1
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Fait A, Silva SF, Abrahamsson JÅH, Ingmer H. Staphylococcus aureus response and adaptation to vancomycin. Adv Microb Physiol 2024; 85:201-258. [PMID: 39059821 DOI: 10.1016/bs.ampbs.2024.04.006] [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] [Indexed: 07/28/2024]
Abstract
Antibiotic resistance is an increasing challenge for the human pathogen Staphylococcus aureus. Methicillin-resistant S. aureus (MRSA) clones have spread globally, and a growing number display decreased susceptibility to vancomycin, the favoured antibiotic for treatment of MRSA infections. These vancomycin-intermediate S. aureus (VISA) or heterogeneous vancomycin-intermediate S. aureus (hVISA) strains arise from accumulation of a variety of point mutations, leading to cell wall thickening and reduced vancomycin binding to the cell wall building block, Lipid II, at the septum. They display only minor changes in vancomycin susceptibility, with varying tolerance between cells in a population, and therefore, they can be difficult to detect. In this review, we summarize current knowledge of VISA and hVISA. We discuss the role of genetic strain background or epistasis for VISA development and the possibility of strains being 'transient' VISA with gene expression changes mediated by, for example, VraTSR, GraXSR, or WalRK signal transduction systems, leading to temporary vancomycin tolerance. Additionally, we address collateral susceptibility to other antibiotics than vancomycin. Specifically, we estimate how mutations in rpoB, encoding the β-subunit of the RNA polymerase, affect overall protein structure and compare changes with rifampicin resistance. Ultimately, such in-depth analysis of VISA and hVISA strains in terms of genetic and transcriptional changes, as well as changes in protein structures, may pave the way for improved detection and guide antibiotic therapy by revealing strains at risk of VISA development. Such tools will be valuable for keeping vancomycin an asset also in the future.
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Affiliation(s)
- Anaëlle Fait
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark; Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Stephanie Fulaz Silva
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark.
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2
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Qiu Z, Huang R, Wu Y, Li X, Sun C, Ma Y. Decoding the Structural Diversity: A New Horizon in Antimicrobial Prospecting and Mechanistic Investigation. Microb Drug Resist 2024; 30:254-272. [PMID: 38648550 DOI: 10.1089/mdr.2023.0232] [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] [Indexed: 04/25/2024] Open
Abstract
The escalating crisis of antimicrobial resistance (AMR) underscores the urgent need for novel antimicrobials. One promising strategy is the exploration of structural diversity, as diverse structures can lead to diverse biological activities and mechanisms of action. This review delves into the role of structural diversity in antimicrobial discovery, highlighting its influence on factors such as target selectivity, binding affinity, pharmacokinetic properties, and the ability to overcome resistance mechanisms. We discuss various approaches for exploring structural diversity, including combinatorial chemistry, diversity-oriented synthesis, and natural product screening, and provide an overview of the common mechanisms of action of antimicrobials. We also describe techniques for investigating these mechanisms, such as genomics, proteomics, and structural biology. Despite significant progress, several challenges remain, including the synthesis of diverse compound libraries, the identification of active compounds, the elucidation of complex mechanisms of action, the emergence of AMR, and the translation of laboratory discoveries to clinical applications. However, emerging trends and technologies, such as artificial intelligence, high-throughput screening, next-generation sequencing, and open-source drug discovery, offer new avenues to overcome these challenges. Looking ahead, we envisage an exciting future for structural diversity-oriented antimicrobial discovery, with opportunities for expanding the chemical space, harnessing the power of nature, deepening our understanding of mechanisms of action, and moving toward personalized medicine and collaborative drug discovery. As we face the continued challenge of AMR, the exploration of structural diversity will be crucial in our search for new and effective antimicrobials.
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Affiliation(s)
- Ziying Qiu
- School of Pharmacy, Binzhou Medical University, Yantai, China
| | - Rongkun Huang
- School of Pharmacy, Binzhou Medical University, Yantai, China
| | - Yuxuan Wu
- School of Pharmacy, Binzhou Medical University, Yantai, China
| | - Xinghao Li
- School of Pharmacy, Binzhou Medical University, Yantai, China
| | - Chunyu Sun
- School of Pharmacy, Binzhou Medical University, Yantai, China
| | - Yunqi Ma
- School of Pharmacy, Binzhou Medical University, Yantai, China
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3
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Rotsides P, Lee PJ, Webber N, Grasty KC, Beld J, Loll PJ. Diazirine Photoprobes for the Identification of Vancomycin-Binding Proteins. ACS BIO & MED CHEM AU 2024; 4:86-94. [PMID: 38645928 PMCID: PMC11027123 DOI: 10.1021/acsbiomedchemau.3c00067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/15/2023] [Accepted: 11/15/2023] [Indexed: 04/23/2024]
Abstract
Vancomycin's interactions with cellular targets drive its antimicrobial activity and also trigger expression of resistance against the antibiotic. Interaction partners for vancomycin have previously been identified using photoaffinity probes, which have proven to be useful tools for exploring vancomycin's interactome. This work seeks to develop diazirine-based vancomycin photoprobes that display enhanced specificity and bear fewer chemical modifications as compared to previous photoprobes. Using proteins fused to vancomycin's main cell-wall target, d-alanyl-d-alanine, we used mass spectrometry to show that these photoprobes specifically label known vancomycin-binding partners within minutes. In a complementary approach, we developed a Western-blot strategy targeting the vancomycin adduct of the photoprobes, eliminating the need for affinity tags and simplifying the analysis of photolabeling reactions. Together, the probes and identification strategy provide a novel and streamlined pipeline for identifying vancomycin-binding proteins.
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Affiliation(s)
- Photis Rotsides
- Department
of Biochemistry & Molecular Biology and Department of Microbiology &
Immunology, Drexel University College of
Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Paula J. Lee
- Department
of Biochemistry & Molecular Biology and Department of Microbiology &
Immunology, Drexel University College of
Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Nakoa Webber
- Department
of Biochemistry & Molecular Biology and Department of Microbiology &
Immunology, Drexel University College of
Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Kimberly C. Grasty
- Department
of Biochemistry & Molecular Biology and Department of Microbiology &
Immunology, Drexel University College of
Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Joris Beld
- Department
of Biochemistry & Molecular Biology and Department of Microbiology &
Immunology, Drexel University College of
Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Patrick J. Loll
- Department
of Biochemistry & Molecular Biology and Department of Microbiology &
Immunology, Drexel University College of
Medicine, Philadelphia, Pennsylvania 19102, United States
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4
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Fouad A, El-Sayed DH, Salman BE, Bakr HH, Adel SE, Alzarak TM, Mahmoud A. Macrocyclic Antibiotics as Effective Chiral Selectors in Liquid Chromatography for Enantiomeric Separation of Pharmaceutical Compounds: A Review. Crit Rev Anal Chem 2023:1-19. [PMID: 37342891 DOI: 10.1080/10408347.2023.2224442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2023]
Abstract
Chiral separation techniques play a crucial role in the pharmaceutical industry, where the enantiomeric purity of drugs can have a significant impact on their efficacy and safety. Macrocyclic antibiotics are highly effective chiral selectors used in various chiral separation techniques, including LC, HPLC, SMB, and TLC, offering reproducible results and a wide range of applications. However, developing robust and efficient immobilization mechanisms for these chiral selectors remains a challenge. This review article focuses on various immobilization approaches, such as immobilization, coating, encapsulation, and photosynthesis, that have been applied to immobilize macrocyclic antibiotics on their support. Commercially available macrocyclic antibiotics for conventional liquid chromatography include Vancomycin, Norvancomycin, Eremomycin, Teicoplanin, Ristocetin A, Rifamycin, Avoparcin, Bacitracin, and others. In addition, capillary (nano) liquid chromatography has also been used in chiral separation utilizing Vancomycin, Polymyxin B, Daptomycin, and Colistin Sulfate. Macrocyclic antibiotic-based CSPs have been extensively applied due to their reproducible results, ease of use, and broad range of applications, capable of separating a large number of racemates.
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Affiliation(s)
- Ali Fouad
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Al-Azhar University, Assiut, Egypt
| | | | | | - Hanan H Bakr
- Faculty of Science, Tanta University, Tanta, Egypt
| | - Shahd E Adel
- Faculty of Science, Tanta University, Tanta, Egypt
| | | | - Abdelrahman Mahmoud
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Al-Azhar University, Assiut, Egypt
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5
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Britton S, Lee K, Azizova L, Shaw G, Ayre WN, Mansell JP. Immobilised teicoplanin does not demonstrate antimicrobial activity against Staphylococcus aureus. Sci Rep 2022; 12:16661. [PMID: 36198734 PMCID: PMC9534865 DOI: 10.1038/s41598-022-20310-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 09/12/2022] [Indexed: 11/09/2022] Open
Abstract
Antibacterial bone biomaterial coatings appeal to orthopaedics, dentistry and veterinary medicine. Achieving the successful, stable conjugation of suitable compounds to biomaterial surfaces is a major challenge. A pragmatic starting point is to make use of existing, approved antibiotics which are known to remain functional in a stationary, immobilised state. This includes the macrocyclic glycopeptide, teicoplanin, following the discovery, in the 1990's, that it could be used as a chiral selector in chromatographic enantiomeric separations. Importantly teicoplanin works at the level of the bacterial cell wall making it a potential candidate for biomaterial functionalisations. We initially sought to functionalise titanium (Ti) with polydopamine and use this platform to capture teicoplanin, however we were unable to avoid the natural affinity of the antibiotic to the oxide surface of the metal. Whilst the interaction between teicoplanin and Ti was robust, we found that phosphate resulted in antibiotic loss. Before contemplating the covalent attachment of teicoplanin to Ti we examined whether a commercial teicoplanin stationary phase could kill staphylococci. Whilst this commercially available material could bind N-Acetyl-L-Lys-D-Ala-D-Ala it was unable to kill bacteria. We therefore strongly discourage attempts at covalently immobilising teicoplanin and/or other glycopeptide antibiotics in the pursuit of novel antibacterial bone biomaterials.
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Affiliation(s)
- S Britton
- Department of Applied Sciences, University of the West of England, Coldharbour Lane, Bristol, BS16 1QY, UK
| | - K Lee
- Department of Chemistry, Green-Nano Materials Research Center, Kyungpook National University, Daegu, 41566, South Korea
| | - L Azizova
- School of Dentistry, Cardiff University, Cardiff, CF14 4XY, UK
| | - G Shaw
- School of Dentistry, Cardiff University, Cardiff, CF14 4XY, UK
| | - W Nishio Ayre
- School of Dentistry, Cardiff University, Cardiff, CF14 4XY, UK
| | - J P Mansell
- Department of Applied Sciences, University of the West of England, Coldharbour Lane, Bristol, BS16 1QY, UK.
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6
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van Groesen E, Innocenti P, Martin NI. Recent Advances in the Development of Semisynthetic Glycopeptide Antibiotics: 2014-2022. ACS Infect Dis 2022; 8:1381-1407. [PMID: 35895325 PMCID: PMC9379927 DOI: 10.1021/acsinfecdis.2c00253] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The accelerated appearance of drug-resistant bacteria poses an ever-growing threat to modern medicine's capacity to fight infectious diseases. Gram-positive species such as methicillin-resistant Staphylococcus aureus (MRSA) and Streptococcus pneumoniae continue to contribute significantly to the global burden of antimicrobial resistance. For decades, the treatment of serious Gram-positive infections relied upon the glycopeptide family of antibiotics, typified by vancomycin, as a last line of defense. With the emergence of vancomycin resistance, the semisynthetic glycopeptides telavancin, dalbavancin, and oritavancin were developed. The clinical use of these compounds is somewhat limited due to toxicity concerns and their unusual pharmacokinetics, highlighting the importance of developing next-generation semisynthetic glycopeptides with enhanced antibacterial activities and improved safety profiles. This Review provides an updated overview of recent advancements made in the development of novel semisynthetic glycopeptides, spanning the period from 2014 to today. A wide range of approaches are covered, encompassing innovative strategies that have delivered semisynthetic glycopeptides with potent activities against Gram-positive bacteria, including drug-resistant strains. We also address recent efforts aimed at developing targeted therapies and advances made in extending the activity of the glycopeptides toward Gram-negative organisms.
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Affiliation(s)
- Emma van Groesen
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University 2333 BE Leiden, The Netherlands
| | - Paolo Innocenti
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University 2333 BE Leiden, The Netherlands
| | - Nathaniel I Martin
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University 2333 BE Leiden, The Netherlands
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7
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Vimberg V, Buriánková K, Mazumdar A, Branny P, Novotná GB. Role of membrane proteins in bacterial resistance to antimicrobial peptides. Med Res Rev 2021; 42:1023-1036. [PMID: 34796517 DOI: 10.1002/med.21869] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 09/19/2021] [Accepted: 10/21/2021] [Indexed: 11/07/2022]
Abstract
Several natural antimicrobial peptides (AMPs), including the novel semisynthetic lipoglycopeptide antibiotics telavancin, dalbavancin, and oritavancin, have been approved for clinical use to address the growing problem of multiple antibiotic-resistant Gram-positive bacterial infections. Nevertheless, the efficacy of these antibiotics has already been compromised. The SARS-CoV-2 pandemic led to the increased clinical use of all antibiotics, further promoting the development of bacterial resistance. Therefore, it is critical to gain a deeper understanding of the role of resistance mechanisms to minimize the consequential risks of long-term antibiotic use and misuse. Here, we summarize for the first time the current knowledge of resistance mechanisms that have been shown to cause resistance to clinically used AMPs, with particular focus on membrane proteins that have been reported to interfere with the activity of AMPs by affecting the binding of AMPs to bacteria.
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Affiliation(s)
- Vladimir Vimberg
- Laboratory for Biology of Secondary Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Karolína Buriánková
- Laboratory of Cell Signaling, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Aninda Mazumdar
- Laboratory for Biology of Secondary Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Pavel Branny
- Laboratory of Cell Signaling, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Gabriela B Novotná
- Laboratory for Biology of Secondary Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
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8
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Two Novel Semisynthetic Lipoglycopeptides Active against Staphylococcus aureus Biofilms and Cells in Late Stationary Growth Phase. Pharmaceuticals (Basel) 2021; 14:ph14111182. [PMID: 34832964 PMCID: PMC8619453 DOI: 10.3390/ph14111182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/06/2021] [Accepted: 11/17/2021] [Indexed: 11/16/2022] Open
Abstract
The increase in antibiotic resistance among Gram-positive bacteria underscores the urgent need to develop new antibiotics. New antibiotics should target actively growing susceptible bacteria that are resistant to clinically accepted antibiotics including bacteria that are not growing or are protected in a biofilm environment. In this paper, we compare the in vitro activities of two new semisynthetic glycopeptide antibiotics, MA79 and ERJ390, with two clinically used glycopeptide antibiotics-vancomycin and teicoplanin. The new antibiotics effectively killed not only exponentially growing cells of Staphylococcus aureus, but also cells in the stationary growth phase and biofilm.
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9
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Capriotti AL, Montone CM, Antonelli M, Cavaliere C, Gasparrini F, La Barbera G, Piovesana S, Laganà A. Simultaneous Preconcentration, Identification, and Quantitation of Selenoamino Acids in Oils by Enantioselective High Performance Liquid Chromatography and Mass Spectrometry. Anal Chem 2018; 90:8326-8330. [DOI: 10.1021/acs.analchem.8b02089] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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10
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Zeng D, Debabov D, Hartsell TL, Cano RJ, Adams S, Schuyler JA, McMillan R, Pace JL. Approved Glycopeptide Antibacterial Drugs: Mechanism of Action and Resistance. Cold Spring Harb Perspect Med 2016; 6:cshperspect.a026989. [PMID: 27663982 DOI: 10.1101/cshperspect.a026989] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The glycopeptide antimicrobials are a group of natural product and semisynthetic glycosylated peptides that show antibacterial activity against Gram-positive organisms through inhibition of cell-wall synthesis. This is achieved primarily through binding to the d-alanyl-d-alanine terminus of the lipid II bacterial cell-wall precursor, preventing cross-linking of the peptidoglycan layer. Vancomycin is the foundational member of the class, showing both clinical longevity and a still preferential role in the therapy of methicillin-resistant Staphylococcus aureus and of susceptible Enterococcus spp. Newer lipoglycopeptide derivatives (telavancin, dalbavancin, and oritavancin) were designed in a targeted fashion to increase antibacterial activity, in some cases through secondary mechanisms of action. Resistance to the glycopeptides emerged in delayed fashion and occurs via a spectrum of chromosome- and plasmid-associated elements that lead to structural alteration of the bacterial cell-wall precursor substrates.
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Affiliation(s)
- Daina Zeng
- Agile Sciences, Raleigh, North Carolina 27606
| | | | - Theresa L Hartsell
- Department of Anesthesiology/Critical Care Medicine, The Johns Hopkins School of Medicine and Nursing, Baltimore, Maryland 21287
| | - Raul J Cano
- ATCC Center for Translational Microbiology, Union, New Jersey 07083.,Biological Sciences Department, California Polytechnic State University, San Luis Obispo, California 93407
| | - Stacy Adams
- Center for Skin Biology, GlaxoSmithKline, Durham, North Carolina 27703
| | | | - Ronald McMillan
- ATCC Center for Translational Microbiology, Union, New Jersey 07083
| | - John L Pace
- ATCC Center for Translational Microbiology, Union, New Jersey 07083.,STEM Program, Kean University, Union, New Jersey 07083.,Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, Durham, North Carolina 27707
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11
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Dutta S, Dimitropoulos D, Feng Z, Persikova I, Sen S, Shao C, Westbrook J, Young J, Zhuravleva MA, Kleywegt GJ, Berman HM. Improving the representation of peptide-like inhibitor and antibiotic molecules in the Protein Data Bank. Biopolymers 2016; 101:659-68. [PMID: 24173824 PMCID: PMC3992913 DOI: 10.1002/bip.22434] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 10/27/2013] [Indexed: 11/08/2022]
Abstract
With the accumulation of a large number and variety of molecules in the Protein Data Bank (PDB) comes the need on occasion to review and improve their representation. The Worldwide PDB (wwPDB) partners have periodically updated various aspects of structural data representation to improve the integrity and consistency of the archive. The remediation effort described here was focused on improving the representation of peptide-like inhibitor and antibiotic molecules so that they can be easily identified and analyzed. Peptide-like inhibitors or antibiotics were identified in over 1000 PDB entries, systematically reviewed and represented either as peptides with polymer sequence or as single components. For the majority of the single-component molecules, their peptide-like composition was captured in a new representation, called the subcomponent sequence. A novel concept called “group” was developed for representing complex peptide-like antibiotics and inhibitors that are composed of multiple polymer and nonpolymer components. In addition, a reference dictionary was developed with detailed information about these peptide-like molecules to aid in their annotation, identification and analysis. Based on the experience gained in this remediation, guidelines, procedures, and tools were developed to annotate new depositions containing peptide-like inhibitors and antibiotics accurately and consistently. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 659–668, 2014.
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Affiliation(s)
- Shuchismita Dutta
- RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854-8076
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12
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Haslinger K, Redfield C, Cryle MJ. Structure of the terminal PCP domain of the non-ribosomal peptide synthetase in teicoplanin biosynthesis. Proteins 2015; 83:711-21. [PMID: 25586301 DOI: 10.1002/prot.24758] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 12/17/2014] [Accepted: 12/31/2014] [Indexed: 01/19/2023]
Abstract
The biosynthesis of the glycopeptide antibiotics, of which teicoplanin and vancomycin are representative members, relies on the combination of non-ribosomal peptide synthesis and modification of the peptide by cytochrome P450 (Oxy) enzymes while the peptide remains bound to the peptide synthesis machinery. We have structurally characterized the final peptidyl carrier protein domain of the teicoplanin non-ribosomal peptide synthetase machinery: this domain is believed to mediate the interactions with tailoring Oxy enzymes in addition to its function as a shuttle for intermediates between multiple non-ribosomal peptide synthetase domains. Using solution state NMR, we have determined structures of this PCP domain in two states, the apo and the post-translationally modified holo state, both of which conform to a four-helix bundle assembly. The structures exhibit the same general fold as the majority of known carrier protein structures, in spite of the complex biosynthetic role that PCP domains from the final non-ribosomal peptide synthetase module must play in glycopeptide antibiotic biosynthesis. These structures thus support the hypothesis that it is subtle rearrangements, rather than dramatic conformational changes, which govern carrier protein interactions and selectivity during non-ribosomal peptide synthesis.
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Affiliation(s)
- Kristina Haslinger
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, 69120, Germany
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13
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Haslinger K, Maximowitsch E, Brieke C, Koch A, Cryle MJ. Cytochrome P450 OxyBteiCatalyzes the First Phenolic Coupling Step in Teicoplanin Biosynthesis. Chembiochem 2014; 15:2719-28. [DOI: 10.1002/cbic.201402441] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Indexed: 01/25/2023]
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14
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Loll PJ, Xu P, Schmidt JT, Melideo SL. Enhancing ubiquitin crystallization through surface-entropy reduction. Acta Crystallogr F Struct Biol Commun 2014; 70:1434-42. [PMID: 25286958 PMCID: PMC4188098 DOI: 10.1107/s2053230x14019244] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 08/26/2014] [Indexed: 11/11/2022] Open
Abstract
Ubiquitin has many attributes suitable for a crystallization chaperone, including high stability and ease of expression. However, ubiquitin contains a high surface density of lysine residues and the doctrine of surface-entropy reduction suggests that these lysines will resist participating in packing interactions and thereby impede crystallization. To assess the contributions of these residues to crystallization behavior, each of the seven lysines of ubiquitin was mutated to serine and the corresponding single-site mutant proteins were expressed and purified. The behavior of these seven mutants was then compared with that of the wild-type protein in a 384-condition crystallization screen. The likelihood of obtaining crystals varied by two orders of magnitude within this set of eight proteins. Some mutants crystallized much more readily than the wild type, while others crystallized less readily. X-ray crystal structures were determined for three readily crystallized variants: K11S, K33S and the K11S/K63S double mutant. These structures revealed that the mutant serine residues can directly promote crystallization by participating in favorable packing interactions; the mutations can also exert permissive effects, wherein crystallization appears to be driven by removal of the lysine rather than by addition of a serine. Presumably, such permissive effects reflect the elimination of steric and electrostatic barriers to crystallization.
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Affiliation(s)
- Patrick J. Loll
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Peining Xu
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - John T. Schmidt
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Scott L. Melideo
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
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15
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Han S, Le BV, Hajare HS, Baxter RHG, Miller SJ. X-ray crystal structure of teicoplanin A₂-2 bound to a catalytic peptide sequence via the carrier protein strategy. J Org Chem 2014; 79:8550-6. [PMID: 25147913 PMCID: PMC4168787 DOI: 10.1021/jo501625f] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
![]()
We
report the X-ray crystal structure of a site-selective peptide
catalyst moiety and teicoplanin A2-2 complex. The expressed
protein ligation technique was used to couple T4 lysozyme (T4L) and
a synthetic peptide catalyst responsible for the selective phosphorylation
of the N-acetylglucosamine sugar in a teicoplanin
A2-2 derivative. The T4L-Pmh-dPro-Aib-dAla-dAla construct was crystallized in the presence of teicoplanin
A2-2. The resulting 2.3 Å resolution protein–peptide–teicoplanin
complex crystal structure revealed that the nucleophilic nitrogen
of N-methylimidazole in the Pmh residue is in closer
proximity (7.6 Å) to the N-acetylglucosamine
than the two other sugar rings present in teicoplanin (9.3 and 20.3
Å, respectively). This molecular arrangement is consistent with
the observed selectivity afforded by the peptide-based catalyst when
it is applied to a site-selective phosphorylation reaction involving
a teicoplanin A2-2 derivative.
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Affiliation(s)
- Sunkyu Han
- Department of Chemistry, Yale University , New Haven, Connecticut 06511, United States
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16
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Treviño J, Bayón C, Ardá A, Marinelli F, Gandolfi R, Molinari F, Jimenez-Barbero J, Hernáiz MJ. New Insights into Glycopeptide Antibiotic Binding to Cell Wall Precursors using SPR and NMR Spectroscopy. Chemistry 2014; 20:7363-72. [DOI: 10.1002/chem.201303310] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 04/02/2014] [Indexed: 11/09/2022]
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17
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Cheng M, Ziora ZM, Hansford KA, Blaskovich MA, Butler MS, Cooper MA. Anti-cooperative ligand binding and dimerisation in the glycopeptide antibiotic dalbavancin. Org Biomol Chem 2014; 12:2568-75. [PMID: 24608916 PMCID: PMC4082399 DOI: 10.1039/c3ob42428f] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 01/22/2014] [Indexed: 12/22/2022]
Abstract
Dalbavancin, a semi-synthetic glycopeptide with enhanced antibiotic activity compared to vancomycin and teicoplanin, binds to the C-terminal lysyl-d-alanyl-d-alanine subunit of Lipid II, inhibiting peptidoglycan biosynthesis. In this study, micro-calorimetry and electrospray ionization (ESI)-MS have been used to investigate the relationship between oligomerisation of dalbavancin and binding of a Lipid II peptide mimic, diacetyl-Lys-d-Ala-d-Ala (Ac2-Kaa). Dalbavancin dimerised strongly in an anti-cooperative manner with ligand-binding, as was the case for ristocetin A, but not for vancomycin and teicoplanin. Dalbavancin and ristocetin A both adopt an 'closed' conformation upon ligand binding, suggesting anti-cooperative dimerisation with ligand-binding may be a general feature of dalbavancin/ristocetin A-like glycopeptides. Understanding these effects may provide insight into design of novel dalbavancin derivatives with cooperative ligand-binding and dimerisation characteristics that could enhance antibiotic activity.
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Affiliation(s)
- Mu Cheng
- Division of Chemistry and Structural Biology , Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia . ; Tel: +61-7-3346-2044
| | - Zyta M. Ziora
- Division of Chemistry and Structural Biology , Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia . ; Tel: +61-7-3346-2044
| | - Karl A. Hansford
- Division of Chemistry and Structural Biology , Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia . ; Tel: +61-7-3346-2044
| | - Mark A. Blaskovich
- Division of Chemistry and Structural Biology , Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia . ; Tel: +61-7-3346-2044
| | - Mark S. Butler
- Division of Chemistry and Structural Biology , Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia . ; Tel: +61-7-3346-2044
| | - Matthew A. Cooper
- Division of Chemistry and Structural Biology , Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia . ; Tel: +61-7-3346-2044
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