-resistant bacterial pathogens. In this chapter, we introduce some of the concepts currently being employed in the field of antibiotic discovery. In particular, we will exemplarily illustrate three approaches: (1) Current sources for novel compounds are mainly soil-dwelling bacteria. In the course of our antimicrobial discovery program, a biodiverse collection of myxobacterial strains has been established and screened for antibiotic activities. Based on this effort, one successful example is presented in this chapter: Antibacterial cystobactamids were discovered and their molecular target, the DNA gyrase, was identified soon after the analysis of myxobacterial self-resistance making use of the information found in the respective biosynthesis gene cluster. (2) Besides our focus on novel natural products, we also apply strategies to further develop either neglected drugs or widely used antibiotics for which development of resistance in the clinical setting is an issue: Antimycobacterial griselimycins were first described in the 1960s but their development and use in tuberculosis therapy was not further pursued. We show how a griselimycin derivative with improved pharmacokinetic properties and enhanced potency against Mycobacterium tuberculosis revealed and validated a novel target for antibacterial therapy, the DNA sliding clamp. (3) In a third approach, biosynthetic engineering was used to modify and optimize natural products regarding their pharmaceutical properties and their production scale: The atypical tetracycline chelocardin is a natural product scaffold that was modified to yield a more potent derivative exhibiting activity against multidrug-resistant pathogens. This was achieved by genetic engineering of the producer strain and the resulting compound is now subject to further optimization by medicinal chemistry approaches.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Anonymous (1962) New antibiotic product, its preparation and compositions containing it. GB Patent 966,124
Arias CA, Murray BE (2009) Antibiotic-resistant bugs in the 21st century—a clinical super-challenge. N Engl J Med 360:439–443
Baltz RH (2009) Daptomycin: mechanisms of action and resistance, and biosynthetic engineering. Curr Opin Chem Biol 13(2):144–151
Baumann S, Herrmann J, Raju R, Steinmetz H, Mohr KI, Hüttel S, Harmrolfs K, Stadler M, Müller R (2014) Cystobactamids: myxobacterial topoisomerase inhibitors exhibiting potent antibacterial activity. Angew Chem Int Ed 53(52):14605–14609
Bielecki P, Lukat P, Hüsecken K, Dötsch A, Steinmetz H, Hartmann RW, Häussler S (2012) Mutation in Elongation Factor G Confers Resistance to the Antibiotic Argyrin in the Opportunistic Pathogen Pseudomonas aeruginosa. ChemBioChem 13(16):2339–2345
Broenstrup M, Koenig C, Toti L, Wink J, Leuschner W, Gassenhuber J, Müller R, Wenzel S, Binz T, Volz C (2014) Gene cluster for biosynthesis of griselimycin and methylgriselimycin. United States Patent US2014/0295457 A1
Challinor VL, Bode HB (2015) Bioactive natural products from novel microbial sources. Ann N Y Acad Sci 1354:82–97
Chopra I, Roberts M (2001) Tetracycline antibiotics: mode of action, applications, molecular biology, and epidemiology of bacterial resistance. Microbiol Mol Biol Rev 65(2):232–260
Cummings M, Breitling R, Takano E (2014) Steps towards the synthetic biology of polyketide biosynthesis. FEMS Microbiol Lett 351(2):116–125
Emmerson AM, Jones AM (2003) The quinolones: decades of development and use. J Antimicrob Chemother 51(Suppl 1):13–20
Fischbach MA, Walsh CT (2006) Assembly-line enzymology for polyketide and nonribosomal Peptide antibiotics: logic, machinery, and mechanisms. Chem Rev 106(8):3468–3496
Garcia R, Gerth K, Stadler M, Dogma IJ Jr, Müller R (2010) Expanded phylogeny of myxobacteria and evidence for cultivation of the ‘unculturables’. Mol Phylogenet Evol 57(2):878–887
Garcia R, Stadler M, Gemperlein K, Müller R (2015) Aetherobacter fasciculatus gen. nov., sp. nov. and Aetherobacter rufus gen. nov., sp. nov., two novel myxobacteria with promising biotechnological applications. Int J Syst Evol Microbiol. doi:10.1099/ijsem.0.000813
Garrido MC, Herrero M, Kolter R (1988) The export of the DNA replication inhibitor microcin B17 provides immunity for the host cell. EMBO J 7(6):1853–1862
Goss RJ, Shankar S, Fayad AA (2012) The generation of “unnatural” products: synthetic biology meets synthetic chemistry. Nat Prod Rep 29(8):870–889
Gruger T, Nitiss JL, Maxwell A, Zechiedrich EL, Heisig P, Seeber S, Pommier Y, Strumberg D (2004) A mutation in escherichia coli DNA gyrase conferring quinolone resistance results in sensitivity to drugs targeting eukaryotic topoisomerase II. Antimicrob Agents Chemother 48(12):4495–4504
Hashimi SM, Wall MK, Smith AB, Maxwell A, Birch RG (2007) The phytotoxin albicidin is a novel inhibitor of DNA gyrase. Antimicrob Agents Chemother 51(1):181–187
Hoffmann H, Kogler H, Heyse W, Matter H, Caspers M, Schummer D, Klemke-Jahn C, Bauer A, Penarier G, Debussche L, Brönstrup M (2015) Discovery, structure elucidation, and biological characterization of nannocystin A, a macrocyclic myxobacterial metabolite with potent antiproliferative properties. Angew Chem Int Ed 54(35):10145–10148
Kadota I, Takamura H, Nishii H, Yamamoto Y (2005) Total synthesis of brevetoxin B. J Am Chem Soc 127(25):9246–9250
Kirschning A, Hahn F (2012) Merging chemical synthesis and biosynthesis: a new chapter in the total synthesis of natural products and natural product libraries. Angew Chem Int Ed 51(17):4012–4022
Kling A, Lukat P, Almeida DV, Bauer A, Fontaine E, Sordello S, Zaburannyi N, Herrmann J, Wenzel SC, König C, Ammerman NC, Barrio MB, Borchers K, Bordon-Pallier F, Brönstrup M, Courtemanche G, Gerlitz M, Geslin M, Hammann P, Heinz DW, Hoffmann H, Klieber S, Kohlmann M, Kurz M, Lair C, Matter H, Nuermberger E, Tyagi S, Fraisse L, Grosset JH, Lagrange S, Müller R (2015) Targeting DnaN for tuberculosis therapy using novel griselimycins. Science 348(6239):1106–1112
Koehn FE, Carter GT (2005) The evolving role of natural products in drug discovery. Nat Rev Drug Discov 4:206–220
Kretz J, Kerwat D, Schubert V, Grätz S, Pesic A, Semsary S, Cociancich S, Royer M, Süssmuth RD (2015) Total synthesis of albicidin: a lead structure from xanthomonas albilineans for potent antibacterial gyrase inhibitors. Angew Chem Int Ed 54(6):1969–1973
Laxminarayan R, Duse A, Wattal C, Zaidi AKM, Wertheim HFL, Sumpradit N, Vlieghe E, Hara GL, Gould IM, Goossens H, Greko C, So AD, Bigdeli M, Tomson G, Woobhous W, Ombaka E, Peralta AQ, Qarnar FN, Mir F, Kariuki S, Bhutta ZA, Coates A, Bergstrom R, Wrigh GD, Brown ED, Cars O (2013) Antibiotic resistance-the need for global solutions. Lancet Infect Dis 13(12):1057–1098
Lešnik U, Lukežič T, Podgoršek A, Horvat J, Polak T, Šala M, Jenko B, Harmrolfs K, Ocampo-Sosa A, Martínez-Martínez L, Herron PR, Fujs Š, Kosec G, Hunter IS, Müller R, Petković H (2015) Construction of a new class of tetracycline lead structures with potent antibacterial activity through biosynthetic engineering. Angew Chem Int Ed Engl 54(13):3937–3940
Lewis K (2013) Platforms for antibiotic discovery. Nat Rev Drug Discov 12(5):371–387
Li JWH, Vederas JC (2009) Drug discovery and natural products: end of an era or an endless frontier? Science 325(5937):161–165
Lukežič T, Lešnik U, Podgoršek A, Horvat J, Polak T, Šala M, Jenko B, Raspor P, Herron PR, Hunter IS, Petković H (2013) Identification of the chelocardin biosynthetic gene cluster from Amycolatopsis sulphurea: a platform for producing novel tetracycline antibiotics. Microbiology 159(12):2524–2532
Mendez C, Salas JA (2001) Altering the glycosylation pattern of bioactive compounds. Trends Biotechnol 19(11):449–456
Molnar V, Matković Z, Tambić T, Kozma C (1977) Clinico-pharmacological investigation of chelocardine in patients suffering from urinary tract infection (author’s transl). Lijec Vjesn 99(9):560–562
Montero C, Mateu G, Rodriguez R, Takiff H (2001) Intrinsic resistance of mycobacterium smegmatis to fluoroquinolones may be influenced by new pentapeptide protein MfpA. Antimicrob Agents Chemother 45(12):3387–3392
Moreno M, Elgaher WAM, Hermann J, Schläger N, Hamed MM, Baumann S, Müller R, Hartmann RW, Kirschning A (2015) Synthesis and biological evaluation of cystobactamid 507: a bacterial topoisomerase inhibitor from cystobacter sp. Synlett 26(09):1175–1178
Müller R, Wink J (2014) Future potential for anti-infectives from bacteria—how to exploit biodiversity and genomic potential. Int J Med Microbiol 304(1):3–13
Nelson ML (1998) Chemical and biological dynamics of tetracyclines. Adv Dent Res 12(2):5–11
Newman DJ (2008) Natural products as leads to potential drugs: an old process or the new hope for drug discovery? J Med Chem 51(9):2589–2599
Nicolaou KC, Winssinger N, Pastor J, Ninkovic S, Sarabia F, He Y, Vourloumis D, Yang Z, Li T, Giannakakou P, Hamel E (1997) Synthesis of epothilones A and B in solid and solution phase. Nature 387(6630):268–272
Oliver TJ, Sinclair AC (1964) Antibiotic M-319. United States Patent US3155582
Payne DJ, Gwynn MN, Holmes DJ, Pompliano DL (2007) Drugs for bad bugs: confronting the challenges of antibacterial discovery. Nat Rev Drug Discov 6:29–40
Pendleton JN, Gorman SP, Gilmore BF (2013) Clinical relevance of the ESKAPE pathogens. Expert Rev Anti Infect Ther 11(3):297–308
Pickens LB, Tang Y (2010) Oxytetracycline biosynthesis. J Biol Chem 285(36):27509–27515
Plaza A, Garcia R, Bifulco G, Martinez JP, Hüttel S, Sasse F, Meyerhans A, Stadler M, Müller R (2012) Aetheramides A and B, potent HIV-inhibitory depsipeptides from a myxobacterium of the new genus “aetherobacter”. Org Lett 14(11):2854–2857
Power P, Dunne T, Murphy B, Lochlainn LN, Rai D, Borissow C, Rawlings B, Caffrey P (2008) Engineered synthesis of 7-oxo- and 15-deoxy-15-oxo-amphotericins: insights into structure-activity relationships in polyene antibiotics. Chem Biol 15(1):78–86
Proctor R, Craig W, Kunin C (1978) Cetocycline, tetracycline analog: in vitro studies of antimicrobial activity, serum binding, lipid solubility, and uptake by bacteria. Antimicrob Agents Chemother 13(4):598–604
Rahn N, Kalesse M (2008) The total synthesis of Chlorotonil A. Angew Chem Int Ed Engl 47(3):2232–2247
Rangel-Vega A, Bernstein LR, Mandujano-Tinoco EA, Garcia-Cibtreras SJ, Contreras SJ, Garcia-Contreras R (2015) Drug repurposing as an alternative for the treatment of recalcitrant bacterial infections. Front Microbiol 6:1–8
Seiple IB, Zhang Z, Jakubec P, Langlois-Mercier A, Wright PM, Hog DT, Yabu K, Allu SR, Fukuzaki T, Carlsen PN, Kitamura Y, Zhou X, Condakes ML, Szczypiński FT, Green WD, Myers AG (2016) A platform for the discovery of new macrolide antibiotics. Nature 533(7603):338–345
Stepanek JJ, Lukežič T, Teichert I, Petković H, Bandow JE (2016) Dual mechanism of action of the atypical tetracycline chelocardin. Biochim Biophys Acta 1864(6):645–654
Strieker M, Tanovic A, Marahiel MA (2010) Nonribosomal peptide synthetases: structures and dynamics. Curr Opin Struct Biol 20(2):234–240
Sun H, Liu Z, Zhao H, Ang EL (2015) Recent advances in combinatorial biosynthesis for drug discovery. Drug Des Devel Ther 9:823–833
Surup F, Viehrig K, Mohr KI, Herrmann J, Jansen R, Müller R (2014) Disciformycins A and B: 12-membered macrolide glycoside antibiotics from the myxobacterium Pyxidicoccus fallax active against multiresistant staphylococci. Angew Chem Int Ed 53(49):13588–13591
Tanner NA, Tolun G, Loparo JJ, Jergic S, Griffith JD, Dixon NE, van Oijen AM (2011) E. coli DNA replication in the absence of free β clamps. EMBO J 30(9):1830–1840
Terlain B, Thomas JP (1971) Structure of griselimycin, polypeptide antibiotic extracted from streptomyces cultures. Bull Soc Chim Fr 3:2349–2365
Tran JH, Jacoby GA (2002) Mechanism of plasmid-mediated quinolone resistance. Proc Natl Acad Sci USA 99(8):5638–5642
Vos SM, Tretter EM, Schmidt BH, Berger JM (2011) All tangled up: how cells direct, manage and exploit topoisomerase function. Nat Rev Mol Cell Biol 12(12):827–841
Walsh CT, Haynes ST, Ames BD (2012) Aminobenzoates as building blocks for natural product assembly lines. Nat Prod Rep 29(1):37–59
Wang P, Gao X, Chooi YH, Deng Z, Tang Y (2011) Genetic characterization of enzymes involved in the priming steps of oxytetracycline biosynthesis in Streptomyces rimosus. Microbiology-(UK) 157:2401–2409
Weissman KJ, Müller R (2010) Myxobacterial secondary metabolites: bioactivities and modes-of-action. Nat Prod Rep 27(9):1276–1295
Wenzel SC, Müller R (2009) The impact of genomics on the exploitation of the myxobacterial secondary metabolome. Nat Prod Rep 26(11):1385–1407
Williams GJ (2013) Engineering polyketide synthases and nonribosomal peptide synthetases. Curr Opin Struct Biol 23(4):603–612
Wong FT, Khosla C (2012) Combinatorial biosynthesis of polyketides—a perspective. Curr Opin Chem Biol 16(1–2):117–123
Zhang W, Ames BD, Tsai SC, Tang Y (2006) Engineered biosynthesis of a novel amidated polyketide, using the malonamyl-specific initiation module from the oxytetracycline polyketide synthase. Appl Environ Microbiol 72(4):2573–2580
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2016 Springer International Publishing AG
About this chapter
Cite this chapter
Herrmann, J. et al. (2016). Strategies for the Discovery and Development of New Antibiotics from Natural Products: Three Case Studies. In: Stadler, M., Dersch, P. (eds) How to Overcome the Antibiotic Crisis . Current Topics in Microbiology and Immunology, vol 398. Springer, Cham. https://doi.org/10.1007/82_2016_498
Download citation
DOI: https://doi.org/10.1007/82_2016_498
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-49282-7
Online ISBN: 978-3-319-49284-1
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)