1
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Paquette AR, Brazeau-Henrie JT, Boddy CN. Thioesterases as tools for chemoenzymatic synthesis of macrolactones. Chem Commun (Camb) 2024; 60:3379-3388. [PMID: 38456624 DOI: 10.1039/d4cc00401a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
Macrocycles are a key functional group that can impart unique properties into molecules. Their synthesis has led to the development of many outstanding chemical methodologies and yet still remains challenging. Thioesterase (TE) domains are frequently responsible for macrocyclization in natural product biosynthesis and provide unique strengths for the enzymatic synthesis of macrocycles. In this feature article, we describe our work to characterize the substrate selectivity of TEs and to use these enzymes as biocatalysts. Our efforts have shown that the linear thioester activated substrates are loaded on TEs with limited substrate selectivity to generate acyl-enzyme intermediates. We show that cyclization of the acyl-enzyme intermediates can be highly selective, with competing hydrolysis of the acyl-enzyme intermediates. The mechanisms controlling TE-mediated macrocyclization versus hydrolysis are a significant unsolved problem in TE biochemistry. The potential of TEs as biocatalysts was demonstrated by using them in the chemoenzymatic total synthesis of macrocyclic depsipeptide natural products. This article highlights the strengths and potential of TEs as biocatalysts as well as their limitations, opening exciting research opportunities including TE engineering to optimize these powerful biocatalysts.
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Affiliation(s)
- André R Paquette
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada K1N 6N5.
| | - Jordan T Brazeau-Henrie
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada K1N 6N5.
| | - Christopher N Boddy
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada K1N 6N5.
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2
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Konno S, Tanaka M, Mizuguchi T, Toyokai H, Taguchi A, Taniguchi A, Hayashi Y. Peptide mixed phosphonates for covalent complex formation with thioesterases in nonribosomal peptide synthetases. J Pept Sci 2024; 30:e3532. [PMID: 37423887 DOI: 10.1002/psc.3532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/11/2023]
Abstract
Natural macrocyclic peptides derived from microorganisms are medicinal resources that are important for the development of new therapeutic agents. Most of these molecules are biosynthesized by a nonribosomal peptide synthetase (NRPS). The thioesterase (TE) domain in NRPS is responsible for the macrocyclization of mature linear peptide thioesters in a final biosynthetic step. NRPS-TEs can cyclize synthetic linear peptide analogs and can be utilized as biocatalysts for the preparation of natural product derivatives. Although the structures and enzymatic activities of TEs have been investigated, the substrate recognition and substrate-TE interaction during the macrocyclization step are still unknown. To understand the TE-mediated macrocyclization, here we report the development of a substrate-based analog with mixed phosphonate warheads, which can react irreversibly with the Ser residue at the active site of TE. We have demonstrated that the tyrocidine A linear peptide (TLP) with a p-nitrophenyl phosphonate (PNP) enables efficient complex formation with tyrocidine synthetase C (TycC)-TE containing tyrocidine synthetase.
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Affiliation(s)
- Sho Konno
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Miyu Tanaka
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Tomoe Mizuguchi
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Haruka Toyokai
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Akihiro Taguchi
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Atsuhiko Taniguchi
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Yoshio Hayashi
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
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3
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Hennrich O, Weinmann L, Kulik A, Harms K, Klahn P, Youn JW, Surup F, Mast Y. Biotransformation-coupled mutasynthesis for the generation of novel pristinamycin derivatives by engineering the phenylglycine residue. RSC Chem Biol 2023; 4:1050-1063. [PMID: 38033732 PMCID: PMC10685826 DOI: 10.1039/d3cb00143a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 10/06/2023] [Indexed: 12/02/2023] Open
Abstract
Streptogramins are the last line of defense antimicrobials with pristinamycin as a representative substance used as therapeutics against highly resistant pathogenic bacteria. However, the emergence of (multi)drug-resistant pathogens renders these valuable antibiotics useless; making it necessary to derivatize compounds for new compound characteristics, which is often difficult by chemical de novo synthesis due to the complex nature of the molecules. An alternative to substance derivatization is mutasynthesis. Herein, we report about a mutasynthesis approach, targeting the phenylglycine (Phg) residue for substance derivatization, a pivotal component of streptogramin antibiotics. Mutasynthesis with halogenated Phg(-like) derivatives altogether led to the production of two new derivatized natural compounds, as there are 6-chloropristinamycin I and 6-fluoropristinamycin I based on LC-MS/MS analysis. 6-Chloropristinamycin I and 6-fluoropristinamycin I were isolated by preparative HPLC, structurally confirmed using NMR spectroscopy and tested for antimicrobial bioactivity. In a whole-cell biotransformation approach using an engineered E. coli BL21(DE3) pET28-hmo/pACYC-bcd-gdh strain, Phg derivatives were generated fermentatively. Supplementation with the E. coli biotransformation fermentation broth containing 4-fluorophenylglycine to the pristinamycin mutasynthesis strain resulted in the production of 6-fluoropristinamycin I, demonstrating an advanced level of mutasynthesis.
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Affiliation(s)
- Oliver Hennrich
- Department Bioresources for Bioeconomy and Health Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B 38124 Braunschweig Germany
| | - Leoni Weinmann
- Institute of Microbiology, University Stuttgart, Allmandring 31 D-70569 Stuttgart Germany
| | - Andreas Kulik
- Department Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, Faculty of Science, University of Tübingen, Auf der Morgenstelle 28 D-72076 Tübingen Germany
| | - Karen Harms
- Microbial Drugs Department, Helmholtz-Centre for Infection Research 38124 Braunschweig Germany
| | - Philipp Klahn
- Division of Organic and Medicinal Chemistry, Department of Chemistry and Molecular Biology, University of Gothenburg, Kemigården 4 412 96 Göteborg Sweden
- Centre of Antimicrobial Resistance Research in Gothenburg (CARe) Gothenburg Sweden
| | - Jung-Won Youn
- Institute of Microbiology, University Stuttgart, Allmandring 31 D-70569 Stuttgart Germany
| | - Frank Surup
- Microbial Drugs Department, Helmholtz-Centre for Infection Research 38124 Braunschweig Germany
| | - Yvonne Mast
- Department Bioresources for Bioeconomy and Health Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B 38124 Braunschweig Germany
- Technische Universität Braunschweig, Institut für Mikrobiologie, Rebenring 56 38106 Braunschweig Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen Tübingen Germany
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4
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Affiliation(s)
- Rustam Aminov
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, United Kingdom
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5
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Jing X, Jin K. A gold mine for drug discovery: Strategies to develop cyclic peptides into therapies. Med Res Rev 2019; 40:753-810. [PMID: 31599007 DOI: 10.1002/med.21639] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/05/2019] [Accepted: 09/26/2019] [Indexed: 12/19/2022]
Abstract
As a versatile therapeutic modality, peptides attract much attention because of their great binding affinity, low toxicity, and the capability of targeting traditionally "undruggable" protein surfaces. However, the deficiency of cell permeability and metabolic stability always limits the success of in vitro bioactive peptides as drug candidates. Peptide macrocyclization is one of the most established strategies to overcome these limitations. Over the past decades, more than 40 cyclic peptide drugs have been clinically approved, the vast majority of which are derived from natural products. The de novo discovered cyclic peptides on the basis of rational design and in vitro evolution, have also enabled the binding with targets for which nature provides no solutions. The current review summarizes different classes of cyclic peptides with diverse biological activities, and presents an overview of various approaches to develop cyclic peptide-based drug candidates, drawing upon series of examples to illustrate each strategy.
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Affiliation(s)
- Xiaoshu Jing
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Kang Jin
- Department of Medicinal Chemistry, School of Pharmacy, Shandong University, Jinan, Shandong, China
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6
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Vosloo J, Snoep J, Rautenbach M. Modelling the variable incorporation of aromatic amino acids in the tyrocidines and analogous cyclodecapeptides. J Appl Microbiol 2019; 127:1665-1676. [DOI: 10.1111/jam.14430] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 08/02/2019] [Accepted: 08/18/2019] [Indexed: 11/28/2022]
Affiliation(s)
- J.A. Vosloo
- Department of Biochemistry Faculty of Science Stellenbosch University Stellenbosch South Africa
| | - J.L. Snoep
- Department of Biochemistry Faculty of Science Stellenbosch University Stellenbosch South Africa
- Molecular Cell Physiology Vrije Universiteit Amsterdam HV Amsterdam The Netherlands
- MIB University of Manchester Manchester UK
| | - M. Rautenbach
- Department of Biochemistry Faculty of Science Stellenbosch University Stellenbosch South Africa
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7
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Drug combinations: a strategy to extend the life of antibiotics in the 21st century. Nat Rev Microbiol 2019; 17:141-155. [PMID: 30683887 DOI: 10.1038/s41579-018-0141-x] [Citation(s) in RCA: 447] [Impact Index Per Article: 89.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 11/22/2018] [Indexed: 01/03/2023]
Abstract
Antimicrobial resistance threatens a resurgence of life-threatening bacterial infections and the potential demise of many aspects of modern medicine. Despite intensive drug discovery efforts, no new classes of antibiotics have been developed into new medicines for decades, in large part owing to the stringent chemical, biological and pharmacological requisites for effective antibiotic drugs. Combinations of antibiotics and of antibiotics with non-antibiotic activity-enhancing compounds offer a productive strategy to address the widespread emergence of antibiotic-resistant strains. In this Review, we outline a theoretical and practical framework for the development of effective antibiotic combinations.
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8
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Aminov R. History of antimicrobial drug discovery: Major classes and health impact. Biochem Pharmacol 2016; 133:4-19. [PMID: 27720719 DOI: 10.1016/j.bcp.2016.10.001] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 10/04/2016] [Indexed: 12/12/2022]
Abstract
The introduction of antibiotics into clinical practice revolutionized the treatment and management of infectious diseases. Before the introduction of antibiotics, these diseases were the leading cause of morbidity and mortality in human populations. This review presents a brief history of discovery of the main antimicrobial classes (arsphenamines, β-lactams, sulphonamides, polypeptides, aminoglycosides, tetracyclines, amphenicols, lipopeptides, macrolides, oxazolidinones, glycopeptides, streptogramins, ansamycins, quinolones, and lincosamides) that have changed the landscape of contemporary medicine. Given within a historical timeline context, the review discusses how the introduction of certain antimicrobial classes affected the morbidity and mortality rates due to bacterial infectious diseases in human populations. Problems of resistance to antibiotics of different classes are also extensively discussed.
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Affiliation(s)
- Rustam Aminov
- School of Medicine and Dentistry, University of Aberdeen, Aberdeen AB25 2ZD, United Kingdom.
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9
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Horsman ME, Hari TPA, Boddy CN. Polyketide synthase and non-ribosomal peptide synthetase thioesterase selectivity: logic gate or a victim of fate? Nat Prod Rep 2016; 33:183-202. [DOI: 10.1039/c4np00148f] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thioesterases (TEs) are product offloading enzymes from FAS, PKS, and NRPS complexes. We review the diversity, structure, and mechanism of PKS and NRPS TEs and analyze TE loading and release steps as possible logic gates with a view to predicting TE function in new pathways.
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Affiliation(s)
- Mark E. Horsman
- Department of chemistry
- Centre for Catalysis Research and Innovation
- University of Ottawa
- Canada
| | - Taylor P. A. Hari
- Department of chemistry
- Centre for Catalysis Research and Innovation
- University of Ottawa
- Canada
| | - Christopher N. Boddy
- Department of chemistry
- Centre for Catalysis Research and Innovation
- University of Ottawa
- Canada
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10
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Tevyashova AN, Olsufyeva EN, Preobrazhenskaya MN. Design of dual action antibiotics as an approach to search for new promising drugs. RUSSIAN CHEMICAL REVIEWS 2015. [DOI: 10.1070/rcr4448] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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11
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Makobongo MO, Einck L, Peek RM, Merrell DS. In vitro characterization of the anti-bacterial activity of SQ109 against Helicobacter pylori. PLoS One 2013; 8:e68917. [PMID: 23935905 PMCID: PMC3723868 DOI: 10.1371/journal.pone.0068917] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 06/04/2013] [Indexed: 12/29/2022] Open
Abstract
The most evident challenge to treatment of Helicobacter pylori, a bacterium responsible for gastritis, peptic ulcers and gastric cancer, is the increasing rate of resistance to all currently used therapeutic antibiotics. Thus, the development of novel therapies is urgently required. N-geranyl-N'-(2-adamantyl) ethane-1, 2-diamine (SQ109) is an ethylene diamine-based antitubercular drug that is currently in clinical trials for the treatment of tuberculosis (TB). Previous pharmacokinetic studies of SQ109 revealed that persistently high concentrations of SQ109 remain in the stomach 4 hours post oral administration in rats. This finding, combined with the need for new anti-Helicobacter therapies, prompted us to define the in vitro efficacy of SQ109 against H. pylori. Liquid broth micro-dilution was used for susceptibility studies to determine the antimicrobial activity of SQ109 against a total of 6 laboratory strains and 20 clinical isolates of H. pylori; the clinical isolates included a multi-drug resistant strain. All strains tested were susceptible to SQ109 with MIC and MBC ranges of 6-10 µM and 50-60 µM, respectively. SQ109 killing kinetics were concentration- and time-dependent. SQ109 killed H. pylori in 8-10 h at 140 µM (2MBCs) or 4-6 h at 200 µM (~3MBCs). Importantly, though the kinetics of killing were altered, SQ109 retained potent bactericidal activity against H. pylori at low pH. Additionally, SQ109 demonstrated robust thermal stability and was effective at killing slow growing or static bacteria. In fact, pretreatment of cultures with a bacteriostatic concentration of chloramphenicol (Cm) synergized the effects of typically bacteriostatic concentrations of SQ109 to the level of five-logs of bacterial killing. A molar-to-molar comparison of the efficacy of SQ109 as compared to metronidazole (MTZ), amoxicillin (AMX), rifampicin (RIF) and clarithromycin (CLR), revealed that SQ109 was superior to MTZ, AMX and RIF but not to CLR. Finally, the frequency of resistance to SQ109 was low and electron microscopy studies revealed that SQ109 interacted with bacterial inner membrane and cytoplasmic content(s). Collectively, our in vitro data demonstrate that SQ109 is an effective monotherapy against susceptible and multi-drug resistant strains of H. pylori and may be useful alone or in combination with other antibiotics for development as a new class of anti-Helicobacter drugs.
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Affiliation(s)
- Morris O. Makobongo
- Department of Microbiology and Immunology, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Leo Einck
- Sequella, Inc., Rockville, Maryland, United States of America
| | - Richard M. Peek
- Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - D. Scott Merrell
- Department of Microbiology and Immunology, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
- * E-mail:
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12
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The oligo-acyl lysyl antimicrobial peptide C₁₂K-2β₁₂ exhibits a dual mechanism of action and demonstrates strong in vivo efficacy against Helicobacter pylori. Antimicrob Agents Chemother 2011; 56:378-90. [PMID: 22064541 DOI: 10.1128/aac.00689-11] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Helicobacter pylori has developed antimicrobial resistance to virtually all current antibiotics. Thus, there is a pressing need to develop new anti-H. pylori therapies. We recently described a novel oligo-acyl-lysyl (OAK) antimicrobial peptidomimetic, C(12)K-2β(12), that shows potent in vitro bactericidal activity against H. pylori. Herein, we define the mechanism of action and evaluate the in vivo efficacy of C(12)K-2β(12) against H. pylori after experimental infection of Mongolian gerbils. We demonstrate using a 1-N-phenylnaphthylamine (fluorescent probe) uptake assay and electron microscopy that C(12)K-2β(12) rapidly permeabilizes the bacterial membrane and creates pores that cause bacterial cell lysis. Furthermore, using nucleic acid binding assays, Western blots, and confocal microscopy, we show that C(12)K-2β(12) can cross the bacterial membranes into the cytoplasm and tightly bind to bacterial DNA, RNA, and proteins, a property that may result in inhibition of enzymatic activities and macromolecule synthesis. To define the in vivo efficacy of C(12)K-2β(12), H. pylori-infected gerbils were orogastrically treated with increasing doses and concentrations of C(12)K-2β(12) 1 day or 1 week postinfection. The efficacy of C(12)K-2β(12) was strongest in animals that received the largest number of doses at the highest concentration, indicating dose-dependent activity of the peptide (P < 0.001 by analysis of variance [ANOVA]) regardless of the timing of the treatment with C(12)K-2β(12). Overall, our results demonstrate a dual mode of action of C(12)K-2β(12) against the H. pylori membrane and cytoplasmic components. Moreover, and consistent with the previously reported in vitro efficacy, C(12)K-2β(12) shows significant in vivo efficacy against H. pylori when used as monotherapy. Therefore, OAK peptides may be a valuable resource for therapeutic treatment of H. pylori infection.
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13
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Fabbretti A, Gualerzi CO, Brandi L. How to cope with the quest for new antibiotics. FEBS Lett 2011; 585:1673-81. [PMID: 21513713 DOI: 10.1016/j.febslet.2011.04.029] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 04/11/2011] [Accepted: 04/12/2011] [Indexed: 10/18/2022]
Abstract
Since their introduction in therapy, antibiotics have played an essential role in human society, saving millions of lives, allowing safe surgery, organ transplants, cancer therapy. Antibiotics have also helped to elucidate several biological mechanisms and boosted the birth and growth of pharmaceutical companies, generating profits and royalties. The golden era of antibiotics and the scientific and economical drive of big pharma towards these molecules is long gone, but the need for effective antibiotics is increased as their pipelines dwindle and multi-resistant pathogenic strains spread. Here we outline some strategies that could help meet this emergency and list promising new targets.
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Affiliation(s)
- Attilio Fabbretti
- Laboratory of Genetics, Department of Biosciences and Biotechnology, University of Camerino, Camerino (MC), Italy
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14
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Kopp F, Marahiel MA. Where chemistry meets biology: the chemoenzymatic synthesis of nonribosomal peptides and polyketides. Curr Opin Biotechnol 2007; 18:513-20. [DOI: 10.1016/j.copbio.2007.09.009] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2007] [Revised: 09/21/2007] [Accepted: 09/24/2007] [Indexed: 11/26/2022]
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15
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Marques MA, Citron DM, Wang CC. Development of Tyrocidine A analogues with improved antibacterial activity. Bioorg Med Chem 2007; 15:6667-77. [PMID: 17728134 PMCID: PMC2706120 DOI: 10.1016/j.bmc.2007.08.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2007] [Revised: 07/05/2007] [Accepted: 08/07/2007] [Indexed: 11/25/2022]
Abstract
The development of new antibacterial therapeutic agents capable of halting microbial resistance is a chief pursuit in clinical medicine. Classes of antibiotics that target and destroy bacterial membranes are attractive due to the decreased likelihood that bacteria will be able to generate resistance to this mechanism. The amphipathic cyclic decapeptide, Tyrocidine A, is a model for this class of antibiotics. Tyrocidine A is composed of a hydrophobic and a hydrophilic face, allowing for insertion into bacterial membranes, creating porous channels and destroying membrane integrity. We have used a combination of molecular modeling and solid phase synthesis to prepare Tyrocidine A and analogues 1-8. The minimum inhibitory concentrations (MICs) of these compounds were determined for a host of gram positive species and E. coli as a representative gram negative bacterium. Analogues 2 and 5 demonstrated moderate 2- to 8-fold increases in antibacterial activity over the parent Tyrocidine A for a variety of pathogenic microbes (best MICs for E. coli 32 microg/mL and 2 microg/mL for most gram positives). Examination of the structure- activity relationship between the analogues demonstrated a preference for increased amphipathicity but did not show a clear preference for increasing hydrophilicity versus hydrophobicity in improving antibacterial activity. Of note, movement of positively charged lysine residues or neutral pentafluorophenyl residues to different positions within the cyclopeptide ring system demonstrated improvements in antibacterial activity.
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Affiliation(s)
- Michael A. Marques
- Department of Pharmacology and Department of Chemistry, University of Southern California, 1985 Zonal Ave, Los Angeles California 90089
| | - Diane M. Citron
- Microbial Research Lab, Los Angeles County, University of Southern California Medical Center, 1801 East Marengo Street 2G-24, Los Angeles, California 90033
| | - Clay C. Wang
- Department of Pharmacology and Department of Chemistry, University of Southern California, 1985 Zonal Ave, Los Angeles California 90089
- Corresponding Author: Clay C. Wang, Department of Pharmacology and Department of Chemistry, University of Southern California, 1985 Zonal Ave, Los Angeles, California 90089, Phone: (323) 442-1670, Fax: (323) 442-1365,
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16
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Korczynska M, Mukhtar TA, Wright GD, Berghuis AM. Structural basis for streptogramin B resistance in Staphylococcus aureus by virginiamycin B lyase. Proc Natl Acad Sci U S A 2007; 104:10388-93. [PMID: 17563376 PMCID: PMC1965523 DOI: 10.1073/pnas.0701809104] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The streptogramin combination therapy of quinupristin-dalfopristin (Synercid) is used to treat infections caused by bacterial pathogens, such as methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecium. However, the effectiveness of this therapy is being compromised because of an increased incidence of streptogramin resistance. One of the clinically observed mechanisms of resistance is enzymatic inactivation of the type B streptogramins, such as quinupristin, by a streptogramin B lyase, i.e., virginiamycin B lyase (Vgb). The enzyme catalyzes the linearization of the cyclic antibiotic via a cleavage that requires a divalent metal ion. Here, we present crystal structures of Vgb from S. aureus in its apoenzyme form and in complex with quinupristin and Mg2+ at 1.65- and 2.8-A resolution, respectively. The fold of the enzyme is that of a seven-bladed beta-propeller, although the sequence reveals no similarity to other known members of this structural family. Quinupristin binds to a large depression on the surface of the enzyme, where it predominantly forms van der Waals interactions. Validated by site-directed mutagenesis studies, a reaction mechanism is proposed in which the initial abstraction of a proton is facilitated by a Mg2+ -linked conjugated system. Analysis of the Vgb-quinupristin structure and comparison with the complex between quinupristin and its natural target, the 50S ribosomal subunit, reveals features that can be exploited for developing streptogramins that are impervious to Vgb-mediated resistance.
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Affiliation(s)
- Magdalena Korczynska
- *Departments of Biochemistry and Microbiology and Immunology, McGill University, Montreal, QC, Canada H3A 4A2; and
| | - Tariq A. Mukhtar
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada L8N 3Z5
| | - Gerard D. Wright
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada L8N 3Z5
| | - Albert M. Berghuis
- *Departments of Biochemistry and Microbiology and Immunology, McGill University, Montreal, QC, Canada H3A 4A2; and
- To whom correspondence should be addressed. E-mail:
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17
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Kopp F, Marahiel MA. Macrocyclization strategies in polyketide and nonribosomal peptide biosynthesis. Nat Prod Rep 2007; 24:735-49. [PMID: 17653357 DOI: 10.1039/b613652b] [Citation(s) in RCA: 149] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nonribosomal peptides and polyketides have attracted considerable attention in basic and applied research and have given rise to a multitude of therapeutic agents. The biological activity of many of these complex natural products, including for example the peptide antibiotics daptomycin and bacitracin or the polyketide anticancer agents epothilone and geldanamycin, specifically relies on the macrocyclization of linear acyl chains that form the backbone of these highly valuable molecules. The construction of the linear acyl precursors is accomplished by modular protein templates that follow comparable assembly line logic. As an enzymatic key step, macrocyclization is introduced after the consecutive condensation of amino acid or acyl-CoA building blocks by dedicated catalysts, and the mature product is released from the biosynthetic machinery. The diverse chain termination strategies of nonribosomal peptide and polyketide assembly lines, the structures and mechanisms of the versatile macrocyclization catalysts, and chemoenzymatic approaches for the development of new therapeutics are the focus of this review. Further, it is illustrated that macrocyclization is not restricted to secondary metabolites, but represents a commonly found structural motif of other biologically active proteins and peptides.
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Affiliation(s)
- Florian Kopp
- Fachbereich Chemie/Biochemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35043, Marburg, Germany
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18
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Grünewald J, Marahiel MA. Chemoenzymatic and template-directed synthesis of bioactive macrocyclic peptides. Microbiol Mol Biol Rev 2006; 70:121-46. [PMID: 16524919 PMCID: PMC1393257 DOI: 10.1128/mmbr.70.1.121-146.2006] [Citation(s) in RCA: 183] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Non-ribosomally synthesized peptides have compelling biological activities ranging from antimicrobial to immunosuppressive and from cytostatic to antitumor. The broad spectrum of applications in modern medicine is reflected in the great structural diversity of these natural products. They contain unique building blocks, such as d-amino acids, fatty acids, sugar moieties, and heterocyclic elements, as well as halogenated, methylated, and formylated residues. In the past decades, significant progress has been made toward the understanding of the biosynthesis of these secondary metabolites by nonribosomal peptide synthetases (NRPSs) and their associated tailoring enzymes. Guided by this knowledge, researchers genetically redesigned the NRPS template to synthesize new peptide products. Moreover, chemoenzymatic strategies were developed to rationally engineer nonribosomal peptides products in order to increase or alter their bioactivities. Specifically, chemical synthesis combined with peptide cyclization mediated by nonribosomal thioesterase domains enabled the synthesis of glycosylated cyclopeptides, inhibitors of integrin receptors, peptide/polyketide hybrids, lipopeptide antibiotics, and streptogramin B antibiotics. In addition to the synthetic potential of these cyclization catalysts, which is the main focus of this review, different enzymes for tailoring of peptide scaffolds as well as the manipulation of carrier proteins with reporter-labeled coenzyme A analogs are discussed.
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Affiliation(s)
- Jan Grünewald
- Fachbereich Chemie/Biochemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse, D-35032 Marburg, Germany
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Mahlert C, Sieber SA, Grünewald J, Marahiel MA. Chemoenzymatic approach to enantiopure streptogramin B variants: characterization of stereoselective pristinamycin I cyclase from Streptomyces pristinaespiralis. J Am Chem Soc 2005; 127:9571-80. [PMID: 15984884 DOI: 10.1021/ja051254t] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Streptogramin B antibiotics are cyclic peptide natural products produced by Streptomyces species. In combination with the synergistic group A component, they are "last line of defense" antimicrobial agents against multiresistant cocci. The racemization sensitivity of the phenylglycine (Phg(7)) ester is a complex challenge in total chemical synthesis of streptogramin B molecules. To provide fast and easy access to novel streptogramin antibiotics, we introduce a novel chemoenzymatic strategy in which diversity is generated by standard solid phase protocols and stereoselectivity by subsequent enzymatic cyclization. For this approach, we cloned, overproduced, and biochemically characterized the recombinant thioesterase domain SnbDE TE of the pristinamycin I nonribosomal peptide synthetase from Streptomyces pristinaespiralis. SnbDE TE catalyzes regioselective ring closure of linear peptide thioester analogues of pristinamycin I as well as stereoselective cyclization out of complex in situ racemizing substrate mixtures, enabling synthesis of Streptogramin B variants via a dynamic kinetic resolution assay. A remarkable substrate tolerance was detected for the enzymatic cyclization including all the seven positions of the peptide backbone. Interestingly, SnbDE TE was observed to be the first cyclase from a macrolactone forming NRPS which is additionally able to catalyze macrolactamization of peptide thioester substrates. An N-methylated peptide bond between positions 4 and 5 is mandatory for a high substrate turnover. The presented strategy is potent to screen for analogues with improved activity and guides our understanding of structure--activity relationships in the important class of streptogramin antibiotics.
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Affiliation(s)
- Christoph Mahlert
- Fachbereich Chemie/Biochemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse, D-35032 Marburg, Germany
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Sutcliffe JA. Improving on nature: antibiotics that target the ribosome. Curr Opin Microbiol 2005; 8:534-42. [PMID: 16111914 DOI: 10.1016/j.mib.2005.08.004] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2005] [Accepted: 08/08/2005] [Indexed: 11/28/2022]
Abstract
Antibiotic resistance, along with the resolution of antibiotic-ribosomal subunit complexes at the atomic level, has provided new insights into modifications of clinically relevant antimicrobials that target the ribosome. Modifications to the aminoglycoside or negamycin scaffolds have been reported in the past, but few derivatives appear to be greatly improved compared to their parent compound. Computational and/or traditional screening efforts have yielded novel compounds that bind to the decoding site of the small (30S) ribosomal subunit; naphthyridones appear to bind only in the presence of poly(U) and tRNA(Phe), whereas quinolines bind in a similar manner to aminoglycosides. Streptogramin B analogs were designed that have an amide replacement of the labile ester bond. The resultant molecules were not substrates for the inactivating lyase, but were no longer inhibitors of translation. The synthesis of 16-membered macrolides that are modified at the C6 position with peptidyl moieties as well as conjugates of chloramphenicol to either nucleotide groups or pyrene have been described, but no antibacterial activity has been reported. X-ray crystal structures are now available that can be used to improve on natural or synthetic antibiotics that bind to either the 30S or the 50S ribosomal subunit.
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Mercer AC, Burkart MD. Enzyme-assisted antibiotic engineering--the Wright way. CHEMISTRY & BIOLOGY 2005; 12:147-8. [PMID: 15734642 DOI: 10.1016/j.chembiol.2005.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Affiliation(s)
- Andrew C Mercer
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
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