Old dogs and new tricks in antimicrobial discovery

McKenna, 2013, Antibiotic resistance: the last resort, Nature, 499, 394, 10.1038/499394a Butler, 2013, Antibiotics in the clinical pipeline in 2013, J Antibiot, 66, 571, 10.1038/ja.2013.86 Baltz, 2006, Marcel Faber roundtable: is our antibiotic pipeline unproductive because of starvation, constipation or lack of inspiration?, J Ind Microbiol Biotechnol, 33, 507, 10.1007/s10295-005-0077-9 Carrano, 2015, The relevance of chemical dereplication in microbial natural product screening, J Appl Bioanal, 1, 55, 10.17145/jab.15.010 Tringe, 2005, Comparative metagenomics of microbial communities, Science, 308, 554, 10.1126/science.1107851 Cimermancic, 2014, Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters, Cell, 158, 412, 10.1016/j.cell.2014.06.034 Bentley, 2002, Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2), Nature, 417, 141, 10.1038/417141a Ikeda, 2003, Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis, Nat Biotechnol, 21, 526, 10.1038/nbt820 Donia, 2014, A systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics, Cell, 158, 1402, 10.1016/j.cell.2014.08.032 Doroghazi, 2014, A roadmap for natural product discovery based on large-scale genomics and metabolomics, Nat Chem Biol, 10, 963, 10.1038/nchembio.1659 Ju, 2015, Discovery of phosphonic acid natural products by mining the genomes of 10,000 actinomycetes, Proc Natl Acad Sci U S A, 112, 12175, 10.1073/pnas.1500873112 Wang, 2014, Atlas of nonribosomal peptide and polyketide biosynthetic pathways reveals common occurrence of nonmodular enzymes, Proc Natl Acad Sci U S A, 111, 9259, 10.1073/pnas.1401734111 McClerren, 2006, Discovery and in vitro biosynthesis of haloduracin, a two-component lantibiotic, Proc Natl Acad Sci U S A, 103, 17243, 10.1073/pnas.0606088103 Oman, 2011, Haloduracin α binds the peptidoglycan precursor lipid II with 2:1 stoichiometry, J Am Chem Soc, 133, 17544, 10.1021/ja206281k Yamanaka, 2014, Direct cloning and refactoring of a silent lipopeptide biosynthetic gene cluster yields the antibiotic taromycin A, Proc Natl Acad Sci U S A, 111, 1957, 10.1073/pnas.1319584111 Brady, 2007, Construction of soil environmental DNA cosmid libraries and screening for clones that produce biologically active small molecules, Nat Protoc, 2, 1297, 10.1038/nprot.2007.195 Milshteyn, 2014, Mining the metabiome: identifying novel natural products from microbial communities, Chem Biol, 21, 1211, 10.1016/j.chembiol.2014.08.006 Chang, 2013, Discovery of indolotryptoline antiproliferative agents by homology-guided metagenomic screening, Proc Natl Acad Sci U S A, 110, 2478, 10.1073/pnas.1218073110 Feng, 2011, Functional analysis of environmental DNA-derived type ii polyketide synthases reveals structurally diverse secondary metabolites, Proc Natl Acad Sci U S A, 108, 12629, 10.1073/pnas.1103921108 Feng, 2010, Fluostatins produced by the heterologous expression of a TAR reassembled environmental DNA derived type ii PKS gene cluster, J Am Chem Soc, 132, 11902, 10.1021/ja104550p Kang, 2013, Arimetamycin A: improving clinically relevant families of natural products through sequence-guided screening of soil metagenomes, Angew Chem Int Ed Engl, 52, 11063, 10.1002/anie.201305109 Banik, 2010, Tailoring enzyme-rich environmental DNA clones: a source of enzymes for generating libraries of unnatural natural products, J Am Chem Soc, 132, 15661, 10.1021/ja105825a Bauer, 2010, Utahmycins A and B, azaquinones produced by an environmental DNA clone, J Nat Prod, 73, 976, 10.1021/np900786s Owen, 2013, Mapping gene clusters within arrayed metagenomic libraries to expand the structural diversity of biomedically relevant natural products, Proc Natl Acad Sci U S A, 110, 11797, 10.1073/pnas.1222159110 Feng, 2012, Environmental DNA-encoded antibiotics fasamycins A and B inhibit FabF in type II fatty acid biosynthesis, J Am Chem Soc, 134, 2981, 10.1021/ja207662w Kallifidas, 2012, Tetarimycin A, an MRSA-active antibiotic identified through induced expression of environmental DNA gene clusters, J Am Chem Soc, 134, 19552, 10.1021/ja3093828 Charlop-Powers, 2014, Chemical-biogeographic survey of secondary metabolism in soil, Proc Natl Acad Sci U S A, 111, 3757, 10.1073/pnas.1318021111 Owen, 2015, Multiplexed metagenome mining using short DNA sequence tags facilitates targeted discovery of epoxyketone proteasome inhibitors, Proc Natl Acad Sci U S A, 112, 4221, 10.1073/pnas.1501124112 Reddy, 2014, eSNaPD: a versatile, web-based bioinformatics platform for surveying and mining natural product biosynthetic diversity from metagenomes, Chem Biol, 21, 1023, 10.1016/j.chembiol.2014.06.007 Weber, 2015, AntiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters, Nucleic Acids Res, 43, W237, 10.1093/nar/gkv437 Ziemert, 2012, The natural product domain seeker NaPDoS: a phylogeny based bioinformatic tool to classify secondary metabolite gene diversity, PLoS One, 7, e34064, 10.1371/journal.pone.0034064 Skinnider, 2015, Genomes to natural products PRediction Informatics for Secondary Metabolomes (PRISM), Nucleic Acids Res, 43, 9645 Kersten, 2011, A mass spectrometry-guided genome mining approach for natural product peptidogenomics, Nat Chem Biol, 7, 794, 10.1038/nchembio.684 Goering, 2016, Metabologenomics. Correlation of microbial gene clusters with metabolites drives discovery of a nonribosomal peptide with an unusual amino acid monomer, ACS Cent Sci, 2, 99, 10.1021/acscentsci.5b00331 Duncan, 2015, Molecular networking and pattern-based genome mining improves discovery of biosynthetic gene clusters and their products from Salinispora species, Chem Biol, 22, 460, 10.1016/j.chembiol.2015.03.010 Kersten, 2013, Glycogenomics as a mass spectrometry-guided genome-mining method for microbial glycosylated molecules, Proc Natl Acad Sci U S A, 110, E4407, 10.1073/pnas.1315492110 Johnston, 2015, An automated Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products, Nat Commun, 6, 8421, 10.1038/ncomms9421 Mohimani, 2014, NRPquest: coupling mass spectrometry and genome mining for nonribosomal peptide discovery, J Nat Prod, 77, 1902, 10.1021/np500370c Chan, 2013, Antibacterial drugs, 389 Wright, 2014, The evolving role of chemical synthesis in antibacterial drug discovery, Angew Chem Int Ed Engl, 53, 8840, 10.1002/anie.201310843 Rolinson, 2007, The 50th anniversary of the discovery of 6-aminopenicillanic acid (6-APA), Int J Antimicrob Ag, 29, 3, 10.1016/j.ijantimicag.2006.09.003 Butler, 2014, Glycopeptide antibiotics: back to the future, J Antibiot, 67, 631, 10.1038/ja.2014.111 Leadbetter, 2004, Hydrophobic vancomycin derivatives with improved adme properties: discovery of telavancin (TD-6424), J Antibiot, 57, 326, 10.7164/antibiotics.57.326 Leadbetter, 2004, Hydrophobic vancomycin derivatives with improved ADME properties: discovery of telavancin (TD-6424), J Antibiot, 57, 326, 10.7164/antibiotics.57.326 Bouza, 2010, Oritavancin: a novel lipoglycopeptide active against gram-positive pathogens including multiresistant strains, Int J Antimicrob Ag, 36, 401, 10.1016/j.ijantimicag.2010.06.048 Cooper, 2015 Yarlagadda, 2014, Membrane active vancomycin analogues: a strategy to combat bacterial resistance, J Med Chem, 57, 4558, 10.1021/jm500270w Yarlagadda, 2015, Membrane disruption and enhanced inhibition of cell-wall biosynthesis: a synergistic approach to tackle vancomycin-resistant bacteria, Angew Chem Int Ed Engl, 54, 13644, 10.1002/anie.201507567 Albayati, 2015, Novel bone-targeting agent for enhanced delivery of vancomycin to bone, Antimicrob Agents Chemother, 60, 1865, 10.1128/AAC.01609-15 Goldstein, 1993, In vitro antimicrobial activity of a new antibiotic, MDL 62,879 (GE2270 A), Antimicrob Agents Chemother, 37, 741, 10.1128/AAC.37.4.741 Selva, 1991, Antibiotic GE2270 A: a novel inhibitor of bacterial protein synthesis. I. Isolation and characterization, J Antibiot, 44, 693, 10.7164/antibiotics.44.693 Parmeggiani, 2006, Structural basis of the action of pulvomycin and GE2270 A on elongation factor Tu, Biochemistry, 45, 6846, 10.1021/bi0525122 Tavecchia, 1995, Degradation studies of antibiotic MDL 62,879 (GE2270A) and revision of the structure, Tetrahedron, 51, 4867, 10.1016/0040-4020(95)00171-4 LaMarche, 2012, Discovery of LFF571: an investigational agent for Clostridium difficile infection, J Med Chem, 55, 2376, 10.1021/jm201685h Mullane, 2015, Multicenter, randomized clinical trial to compare the safety and efficacy of LFF571 and vancomycin for Clostridium difficile infections, Antimicrob Agents Chemother, 59, 1435, 10.1128/AAC.04251-14 Fabbretti, 2015, A derivative of the thiopeptide GE2270A highly selective against Propionibacterium acnes, Antimicrob Agents Chemother, 59, 4560, 10.1128/AAC.05155-14 Huber, 1988, The formation of daptomycin by supplying decanoic acid to Streptomyces roseosporus cultures producing the antibiotic complex A21978C, J Biotechnol, 7, 283, 10.1016/0168-1656(88)90040-5 Yin, 2015, Structure–activity relationship studies of a series of semisynthetic lipopeptides leading to the discovery of surotomycin, a novel cyclic lipopeptide being developed for the treatment of Clostridium difficile-associated diarrhea, J Med Chem, 58, 5137, 10.1021/acs.jmedchem.5b00366 Knight-Connoni, 2015, Discovery and development of surotomycin for the treatment of Clostridium difficile, J Ind Microbiol Biotechnol, 43, 195, 10.1007/s10295-015-1714-6 Craig, 2010, In vivo pharmacodynamics of new lipopeptide MX-2401, Antimicrob Agents Chemother, 54, 5092, 10.1128/AAC.00238-10 Rubinchik, 2011, Mechanism of action and limited cross-resistance of new lipopeptide MX-2401, Antimicrob Agents Chemother, 55, 2743, 10.1128/AAC.00170-11 Gallardo-Godoy, 2016, Activity and predicted nephrotoxicity of synthetic antibiotics based on polymyxin B, J Med Chem, 59, 1068, 10.1021/acs.jmedchem.5b01593 Fu, 2015, Biosynthetic studies of telomycin reveal new lipopeptides with enhanced activity, J Am Chem Soc, 137, 7692, 10.1021/jacs.5b01794 Johnston, 2016, Assembly and clustering of natural antibiotics guides target identification, Nat Chem Biol, 12, 233, 10.1038/nchembio.2018 Klinker, 2015, Beyond vancomycin: the tail of the lipoglycopeptides, Clin Ther, 37, 2619, 10.1016/j.clinthera.2015.11.007 Blaskovich, 2015, Helping chemists discover new antibiotics, ACS Infect Dis, 1, 285, 10.1021/acsinfecdis.5b00044 Cooper, 2015, A community-based approach to new antibiotic discovery, Nat Rev Drug Discov, 14, 587, 10.1038/nrd4706 Kumarasamy, 2010, Emergence of a new antibiotic resistance mechanism in India, Pakistan, and the UK: a molecular, biological, and epidemiological study, Lancet Infect Dis, 10, 597, 10.1016/S1473-3099(10)70143-2