23 results on '"Bader CD"'
Search Results
2. Dynamic Combinatorial Chemistry Unveils Nsp10 Inhibitors with Antiviral Potential Against SARS-CoV-2.
- Author
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Jumde RP, Jézéquel G, Saramago M, Frank N, Adam S, Cunha MV, Bader CD, Gunesch AP, Köhler NM, Johannsen S, Bousis S, Pietschmann T, Matos RG, Müller R, Arraiano CM, and Hirsch AKH
- Abstract
The development of antiviral drugs against the Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) responsible for the recent Covid-19 pandemic is crucial, as treatment options remain limited and vaccination does not prevent (re)infection. Two relatively underexplored targets of this virus are the 3'-5' exoribonuclease (ExoN) and the 2'-O-methyltransferase (2'-O-MTase), both essential for viral viability. The non-structural proteins Nsp14 and Nsp16 exhibit enzymatic activities for ExoN and 2'-O-MTase, respectively, especially when in complex with their co-factor protein Nsp10. The study focuses on the use of target-directed dynamic combinatorial chemistry (tdDCC) to identify binders of Nsp10, aiming to disturb the protein-protein interactions (PPI) involving Nsp10-Nsp14, as well as Nsp10-Nsp16. We synthesised the hits and evaluated them to assess Nsp10 affinity, ExoN and 2'-O-MTase activities inhibition, and antiviral activity in hCoV-229E and SARS-CoV-2-infected whole-cell settings. This study reports a novel class of ExoN and/or 2'-O-MTase inhibitors exhibiting antiviral activity against coronaviruses., (© 2024 The Author(s). Chemistry - A European Journal published by Wiley-VCH GmbH.)
- Published
- 2024
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3. MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration.
- Author
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Zdouc MM, Blin K, Louwen NLL, Navarro J, Loureiro C, Bader CD, Bailey CB, Barra L, Booth TJ, Bozhüyük KAJ, Cediel-Becerra JDD, Charlop-Powers Z, Chevrette MG, Chooi YH, D'Agostino PM, de Rond T, Del Pup E, Duncan KR, Gu W, Hanif N, Helfrich EJN, Jenner M, Katsuyama Y, Korenskaia A, Krug D, Libis V, Lund GA, Mantri S, Morgan KD, Owen C, Phan CS, Philmus B, Reitz ZL, Robinson SL, Singh KS, Teufel R, Tong Y, Tugizimana F, Ulanova D, Winter JM, Aguilar C, Akiyama DY, Al-Salihi SAA, Alanjary M, Alberti F, Aleti G, Alharthi SA, Rojo MYA, Arishi AA, Augustijn HE, Avalon NE, Avelar-Rivas JA, Axt KK, Barbieri HB, Barbosa JCJ, Barboza Segato LG, Barrett SE, Baunach M, Beemelmanns C, Beqaj D, Berger T, Bernaldo-Agüero J, Bettenbühl SM, Bielinski VA, Biermann F, Borges RM, Borriss R, Breitenbach M, Bretscher KM, Brigham MW, Buedenbender L, Bulcock BW, Cano-Prieto C, Capela J, Carrion VJ, Carter RS, Castelo-Branco R, Castro-Falcón G, Chagas FO, Charria-Girón E, Chaudhri AA, Chaudhry V, Choi H, Choi Y, Choupannejad R, Chromy J, Donahey MSC, Collemare J, Connolly JA, Creamer KE, Crüsemann M, Cruz AA, Cumsille A, Dallery JF, Damas-Ramos LC, Damiani T, de Kruijff M, Martín BD, Sala GD, Dillen J, Doering DT, Dommaraju SR, Durusu S, Egbert S, Ellerhorst M, Faussurier B, Fetter A, Feuermann M, Fewer DP, Foldi J, Frediansyah A, Garza EA, Gavriilidou A, Gentile A, Gerke J, Gerstmans H, Gomez-Escribano JP, González-Salazar LA, Grayson NE, Greco C, Gomez JEG, Guerra S, Flores SG, Gurevich A, Gutiérrez-García K, Hart L, Haslinger K, He B, Hebra T, Hemmann JL, Hindra H, Höing L, Holland DC, Holme JE, Horch T, Hrab P, Hu J, Huynh TH, Hwang JY, Iacovelli R, Iftime D, Iorio M, Jayachandran S, Jeong E, Jing J, Jung JJ, Kakumu Y, Kalkreuter E, Kang KB, Kang S, Kim W, Kim GJ, Kim H, Kim HU, Klapper M, Koetsier RA, Kollten C, Kovács ÁT, Kriukova Y, Kubach N, Kunjapur AM, Kushnareva AK, Kust A, Lamber J, Larralde M, Larsen NJ, Launay AP, Le NT, Lebeer S, Lee BT, Lee K, Lev KL, Li SM, Li YX, Licona-Cassani C, Lien A, Liu J, Lopez JAV, Machushynets NV, Macias MI, Mahmud T, Maleckis M, Martinez-Martinez AM, Mast Y, Maximo MF, McBride CM, McLellan RM, Bhatt KM, Melkonian C, Merrild A, Metsä-Ketelä M, Mitchell DA, Müller AV, Nguyen GS, Nguyen HT, Niedermeyer THJ, O'Hare JH, Ossowicki A, Ostash BO, Otani H, Padva L, Paliyal S, Pan X, Panghal M, Parade DS, Park J, Parra J, Rubio MP, Pham HT, Pidot SJ, Piel J, Pourmohsenin B, Rakhmanov M, Ramesh S, Rasmussen MH, Rego A, Reher R, Rice AJ, Rigolet A, Romero-Otero A, Rosas-Becerra LR, Rosiles PY, Rutz A, Ryu B, Sahadeo LA, Saldanha M, Salvi L, Sánchez-Carvajal E, Santos-Medellin C, Sbaraini N, Schoellhorn SM, Schumm C, Sehnal L, Selem N, Shah AD, Shishido TK, Sieber S, Silviani V, Singh G, Singh H, Sokolova N, Sonnenschein EC, Sosio M, Sowa ST, Steffen K, Stegmann E, Streiff AB, Strüder A, Surup F, Svenningsen T, Sweeney D, Szenei J, Tagirdzhanov A, Tan B, Tarnowski MJ, Terlouw BR, Rey T, Thome NU, Torres Ortega LR, Tørring T, Trindade M, Truman AW, Tvilum M, Udwary DW, Ulbricht C, Vader L, van Wezel GP, Walmsley M, Warnasinghe R, Weddeling HG, Weir ANM, Williams K, Williams SE, Witte TE, Rocca SMW, Yamada K, Yang D, Yang D, Yu J, Zhou Z, Ziemert N, Zimmer L, Zimmermann A, Zimmermann C, van der Hooft JJJ, Linington RG, Weber T, and Medema MH
- Abstract
Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)
- Published
- 2024
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4. The Natural Products Discovery Center: Release of the First 8490 Sequenced Strains for Exploring Actinobacteria Biosynthetic Diversity.
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Kalkreuter E, Kautsar SA, Yang D, Bader CD, Teijaro CN, Fluegel LL, Davis CM, Simpson JR, Lauterbach L, Steele AD, Gui C, Meng S, Li G, Viehrig K, Ye F, Su P, Kiefer AF, Nichols A, Cepeda AJ, Yan W, Fan B, Jiang Y, Adhikari A, Zheng CJ, Schuster L, Cowan TM, Smanski MJ, Chevrette MG, de Carvalho LPS, and Shen B
- Abstract
Actinobacteria, the bacterial phylum most renowned for natural product discovery, has been established as a valuable source for drug discovery and biotechnology but is underrepresented within accessible genome and strain collections. Herein, we introduce the Natural Products Discovery Center (NPDC), featuring 122,449 strains assembled over eight decades, the genomes of the first 8490 NPDC strains (7142 Actinobacteria), and the online NPDC Portal making both strains and genomes publicly available. A comparative survey of RefSeq and NPDC Actinobacteria highlights the taxonomic and biosynthetic diversity within the NPDC collection, including three new genera, hundreds of new species, and ~7000 new gene cluster families. Selected examples demonstrate how the NPDC Portal's strain metadata, genomes, and biosynthetic gene clusters can be leveraged using genome mining approaches. Our findings underscore the ongoing significance of Actinobacteria in natural product discovery, and the NPDC serves as an unparalleled resource for both Actinobacteria strains and genomes., Competing Interests: Competing Interest Statement: The authors declare that they have no conflict of interest.
- Published
- 2024
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5. Elucidation of unusual biosynthesis and DnaN-targeting mode of action of potent anti-tuberculosis antibiotics Mycoplanecins.
- Author
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Fu C, Liu Y, Walt C, Rasheed S, Bader CD, Lukat P, Neuber M, Haeckl FPJ, Blankenfeldt W, Kalinina OV, and Müller R
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- Humans, Anti-Bacterial Agents pharmacology, Anti-Bacterial Agents chemistry, DNA Polymerase III metabolism, Microbial Sensitivity Tests, Tuberculosis, Mycobacterium tuberculosis metabolism
- Abstract
DNA polymerase III sliding clamp (DnaN) was recently validated as a new anti-tuberculosis target employing griselimycins. Three (2 S,4 R)-4-methylproline moieties of methylgriselimycin play significant roles in target binding and metabolic stability. Here, we identify the mycoplanecin biosynthetic gene cluster by genome mining using bait genes from the 4-methylproline pathway. We isolate and structurally elucidate four mycoplanecins comprising scarce homo-amino acids and 4-alkylprolines. Evaluating mycoplanecin E against Mycobacterium tuberculosis surprisingly reveals an excitingly low minimum inhibition concentration at 83 ng/mL, thus outcompeting griselimycin by approximately 24-fold. We show that mycoplanecins bind DnaN with nanomolar affinity and provide a co-crystal structure of mycoplanecin A-bound DnaN. Additionally, we reconstitute the biosyntheses of the unusual L-homoleucine, L-homonorleucine, and (2 S,4 R)-4-ethylproline building blocks by characterizing in vitro the full set of eight enzymes involved. The biosynthetic study, bioactivity evaluation, and drug target validation of mycoplanecins pave the way for their further development to tackle multidrug-resistant mycobacterial infections., (© 2024. The Author(s).)
- Published
- 2024
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6. Interplay of emerging and established technologies drives innovation in natural product antibiotic discovery.
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Bader CD, Nichols AL, Yang D, and Shen B
- Subjects
- Drug Discovery, Anti-Bacterial Agents pharmacology, Anti-Bacterial Agents chemistry, Computational Biology, Biological Products pharmacology, Biological Products chemistry
- Abstract
A continued rise of antibiotic resistance and shortages of effective antibiotics necessitate the discovery and development of new antibiotics with novel modes of action (MoAs) against resistant pathogens. While natural products remain the best resource for antibiotic discovery, their exploration faces many challenges, including (i) unknown MoAs, (ii) high rediscovery rates, (iii) tedious isolation and structure elucidation, and (iv) insufficient production for further development. We have identified recent innovations in screening methods, microbiology, bioinformatics, and metabolomics technologies, as well as natural product-inspired synthesis and synthetic biology, that have contributed to new natural product antibiotics in the past two years. We highlight their interplay as the key element for successful applications, driving future opportunities to increase the pool of natural product-based antibacterial antibiotics., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier Ltd.)
- Published
- 2023
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7. Genome-Guided Discovery of the Myxobacterial Thiolactone-Containing Sorangibactins.
- Author
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Gao Y, Walt C, Bader CD, and Müller R
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- Phenols metabolism, Oxazoles metabolism, Myxococcales genetics, Myxococcales metabolism, Myxococcus xanthus genetics, Myxococcus xanthus metabolism
- Abstract
In this study, an unprecedented myxobacterial siderophore termed sorangibactin was discovered by heterologous expression of a coelibactin-like nonribosomal peptide synthetase (NRPS) gene cluster from the Sorangiineae strain MSr11367 in the host Myxococcus xanthus DK1622. De novo structure elucidation uncovered a linear polycyclic structure consisting of an N-terminal phenol group, an oxazole, tandem N -methyl-thiazolidines, and an unusual C-terminal γ-thiolactone moiety. Except for the unprecedented oxazoline dehydrogenation to form an oxazole, which we show to be catalyzed by a cytochrome P450-dependent enzyme, other tailoring steps were found necessary for efficient downstream processing. The unusual thioesterase (TE) domain is proposed to select homocysteine or methionine for offloading involving an intramolecular γ-thiolactone formation. Its active site comprises a rare cysteine, which was found essential for product formation by point mutation to alanine or serine, which both abolished its activity. This unusual release mechanism and the resulting rare thiolactone structure can serve as a starting point for detailed biochemical investigations.
- Published
- 2023
- Full Text
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8. Darobactins Exhibiting Superior Antibiotic Activity by Cryo-EM Structure Guided Biosynthetic Engineering.
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Seyfert CE, Porten C, Yuan B, Deckarm S, Panter F, Bader CD, Coetzee J, Deschner F, Tehrani KHME, Higgins PG, Seifert H, Marlovits TC, Herrmann J, and Müller R
- Subjects
- Anti-Bacterial Agents pharmacology, Anti-Bacterial Agents chemistry, Cryoelectron Microscopy, Gram-Negative Bacteria, Microbial Sensitivity Tests, Phenylpropionates pharmacology, Acinetobacter baumannii
- Abstract
Over recent decades, the pipeline of antibiotics acting against Gram-negative bacteria is running dry, as most discovered candidate antibiotics suffer from insufficient potency, pharmacokinetic properties, or toxicity. The darobactins, a promising new small peptide class of drug candidates, bind to novel antibiotic target BamA, an outer membrane protein. Previously, we reported that biosynthetic engineering in a heterologous host generated novel darobactins with enhanced antibacterial activity. Here we utilize an optimized purification method and present cryo-EM structures of the Bam complex with darobactin 9 (D9), which served as a blueprint for the biotechnological generation of twenty new darobactins including halogenated analogs. The newly engineered darobactin 22 binds more tightly to BamA and outperforms the favorable activity profile of D9 against clinically relevant pathogens such as carbapenem-resistant Acinetobacter baumannii up to 32-fold, without observing toxic effects., (© 2022 The Authors. Angewandte Chemie International Edition published by Wiley-VCH GmbH.)
- Published
- 2023
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9. Thiamyxins: Structure and Biosynthesis of Myxobacterial RNA-Virus Inhibitors.
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Haack PA, Harmrolfs K, Bader CD, Garcia R, Gunesch AP, Haid S, Popoff A, Voltz A, Kim H, Bartenschlager R, Pietschmann T, and Müller R
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- Humans, RNA, Polyketide Synthases genetics, Polyketide Synthases metabolism, Multigene Family, Myxococcales metabolism, Polyketides, Zika Virus, Zika Virus Infection genetics
- Abstract
During our search for novel myxobacterial natural products, we discovered the thiamyxins: thiazole- and thiazoline-rich non-ribosomal peptide-polyketide hybrids with potent antiviral activity. We isolated four congeners of this unprecedented natural product family with the non-cyclized thiamyxin D fused to a glycerol unit at the C-terminus. Alongside their structure elucidation, we present a concise biosynthesis model based on biosynthetic gene cluster analysis and isotopically labelled precursor feeding. We report incorporation of a 2-(hydroxymethyl)-4-methylpent-3-enoic acid moiety by a GCN5-related N-acetyltransferase-like decarboxylase domain featuring polyketide synthase. The thiamyxins show potent inhibition of RNA viruses in cell culture models of corona, zika and dengue virus infection. Their potency up to a half maximal inhibitory concentration of 560 nM combined with milder cytotoxic effects on human cell lines indicate the potential for further development of the thiamyxins., (© 2022 The Authors. Angewandte Chemie International Edition published by Wiley-VCH GmbH.)
- Published
- 2022
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10. Large-Scale Interlaboratory DI-FT-ICR MS Comparability Study Employing Various Systems.
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Forcisi S, Moritz F, Thompson CJ, Kanawati B, Uhl J, Afonso C, Bader CD, Barsch A, Boughton BA, Chu RK, Ferey J, Fernandez-Lima F, Guéguen C, Heintz D, Gomez-Hernandez M, Jang KS, Kessler N, Mangal V, Müller R, Nakabayashi R, Nicol E, Nicolardi S, Palmblad M, Paša-Tolić L, Porter J, Schmitz-Afonso I, Seo JB, Sommella E, van der Burgt YEM, Villette C, Witt M, Wittrig A, Wolff JJ, Easterling ML, Laukien FH, and Schmitt-Kopplin P
- Abstract
Ultrahigh resolution mass spectrometry (UHR-MS) coupled with direct infusion (DI) electrospray ionization offers a fast solution for accurate untargeted profiling. Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometers have been shown to produce a wealth of insights into complex chemical systems because they enable unambiguous molecular formula assignment even if the vast majority of signals is of unknown identity. Interlaboratory comparisons are required to apply this type of instrumentation in quality control (for food industry or pharmaceuticals), large-scale environmental studies, or clinical diagnostics. Extended comparisons employing different FT-ICR MS instruments with qualitative direct infusion analysis are scarce since the majority of detected compounds cannot be quantified. The extent to which observations can be reproduced by different laboratories remains unknown. We set up a preliminary study which encompassed a set of 17 laboratories around the globe, diverse in instrumental characteristics and applications, to analyze the same sets of extracts from commercially available standard human blood plasma and Standard Reference Material (SRM) for blood plasma (SRM1950), which were delivered at different dilutions or spiked with different concentrations of pesticides. The aim of this study was to assess the extent to which the outputs of differently tuned FT-ICR mass spectrometers, with different technical specifications, are comparable for setting the frames of a future DI-FT-ICR MS ring trial. We concluded that a cluster of five laboratories, with diverse instrumental characteristics, showed comparable and representative performance across all experiments, setting a reference to be used in a future ring trial on blood plasma.
- Published
- 2022
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11. Identification and Biochemical Characterization of Pyrrolidinediones as Novel Inhibitors of the Bacterial Enzyme MurA.
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Fathalla RK, Fröhner W, Bader CD, Fischer PD, Dahlem C, Chatterjee D, Mathea S, Kiemer AK, Arthanari H, Müller R, Abdel-Halim M, Ducho C, and Engel M
- Subjects
- Humans, Succinimides, Peptidoglycan, Anti-Bacterial Agents pharmacology, Bacteria metabolism, Enzyme Inhibitors chemistry, Fosfomycin chemistry, Alkyl and Aryl Transferases
- Abstract
To develop novel antibiotics, targeting the early steps of cell wall peptidoglycan biosynthesis seems to be a promising strategy that is still underutilized. MurA, the first enzyme in this pathway, is targeted by the clinically used irreversible inhibitor fosfomycin. However, mutations in its binding site can cause bacterial resistance. We herein report a series of novel reversible pyrrolidinedione-based MurA inhibitors that equally inhibit wild type (WT) MurA and the fosfomycin-resistant MurA C115D mutant, showing an additive effect with fosfomycin for the inhibition of WT MurA. For the most potent inhibitor 46 (IC
50 = 4.5 μM), the mode of inhibition was analyzed using native mass spectrometry and protein NMR spectroscopy. The compound class was nontoxic against human cells and highly stable in human S9 fraction, human plasma, and bacterial cell lysate. Taken together, this novel compound class might be further developed toward antibiotic drug candidates that inhibit cell wall synthesis.- Published
- 2022
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12. Sandacrabins - Structurally Unique Antiviral RNA Polymerase Inhibitors from a Rare Myxobacterium.
- Author
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Bader CD, Panter F, Garcia R, Tchesnokov EP, Haid S, Walt C, Spröer C, Kiefer AF, Götte M, Overmann J, Pietschmann T, and Müller R
- Subjects
- Antiviral Agents chemistry, Antiviral Agents pharmacology, DNA-Directed RNA Polymerases antagonists & inhibitors, Myxococcales chemistry, SARS-CoV-2 drug effects
- Abstract
Structure elucidation and total synthesis of five unprecedented terpenoid-alkaloids, the sandacrabins, are reported, alongside with the first description of their producing organism Sandaracinus defensii MSr10575, which expands the Sandaracineae family by only its second member. The genome sequence of S. defensii as presented in this study was utilized to identify enzymes responsible for sandacrabin formation, whereby dimethylbenzimidazol, deriving from cobalamin biosynthesis, was identified as key intermediate. Biological activity profiling revealed that all sandacrabins except congener A exhibit potent antiviral activity against the human pathogenic coronavirus HCoV229E in the three digit nanomolar range. Investigation of the underlying mode of action discloses that the sandacrabins inhibit the SARS-CoV-2 RNA-dependent RNA polymerase complex, highlighting them as structurally distinct non-nucleoside RNA synthesis inhibitors. The observed segregation between cell toxicity at higher concentrations and viral inhibition opens the possibility for their medicinal chemistry optimization towards selective inhibitors., (© 2022 The Authors. Chemistry - A European Journal published by Wiley-VCH GmbH.)
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- 2022
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13. Improved broad-spectrum antibiotics against Gram-negative pathogens via darobactin biosynthetic pathway engineering.
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Groß S, Panter F, Pogorevc D, Seyfert CE, Deckarm S, Bader CD, Herrmann J, and Müller R
- Abstract
The development of new antibiotics is imperative to fight increasing mortality rates connected to infections caused by multidrug-resistant (MDR) bacteria. In this context, Gram-negative pathogens listed in the WHO priority list are particularly problematic. Darobactin is a ribosomally produced and post-translationally modified bicyclic heptapeptide antibiotic selectively killing Gram-negative bacteria by targeting the outer membrane protein BamA. The native darobactin A producer Photorhabdus khanii HGB1456 shows very limited production under laboratory cultivation conditions. Herein, we present the design and heterologous expression of a synthetically engineered darobactin biosynthetic gene cluster (BGC) in Escherichia coli to reach an average darobactin A production titre of 13.4 mg L
-1 . Rational design of darA variants, encoding the darobactin precursor peptide with altered core sequences, resulted in the production of 13 new 'non-natural' darobactin derivatives and 4 previously hypothetical natural darobactins. One of the non-natural compounds, darobactin 9, was more potent than darobactin A, and showed significantly improved activity especially against Pseudomonas aeruginosa (0.125 μg mL-1 ) and Acinetobacter baumannii (1-2 μg mL-1 ). Importantly, it also displayed superior activity against MDR clinical isolates of E . coli (1-2 μg mL-1 ) and Klebsiella pneumoniae (1-4 μg mL-1 ). Independent deletions of genes from the darobactin BGC showed that only darA and darE , encoding a radical forming S -adenosyl-l-methionine-dependent enzyme, are required for darobactin formation. Co-expression of two additional genes associated with the BGCs in hypothetical producer strains identified a proteolytic detoxification mechanism as a potential self-resistance strategy in native producers. Taken together, we describe a versatile heterologous darobactin platform allowing the production of unprecedented active derivatives in good yields, and we provide first experimental evidence for darobactin biosynthesis processes., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)- Published
- 2021
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14. Search for the Active Ingredients from a 2-Aminothiazole DMSO Stock Solution with Antimalarial Activity.
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Ropponen HK, Bader CD, Diamanti E, Illarionov B, Rottmann M, Fischer M, Witschel M, Müller R, and Hirsch AKH
- Subjects
- Antimalarials chemical synthesis, Antimalarials chemistry, Dose-Response Relationship, Drug, Molecular Structure, Parasitic Sensitivity Tests, Solutions, Structure-Activity Relationship, Thiazoles chemical synthesis, Thiazoles chemistry, Antimalarials pharmacology, Dimethyl Sulfoxide chemistry, Plasmodium falciparum drug effects, Thiazoles pharmacology
- Abstract
Chemical decomposition of DMSO stock solutions is a common incident that can mislead biological screening campaigns. Here, we share our case study of 2-aminothiazole 1, originating from an antimalarial class that undergoes chemical decomposition in DMSO at room temperature. As previously measured biological activities observed against Plasmodium falciparum NF54 and for the target enzyme PfIspE were not reproducible for a fresh batch, we tackled the challenge to understand where the activity originated from. Solvent- and temperature-dependent studies using HRMS and NMR spectroscopy to monitor the decomposition led to the isolation and in vitro evaluation of several fractions against PfIspE. After four days of decomposition, we successfully isolated the oxygenated and dimerised compounds using SFC purification and correlated the observed activities to them. Due to the unstable nature of the two isolates, it is likely that they undergo further decomposition contributing to the overall instability of the compound., (© 2021 The Authors. ChemMedChem published by Wiley-VCH GmbH.)
- Published
- 2021
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15. Sesbanimide R, a Novel Cytotoxic Polyketide Produced by Magnetotactic Bacteria.
- Author
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Awal RP, Haack PA, Bader CD, Riese CN, Schüler D, and Müller R
- Subjects
- Bacterial Proteins classification, Bacterial Proteins metabolism, Biological Products metabolism, Phylogeny, Bacterial Proteins biosynthesis, Biosynthetic Pathways, Magnetospirillum metabolism, Polyketides metabolism, Secondary Metabolism
- Abstract
Genomic information from various magnetotactic bacteria suggested that besides their common ability to form magnetosomes, they potentially also represent a source of bioactive natural products. By using targeted deletion and transcriptional activation, we connected a large biosynthetic gene cluster (BGC) of the trans -acyltransferase polyketide synthase ( trans -AT PKS) type to the biosynthesis of a novel polyketide in the alphaproteobacterium Magnetospirillum gryphiswaldense Structure elucidation by mass spectrometry and nuclear magnetic resonance spectroscopy (NMR) revealed that this secondary metabolite resembles sesbanimides, which were very recently reported from other taxa. However, sesbanimide R exhibits an additional arginine moiety the presence of which reconciles inconsistencies in the previously proposed sesbanimide biosynthesis pathway observed when comparing the chemical structure and the potential biochemistry encoded in the BGC. In contrast to the case with sesbanimides D, E, and F, we were able to assign the stereocenter of the arginine moiety experimentally and two of the remaining three stereocenters by predictive biosynthetic tools. Sesbanimide R displayed strong cytotoxic activity against several carcinoma cell lines. IMPORTANCE The findings of this study contribute a new secondary metabolite member to the glutarimide-containing polyketides. The determined structure of sesbanimide R correlates with its cytotoxic bioactivity, characteristic for members of this family. Sesbanimide R represents the first natural product isolated from magnetotactic bacteria and identifies this highly diverse group as a so-far-untapped source for the future discovery of novel secondary metabolites., (Copyright © 2021 Awal et al.)
- Published
- 2021
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16. The Sandarazols are Cryptic and Structurally Unique Plasmid-Encoded Toxins from a Rare Myxobacterium*.
- Author
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Panter F, Bader CD, and Müller R
- Subjects
- Molecular Structure, Multigene Family, Myxococcales metabolism, Toxins, Biological genetics, Toxins, Biological metabolism, Myxococcales chemistry, Toxins, Biological chemistry
- Abstract
Herein, we describe a new plasmid found in Sandaracinus sp. MSr10575 named pSa001 spanning 209.7 kbp that harbors a cryptic secondary metabolite biosynthesis gene cluster (BGC). Activation of this BGC by homologous-recombination-mediated exchange of the native promoter sequence against a vanillate inducible system led to the production and subsequent isolation and structure elucidation of novel secondary metabolites, the sandarazols A-G. The sandarazols contain intriguing structural features and very reactive functional groups such as an α-chlorinated ketone, an epoxyketone, and a (2R)-2-amino-3-(N,N-dimethylamino)-propionic acid building block. In-depth investigation of the underlying biosynthetic machinery led to a concise biosynthetic model for the new compound family, including several uncommon biosynthetic steps. The chlorinated congener sandarazol C shows an IC
50 value of 0.5 μm against HCT 116 cells and a MIC of 14 μm against Mycobacterium smegmatis, which points at the sandarazols' potential function as defensive secondary metabolites or toxins., (© 2021 The Authors. Angewandte Chemie International Edition published by Wiley-VCH GmbH.)- Published
- 2021
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17. Synergizing the potential of bacterial genomics and metabolomics to find novel antibiotics.
- Author
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Panter F, Bader CD, and Müller R
- Abstract
Antibiotic development based on natural products has faced a long lasting decline since the 1970s, while both the speed and the extent of antimicrobial resistance (AMR) development have been severely underestimated. The discovery of antimicrobial natural products of bacterial and fungal origin featuring new chemistry and previously unknown mode of actions is increasingly challenged by rediscovery issues. Natural products that are abundantly produced by the corresponding wild type organisms often featuring strong UV signals have been extensively characterized, especially the ones produced by extensively screened microbial genera such as streptomycetes. Purely synthetic chemistry approaches aiming to replace the declining supply from natural products as starting materials to develop novel antibiotics largely failed to provide significant numbers of antibiotic drug leads. To cope with this fundamental issue, microbial natural products science is being transformed from a 'grind-and-find' study to an integrated approach based on bacterial genomics and metabolomics. Novel technologies in instrumental analytics are increasingly employed to lower detection limits and expand the space of detectable substance classes, while broadening the scope of accessible and potentially bioactive natural products. Furthermore, the almost exponential increase in publicly available bacterial genome data has shown that the biosynthetic potential of the investigated strains by far exceeds the amount of detected metabolites. This can be judged by the discrepancy between the number of biosynthetic gene clusters (BGC) encoded in the genome of each microbial strain and the number of secondary metabolites actually detected, even when considering the increased sensitivity provided by novel analytical instrumentation. In silico annotation tools for biosynthetic gene cluster classification and analysis allow fast prioritization in BGC-to-compound workflows, which is highly important to be able to process the enormous underlying data volumes. BGC prioritization is currently accompanied by novel molecular biology-based approaches to access the so-called orphan BGCs not yet correlated with a secondary metabolite. Integration of metabolomics, in silico genomics and molecular biology approaches into the mainstream of natural product research will critically influence future success and impact the natural product field in pharmaceutical, nutritional and agrochemical applications and especially in anti-infective research., Competing Interests: There are no conflicts of interest to declare., (This journal is © The Royal Society of Chemistry.)
- Published
- 2021
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18. Expanding the Scope of Detectable Microbial Natural Products by Complementary Analytical Methods and Cultivation Systems.
- Author
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Bader CD, Haack PA, Panter F, Krug D, and Müller R
- Subjects
- Biological Products chemistry, Chromatography, Liquid, Mass Spectrometry, Secondary Metabolism, Biological Products analysis, Metabolomics methods, Myxococcales chemistry
- Abstract
Recent advances in genome sequencing have unveiled a large discrepancy between the genome-encoded capacity of microorganisms to produce secondary metabolites and the number detected. In this work, a two-platform mass spectrometry analysis for the comprehensive secondary metabolomics characterization of nine myxobacterial strains, focusing on extending the range of detectable secondary metabolites by diversifying analytical methods and cultivation conditions, is presented. Direct infusion measurements of crude extracts on a Fourier transform ion cyclotron resonance mass spectrometer are compared to a time-of-flight device coupled to liquid chromatography measurements. Both methods are successful in detecting known metabolites, whereas statistical analysis of unknowns highlights their complementarity: Strikingly, 82-99% of molecular features detected with one setup were not detectable with the other. Metabolite profile differences from our set of strains grown in liquid culture versus their swarming colonies on agar plates were evaluated. The detection of up to 96% more molecular features when both liquid and plate cultures were analyzed translates into increased chances to identify new secondary metabolites. Discrimination between primary and secondary metabolism in combination with GNPS molecular networking revealed strain Mx3 as particularly promising for the isolation of novel secondary metabolites among the nine strains investigated in this study.
- Published
- 2021
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19. Supercritical Fluid Extraction Enhances Discovery of Secondary Metabolites from Myxobacteria.
- Author
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Bader CD, Neuber M, Panter F, Krug D, and Müller R
- Subjects
- Anti-Bacterial Agents chemistry, Anti-Bacterial Agents pharmacology, Myxococcales drug effects, Solvents chemistry, Time Factors, Chromatography, Supercritical Fluid methods, Myxococcales metabolism
- Abstract
Supercritical fluid extraction (SFE) is widely used for the isolation of natural products from plants, but its application in efforts to identify structurally and physicochemically often dissimilar microbial natural products is limited to date. In this study, we evaluated the impact of SFE on the extractability of myxobacterial secondary metabolites, aiming to improve the prospects of discovering novel natural products. We investigated the influence of different co-solvents on the extraction efficiency of secondary metabolites from three myxobacterial strains and the antimicrobial activity profiles of the corresponding extracts. For each known secondary metabolite, we found extraction conditions using SFE leading to superior yields in the extracts compared to conventional solvent extraction. Compounds with a log P higher than 3 showed the best extraction efficiency using 20% EtOAc as a co-solvent, whereas compounds with log P values lower than 3 were better extractable using more polar co-solvents such as MeOH. Extracts generated with SFE showed increased antimicrobial activities including the presence of activities not explained by known myxobacterial secondary metabolites, highlighting the advantage of SFE for bioactivity-guided isolation. Moreover, non-targeted metabolomics analysis revealed a group of chlorinated metabolites produced by the well-studied model myxobacterium Myxococcus xanthus DK1622, which were not accessible previously due to their low concentration in conventional extracts. The enriched SF extracts were used for isolation and subsequent structure elucidation of chloroxanthic acid A as the founding member of a novel secondary metabolite family. Our findings encourage the increased utilization of SFE as a part of future screening workflows of microbial natural products.
- Published
- 2020
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- View/download PDF
20. In depth natural product discovery - Myxobacterial strains that provided multiple secondary metabolites.
- Author
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Bader CD, Panter F, and Müller R
- Subjects
- Actinobacteria, Biological Products, Genome, Bacterial, Multigene Family, Myxococcales
- Abstract
In recognition of many microorganisms ability to produce a variety of secondary metabolites in parallel, Zeeck and coworkers introduced the term "OSMAC" (one strain many compounds) around the turn of the century. Since then, additional efforts focused on the systematic characterization of a single bacterial species ability to form multiple secondary metabolite scaffolds. With the beginning of the genomic era mainly initiated by a dramatic reduction of sequencing costs, investigations of the genome encoded biosynthetic potential and especially the exploitation of biosynthetic gene clusters of undefined function gained attention. This was seen as a novel means to extend range and diversity of bacterial secondary metabolites. Genome analyses showed that even for well-studied bacterial strains, like the myxobacterium Myxococcus xanthus DK1622, many biosynthetic gene clusters are not yet assigned to their corresponding hypothetical secondary metabolites. In contrast to the results from emerging genome and metabolome mining techniques that show the large untapped biosynthetic potential per strain, many newly isolated bacterial species are still used for the isolation of only one target compound class and successively abandoned in the sense that no follow up studies are published from the same species. This work provides an overview about myxobacterial bacterial strains, from which not just one but multiple different secondary metabolite classes were successfully isolated. The underlying methods used for strain prioritization and natural product discovery such as biological characterization of crude extracts against a panel of pathogens, in-silico prediction of secondary metabolite abundance from genome data and state of the art instrumental analytics required for new natural product scaffold discovery in comparative settings are summarized and classified according to their output. Furthermore, for each approach selected studies performed with actinobacteria are shown to underline especially innovative methods used for natural product discovery., Competing Interests: Declaration of Competing Interest The authors declare no conflict of interest. 2019 by the authors. Submitted for possible open access publication under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/)., (Copyright © 2019 Elsevier Inc. All rights reserved.)
- Published
- 2020
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21. Synthesis of New Cyclomarin Derivatives and Their Biological Evaluation towards Mycobacterium Tuberculosis and Plasmodium Falciparum.
- Author
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Kiefer A, Bader CD, Held J, Esser A, Rybniker J, Empting M, Müller R, and Kazmaier U
- Subjects
- Anti-Bacterial Agents pharmacology, Antimalarials pharmacology, Inhibitory Concentration 50, Oligopeptides chemistry, Oligopeptides pharmacology, Peptides, Cyclic chemistry, Stereoisomerism, Structure-Activity Relationship, Anti-Bacterial Agents chemical synthesis, Antimalarials chemical synthesis, Mycobacterium tuberculosis drug effects, Peptides, Cyclic pharmacology, Plasmodium falciparum drug effects
- Abstract
Cyclomarins are highly potent antimycobacterial and antiplasmodial cyclopeptides isolated from a marine bacterium (Streptomyces sp.). Previous studies have identified the target proteins and elucidated a novel mode of action, however there are currently only a few studies examining the structure-activity relationship (SAR) for both pathogens. Herein, we report the synthesis and biological evaluation of 17 novel desoxycyclomarin-inspired analogues. Optimization via side chain modifications of the non-canonical amino acids led to potent lead structures for each pathogen., (© 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)
- Published
- 2019
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22. Concepts and Methods to Access Novel Antibiotics from Actinomycetes.
- Author
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Hug JJ, Bader CD, Remškar M, Cirnski K, and Müller R
- Abstract
Actinomycetes have been proven to be an excellent source of secondary metabolites for more than half a century. Exhibiting various bioactivities, they provide valuable approved drugs in clinical use. Most microorganisms are still untapped in terms of their capacity to produce secondary metabolites, since only a small fraction can be cultured in the laboratory. Thus, improving cultivation techniques to extend the range of secondary metabolite producers accessible under laboratory conditions is an important first step in prospecting underexplored sources for the isolation of novel antibiotics. Currently uncultured actinobacteria can be made available by bioprospecting extreme or simply habitats other than soil. Furthermore, bioinformatic analysis of genomes reveals most producers to harbour many more biosynthetic gene clusters than compounds identified from any single strain, which translates into a silent biosynthetic potential of the microbial world for the production of yet unknown natural products. This review covers discovery strategies and innovative methods recently employed to access the untapped reservoir of natural products. The focus is the order of actinomycetes although most approaches are similarly applicable to other microbes. Advanced cultivation methods, genomics- and metagenomics-based approaches, as well as modern metabolomics-inspired methods are highlighted to emphasise the interplay of different disciplines to improve access to novel natural products.
- Published
- 2018
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23. Bipolar disorder not otherwise specified in relation to the bipolar spectrum.
- Author
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Bader CD and Dunner DL
- Subjects
- Adolescent, Adult, Aged, Analysis of Variance, Bipolar Disorder psychology, Chi-Square Distribution, Diagnosis, Differential, Diagnostic and Statistical Manual of Mental Disorders, Female, Humans, Male, Medical History Taking, Middle Aged, Retrospective Studies, Severity of Illness Index, Suicide, Attempted statistics & numerical data, Bipolar Disorder classification, Bipolar Disorder epidemiology, Bipolar Disorder physiopathology
- Abstract
Background: The purpose of this study was to determine the clinical characteristics of patients who are diagnosed with bipolar disorder not otherwise specified (BPD NOS) and who are considered to represent part of the bipolar spectrum. The lifetime prevalence of BPD in the general population may be as high as 6% when the full spectrum of bipolar disorders is accounted for. Correct identification of true bipolar patients in clinical settings may result in more appropriate treatment. Our hypothesis was that patients with BPD NOS would be more similar to other bipolar patients than major depressive disorder (MDD) patients in terms of age of onset, history of suicidal behavior and family history of BPD., Methods: We conducted a retrospective chart review to extract and analyze data on the family history, disease course and clinical characteristics of 305 bipolar disorder I (BPD I), bipolar disorder II (BPD II), bipolar disorder not otherwise specified (BPD NOS) or major depressive disorder (MDD) patients who were then grouped by diagnosis for analysis. Nominal variables were compared between groups using chi-square tests and ANOVA was used to compare means between groups for continuous variables. Significant F values were followed by independent-samples t-tests., Results: Patients with BPD I, BPD II and BPD NOS were all found to have a significantly earlier mean age of onset of depression than MDD patients. A significantly higher incidence of bipolar illness in a first-degree relative was found in all BPD groups (27-32%) compared with MDD patients (11%). Only the BPD I group had a significantly higher rate of suicide attempts (42%), compared with the BPD NOS (17%) and MDD recurrent (16%) groups., Conclusions: Our data support the conclusions of others that an early age of onset and a positive family history of bipolar illness are associated not only with BPD I and II but also with 'softer' forms of bipolar illness, which DSM-IV classifies as BPD NOS and the current literature refers to as a category of 'bipolar spectrum disorder', albeit with varying proposed definitions and diagnostic criteria. Suicide attempt history may be more useful in identifying the severity of illness than distinguishing the bipolar spectrum from depressive disorders. Further research is needed to clearly define the boundaries of the bipolar spectrum.
- Published
- 2007
- Full Text
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