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Fernández-Pastor I, Ortiz-López FJ, Oves-Costales D, Martín J, Sánchez P, Melguizo Á, Reyes F, Weber T, Genilloud O. Dilarmycins A-C, Calcium-Dependent Lipopeptide Antibiotics with a Non-canonical Ca 2+-Binding Motif. Org Lett 2024; 26:1343-1347. [PMID: 38329455 DOI: 10.1021/acs.orglett.3c04195] [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: 02/09/2024]
Abstract
Genome analysis of strain Streptomyces sp. CA-278952 revealed a biosynthetic gene cluster encoding a putative lipopeptide with a sequence containing an Asp-Gly-Glu-Ala motif. We envisioned that this motif could mimic the canonical Asp-X-Asp-Gly sequence found in previously reported calcium-dependent lipopeptide antibiotics. Chemical investigation of the producing strain led to the discovery of three novel lipodepsipeptides, dilarmycins A-C. The calcium-dependent antibacterial activity of the new compounds was confirmed against the Gram-positive pathogens methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus.
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Affiliation(s)
- Ignacio Fernández-Pastor
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía. Avenida del Conocimiento, 34, 18016 Armilla, Granada, Spain
| | - Francisco Javier Ortiz-López
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía. Avenida del Conocimiento, 34, 18016 Armilla, Granada, Spain
| | - Daniel Oves-Costales
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía. Avenida del Conocimiento, 34, 18016 Armilla, Granada, Spain
| | - Jesús Martín
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía. Avenida del Conocimiento, 34, 18016 Armilla, Granada, Spain
| | - Pilar Sánchez
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía. Avenida del Conocimiento, 34, 18016 Armilla, Granada, Spain
| | - Ángeles Melguizo
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía. Avenida del Conocimiento, 34, 18016 Armilla, Granada, Spain
| | - Fernando Reyes
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía. Avenida del Conocimiento, 34, 18016 Armilla, Granada, Spain
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltoft Plads, Building 220, 2800 Kongens Lyngby, Denmark
| | - Olga Genilloud
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía. Avenida del Conocimiento, 34, 18016 Armilla, Granada, Spain
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2
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Chiou SL, Chen YJ, Lee CT, Ho MN, Miao J, Kuo PC, Hsu CC, Lin YS, Chu J. A Boron-Dependent Antibiotic Derived from a Calcium-Dependent Antibiotic. Angew Chem Int Ed Engl 2024; 63:e202317522. [PMID: 38085688 PMCID: PMC10872445 DOI: 10.1002/anie.202317522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Indexed: 12/29/2023]
Abstract
The prevalence of drug-resistant bacterial pathogens foreshadows a healthcare crisis. Calcium-dependent antibiotics (CDAs) are promising candidates to combat infectious diseases as many of them show modes of action (MOA) orthogonal to widespread resistance mechanisms. The calcium dependence is nonetheless one of the hurdles toward realizing their full potential. Using laspartomycin C (LspC) as a model, we explored the possibility of reducing, or even eliminating, its calcium dependence. We report herein a synthetic LspC analogue (B1) whose activity no longer depends on calcium and is instead induced by phenylboronic acid (PBA). In LspC, Asp1 and Asp7 coordinate to calcium to anchor it in the active conformation; these residues are replaced by serine in B1 and condense with PBA to form a boronic ester with the same anchoring effect. Using thin-layer chromatography, MS, NMR, and complementation assays, we demonstrate that B1 inhibits bacterial growth via the same MOA as LspC, i.e., sequestering the cell wall biosynthetic intermediate undecaprenyl phosphate. B1 is as potent and effective as LspC against several Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus. Our success in converting a CDA to a boron-dependent antibiotic opens a new avenue in the design and functional control of drug molecules.
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Affiliation(s)
- Shao-Lun Chiou
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei City, 10617, Taiwan
| | - Yi-Ju Chen
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei City, 10617, Taiwan
| | - Chu-Ting Lee
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei City, 10617, Taiwan
| | - Minh Ngoc Ho
- Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford, MA 02155, USA
| | - Jiayuan Miao
- Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford, MA 02155, USA
| | - Po-Cheng Kuo
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei City, 10617, Taiwan
| | - Cheng-Chih Hsu
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei City, 10617, Taiwan
| | - Yu-Shan Lin
- Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford, MA 02155, USA
| | - John Chu
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei City, 10617, Taiwan
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3
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Pilz M, Cavelius P, Qoura F, Awad D, Brück T. Lipopeptides development in cosmetics and pharmaceutical applications: A comprehensive review. Biotechnol Adv 2023; 67:108210. [PMID: 37460047 DOI: 10.1016/j.biotechadv.2023.108210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 07/05/2023] [Accepted: 07/09/2023] [Indexed: 07/25/2023]
Abstract
Lipopeptides are surface active, natural products of bacteria, fungi and green-blue algae origin, having diverse structures and functionalities. In analogy, a number of chemical synthesis techniques generated new designer lipopeptides with desirable features and functions. Lipopetides are self-assembly guided, supramolecular compounds which have the capacity of high-density presentation of the functional epitopes at the surface of the nanostructures. This feature contributes to their successful application in several industry sectors, including food, feed, personal care, and pharmaceutics. In this comprehensive review, the novel class of ribosomally synthesized lipopeptides is introduced alongside the more commonly occuring non-ribosomal lipopeptides. We highlight key representatives of the most researched as well as recently described lipopeptide families, with emphasis on structural features, self-assembly and associated functions. The common biological, chemical and hybrid production routes of lipopeptides, including prominent analogues and derivatives are also discussed. Furthermore, genetic engineering strategies aimed at increasing lipopeptide yields, diversity and biological activity are summarized and exemplified. With respect to application, this work mainly details the potential of lipopeptides in personal care and cosmetics industry as cleansing agents, moisturizer, anti-aging/anti-wrinkling, skin whitening and preservative agents as well as the pharmaceutical industry as anitimicrobial agents, vaccines, immunotherapy, and cancer drugs. Given that this review addresses human applications, we conclude on the topic of safety of lipopeptide formulations and their sustainable production.
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Affiliation(s)
- Melania Pilz
- Werner Siemens-Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Philipp Cavelius
- Werner Siemens-Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Farah Qoura
- Werner Siemens-Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Dania Awad
- Werner Siemens-Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany.
| | - Thomas Brück
- Werner Siemens-Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany.
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4
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Zhang S, Chen Y, Zhu J, Lu Q, Cryle MJ, Zhang Y, Yan F. Structural diversity, biosynthesis, and biological functions of lipopeptides from Streptomyces. Nat Prod Rep 2023; 40:557-594. [PMID: 36484454 DOI: 10.1039/d2np00044j] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: up to 2022Streptomyces are ubiquitous in terrestrial and marine environments, where they display a fascinating metabolic diversity. As a result, these bacteria are a prolific source of active natural products. One important class of these natural products is the nonribosomal lipopeptides, which have diverse biological activities and play important roles in the lifestyle of Streptomyces. The importance of this class is highlighted by the use of related antibiotics in the clinic, such as daptomycin (tradename Cubicin). By virtue of recent advances spanning chemistry and biology, significant progress has been made in biosynthetic studies on the lipopeptide antibiotics produced by Streptomyces. This review will serve as a comprehensive guide for researchers working in this multidisciplinary field, providing a summary of recent progress regarding the investigation of lipopeptides from Streptomyces. In particular, we highlight the structures, properties, biosynthetic mechanisms, chemical and chemoenzymatic synthesis, and biological functions of lipopeptides. In addition, the application of genome mining techniques to Streptomyces that have led to the discovery of many novel lipopeptides is discussed, further demonstrating the potential of lipopeptides from Streptomyces for future development in modern medicine.
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Affiliation(s)
- Songya Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yunliang Chen
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
- The Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 1000050, China.
| | - Jing Zhu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Qiujie Lu
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
| | - Max J Cryle
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800 Australia
- EMBL Australia, Monash University, Clayton, Victoria, 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, Victoria, 3800 Australia
| | - Youming Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
| | - Fu Yan
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
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5
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Miller LN, Blake MJ, Page EF, Castillo HB, Calhoun TR. Phosphate Ions Alter the Binding of Daptomycin to Living Bacterial Cell Surfaces. ACS Infect Dis 2021; 7:3088-3095. [PMID: 34605244 DOI: 10.1021/acsinfecdis.1c00397] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Advancements in antibiotic drug design are often hindered by missing information on how these small molecules interact with living cells. The antibiotic, daptomycin, has found clinical success and an emerging resistance, but a comprehensive picture of its mechanism of action has remained elusive. Using a surface-specific spectroscopy technique, second harmonic generation, we are able to quantitatively assess the binding of daptomycin to living cell membranes without the addition of exogenous labels. Our results reveal similar binding affinities for both Gram-positive and Gram-negative bacteria studied, including Escherichia coli. More importantly, we show that the presence of phosphate ions influences the binding of daptomycin to the Gram-positive bacterium Enterococcus faecalis. The role of environmental phosphate has not previously been considered in any proposed mechanism, and its implications are expected to be important in vivo.
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Affiliation(s)
- Lindsey N. Miller
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Marea J. Blake
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Eleanor F. Page
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Hannah B. Castillo
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Tessa R. Calhoun
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
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6
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Rius J, Torrelles X. A new density-modification procedure extending the application of the recent |ρ|-based phasing algorithm to larger crystal structures. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2021; 77:339-347. [PMID: 34196295 PMCID: PMC8248888 DOI: 10.1107/s2053273321004915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/10/2021] [Indexed: 11/10/2022]
Abstract
The incorporation of the new peakness-enhancing fast Fourier transform compatible ipp procedure (ipp = inner-pixel preservation) into the recently published SM algorithm based on |ρ| [Rius (2020). Acta Cryst A76, 489-493] improves its phasing efficiency for larger crystal structures with atomic resolution data. Its effectiveness is clearly demonstrated via a collection of test crystal structures (taken from the Protein Data Bank) either starting from random phase values or by using the randomly shifted modulus function (a Patterson-type synthesis) as initial ρ estimate. It has been found that in the presence of medium scatterers (e.g. S or Cl atoms) crystal structures with 1500 × c atoms in the unit cell (c = number of centerings) can be routinely solved. In the presence of strong scatterers like Fe, Cu or Zn atoms this number increases to around 5000 × c atoms. The implementation of this strengthened SM algorithm is simple, since it only includes a few easy-to-adjust parameters.
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Affiliation(s)
- Jordi Rius
- Institut de Ciència de Materials de Barcelona, CSIC, Campus de la UAB, Bellaterra, Catalonia 08193, Spain
| | - Xavier Torrelles
- Institut de Ciència de Materials de Barcelona, CSIC, Campus de la UAB, Bellaterra, Catalonia 08193, Spain
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7
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Cardoso P, Glossop H, Meikle TG, Aburto-Medina A, Conn CE, Sarojini V, Valery C. Molecular engineering of antimicrobial peptides: microbial targets, peptide motifs and translation opportunities. Biophys Rev 2021; 13:35-69. [PMID: 33495702 PMCID: PMC7817352 DOI: 10.1007/s12551-021-00784-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 01/07/2021] [Indexed: 02/07/2023] Open
Abstract
The global public health threat of antimicrobial resistance has led the scientific community to highly engage into research on alternative strategies to the traditional small molecule therapeutics. Here, we review one of the most popular alternatives amongst basic and applied research scientists, synthetic antimicrobial peptides. The ease of peptide chemical synthesis combined with emerging engineering principles and potent broad-spectrum activity, including against multidrug-resistant strains, has motivated intense scientific focus on these compounds for the past decade. This global effort has resulted in significant advances in our understanding of peptide antimicrobial activity at the molecular scale. Recent evidence of molecular targets other than the microbial lipid membrane, and efforts towards consensus antimicrobial peptide motifs, have supported the rise of molecular engineering approaches and design tools, including machine learning. Beyond molecular concepts, supramolecular chemistry has been lately added to the debate; and helped unravel the impact of peptide self-assembly on activity, including on biofilms and secondary targets, while providing new directions in pharmaceutical formulation through taking advantage of peptide self-assembled nanostructures. We argue that these basic research advances constitute a solid basis for promising industry translation of rationally designed synthetic peptide antimicrobials, not only as novel drugs against multidrug-resistant strains but also as components of emerging antimicrobial biomaterials. This perspective is supported by recent developments of innovative peptide-based and peptide-carrier nanobiomaterials that we also review.
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Affiliation(s)
- Priscila Cardoso
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia.,School of Science, RMIT University, Melbourne, Australia
| | - Hugh Glossop
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | | | | | | | | | - Celine Valery
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia
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8
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Ca 2+-Daptomycin targets cell wall biosynthesis by forming a tripartite complex with undecaprenyl-coupled intermediates and membrane lipids. Nat Commun 2020; 11:1455. [PMID: 32193379 PMCID: PMC7081307 DOI: 10.1038/s41467-020-15257-1] [Citation(s) in RCA: 114] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 02/25/2020] [Indexed: 11/08/2022] Open
Abstract
The lipopeptide daptomycin is used as an antibiotic to treat severe infections with gram-positive pathogens, such as methicillin resistant Staphylococcus aureus (MRSA) and drug-resistant enterococci. Its precise mechanism of action is incompletely understood, and a specific molecular target has not been identified. Here we show that Ca2+-daptomycin specifically interacts with undecaprenyl-coupled cell envelope precursors in the presence of the anionic phospholipid phosphatidylglycerol, forming a tripartite complex. We use microbiological and biochemical assays, in combination with fluorescence and optical sectioning microscopy of intact staphylococcal cells and model membrane systems. Binding primarily occurs at the staphylococcal septum and interrupts cell wall biosynthesis. This is followed by delocalisation of components of the peptidoglycan biosynthesis machinery and massive membrane rearrangements, which may account for the pleiotropic cellular events previously reported. The identification of carrier-bound cell wall precursors as specific targets explains the specificity of daptomycin for bacterial cells. Our work reconciles apparently inconsistent previous results, and supports a concise model for the mode of action of daptomycin.
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9
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Munusamy S, Conde R, Bertrand B, Munoz-Garay C. Biophysical approaches for exploring lipopeptide-lipid interactions. Biochimie 2020; 170:173-202. [PMID: 31978418 PMCID: PMC7116911 DOI: 10.1016/j.biochi.2020.01.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 01/19/2020] [Indexed: 02/07/2023]
Abstract
In recent years, lipopeptides (LPs) have attracted a lot of attention in the pharmaceutical industry due to their broad-spectrum of antimicrobial activity against a variety of pathogens and their unique mode of action. This class of compounds has enormous potential for application as an alternative to conventional antibiotics and for pest control. Understanding how LPs work from a structural and biophysical standpoint through investigating their interaction with cell membranes is crucial for the rational design of these biomolecules. Various analytical techniques have been developed for studying intramolecular interactions with high resolution. However, these tools have been barely exploited in lipopeptide-lipid interactions studies. These biophysical approaches would give precise insight on these interactions. Here, we reviewed these state-of-the-art analytical techniques. Knowledge at this level is indispensable for understanding LPs activity and particularly their potential specificity, which is relevant information for safe application. Additionally, the principle of each analytical technique is presented and the information acquired is discussed. The key challenges, such as the selection of the membrane model are also been briefly reviewed. A brief overview of topics to understand the generalities of lipopeptide (LP) science. Main analytical techniques used to reveal the interaction and the distorting effect of LP on artificial membranes. Guidelines for selecting of the most adequate membrane models for the given analytical technique.
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Affiliation(s)
- Sathishkumar Munusamy
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Mexico
| | - Renaud Conde
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, Mexico
| | - Brandt Bertrand
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Mexico
| | - Carlos Munoz-Garay
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Mexico.
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10
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Götze S, Stallforth P. Structure elucidation of bacterial nonribosomal lipopeptides. Org Biomol Chem 2020; 18:1710-1727. [DOI: 10.1039/c9ob02539a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We provide a summary of the tools, which allow elucidate the structures of nonribosomal lipopetides.
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Affiliation(s)
- Sebastian Götze
- Department of Paleobiotechnology
- Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute (HKI)
- 07745 Jena
- Germany
| | - Pierre Stallforth
- Department of Paleobiotechnology
- Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute (HKI)
- 07745 Jena
- Germany
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11
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Xu B, Hermant Y, Yang S, Harris PWR, Brimble MA. A Versatile Boc Solid Phase Synthesis of Daptomycin and Analogues Using Site Specific, On‐Resin Ozonolysis to Install the Kynurenine Residue. Chemistry 2019; 25:14101-14107. [DOI: 10.1002/chem.201903725] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Buzhe Xu
- School of Chemical SciencesThe University of Auckland 23 Symonds Street Auckland 1142 New Zealand
- Maurice Wilkins Centre for Molecular BiodiscoverySchool of Biological SciencesThe University of Auckland Auckland 1142 New Zealand
| | - Yann Hermant
- School of Chemical SciencesThe University of Auckland 23 Symonds Street Auckland 1142 New Zealand
- Maurice Wilkins Centre for Molecular BiodiscoverySchool of Biological SciencesThe University of Auckland Auckland 1142 New Zealand
| | - Sung‐Hyun Yang
- School of Chemical SciencesThe University of Auckland 23 Symonds Street Auckland 1142 New Zealand
| | - Paul W. R. Harris
- School of Chemical SciencesThe University of Auckland 23 Symonds Street Auckland 1142 New Zealand
- School of Biological SciencesThe University of Auckland 3A Symonds Street Auckland 1142 New Zealand
- Maurice Wilkins Centre for Molecular BiodiscoverySchool of Biological SciencesThe University of Auckland Auckland 1142 New Zealand
| | - Margaret A. Brimble
- School of Chemical SciencesThe University of Auckland 23 Symonds Street Auckland 1142 New Zealand
- School of Biological SciencesThe University of Auckland 3A Symonds Street Auckland 1142 New Zealand
- Maurice Wilkins Centre for Molecular BiodiscoverySchool of Biological SciencesThe University of Auckland Auckland 1142 New Zealand
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12
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Wood TM, Martin NI. The calcium-dependent lipopeptide antibiotics: structure, mechanism, & medicinal chemistry. MEDCHEMCOMM 2019; 10:634-646. [PMID: 31191855 DOI: 10.1039/c9md00126c] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 03/20/2019] [Indexed: 12/19/2022]
Abstract
To push back the growing tide of antibacterial resistance the discovery and development of new antibiotics is a must. In recent years the calcium-dependent lipopeptide antibiotics (CDAs) have emerged as a potential source of new antibacterial agents rich in structural and mechanistic diversity. All CDAs share a common lipidated cyclic peptide motif containing amino acid side chains that specifically chelate calcium. It is only in the calcium bound state that the CDAs achieve their potent antibacterial activities. Interestingly, despite their common structural features, the mechanisms by which different CDAs target bacteria can vary dramatically. This review provides both a historic context for the CDAs while also addressing the state of the art with regards to their discovery, optimization, and antibacterial mechanisms.
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Affiliation(s)
- Thomas M Wood
- Department of Chemical Biology & Drug Discovery , Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands.,Biological Chemistry Group , Institute of Biology Leiden , Leiden University , Sylvius Laboratories , Sylviusweg 72 , 2333 BE Leiden , The Netherlands . ; Tel: +31 (0)6 1878 5274
| | - Nathaniel I Martin
- Biological Chemistry Group , Institute of Biology Leiden , Leiden University , Sylvius Laboratories , Sylviusweg 72 , 2333 BE Leiden , The Netherlands . ; Tel: +31 (0)6 1878 5274
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13
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Pokorny A, Khatib TO, Stevenson H. A Quantitative Model of Daptomycin Binding to Lipid Bilayers. J Phys Chem B 2018; 122:9137-9146. [DOI: 10.1021/acs.jpcb.8b07503] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Antje Pokorny
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina 28403, United States
| | - Tala O. Khatib
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina 28403, United States
| | - Heather Stevenson
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina 28403, United States
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14
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Tyurin AP, Alferova VA, Paramonov AS, Shuvalov MV, Malanicheva IA, Grammatikova NE, Solyev PN, Liu S, Sun C, Prokhorenko IA, Efimenko TA, Terekhova LP, Efremenkova OV, Shenkarev ZO, Korshun VA. Crystallomycin revisited after 60 years: aspartocins B and C. MEDCHEMCOMM 2018; 9:667-675. [PMID: 30108957 PMCID: PMC6071864 DOI: 10.1039/c8md00002f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 02/25/2018] [Indexed: 11/21/2022]
Abstract
The study of an archived sample of crystallomycin complex using HPLC, ESI HRMS, and 2D NMR showed that two major components of the antibiotic, compounds 1 and 2, are lipopeptides having the same peptide core, Asp1-cyclo(Dab2-Pip3-MeAsp4-Asp5-Gly6-Asp7-Gly8-Dab9-Val10-Pro11-), N-acylated either with Δ3-iso-tetradecenoyl or Δ3-anteiso-pentadecenoyl that are identical to aspartocins C and B, respectively. According to the 2D NMR study, compound 2 in DMSO solution exists as a mixture of four conformers. The producing strain was identified as Streptomyces griseorubens. Compounds 1 and 2 have considerable Ca2+-dependent activity against Gram-positive bacteria including five MRSA strains.
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Affiliation(s)
- Anton P Tyurin
- Gause Institute of New Antibiotics , B. Pirogovskaya 11 , Moscow 119021 , Russia .
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Miklukho-Maklaya 16/10 , Moscow 117997 , Russia .
| | - Vera A Alferova
- Gause Institute of New Antibiotics , B. Pirogovskaya 11 , Moscow 119021 , Russia .
| | - Alexander S Paramonov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Miklukho-Maklaya 16/10 , Moscow 117997 , Russia .
| | - Maxim V Shuvalov
- Gause Institute of New Antibiotics , B. Pirogovskaya 11 , Moscow 119021 , Russia .
- Department of Chemistry , Lomonosov Moscow State University , 1-3 Leninskie Gory , Moscow 119992 , Russia
| | - Irina A Malanicheva
- Gause Institute of New Antibiotics , B. Pirogovskaya 11 , Moscow 119021 , Russia .
| | | | - Pavel N Solyev
- Engelhardt Institute of Molecular Biology , Vavilova 32 , Moscow 119991 , Russia
| | - Shaowei Liu
- Institute of Medicinal Biotechnology , Chinese Academy of Medical Sciences & Peking Union Medical College , Tian Tan Xi Li 1 , Beijing 100050 , China
| | - Chenghang Sun
- Institute of Medicinal Biotechnology , Chinese Academy of Medical Sciences & Peking Union Medical College , Tian Tan Xi Li 1 , Beijing 100050 , China
| | - Igor A Prokhorenko
- Gause Institute of New Antibiotics , B. Pirogovskaya 11 , Moscow 119021 , Russia .
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Miklukho-Maklaya 16/10 , Moscow 117997 , Russia .
| | - Tatyana A Efimenko
- Gause Institute of New Antibiotics , B. Pirogovskaya 11 , Moscow 119021 , Russia .
| | - Larisa P Terekhova
- Gause Institute of New Antibiotics , B. Pirogovskaya 11 , Moscow 119021 , Russia .
| | - Olga V Efremenkova
- Gause Institute of New Antibiotics , B. Pirogovskaya 11 , Moscow 119021 , Russia .
| | - Zakhar O Shenkarev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Miklukho-Maklaya 16/10 , Moscow 117997 , Russia .
- Moscow Institute of Physics and Technology , Institutsky lane 9, Dolgoprydny , Moscow region 141700 , Russia
| | - Vladimir A Korshun
- Gause Institute of New Antibiotics , B. Pirogovskaya 11 , Moscow 119021 , Russia .
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Miklukho-Maklaya 16/10 , Moscow 117997 , Russia .
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15
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Hover BM, Kim SH, Katz M, Charlop-Powers Z, Owen JG, Ternei MA, Maniko J, Estrela AB, Molina H, Park S, Perlin DS, Brady SF. Culture-independent discovery of the malacidins as calcium-dependent antibiotics with activity against multidrug-resistant Gram-positive pathogens. Nat Microbiol 2018; 3:415-422. [PMID: 29434326 PMCID: PMC5874163 DOI: 10.1038/s41564-018-0110-1] [Citation(s) in RCA: 246] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Accepted: 01/03/2018] [Indexed: 11/09/2022]
Abstract
Despite the wide availability of antibiotics, infectious diseases remain a leading cause of death worldwide 1 . In the absence of new therapies, mortality rates due to untreatable infections are predicted to rise more than tenfold by 2050. Natural products (NPs) made by cultured bacteria have been a major source of clinically useful antibiotics. In spite of decades of productivity, the use of bacteria in the search for new antibiotics was largely abandoned due to high rediscovery rates2,3. As only a fraction of bacterial diversity is regularly cultivated in the laboratory and just a fraction of the chemistries encoded by cultured bacteria are detected in fermentation experiments, most bacterial NPs remain hidden in the global microbiome. In an effort to access these hidden NPs, we have developed a culture-independent NP discovery platform that involves sequencing, bioinformatic analysis and heterologous expression of biosynthetic gene clusters captured on DNA extracted from environmental samples. Here, we describe the application of this platform to the discovery of the malacidins, a distinctive class of antibiotics that are commonly encoded in soil microbiomes but have never been reported in culture-based NP discovery efforts. The malacidins are active against multidrug-resistant pathogens, sterilize methicillin-resistant Staphylococcus aureus skin infections in an animal wound model and did not select for resistance under our laboratory conditions.
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Affiliation(s)
- Bradley M Hover
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Seong-Hwan Kim
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Micah Katz
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Zachary Charlop-Powers
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Jeremy G Owen
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Melinda A Ternei
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Jeffrey Maniko
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Andreia B Estrela
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Steven Park
- Public Health Research Institute, Rutgers University-New Jersey Medical School, Newark, NJ, USA
| | - David S Perlin
- Public Health Research Institute, Rutgers University-New Jersey Medical School, Newark, NJ, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA.
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16
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Kleijn LHJ, Vlieg HC, Wood TM, Sastre Toraño J, Janssen BJC, Martin NI. A High-Resolution Crystal Structure that Reveals Molecular Details of Target Recognition by the Calcium-Dependent Lipopeptide Antibiotic Laspartomycin C. Angew Chem Int Ed Engl 2017; 56:16546-16549. [PMID: 29108098 PMCID: PMC5767759 DOI: 10.1002/anie.201709240] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 10/21/2017] [Indexed: 12/15/2022]
Abstract
The calcium‐dependent antibiotics (CDAs) are an important emerging class of antibiotics. The crystal structure of the CDA laspartomycin C in complex with calcium and the ligand geranyl‐phosphate at a resolution of 1.28 Å is reported. This is the first crystal structure of a CDA bound to its bacterial target. The structure is also the first to be reported for an antibiotic that binds the essential bacterial phospholipid undecaprenyl phosphate (C55‐P). These structural insights are of great value in the design of antibiotics capable of exploiting this unique bacterial target.
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Affiliation(s)
- Laurens H J Kleijn
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584, CG, Utrecht, The Netherlands
| | - Hedwich C Vlieg
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Thomas M Wood
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584, CG, Utrecht, The Netherlands
| | - Javier Sastre Toraño
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584, CG, Utrecht, The Netherlands
| | - Bert J C Janssen
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Nathaniel I Martin
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584, CG, Utrecht, The Netherlands
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17
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Kleijn LHJ, Vlieg HC, Wood TM, Sastre Toraño J, Janssen BJC, Martin NI. A High-Resolution Crystal Structure that Reveals Molecular Details of Target Recognition by the Calcium-Dependent Lipopeptide Antibiotic Laspartomycin C. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201709240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Laurens H. J. Kleijn
- Department of Chemical Biology & Drug Discovery; Utrecht Institute for Pharmaceutical Sciences; Utrecht University; Universiteitsweg 99 3584 CG Utrecht The Netherlands
| | - Hedwich C. Vlieg
- Crystal and Structural Chemistry; Bijvoet Center for Biomolecular Research; Utrecht University; Padualaan 8 3584 CH Utrecht The Netherlands
| | - Thomas M. Wood
- Department of Chemical Biology & Drug Discovery; Utrecht Institute for Pharmaceutical Sciences; Utrecht University; Universiteitsweg 99 3584 CG Utrecht The Netherlands
| | - Javier Sastre Toraño
- Department of Chemical Biology & Drug Discovery; Utrecht Institute for Pharmaceutical Sciences; Utrecht University; Universiteitsweg 99 3584 CG Utrecht The Netherlands
| | - Bert J. C. Janssen
- Crystal and Structural Chemistry; Bijvoet Center for Biomolecular Research; Utrecht University; Padualaan 8 3584 CH Utrecht The Netherlands
| | - Nathaniel I. Martin
- Department of Chemical Biology & Drug Discovery; Utrecht Institute for Pharmaceutical Sciences; Utrecht University; Universiteitsweg 99 3584 CG Utrecht The Netherlands
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18
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Zhang J, Scott WRP, Gabel F, Wu M, Desmond R, Bae J, Zaccai G, Algar WR, Straus SK. On the quest for the elusive mechanism of action of daptomycin: Binding, fusion, and oligomerization. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1490-1499. [PMID: 28844744 DOI: 10.1016/j.bbapap.2017.07.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 07/05/2017] [Accepted: 07/31/2017] [Indexed: 01/27/2023]
Abstract
Daptomycin, sold under the trade name CUBICIN, is the first lipopeptide antibiotic to be approved for use against Gram-positive organisms, including a number of highly resistant species. Over the last few decades, a number of studies have tried to pinpoint the mechanism of action of daptomycin. These proposed modes of action often have points in common (e.g. the requirement for Ca2+ and lipid membranes containing a high proportion of phosphatidylglycerol (PG) headgroups), but also points of divergence (e.g. oligomerization in solution and in membranes, membrane perturbation vs. inhibition of cell envelope synthesis). In this study, we investigate how concentration effects may have an impact on the interpretation of the biophysical data used to support a given mechanism of action. Results obtained from small angle neutron scattering (SANS) experiments and molecular dynamics (MD) simulations show that daptomycin oligomerizes at high concentrations (both with and without Ca2+) in solution, but that this oligomer readily falls apart. Photon correlation spectroscopy (PCS) experiments demonstrate that daptomycin causes fusion more readily in DMPC/PG membranes than in POPC/PG, suggesting that the latter may be a better model system. Finally, fluorescence and Förster resonance energy transfer (FRET) experiments reveal that daptomycin binds strongly to the lipid membrane and that oligomerization occurs in a concentration-dependent manner. The combined experiments provide an improved framework for more general and rigorous biophysical studies toward understanding the elusive mechanism of action of daptomycin. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
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Affiliation(s)
- Jin Zhang
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Walter R P Scott
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Frank Gabel
- Institut de Biologie Structurale, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France; Institut Laue Langevin, 6 rue Jules Horowitz, 38042 Grenoble Cedex 9, France
| | - Miao Wu
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Ruqaiba Desmond
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - JungHwan Bae
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Giuseppe Zaccai
- Institut Laue Langevin, 6 rue Jules Horowitz, 38042 Grenoble Cedex 9, France
| | - W Russ Algar
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada.
| | - Suzana K Straus
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada.
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19
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Müller A, Klöckner A, Schneider T. Targeting a cell wall biosynthesis hot spot. Nat Prod Rep 2017; 34:909-932. [PMID: 28675405 DOI: 10.1039/c7np00012j] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Covering: up to 2017History points to the bacterial cell wall biosynthetic network as a very effective target for antibiotic intervention, and numerous natural product inhibitors have been discovered. In addition to the inhibition of enzymes involved in the multistep synthesis of the macromolecular layer, in particular, interference with membrane-bound substrates and intermediates essential for the biosynthetic reactions has proven a valuable antibacterial strategy. A prominent target within the peptidoglycan biosynthetic pathway is lipid II, which represents a particular "Achilles' heel" for antibiotic attack, as it is readily accessible on the outside of the cytoplasmic membrane. Lipid II is a unique non-protein target that is one of the structurally most conserved molecules in bacterial cells. Notably, lipid II is more than just a target molecule, since sequestration of the cell wall precursor may be combined with additional antibiotic activities, such as the disruption of membrane integrity or disintegration of membrane-bound multi-enzyme machineries. Within the membrane bilayer lipid II is likely organized in specific anionic phospholipid patches that form a particular "landing platform" for antibiotics. Nature has invented a variety of different "lipid II binders" of at least 5 chemical classes, and their antibiotic activities can vary substantially depending on the compounds' physicochemical properties, such as amphiphilicity and charge, and thus trigger diverse cellular effects that are decisive for antibiotic activity.
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Affiliation(s)
- Anna Müller
- Institute of Pharmaceutical Microbiology, University of Bonn, Bonn, Germany.
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20
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The action mechanism of daptomycin. Bioorg Med Chem 2016; 24:6253-6268. [DOI: 10.1016/j.bmc.2016.05.052] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/20/2016] [Accepted: 05/26/2016] [Indexed: 11/15/2022]
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21
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New antibiotics from Nature’s chemical inventory. Bioorg Med Chem 2016; 24:6227-6252. [DOI: 10.1016/j.bmc.2016.09.014] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/07/2016] [Indexed: 01/07/2023]
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22
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Solid-state NMR characterization of amphomycin effects on peptidoglycan and wall teichoic acid biosyntheses in Staphylococcus aureus. Sci Rep 2016; 6:31757. [PMID: 27538449 PMCID: PMC4990924 DOI: 10.1038/srep31757] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 07/27/2016] [Indexed: 11/09/2022] Open
Abstract
Amphomycin and MX-2401 are cyclic lipopeptides exhibiting bactericidal activities against Gram-positive pathogens. Amphomycin and MX-2401 share structural similarities with daptomycin, but unlike daptomycin they do not target bacterial membrane. In this study, we investigate in vivo modes of action for amphomycin and MX-2401 in intact whole cells of Staphylococcus aureus by measuring the changes of peptidoglycan and wall teichoic acid compositions using solid-state NMR. S. aureus were grown in a defined media containing isotope labels [1-13C]glycine and L-[ε-15N]lysin, L-[1-13C]lysine and D-[15N]alanine, or D-[1-13C]alanine and [15N]glycine, to selectively 13C-15N pair label peptidoglycan bridge-link, stem-link, and cross-link, respectively. 13C{15N} and 15N{13C} rotational-echo double resonance NMR measurements determined that cyclic lipopeptide-treated S. aureus exhibited thinning of the cell wall, accumulation of Park’s nucleotide, inhibition of glycine utilization for purine biosynthesis, reduction of ester-linked D-Ala in teichoic acids, and reduction of peptidoglycan cross-linking. Whole cell NMR analysis also revealed that S. aureus, in presence of amphomycin and MX-2401, maintained the incorporation of D-Ala during peptidoglycan biosynthesis while the incorporation of D-Ala into teichoic acids was inhibited. These effects are consistent with amphomycin’s dual inhibition of both peptidoglycan and wall teichoic acid biosyntheses in S. aureus.
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23
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Structure and mode of action of cyclic lipopeptide pseudofactin II with divalent metal ions. Colloids Surf B Biointerfaces 2016; 146:498-506. [PMID: 27416562 DOI: 10.1016/j.colsurfb.2016.06.055] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 06/22/2016] [Accepted: 06/27/2016] [Indexed: 12/21/2022]
Abstract
The interaction of natural lipopeptide pseudofactin II with a series of doubly charged metal cations was examined by matrix-assisted laser-desorption ionization-time of flight (MALDI-TOF) mass spectrometry and molecular modelling. The molecular modelling for metal-pseudofactin II provides information on the metal-peptide binding sites. Overall, Mg(2+), Ca(2+) and Zn(2+) favor the association with oxygen atoms spanning the peptide backbone, whereas Cu(2+) is coordinated by three nitrogens. Circular dichroism (CD) results confirmed that Zn(2+) and Cu(2+) can disrupt the secondary structure of pseudofactin II at high concentrations, while Ca(2+) and Mg(2+) did not essentially affect the structure of the lipopeptide. Interestingly, our results showed that the addition of Zn(2+) and Cu(2+) helped smaller micelles to form larger micellar aggregates. Since pseudofactin II binds metals, we tested whether this phenomena was somehow related to its antimicrobial activity against Staphylococcus epidermidis and Proteus mirabilis. We found that the antimicrobial effect of pseudofactin II was increased by supplementation of culture media with all tested divalent metal ions. Finally, by using Gram-positive and Gram-negative bacteria we showed that the higher antimicrobial activity of metal complexes of pseudofactin II is attributed to the disruption of the cytoplasmic membrane.
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24
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References. Antibiotics (Basel) 2015. [DOI: 10.1128/9781555819316.refs] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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25
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Abstract
Macrocycles possess desirable properties that make them promising candidates for the discovery of novel drugs. They present structural features to favor bioactive conformations, selectivity to the receptors, cell permeability and metabolic stability. More effective and nontoxic drugs to cure human African trypanosomiasis, Leishmaniasis and Chagas disease are needed, especially because resistance has been detected. Therefore, major efforts should be made for investigation in new bioactive compounds exhibiting different mechanisms of action. Macrocycles might fulfill the expectations for the development of new drugs to treat those diseases. In the current review, we focus on macrocycles exhibiting biological activities as antitrypanosomal and/or antileishmanial. The isolation, synthetic and biological studies of this class of compounds published from 2005 to 2014 are summarized.
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26
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Schneider T, Müller A, Miess H, Gross H. Cyclic lipopeptides as antibacterial agents – Potent antibiotic activity mediated by intriguing mode of actions. Int J Med Microbiol 2014; 304:37-43. [DOI: 10.1016/j.ijmm.2013.08.009] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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27
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Rubinchik E, Schneider T, Elliott M, Scott WRP, Pan J, Anklin C, Yang H, Dugourd D, Müller A, Gries K, Straus SK, Sahl HG, Hancock REW. Mechanism of action and limited cross-resistance of new lipopeptide MX-2401. Antimicrob Agents Chemother 2011; 55:2743-54. [PMID: 21464247 PMCID: PMC3101398 DOI: 10.1128/aac.00170-11] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Revised: 03/11/2011] [Accepted: 03/25/2011] [Indexed: 11/20/2022] Open
Abstract
MX-2401 is a semisynthetic calcium-dependent lipopeptide antibiotic (analogue of amphomycin) in preclinical development for the treatment of serious Gram-positive infections. In vitro and in vivo, MX-2401 demonstrates broad-spectrum bactericidal activity against Gram-positive organisms, including antibiotic-resistant strains. The objective of this study was to investigate the mechanism of action of MX-2401 and compare it with that of the lipopeptide daptomycin. The results indicated that although both daptomycin and MX-2401 are in the structural class of Ca²⁺-dependent lipopeptide antibiotics, the latter has a different mechanism of action. Specifically, MX-2401 inhibits peptidoglycan synthesis by binding to the substrate undecaprenylphosphate (C₅₅-P), the universal carbohydrate carrier involved in several biosynthetic pathways. This interaction resulted in inhibition, in a dose-dependent manner, of the biosynthesis of the cell wall precursors lipids I and II and the wall teichoic acid precursor lipid III, while daptomycin had no significant effect on these processes. MX-2401 induced very slow membrane depolarization that was observed only at high concentrations. Unlike daptomycin, membrane depolarization by MX-2401 did not correlate with its bactericidal activity and did not affect general membrane permeability. In contrast to daptomycin, MX-2401 had no effect on lipid flip-flop, calcein release, or membrane fusion with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (sodium salt) (POPG) liposomes. MX-2401 adopts a more defined structure than daptomycin, presumably to facilitate interaction with C₅₅-P. Mutants resistant to MX-2401 demonstrated low cross-resistance to other antibiotics. Overall, these results provided strong evidence that the mode of action of MX-2401 is unique and different from that of any of the approved antibiotics, including daptomycin.
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Affiliation(s)
- E. Rubinchik
- BioWest Therapeutics Inc., Suite 400, 1727 West Broadway, Vancouver, British Columbia, Canada V6J 4W6
| | - T. Schneider
- University of Bonn, Institute of Medical Microbiology, Immunology and Parasitology-Pharmaceutical Microbiology Section, Meckenheimer Allee 168 D 53115 Bonn, Germany
| | - M. Elliott
- University of British Columbia, Centre for Microbial Diseases and Immunity Research, Room 232, 2259 Lower Mall Research Station, Vancouver, British Columbia, Canada V6T 1Z4
| | - W. R. P. Scott
- University of British Columbia, Department of Chemistry, Room E213, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1
| | - J. Pan
- University of British Columbia, Department of Chemistry, Room E213, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1
| | - C. Anklin
- Bruker BioSpin Corporation, 15 Fortune Drive, Billerica, Massachusetts 01821-3991
| | - H. Yang
- BioWest Therapeutics Inc., Suite 400, 1727 West Broadway, Vancouver, British Columbia, Canada V6J 4W6
| | - D. Dugourd
- BioWest Therapeutics Inc., Suite 400, 1727 West Broadway, Vancouver, British Columbia, Canada V6J 4W6
| | - A. Müller
- University of Bonn, Institute of Medical Microbiology, Immunology and Parasitology-Pharmaceutical Microbiology Section, Meckenheimer Allee 168 D 53115 Bonn, Germany
| | - K. Gries
- University of Bonn, Institute of Medical Microbiology, Immunology and Parasitology-Pharmaceutical Microbiology Section, Meckenheimer Allee 168 D 53115 Bonn, Germany
| | - S. K. Straus
- University of British Columbia, Department of Chemistry, Room E213, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1
| | - H. G. Sahl
- University of Bonn, Institute of Medical Microbiology, Immunology and Parasitology-Pharmaceutical Microbiology Section, Meckenheimer Allee 168 D 53115 Bonn, Germany
| | - R. E. W. Hancock
- University of British Columbia, Centre for Microbial Diseases and Immunity Research, Room 232, 2259 Lower Mall Research Station, Vancouver, British Columbia, Canada V6T 1Z4
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28
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Ishiyama A, Otoguro K, Iwatsuki M, Iwatsuki M, Namatame M, Nishihara A, Nonaka K, Kinoshita Y, Takahashi Y, Masuma R, Shiomi K, Yamada H, Omura S. In vitro and in vivo antitrypanosomal activities of three peptide antibiotics: leucinostatin A and B, alamethicin I and tsushimycin. J Antibiot (Tokyo) 2009; 62:303-8. [PMID: 19407848 DOI: 10.1038/ja.2009.32] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the course of our screening for antitrypanosomal compounds from soil microorganisms, as well as from the antibiotics library of the Kitasato Institute for Life Sciences, we found three peptide antibiotics, leucinostatin (A and B), alamethicin I and tsushimycin, which exhibited potent or moderate antitrypanosomal activity. We report here the in vitro and in vivo antitrypanosomal properties and cytotoxicities of leucinostatin A and B, alamethicin I and tsushimycin compared with suramin. We also discuss their possible mode of action. This is the first report of in vitro and in vivo trypanocidal activity of leucinostatin A and B, alamethicin I and tsushimycin.
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Affiliation(s)
- Aki Ishiyama
- Research Center for Tropical Diseases, Center for Basic Research, Kitasato Institute for Life Sciences and Graduate School of Infectious Control Sciences, Kitasato University, Tokyo, Japan
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29
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The lipopeptide antibiotic Friulimicin B inhibits cell wall biosynthesis through complex formation with bactoprenol phosphate. Antimicrob Agents Chemother 2009; 53:1610-8. [PMID: 19164139 DOI: 10.1128/aac.01040-08] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Friulimicin B is a naturally occurring cyclic lipopeptide, produced by the actinomycete Actinoplanes friuliensis, with excellent activity against gram-positive pathogens, including multidrug-resistant strains. It consists of a macrocyclic decapeptide core and a lipid tail, interlinked by an exocyclic amino acid. Friulimicin is water soluble and amphiphilic, with an overall negative charge. Amphiphilicity is enhanced in the presence of Ca(2+), which is also indispensable for antimicrobial activity. Friulimicin shares these physicochemical properties with daptomycin, which is suggested to kill gram-positive bacteria through the formation of pores in the cytoplasmic membrane. In spite of the fact that friulimicin shares features of structure and potency with daptomycin, we found that friulimicin has a unique mode of action and severely affects the cell envelope of gram-positive bacteria, acting via a defined target. We found friulimicin to interrupt the cell wall precursor cycle through the formation of a Ca(2+)-dependent complex with the bactoprenol phosphate carrier C(55)-P, which is not targeted by any other antibiotic in use. Since C(55)-P also serves as a carrier in teichoic acid biosynthesis and capsule formation, it is likely that friulimicin blocks multiple pathways that are essential for a functional gram-positive cell envelope.
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30
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Butler MS. Natural products to drugs: natural product-derived compounds in clinical trials. Nat Prod Rep 2008; 25:475-516. [PMID: 18497896 DOI: 10.1039/b514294f] [Citation(s) in RCA: 502] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Natural product and natural product-derived compounds that are being evaluated in clinical trials or are in registration (as at 31st December 2007) have been reviewed, as well as natural product-derived compounds for which clinical trials have been halted or discontinued since 2005. Also discussed are natural product-derived drugs launched since 2005, new natural product templates and late-stage development candidates.
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Affiliation(s)
- Mark S Butler
- MerLion Pharmaceuticals, 1 Science Park Road, The Capricorn 05-01, Singapore Science Park II, Singapore 117528.
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31
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Powell A, Borg M, Amir-Heidari B, Neary JM, Thirlway J, Wilkinson B, Smith CP, Micklefield J. Engineered Biosynthesis of Nonribosomal Lipopeptides with Modified Fatty Acid Side Chains. J Am Chem Soc 2007; 129:15182-91. [DOI: 10.1021/ja074331o] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Amanda Powell
- Contribution from the School of Chemistry and Department of Biomolecular Sciences, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom, and Biotica, Chesterford Research Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Mathew Borg
- Contribution from the School of Chemistry and Department of Biomolecular Sciences, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom, and Biotica, Chesterford Research Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Bagher Amir-Heidari
- Contribution from the School of Chemistry and Department of Biomolecular Sciences, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom, and Biotica, Chesterford Research Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Joanne M. Neary
- Contribution from the School of Chemistry and Department of Biomolecular Sciences, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom, and Biotica, Chesterford Research Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Jenny Thirlway
- Contribution from the School of Chemistry and Department of Biomolecular Sciences, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom, and Biotica, Chesterford Research Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Barrie Wilkinson
- Contribution from the School of Chemistry and Department of Biomolecular Sciences, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom, and Biotica, Chesterford Research Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Colin P. Smith
- Contribution from the School of Chemistry and Department of Biomolecular Sciences, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom, and Biotica, Chesterford Research Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Jason Micklefield
- Contribution from the School of Chemistry and Department of Biomolecular Sciences, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom, and Biotica, Chesterford Research Park, Little Chesterford, Essex CB10 1XL, United Kingdom
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Effect of divalent cations on the structure of the antibiotic daptomycin. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2007; 37:421-33. [PMID: 17968536 DOI: 10.1007/s00249-007-0227-2] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2007] [Revised: 10/02/2007] [Accepted: 10/09/2007] [Indexed: 10/22/2022]
Abstract
Daptomycin, a cyclic anionic lipopeptide antibiotic, whose three-dimensional structure was recently solved using solution state NMR (Ball et al. 2004; Jung et al. 2004; Rotondi and Gierasch 2005), requires calcium for function. To date, the exact nature of the interaction between divalent cations, such as Ca(2+) or Mg(2+), has not been fully characterized. It has, however, been suggested that addition of Ca(2+) to daptomycin in a 1:1 molar ratio induces aggregation. Moreover, it has been suggested that certain residues, e.g. Asp3 and Asp7, which are essential for activity (Grunewald et al. 2004; Kopp et al. 2006), may also be important for Ca(2+) binding (Jung et al. 2004). In this work, we have tried: (1) to further pinpoint how Ca(2+) affects daptomycin structure/oligomerization using analytical ultracentrifugation; and (2) to determine whether a specific calcium binding site exists, based on one-dimensional (13)C NMR spectra and molecular dynamics (MD) simulations. The centrifugation results indicated that daptomycin formed micelles of between 14 and 16 monomers in the presence of a 1:1 molar ratio of Ca(2+) and daptomycin. The (13)C NMR data indicated that addition of calcium had a significant effect on the Trp1 and Kyn13 residues, indicating that either calcium binds in this region or that these residues may be important for oligomerization. Finally, the molecular dynamics simulation results indicated that the conformational change of daptomycin upon calcium binding might not be as significant as originally proposed. Similar studies on the divalent cation Mg(2+) are also presented. The implication of these results for the biological function of daptomycin is discussed.
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Abstract
Lipopeptide daptomycin is one of the few recently approved antibiotics based on the novel mechanism of action. Recent advances in synthetic lipopeptides, driven by the biochemical and biophysical research, expanded their spectrum of antimicrobial activity and reduced their size to achieve economically viable production. Lipopeptides, consisting of a short peptide chain conjugated with an acyl chain, form a structurally defined conformation, which inserts into the bacterial membrane and dissipates its transmembrane potential. In addition to antimicrobial activity, synthetic lipopeptides also suppress inflammation through the neutralization of bacterial agonists of the innate immune response, synergize with conventional antibiotics and have improved proteolytic stability. Activities in animal models indicate that synthetic lipopeptides may surpass the natural lipopeptides as the perspective class of anti-infective agents.
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Affiliation(s)
- Roman Jerala
- National Institute of Chemistry, Department of Biotechnology, Hajdrihova 19, Ljubljana, Slovenia.
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Japelj B, Zorko M, Majerle A, Pristovsek P, Sanchez-Gomez S, Martinez de Tejada G, Moriyon I, Blondelle SE, Brandenburg K, Andrä J, Lohner K, Jerala R. The Acyl Group as the Central Element of the Structural Organization of Antimicrobial Lipopeptide. J Am Chem Soc 2007; 129:1022-3. [PMID: 17263370 DOI: 10.1021/ja067419v] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bostjan Japelj
- Laboratory of Biotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
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35
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Mode of action of the new antibiotic for Gram-positive pathogens daptomycin: comparison with cationic antimicrobial peptides and lipopeptides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2006; 1758:1215-23. [PMID: 16615993 DOI: 10.1016/j.bbamem.2006.02.009] [Citation(s) in RCA: 311] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2005] [Revised: 02/01/2006] [Accepted: 02/02/2006] [Indexed: 11/26/2022]
Abstract
With the steady rise in the number of antibiotic-resistant Gram-positive pathogens, it has become increasingly important to find new antibacterial agents which are highly active and have novel and diversified mechanisms of action. Two classes will be discussed here: the cationic antimicrobial peptides, which are amphiphilic in nature, targeting membranes and increasing their permeability; and lipopeptides, which consist of linear or cyclic peptides with an N-terminus that is acylated with a fatty acid side chain. One member of the cyclic lipopeptide family, the anionic molecule daptomycin, has been extensively studied and is the major focus of this review. Models will be presented on its mode of action and comparisons will be made to the known modes of action of cationic antimicrobial peptides and other lipopeptides.
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36
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Baltz RH, Miao V, Wrigley SK. Natural products to drugs: daptomycin and related lipopeptide antibiotics. Nat Prod Rep 2005; 22:717-41. [PMID: 16311632 DOI: 10.1039/b416648p] [Citation(s) in RCA: 272] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Daptomycin (Cubicin) is a lipopeptide antibiotic approved in the USA in 2003 for the treatment of skin and skin structure infections caused by Gram-positive pathogens. It is a member of the 10-membered cyclic lipopeptide family of antibiotics that includes A54145, calcium-dependent antibiotic (CDA), amphomycin, friulimicin, laspartomycin, and others. This review highlights research on this class of antibiotics from 1953 to 2005, focusing on more recent studies with particular emphasis on the interplay between structural features and antibacterial activities; chemical modifications to improve activity; the genetic organization and biosynthesis of lipopeptides; and the genetic engineering of the daptomycin biosynthetic pathway to produce novel derivatives for further chemical modification to develop candidates for clinical evaluation.
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