1
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Chioti VT, McWhorter KL, Blue TC, Li Y, Xu F, Jeffrey PD, Davis KM, Seyedsayamdost MR. Potent and specific antibiotic combination therapy against Clostridioides difficile. Nat Chem Biol 2024; 20:924-933. [PMID: 38942968 PMCID: PMC11306116 DOI: 10.1038/s41589-024-01651-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 05/15/2024] [Indexed: 06/30/2024]
Abstract
Keratinicyclins and keratinimicins are recently discovered glycopeptide antibiotics. Keratinimicins show broad-spectrum activity against Gram-positive bacteria, while keratinicyclins form a new chemotype by virtue of an unusual oxazolidinone moiety and exhibit specific antibiosis against Clostridioides difficile. Here we report the mechanism of action of keratinicyclin B (KCB). We find that steric constraints preclude KCB from binding peptidoglycan termini. Instead, KCB inhibits C. difficile growth by binding wall teichoic acids (WTAs) and interfering with cell wall remodeling. A computational model, guided by biochemical studies, provides an image of the interaction of KCB with C. difficile WTAs and shows that the same H-bonding framework used by glycopeptide antibiotics to bind peptidoglycan termini is used by KCB for interacting with WTAs. Analysis of KCB in combination with vancomycin (VAN) shows highly synergistic and specific antimicrobial activity, and that nanomolar combinations of the two drugs are sufficient for complete growth inhibition of C. difficile, while leaving common commensal strains unaffected.
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Affiliation(s)
| | | | - Tamra C Blue
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | - Yuchen Li
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Fei Xu
- Institute of Pharmaceutical Biotechnology and Department of Gastroenterology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Philip D Jeffrey
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | | | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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2
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Rabe A, Gesell Salazar M, Michalik S, Kocher T, Below H, Völker U, Welk A. Impact of different oral treatments on the composition of the supragingival plaque microbiome. J Oral Microbiol 2022; 14:2138251. [PMID: 36338832 PMCID: PMC9629129 DOI: 10.1080/20002297.2022.2138251] [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] [Indexed: 11/12/2022] Open
Abstract
Background Dental plaque consists of a diverse microbial community embedded in a complex structure of exopolysaccharides. Dental biofilms form a natural barrier against pathogens but lead to oral diseases in a dysbiotic state. Objective Using a metaproteome approach combined with a standard plaque-regrowth study, this pilot study examined the impact of different concentrations of lactoperoxidase (LPO) on early plaque formation, and active biological processes. Design Sixteen orally healthy subjects received four local treatments as a randomized single-blind study based on a cross-over design. Two lozenges containing components of the LPO-system in different concentrations were compared to a placebo and Listerine®. The newly formed dental plaque was analyzed by mass spectrometry (nLC-MS/MS). Results On average 1,916 metaproteins per sample were identified, which could be assigned to 116 genera and 1,316 protein functions. Listerine® reduced the number of metaproteins and their relative abundance, confirming the plaque inhibiting effect. The LPO-lozenges triggered mainly higher metaprotein abundances of early and secondary colonizers as well as bacteria associated with dental health but also periodontitis. Functional information indicated plaque biofilm growth. Conclusion In conclusion, the mechanisms on plaque biofilm formation of Listerine® and the LPO-system containing lozenges are different. In contrast to Listerine®, the lozenges led to a higher bacterial diversity.
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Affiliation(s)
- Alexander Rabe
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475Greifswald, Germany,CONTACT Alexander Rabe University Medicine Greifswald, Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, Felix-Hausdorff-Str. 8, 17489Greifswald, Germany
| | - Manuela Gesell Salazar
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475Greifswald, Germany
| | - Stephan Michalik
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475Greifswald, Germany
| | - Thomas Kocher
- Center for Dentistry, Oral and Maxillofacial Medicine, Department of Restorative Dentistry, Periodontology, Endodontology, and Preventive and Pediatric Dentistry, Dental School of University Medicine Greifswald, Fleischmannstraße 42-44, 17489
| | - Harald Below
- Institute for Hygiene and Environmental Medicine, University Medicine Greifswald, Walter-Rathenau-Straße 49 A17475Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475Greifswald, Germany
| | - Alexander Welk
- Center for Dentistry, Oral and Maxillofacial Medicine, Department of Restorative Dentistry, Periodontology, Endodontology, and Preventive and Pediatric Dentistry, Dental School of University Medicine Greifswald, Fleischmannstraße 42-44, 17489
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3
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NMR and MD Analysis of the Bonding Interaction of Vancomycin with Muramyl Pentapeptide. Int J Mol Sci 2022; 23:ijms23031146. [PMID: 35163070 PMCID: PMC8835396 DOI: 10.3390/ijms23031146] [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: 12/14/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 02/05/2023] Open
Abstract
The article describes an NMR spectroscopy study of interactions between vancomycin and a muramyl pentapeptide in two complexes: vancomycin and a native muramyl pentapeptide ended with D-alanine (MPP-D-Ala), and vancomycin and a modified muramyl pentapeptide ended with D-serine (MPP-D-Ser). The measurements were made in a 9:1 mixture of H2O and D2O. The obtained results confirmed the presence of hydrogen bonds previously described in the literature. At the same time, thanks to the pentapeptide model used, we were able to prove the presence of two more hydrogen bonds formed by the side chain amino group of L-lysine and oxygen atoms from the vancomycin carboxyl and amide groups. This type of interaction has not been described before. The existence of these hydrogen bonds was confirmed by the 1H NMR and molecular modeling. The formation of these bonds incurs additional through-space interactions, visible in the NOESY spectrum, between the protons of the L-lysine amino group and a vancomycin-facing hydrogen atom in the benzylic position. The presence of such interactions was also confirmed by molecular dynamics trajectory analysis.
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4
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Reeßing F, Bispo M, López-Álvarez M, van Oosten M, Feringa BL, van Dijl JM, Szymański W. A Facile and Reproducible Synthesis of Near-Infrared Fluorescent Conjugates with Small Targeting Molecules for Microbial Infection Imaging. ACS OMEGA 2020; 5:22071-22080. [PMID: 32923765 PMCID: PMC7482087 DOI: 10.1021/acsomega.0c02094] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/11/2020] [Indexed: 05/02/2023]
Abstract
Optical imaging of microbial infections, based on the detection of targeted fluorescent probes, offers high sensitivity and resolution with a relatively simple and portable setup. As the absorbance of near-infrared (NIR) light by human tissues is minimal, using respective tracers, such as IRdye800CW, enables imaging deeper target sites in the body. Herein, we present a general strategy for the conjugation of IRdye800CW and IRdye700DX to small molecules (vancomycin and amphotericin B) to provide conjugates targeted toward bacterial and fungal infections for optical imaging and photodynamic therapy. In particular, we present how the use of coupling agents (such as HBTU or HATU) leads to high yields (over 50%) in the reactions of amines and IRDye-NHS esters and how precipitation can be used as a convenient purification strategy to remove excess of the targeting molecule after the reaction. The high selectivity of the synthesized model compound Vanco-800CW has been proven in vitro, and the development of analogous agents opens up new possibilities for diagnostic and theranostic purposes. In times of increasing microbial resistance, this research gives us access to a platform of new fluorescent tracers for the imaging of infections, enabling early diagnosis and respective treatment.
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Affiliation(s)
- Friederike Reeßing
- Department
of Radiology, Medical Imaging Center, University
of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen 9713GZ, The Netherlands
- Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The
Netherlands
| | - Mafalda Bispo
- Department
of Medical Microbiology, University of Groningen,
University Medical Center Groningen, Hanzeplein 1, Groningen 9713GZ, The Netherlands
| | - Marina López-Álvarez
- Department
of Medical Microbiology, University of Groningen,
University Medical Center Groningen, Hanzeplein 1, Groningen 9713GZ, The Netherlands
| | - Marleen van Oosten
- Department
of Medical Microbiology, University of Groningen,
University Medical Center Groningen, Hanzeplein 1, Groningen 9713GZ, The Netherlands
| | - Ben L. Feringa
- Department
of Radiology, Medical Imaging Center, University
of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen 9713GZ, The Netherlands
- Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The
Netherlands
| | - Jan Maarten van Dijl
- Department
of Medical Microbiology, University of Groningen,
University Medical Center Groningen, Hanzeplein 1, Groningen 9713GZ, The Netherlands
| | - Wiktor Szymański
- Department
of Radiology, Medical Imaging Center, University
of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen 9713GZ, The Netherlands
- Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The
Netherlands
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5
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Samaszko-Fiertek J, Szulc M, Dmochowska B, Jaśkiewicz M, Kamysz W, Ślusarz R, Madaj J. Influence of Carbohydrate Residues on Antibacterial Activity of Vancomycin. LETT ORG CHEM 2020. [DOI: 10.2174/1570178616666190329225748] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
This paper presents synthesis of vancomycin derivatives modified with selected 1- and
2-aminoalditols to carboxylic function and 2,5-anhydro-D-mannose and D-talose to amino function of
vancosamine via reductive alkylation. MIC and MBC of these derivatives were determined for reference
strains of bacteria: Staphylococcus aureus ATCC 25923, ATCC 6538, ATCC 6538/P, S. epidemidis
ATCC 14490, E. faecium PCM 1859, E. faecalis PCM 2673, S. pyogenes PCM 465, and
S. pneumonia ATCC 49619 and compared with the activity of vancomycin and its aglycone. Our findings
confirm that sugar fragments can play an important role in the mechanism of interaction of vancomycin
with bacterial cell wall peptidoglycan.
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Affiliation(s)
| | - Monika Szulc
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Barbara Dmochowska
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Maciej Jaśkiewicz
- Faculty of Pharmacy, Medical University of Gdansk, Al. Gen. Hallera 107, 80-416 Gdansk, Poland
| | - Wojciech Kamysz
- Faculty of Pharmacy, Medical University of Gdansk, Al. Gen. Hallera 107, 80-416 Gdansk, Poland
| | - Rafał Ślusarz
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Janusz Madaj
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
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6
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Yuzuriha K, Yakabe K, Nagai H, Li S, Zendo T, Zai K, Kishimura A, Hase K, Kim YG, Mori T, Katayama Y. Protection of gut microbiome from antibiotics: development of a vancomycin-specific adsorbent with high adsorption capacity. BIOSCIENCE OF MICROBIOTA FOOD AND HEALTH 2020; 39:128-136. [PMID: 32775131 PMCID: PMC7392918 DOI: 10.12938/bmfh.2020-002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 02/14/2020] [Indexed: 01/01/2023]
Abstract
The fraction of administered antibiotics that reach the cecum and colon causes dysbiosis of the gut microbiome, resulting in various diseases. Protection of the gut microbiome
from antibiotics using antibiotic adsorbents in the cecum and colon is a promising method to overcome this issue. Previously, activated charcoal (AC) has been reported to protect
the gut microbiome of host animals. AC is an adsorbent that is widely used to capture toxic compounds and overdosed drugs in the gastrointestinal tract. The specificity of
adsorbents for antibiotics is critical to avoid the risk of unexpected side effects caused by nonspecific adsorption of biological compounds in the intestinal fluid, such as bile
acids and essential micronutrients. Here, we have developed specific adsorbents for vancomycin (VCM), which is known to cause gut dysbiosis. The adsorbents were composed of
polyethyleneglycol-based microparticles (MPs) in which a specific ligand for VCM, D-Ala-D-Ala-OH, was attached via dendrons of D-lysine to raise the content of the ligand in the
MPs. The MPs successfully protected Staphylococcus lentus from VCM in vitro because of the adsorption of VCM in the culture media.
Pre-administration of MPs to mice reduced the amount of free VCM in the feces to an undetectable level. This treatment minimized the effect of VCM on gut microbiota and provided
protection against Clostridioides difficile infection after oral challenge with spores.
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Affiliation(s)
- Kazuki Yuzuriha
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kyosuke Yakabe
- Division of Biochemistry, Faculty of Pharmacy, Keio University, Tokyo 105-8512, Japan.,Research Center for Drug Discovery, Faculty of Pharmacy, Keio University, Tokyo 105-8512, Japan
| | - Haruka Nagai
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Shunyi Li
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Takeshi Zendo
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka 819-039, Japan
| | - Khadijah Zai
- Department of Pharmaceutics, Faculty of Pharmacy, Gadjah Mada University, Yogyakarta 55281, Indonesia
| | - Akihiro Kishimura
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.,Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.,Center for Future Chemistry, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.,International Research Center for Molecular Systems, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Koji Hase
- Division of Biochemistry, Faculty of Pharmacy, Keio University, Tokyo 105-8512, Japan.,Division of Mucosal Barriology, International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Yun-Gi Kim
- Research Center for Drug Discovery, Faculty of Pharmacy, Keio University, Tokyo 105-8512, Japan
| | - Takeshi Mori
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.,Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.,Center for Future Chemistry, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yoshiki Katayama
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.,Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.,Center for Future Chemistry, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.,International Research Center for Molecular Systems, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.,Advanced Medicine Innovation Center, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.,Department of Biomedical Engineering, Chung Yuan Christian University, 200 Chung Pei Rd., Chung Li, 32023 ROC, Taiwan
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7
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Czuban M, Srinivasan S, Yee NA, Agustin E, Koliszak A, Miller E, Khan I, Quinones I, Noory H, Motola C, Volkmer R, Di Luca M, Trampuz A, Royzen M, Mejia Oneto JM. Bio-Orthogonal Chemistry and Reloadable Biomaterial Enable Local Activation of Antibiotic Prodrugs and Enhance Treatments against Staphylococcus aureus Infections. ACS CENTRAL SCIENCE 2018; 4:1624-1632. [PMID: 30648146 PMCID: PMC6311693 DOI: 10.1021/acscentsci.8b00344] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Indexed: 05/08/2023]
Abstract
Systemic administration of antibiotics can cause severe side-effects such as liver and kidney toxicity, destruction of healthy gut bacteria, as well as multidrug resistance. Here, we present a bio-orthogonal chemistry-based strategy toward local prodrug concentration and activation. The strategy is based on the inverse electron-demand Diels-Alder chemistry between trans-cyclooctene and tetrazine and involves a biomaterial that can concentrate and activate multiple doses of systemic antibiotic therapy prodrugs at a local site. We demonstrate that a biomaterial, consisting of alginate hydrogel modified with tetrazine, is efficient at activating multiple doses of prodrugs of vancomycin and daptomycin in vitro as well as in vivo. These results support a drug delivery process that is independent of endogenous environmental markers. This approach is expected to improve therapeutic efficacy with decreased side-effects of antibiotics against bacterial infections. The platform has a wide scope of possible applications such as wound healing, and cancer and immunotherapy.
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Affiliation(s)
- Magdalena Czuban
- Berlin-Brandenburg
Center for Regenerative Therapies and Berlin-Brandenburg School for
Regenerative Therapies, Charité Universitätsmedizin
Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
- Institute
of Chemistry and Biochemistry, Freie Universität, Takustr. 3, 14195 Berlin, Germany
| | | | - Nathan A. Yee
- Shasqi
Inc., 665 Third Street, San Francisco, California 94107, United States
| | - Edgar Agustin
- Department
of Chemistry, University at Albany, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Anna Koliszak
- Berlin-Brandenburg
Center for Regenerative Therapies, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Ethan Miller
- Shasqi
Inc., 665 Third Street, San Francisco, California 94107, United States
| | - Irfan Khan
- Department
of Chemistry, University at Albany, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Ilenis Quinones
- Department
of Chemistry, University at Albany, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Hasina Noory
- Department
of Chemistry, University at Albany, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Christopher Motola
- Department
of Chemistry, University at Albany, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Rudolf Volkmer
- Institute
for Medical Immunology and Leibniz-Institut für Molekulare
Pharmakologie, Charité Universitätsmedizin
Berlin, 10117 Berlin, Germany
| | - Mariagrazia Di Luca
- Berlin-Brandenburg
Center for Regenerative Therapies, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Andrej Trampuz
- Charité −
Universitätsmedizin Berlin, corporate member
of Freie Universität Berlin,
Humboldt-Universitat zu Berlin, and Berlin Institute of Health, Center
for Musculoskeletal Surgery, Charitéplatz 1, 10117 Berlin, Germany
| | - Maksim Royzen
- Department
of Chemistry, University at Albany, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Jose M. Mejia Oneto
- Shasqi
Inc., 665 Third Street, San Francisco, California 94107, United States
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8
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Wu ZC, Isley NA, Boger DL. N-Terminus Alkylation of Vancomycin: Ligand Binding Affinity, Antimicrobial Activity, and Site-Specific Nature of Quaternary Trimethylammonium Salt Modification. ACS Infect Dis 2018; 4:1468-1474. [PMID: 30067012 DOI: 10.1021/acsinfecdis.8b00152] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A series of vancomycin derivatives alkylated at the N-terminus amine were synthesized, including those that contain quaternary trimethylammonium salts either directly at the terminal amine site or with an intervening three-carbon spacer. The examination of their properties provides important comparisons with a C-terminus trimethylammonium salt modification that we recently found to improve the antimicrobial potency of vancomycin analogues through an added mechanism of action. The N-terminus modifications disclosed herein were well-tolerated, minimally altering model ligand binding affinities (d-Ala-d-Ala) and antimicrobial activity, but did not induce membrane permeabilization that was observed with a similar C-terminus modification. The results indicate that our earlier observations with the C-terminus modification are sensitive to the site as well as structure of the trimethylammonium salt modification and are not simply the result of nonspecific effects derived from introduction of a cationic charge.
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Affiliation(s)
- Zhi-Chen Wu
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Nicholas A. Isley
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Dale L. Boger
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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9
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Thaker MN, Wright GD. Opportunities for synthetic biology in antibiotics: expanding glycopeptide chemical diversity. ACS Synth Biol 2015; 4:195-206. [PMID: 23654249 PMCID: PMC4384835 DOI: 10.1021/sb300092n] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Synthetic
biology offers a new path for the exploitation and improvement
of natural products to address the growing crisis in antibiotic resistance.
All antibiotics in clinical use are facing eventual obsolesce as a
result of the evolution and dissemination of resistance mechanisms,
yet there are few new drug leads forthcoming from the pharmaceutical
sector. Natural products of microbial origin have proven over the
past 70 years to be the wellspring of antimicrobial drugs. Harnessing
synthetic biology thinking and strategies can provide new molecules
and expand chemical diversity of known antibiotic scaffolds to provide
much needed new drug leads. The glycopeptide antibiotics offer paradigmatic
scaffolds suitable for such an approach. We review these strategies
here using the glycopeptides as an example and demonstrate how synthetic
biology can expand antibiotic chemical diversity to help address the
growing resistance crisis.
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Affiliation(s)
- Maulik N. Thaker
- M.G. DeGroote
Institute for
Infectious Disease Research, Department of Biochemistry and Biomedical
Sciences, McMaster University, Hamilton, ON, L8S 4K1 Canada
| | - Gerard D. Wright
- M.G. DeGroote
Institute for
Infectious Disease Research, Department of Biochemistry and Biomedical
Sciences, McMaster University, Hamilton, ON, L8S 4K1 Canada
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10
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Jia Z, O'Mara ML, Zuegg J, Cooper MA, Mark AE. Vancomycin: ligand recognition, dimerization and super-complex formation. FEBS J 2013; 280:1294-307. [PMID: 23298227 DOI: 10.1111/febs.12121] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 12/19/2012] [Accepted: 12/21/2012] [Indexed: 11/28/2022]
Abstract
The antibiotic vancomycin targets lipid II, blocking cell wall synthesis in Gram-positive bacteria. Despite extensive study, questions remain regarding how it recognizes its primary ligand and what is the most biologically relevant form of vancomycin. In this study, molecular dynamics simulation techniques have been used to examine the process of ligand binding and dimerization of vancomycin. Starting from one or more vancomycin monomers in solution, together with different peptide ligands derived from lipid II, the simulations predict the structures of the ligated monomeric and dimeric complexes to within 0.1 nm rmsd of the structures determined experimentally. The simulations reproduce the conformation transitions observed by NMR and suggest that proposed differences between the crystal structure and the solution structure are an artifact of the way the NMR data has been interpreted in terms of a structural model. The spontaneous formation of both back-to-back and face-to-face dimers was observed in the simulations. This has allowed a detailed analysis of the origin of the cooperatively between ligand binding and dimerization and suggests that the formation of face-to-face dimers could be functionally significant. The work also highlights the possible role of structural water in stabilizing the vancomycin ligand complex and its role in the manifestation of vancomycin resistance.
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Affiliation(s)
- ZhiGuang Jia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld, Australia
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11
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Fowler BS, Laemmerhold KM, Miller SJ. Catalytic site-selective thiocarbonylations and deoxygenations of vancomycin reveal hydroxyl-dependent conformational effects. J Am Chem Soc 2012; 134:9755-61. [PMID: 22621706 PMCID: PMC3374881 DOI: 10.1021/ja302692j] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We have examined peptide-based catalysts for the site-selective thiocarbonylation of a protected form of vancomycin. Several catalysts were identified that either enhanced or altered the inherent selectivity profile exhibited by the substrate. Two catalysts, one identified through screening and another through rational design, were demonstrated to be effective on 0.50-g scale. Deoxygenations led ultimately to two new deoxy-vancomycin derivatives, and surprising conformational consequences of deoxygenation were revealed for one of the new compounds. These effects were mirrored in the biological activities of the new analogues and support a structural role for certain hydroxyls in the native structure.
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Affiliation(s)
- Brandon S. Fowler
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT 06520-8107
| | - Kai M. Laemmerhold
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT 06520-8107
| | - Scott J. Miller
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT 06520-8107
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12
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Mark LP, Gill MC, Mahut M, Derrick PJ. Dual nano-electrospray for probing solution interactions and fast reactions of complex biomolecules. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2012; 18:439-46. [PMID: 23221113 DOI: 10.1255/ejms.1198] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
A novel nano-electrospray emitter has been developed containing two separated channels running throughout the length of the emitter. The emitters have been fabricated from "theta-shaped" borosilicate capillaries. Loading of different solutions into the two different channels opens up the possibility to study short timescale interactions within a Taylor cone common to both channels. The common Taylor cone constitutes an extremely small "mixing volume" of the order of femtolitres. The products of electrospray from the dual-channel emitters have been analysed by Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry. Results are presented for interactions of vancomycin with diacetyl-L-lysyl-D-alanyl- D-alanine and interactions of vancomycin with deuterated vancomycin. On the basis of these results, it is concluded that, during electrospray, specific non-covalent adducts have been formed and that there have been exchange reactions involving making and breaking of covalent bonds.
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Affiliation(s)
- Lewis P Mark
- Department of Chemistry, University of Warwick, Coventry, UK
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13
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Jia Z, O'Mara M, Zuegg J, Cooper M, Mark A. The effect of environment on the recognition and binding of vancomycin to native and resistant forms of lipid II. Biophys J 2011; 101:2684-92. [PMID: 22261057 PMCID: PMC3297793 DOI: 10.1016/j.bpj.2011.10.047] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 09/10/2011] [Accepted: 10/31/2011] [Indexed: 10/14/2022] Open
Abstract
Molecular dynamics simulations and free energy calculations have been used to examine in detail the mechanism by which a receptor molecule (the glycopeptide antibiotic vancomycin) recognizes and binds to a target molecule (lipid II) embedded within a membrane environment. The simulations show that the direct interaction of vancomycin with lipid II, as opposed to initial binding to the membrane, leads most readily to the formation of a stable complex. The recognition of lipid II by vancomycin occurred via the N-terminal amine group of vancomycin and the C-terminal carboxyl group of lipid II. Despite lying at the membrane-water interface, the interaction of vancomycin with lipid II was found to be essentially identical to that of soluble tripeptide analogs of lipid II (Ac-d-Ala-d-Ala; root mean-square deviation 0.11 nm). Free energy calculations also suggest that the relative binding affinity of vancomycin for native, resistant, and synthetic forms of membrane-bound lipid II was unaffected by the membrane environment. The effect of the dimerization of vancomycin on the binding of lipid II, the position of lipid II within a biological membrane, and the effect of the isoamylene tail of lipid II on membrane fluidity have also been examined.
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Affiliation(s)
- ZhiGuang Jia
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Megan L. O'Mara
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Johannes Zuegg
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | - Matthew A. Cooper
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | - Alan E. Mark
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
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14
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Abstract
AbstractSix complexes of vancomycin and peptidoglycan precursors were studied via molecular dynamics simulations. The interactions between the antibiotic and peptidoglycan fragments were identified and described in detail. All six studied modifications of the peptidoglycan precursor resulted in a weakening of the interaction with vancomycin when comparing to the native D-Ala-D-Ala-terminated fragment. It was confirmed that the N-terminus of the vancomycin is directly responsible for peptidoglycan recognition and antimicrobial activity. In simulated systems, the saccharide part of the antibiotic interacts with peptide precursors, thus it could also be important for antimicrobial activity. The complex terminated with D-Lac is the only one in which there is a weak interaction with the sugar moiety in the simulated systems. Analysis of conformational changes is a major scope of this work. The lack of interactions resulting from modification of the peptidoglycan precursors (D-Lac, D-Ser or other substitution) would be counterbalanced by proper modifications of the vancomycin moiety, especially the saccharide part of vancomycin.
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15
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Tripropeptin C blocks the lipid cycle of cell wall biosynthesis by complex formation with undecaprenyl pyrophosphate. Antimicrob Agents Chemother 2011; 55:3821-8. [PMID: 21628543 DOI: 10.1128/aac.00443-11] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tripropeptin C (TPPC) is a naturally occurring cyclic lipodepsipeptide antibiotic produced by a Lysobacter sp. TPPC exhibits potent antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococci (VRE), and penicillin-resistant Streptococcus pneumoniae. This antibiotic also inhibits the incorporation of N-acetylglucosamine into the peptidoglycan of S. aureus at a 50% inhibitory concentration (IC(50)) of 0.7 μM, which is proportional to its MIC (0.87 μM; equivalent to 1.0 μg/ml). Treatment of exponential-phase S. aureus cells with TPPC resulted in accumulation of UDP-MurNAc-pentapeptide in the cytoplasm. The antimicrobial activity of TPPC was weakened by the addition of prenyl pyrophosphates but not by prenyl phosphates, UDP-linked sugars, or the pentapeptide of peptidoglycan. The direct interaction between TPPC and undecaprenyl pyrophosphate (C(55)-PP) was observed by mass spectrometry and thin-layer chromatography analysis, indicating that TPPC can potentially inhibit C(55)-PP phosphatase activity, which plays a crucial role in the lipid cycle of peptidoglycan synthesis. As expected, TPPC inhibits this enzymatic reaction at an IC(50) of 0.03 to 0.1 μM in vitro, as does bacitracin. From the analysis of accumulation of lipid carrier-related compounds, TPPC was found to cause the accumulation of C(55)-PP in situ, leading to the accumulation of a glycine-containing lipid intermediate. This suggested that the TPPC/C(55)-PP complex also inhibits the transglycosylation step or flippase activity, adding to the inhibition of C(55)-PP dephosphorylation. This mode of action is different from that of currently available drugs such as vancomycin, daptomycin, and bacitracin.
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Dellai A, Maricic I, Kumar V, Arutyunyan S, Bouraoui A, Nefzi A. Parallel synthesis and anti-inflammatory activity of cyclic peptides cyclosquamosin D and Met-cherimolacyclopeptide B and their analogs. Bioorg Med Chem Lett 2010; 20:5653-7. [PMID: 20801649 PMCID: PMC2940269 DOI: 10.1016/j.bmcl.2010.08.033] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Revised: 08/04/2010] [Accepted: 08/06/2010] [Indexed: 11/19/2022]
Abstract
We report the parallel synthesis of two natural cyclopeptides, isolated from the seeds of Annona squamosa, cyclosquamosin D (A1), and Met-cherimolacyclopeptide B (B) and their analogs. All of the compounds were screened for anti-inflammatory activity by evaluating their inhibitory effects on the production of pro-inflammatory cytokines using the lipopolysaccharide stimulated macrophage J774A.1 cell line. Compounds having significant anti-inflammatory activity in suppressing the secretion of IL-6 and TNF-α have been identified, some of which exhibit activity superior to that observed with the natural products.
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Affiliation(s)
- Afef Dellai
- Faculté de Pharmacie, Laboratoire de Pharmacologie Marine, 5000 Monastir, Tunisia
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17
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Parallel synthesis of 19-membered ring macro-heterocycles via intramolecular thioether formation. Tetrahedron Lett 2010. [DOI: 10.1016/j.tetlet.2010.05.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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18
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Poully JC, Lecomte F, Nieuwjaer N, Manil B, Schermann JP, Desfrançois C, Calvo F, Grégoire G. Probing the specific interactions and structures of gas-phase vancomycin antibiotics with cell-wall precursor through IRMPD spectroscopy. Phys Chem Chem Phys 2010; 12:3606-15. [DOI: 10.1039/b923787a] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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19
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Lawson MC, Shoemaker R, Hoth KB, Bowman CN, Anseth KS. Polymerizable vancomycin derivatives for bactericidal biomaterial surface modification: structure-function evaluation. Biomacromolecules 2009; 10:2221-34. [PMID: 19606854 PMCID: PMC2936007 DOI: 10.1021/bm900410a] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
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Surface modification of implantable biomaterials with biologically active functionalities, including antimicrobials, has wide potential for addressing implant-related design problems. Here, four polymerizable vancomycin derivatives bearing either acrylamide or poly(ethylene glycol) (PEG)-acrylate were synthesized and then polymerized through a surface-mediated reaction. Functionalization of vancomycin at either the V3 or the X1 position decreased monomeric activity by 6−75-fold depending on the modification site and the nature of the adduct (P < 0.08 for all comparisons). A 5000 Da PEG chain showed an order of magnitude decrease in activity relative to a 3400 Da counterpart. Molecular dynamics computational simulations were used to explore the mechanisms of this decreased activity. Assays were also conducted to demonstrate the utility of a living radical photopolymerization to create functional, polymeric surfaces with these monomers and to demonstrate surface-based activity against Staphylococcus epidermidis. In particular, the vancomycin−PEG-acrylate derivatives demonstrated a 7−8 log reduction in bacterial colony forming units (CFU) with respect to nonfunctionalized control surfaces.
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Affiliation(s)
- McKinley C Lawson
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80309, USA
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20
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Yang Z, Vorpagel ER, Laskin J. Influence of the charge state on the structures and interactions of vancomycin antibiotics with cell-wall analogue peptides: experimental and theoretical studies. Chemistry 2009; 15:2081-90. [PMID: 19156658 DOI: 10.1002/chem.200802010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Charge matters! The charge state significantly influences the conformation and the binding energy between vancomycin antibiotic and bacterial cell-wall analogue peptides (see figure). Surface-induced dissociation (SID) studies provide a quantitative comparison between the stabilities of different charge states of the complex.In this study we examined the effect of the charge state on the energetics and dynamics of dissociation of the noncovalent complex between the vancomycin and the cell-wall peptide analogue N(alpha),N(epsilon)-diacetyl-L-Lys-D-Ala-D-Ala (V-Ac(2)LKdAdA). The binding energies between the vancomycin and the peptide were obtained from the RRKM (Rice, Ramsperger, Kassel, Marcus) modeling of the time- and energy-resolved surface-induced dissociation (SID) experiments. Our results demonstrate that the stability of the complex towards fragmentation increases in the order: doubly protonated<singly protonated<deprotonated. Dissociation of the singly protonated and singly deprotonated complex is characterized by very large entropy effects, which indicate a substantial increase in the conformational flexibility of the resulting products. The experimental threshold energies of (1.75+/-0.08) eV ((40.3+/-1.8) kcal mol(-1)) and (1.34+/-0.08) eV ((30.9+/-1.8) kcal mol(-1)) obtained for the deprotonated and singly protonated complexes, respectively, are in excellent agreement with the results of density functional theory calculations. The increased stability of the deprotonated complex observed experimentally is attributed to the presence of three charged sites in the deprotonated complex, as compared with only one charged site in the singly protonated complex. The low binding energy of (0.93+/-0.04) eV ((21.4+/-0.9) kcal mol(-1)) obtained for the doubly protonated complex suggests that this ion is destabilized by Coulomb repulsion between the singly protonated vancomycin and the singly protonated peptide comprising the complex.
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Affiliation(s)
- Zhibo Yang
- Chemical and Materials Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999 (K8-88), Richland, WA 99352, USA
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21
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22
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Kell AJ, Stewart G, Ryan S, Peytavi R, Boissinot M, Huletsky A, Bergeron MG, Simard B. Vancomycin-modified nanoparticles for efficient targeting and preconcentration of Gram-positive and Gram-negative bacteria. ACS NANO 2008; 2:1777-88. [PMID: 19206416 DOI: 10.1021/nn700183g] [Citation(s) in RCA: 210] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
A series of vancomycin-modified nanoparticles were developed and employed in magnetic confinement assays to isolate a variety of Gram-positive and Gram-negative bacteria from aqueous solution. We determined that the orientation/architecture of vancomycin on the surface of the nanoparticles and the overall surface coverage is critical in mediating fast and effective interactions between the nanoparticle and the pathogen cell wall surface and only one orientation/architecture in a series of modified nanoparticles leads to the efficient and reproducible capture of several important pathogenic bacteria. Interestingly, as the nanoparticles increase in diameter (from approximately 50 to 2800 nm), it is necessary to incorporate a long linker between the nanoparticle surface and the vancomycin moiety in order for the surface bound probe to efficiently confine Gram-positive bacteria. Finally, we also determined that the time required for efficient labeling and subsequent magnetic confinement significantly decreases as the size of the nanoparticle and the vancomycin surface coverage on the nanoparticle increases. As disease detection technologies transition to "lab-on-a-chip" based platforms it is necessary to develop strategies to effectively and inexpensively preconcentrate cells from large volume to volumes more amenable to these types of microfluidic devices. These small molecule-modified superparamagnetic nanoparticles can provide a means by which this can be accomplished.
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Affiliation(s)
- Arnold J Kell
- Steacie Institute for Molecular Sciences, National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario, Canada K1A 0R6
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23
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Yang Z, Vorpagel ER, Laskin J. Experimental and Theoretical Studies of the Structures and Interactions of Vancomycin Antibiotics with Cell Wall Analogues. J Am Chem Soc 2008; 130:13013-22. [DOI: 10.1021/ja802643g] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Zhibo Yang
- Pacific Northwest National Laboratory, Fundamental Science Directorate, P.O. Box 999 (K8-88), Richland, Washington 99352
| | - Erich R. Vorpagel
- Pacific Northwest National Laboratory, Fundamental Science Directorate, P.O. Box 999 (K8-88), Richland, Washington 99352
| | - Julia Laskin
- Pacific Northwest National Laboratory, Fundamental Science Directorate, P.O. Box 999 (K8-88), Richland, Washington 99352
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24
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Yao N, Wu CY, Xiao W, Lam KS. Discovery of high-affinity peptide ligands for vancomycin. Biopolymers 2008; 90:421-32. [PMID: 18260149 DOI: 10.1002/bip.20949] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Vancomycin, an important antibiotic against medically relevant gram-positive bacteria such as methicillin-resistant Staphylococcus aureus, exerts its antibacterial effects by binding with moderate affinity to the C-terminal Lys-D-Ala-D-Ala motif (Kaa) of the bacterial cell wall peptide precursor. Essential for Kaa binding to vancomcyin is the free-carboxyl group on the terminal D-Ala in Kaa. In efforts to identify other Kaa-based peptides which bind vancomycin with higher affinity, we utilized our one-bead-one-compound (OBOC) combinatorial library approach, a method which has been widely used to discover highly specific ligands against various receptors. In standard OBOC peptide libraries, the C-terminal end of the synthesized peptide is tethered to a solid-support/resin, however, this study reports development of a synthetic strategy for generating OBOC peptide libraries with a free D-Ala-D-Ala carboxyl end. We screened these "OBOC inverted" peptide libraries against vancomycin, and discovered a series of peptide ligands with strong consensus, which bind vancomycin. To further optimize these ligands, two highly focused Kaa-containing OBOC combinatorial peptidomimetic libraries were designed, synthesized, and screened against vancomycin under more stringent conditions. Peptidomimetic ligands which bind vancomycin with higher affinity than Kaa were identified. The dissociation constant of one of these ligands, Lys(Ac)-HOCit-Glu-Cha-Lys(3,5-dihydroxybenzoyl)-D-Ala-D-Ala (9), as determined by surface plasmon resonance, was 1.03 microM, roughly a 50-fold improvement in affinity compared to Kaa (K(D) = 50 microM).
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Affiliation(s)
- Nianhuan Yao
- Division of Hematology and Oncology, Department of Internal Medicine, UC Davis Cancer Center, University of California, Davis, Sacramento, CA 95817, USA
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25
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Hatano M, Asai T, Ishihara K. Enantioselective conjugate addition of dialkylzinc to cyclic enones catalyzed by chiral binaphthyldiamine–copper(I) complexes. Tetrahedron Lett 2007. [DOI: 10.1016/j.tetlet.2007.10.061] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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26
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Williams DH, Maplestone RA. Why are secondary metabolites biosynthesized? Sophistication in the inhibition of cell wall biosynthesis by vancomycin group antibiotics. CIBA FOUNDATION SYMPOSIUM 2007; 171:45-59; discussion 59-63. [PMID: 1302185 DOI: 10.1002/9780470514344.ch4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The evidence that secondary metabolites serve sophisticated roles in the survival strategy of the producer is briefly reviewed. This evidence stems from the common involvement of tens of kilobases of DNA in the programming of their synthesis, of up to several tens of discrete enzymic conversions in their biosynthesis, and of the existence of sophisticated mechanisms in the producers for resistance against their physiological effects. It also stems from a study of the molecular basis for these physiological effects. The molecular basis for the antibacterial action of the vancomycin group antibiotics is presented, and demonstrates that essentially every portion of these molecules appears to be finely honed to promote efficient antibacterial action.
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27
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Waltho JP, Williams DH. The natural design of vancomycin family antibiotics to bind their target peptides. CIBA FOUNDATION SYMPOSIUM 2007; 158:73-86; discussion 87-91, 92-7. [PMID: 1935428 DOI: 10.1002/9780470514085.ch6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The vancomycin family of antibiotics provide a rare opportunity among natural systems to study a molecular recognition process in which both the 'receptor' and the 'ligand' are relatively small molecules. Unlike the vast majority of antibiotics, in the vancomycin family the antibiotic performs the role of the receptor. All members of the family are covalently cross-linked heptapeptides that contain a variety of glycosidic modifications. Their site of action in bacterial cell walls is modelled by simple dipeptides and tripeptides. NMR experiments have been used to characterize the binding of these species through the study of both the complex and the free components. In unbound antibiotics conformational freedom is observed in regions of the molecule not severely restricted by covalent linkages. On binding of the ligand much of this conformational freedom is lost and the hydrophobic side chains of the antibiotics reside close to the intermolecular hydrogen-bonding interactions, thus shielding these interactions from the solvent. The charged amino groups of the N-terminus and disaccharide region of vancomycin are orientated not to optimize intermolecular electrostatic interactions but rather to retain solvation. This causes further hydrophobic faces to be presented to the ligand. Removal of saccharide units from the antibiotics leads to small losses in binding energy but may have considerable influence on the selectivity of the antibiotics. Specific dimerization through the non-ligand-binding faces of ristocetin is observed at millimolar concentrations. The geometry of the dimeric complex enables a close approach of the ligand carboxylate anion and the charged amino group of the novel sugar, ristosamine.
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Affiliation(s)
- J P Waltho
- Department of Molecular Biology and Biotechnology, University of Sheffield, UK
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28
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Zhang LW, Ding L, Zhang XX. Estimation of binding constants of receptors and ligands by affinity capillary electrophoresis. Anal Bioanal Chem 2007; 387:2833-41. [PMID: 17310331 DOI: 10.1007/s00216-007-1167-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2006] [Revised: 01/25/2007] [Accepted: 01/31/2007] [Indexed: 10/23/2022]
Abstract
An estimation method for determination of binding constants of receptors to ligands by affinity capillary electrophoresis was evaluated. On the basis of the theories of pseudostationary phase or so-called dynamic stationary phase, the retention factor (k) was used to represent the interaction between the receptor and ligand. k could be easily deduced from the migration times of the ligand and the receptor. Then, with the linear relationship of k versus the concentration of ligand in the running buffer, the binding constant K(b) was calculated from the slope and intercept. In order to test its feasibility, the calculation method was demonstrated using three model systems: the interactions between vancomycin and N-acetyl-D-Ala-D-Ala, ristocetin and N-acetyl-D-Ala-D-Ala, and carbonic anhydrase B and an arylsulfonamide. Estimated binding constants were compared with those determined by other techniques. The results showed that this estimation method was reliable. This calculation method offers a simple and easy approach to estimating binding constants of ligands to receptors.
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Affiliation(s)
- Li-Wei Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), College of Chemistry, Peking University, Beijing 100871, China
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29
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Yuan J, Xu J, Niu W, Zhao Q, Yan H, Cheng X, He B. AFFINITY ADSORBENTS WITH D-ALANINE AND D,L-ALANINE AS LIGANDS FOR VANCOMYCIN GROUP ANTIBIOTICS. J LIQ CHROMATOGR R T 2007. [DOI: 10.1081/jlc-100106091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Jing Yuan
- a The State Key Laboratory of Functional Polymer Materials, for Adsorption and Separation , Institute of Polymer Chemistry, Nankai University , Tianjin, P. R. China
| | - Junjuan Xu
- b Tianjin College of Traditional Chinese Medicine , Tianjin, P. R. China
| | - Wenqiang Niu
- a The State Key Laboratory of Functional Polymer Materials, for Adsorption and Separation , Institute of Polymer Chemistry, Nankai University , Tianjin, P. R. China
| | - Qingxiang Zhao
- a The State Key Laboratory of Functional Polymer Materials, for Adsorption and Separation , Institute of Polymer Chemistry, Nankai University , Tianjin, P. R. China
| | - Husheng Yan
- c The State Key Laboratory of Functional Polymer Materials, for Adsorption and Separation , Institute of Polymer Chemistry, Nankai University , Tianjin, P. R. China
| | - Xiaohui Cheng
- a The State Key Laboratory of Functional Polymer Materials, for Adsorption and Separation , Institute of Polymer Chemistry, Nankai University , Tianjin, P. R. China
| | - Binglin He
- a The State Key Laboratory of Functional Polymer Materials, for Adsorption and Separation , Institute of Polymer Chemistry, Nankai University , Tianjin, P. R. China
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30
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Balzarini J, Keyaerts E, Vijgen L, Egberink H, De Clercq E, Van Ranst M, Printsevskaya SS, Olsufyeva EN, Solovieva SE, Preobrazhenskaya MN. Inhibition of feline (FIPV) and human (SARS) coronavirus by semisynthetic derivatives of glycopeptide antibiotics. Antiviral Res 2006; 72:20-33. [PMID: 16675038 PMCID: PMC7114212 DOI: 10.1016/j.antiviral.2006.03.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2006] [Revised: 03/13/2006] [Accepted: 03/14/2006] [Indexed: 11/28/2022]
Abstract
Various semisynthetic derivatives of glycopeptide antibiotics including vancomycin, eremomycin, teicoplanin, ristocetin A and DA-40926 have been evaluated for their inhibitory activity against feline infectious peritonitis virus (FIPV) and human (SARS-CoV, Frankfurt-1 strain) coronavirus in cell culture in comparison with their activity against human immunodeficiency virus (HIV). Several glycopeptide derivatives modified with hydrophobic substituents showed selective antiviral activity. For the most active compounds, the 50% effective concentrations (EC50) were in the lower micromolar range. In general, removal of the carbohydrate parts of the molecules did not affect the antiviral activity of the compounds. Some compounds showed inhibitory activity against both, whereas other compounds proved inhibitory to either, FIPV or SARS-CoV. There was no close correlation between the EC50 values of the glycopeptide derivatives for FIPV or SARS-CoV.
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Affiliation(s)
- Jan Balzarini
- Rega Institute for Medical Research, K.U. Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium.
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31
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Yao NH, Liu G, He WY, Niu C, Carlson JR, Lam KS. Solid-phase synthesis and antibacterial evaluations of N-demethylvancomycin derivatives. Bioorg Med Chem Lett 2005; 15:2325-9. [PMID: 15837318 DOI: 10.1016/j.bmcl.2005.02.086] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2005] [Revised: 02/27/2005] [Accepted: 02/28/2005] [Indexed: 11/23/2022]
Abstract
Twenty-five N-demethylvancomycin derivatives were synthesized on solid-support and their structures were determined by LC-MS/MS. Biological evaluation of these compounds indicated that bulky hydrophobic substituent on vancosamine of N-demethylvancomycin can increase antibacterial activity against vancomycin-resistant Enterococcus faecalis.
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Affiliation(s)
- Nian-Huan Yao
- Chinese Academy of Medical Sciences & Peking Union Medical College, Institute of Materia Medica, 1 Xian Nong Tan Street, Beijing 100050, PR China
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32
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Yao NH, He WY, Lam KS, Liu G. Conformational Studies of Resin-Bound Vancomycin and the Complex of Vancomycin and Ac2-l-Lys-d-Ala-d-Ala. ACTA ACUST UNITED AC 2004; 7:123-9. [PMID: 15638491 DOI: 10.1021/cc0498783] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The molecular target of vancomycin, a commonly used glycopeptide antibiotic, is the D-Ala-D-Ala dipeptide subunit on the bacterial cell wall. The molecular basis of interaction between vancomycin and D-Ala-D-Ala in solution is well-known. However, there is no structural data on vancomycin, and its interaction with D-Ala-D-Ala when the drug is tethered to a solid support. In this Article, vancomycin was directly coupled onto TentaGel or PEGA resin through its C terminus. High-resolution magic angle spinning NMR studies indicated that conformation of PEGA bead-bound vancomycin is identical to that of the free drug. Broadening and shifts of the same proton resonances were observed in solution-phase vancomycin or PEGA-bound vancomycin when complexed with Ac(2)-L-Lys-D-Ala-D-Ala. This study demonstrates that bead-bound molecules can behave the same as solution-phase molecules in terms of molecular interaction with its target molecule, thus validating the on-bead screening approach of the "one-bead-one-compound" combinatorial library method.
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Affiliation(s)
- Nian-Huan Yao
- Chinese Academy of Medical Sciences & Peking Union Medical College, Institute of Materia Medica, 1 Xian Nong Tan Street, Beijing 100050, P. R. China
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33
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Greenwald RB, Zhao H, Xia J, Martinez A. Poly(ethylene glycol) Transport Forms of Vancomycin: A Long-Lived Continuous Release Delivery System. J Med Chem 2003; 46:5021-30. [PMID: 14584952 DOI: 10.1021/jm030202g] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The facile reaction of vancomycin with various PEG linkers, at the V(3) position, has been selectively accomplished by using an excess of base in DMF. Using rPEG as a blocking group for V(3) provides crystalline derivatives that can be further PEGylated to give pure V(3)-X(1) latentiated species (transport forms). V(3) tetrameric species were also prepared in order to increase the loading of drug on PEG. All PEG-vancomycin transport forms show significant antibacterial activity that is on the same order of native vancomycin. Significant increases in the AUC were observed for all PEG-vancomycin conjugates thus making them potential single dose therapies.
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Affiliation(s)
- Richard B Greenwald
- Enzon Pharmaceuticals Inc., 20 Kingsbridge Road, Piscataway, New Jersey 00854, USA.
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34
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Efficient approach for the diversity-oriented synthesis of macro-heterocycles on solid-support. Tetrahedron Lett 2003. [DOI: 10.1016/s0040-4039(03)01219-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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35
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Balzarini J, Pannecouque C, De Clercq E, Pavlov AY, Printsevskaya SS, Miroshnikova OV, Reznikova MI, Preobrazhenskaya MN. Antiretroviral activity of semisynthetic derivatives of glycopeptide antibiotics. J Med Chem 2003; 46:2755-64. [PMID: 12801238 DOI: 10.1021/jm0300882] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A variety of semisynthetic derivatives of natural antibacterial glycopeptide antibiotics such as vancomycin, eremomycin, ristocetin A, teicoplanin A(2)-2, DA-40926, their aglycons, and also the products of their partial degradation with a destroyed or modified peptide core show marked anti-retroviral activity in cell culture. In particular, aglycon antibiotic derivatives containing various substituents of a preferably hydrophobic nature displayed activity against human immunodeficiency virus type 1 (HIV-1), HIV-2, and Moloney murine sarcoma virus at a 50% inhibitory concentration in the lower micromolar (1-5 microM) concentration range while not being cytostatic against human lymphocytic cells at 250 microM or higher. The mode of anti-HIV action of the antibiotic aglycon derivatives could be ascribed to inhibition of the viral entry process.
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Affiliation(s)
- Jan Balzarini
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium
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36
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Ahrendt KA, Olsen JA, Wakao M, Trias J, Ellman JA. Identification of potent and broad-spectrum antibiotics from SAR studies of a synthetic vancomycin analogue. Bioorg Med Chem Lett 2003; 13:1683-6. [PMID: 12729641 DOI: 10.1016/s0960-894x(03)00243-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Dimeric vancomycin analogues based on a lead compound identified from a library of synthetic analogues of vancomycin have up to 60-fold greater activity than vancomycin against vancomycin-resistant Enterococcus faecium (VRE, VanA phenotype). Simplified analogues have also been prepared and found to maintain activity against VRE and have broad-spectrum antibiotic activity.
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Affiliation(s)
- Kateri A Ahrendt
- Center for New Directions in Organic Synthesis, Department of Chemistry, University of California, Berkeley 94720, USA
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37
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Losey HC, Jiang J, Biggins JB, Oberthür M, Ye XY, Dong SD, Kahne D, Thorson JS, Walsh CT. Incorporation of glucose analogs by GtfE and GtfD from the vancomycin biosynthetic pathway to generate variant glycopeptides. CHEMISTRY & BIOLOGY 2002; 9:1305-14. [PMID: 12498883 DOI: 10.1016/s1074-5521(02)00270-3] [Citation(s) in RCA: 120] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Analogs of the glycopeptide antibiotics vancomycin and teicoplanin with alterations in one or both sugar moieties of the disaccharide have been prepared by tandem action of the vancomycin pathway glycosyltransferases GtfE and GtfD. All four regioisomers (2-, 3-, 4-, 6-) of TDP-deoxyglucoses and UDP/TDP-aminoglucoses were prepared, predominantly by action of D-glucopyranosyl-1-phosphate thymidylyltransferase, E(p). GtfE transferred the deoxyglucoses or aminoglucoses onto the 4-OH of 4-hydroxyphenylglycine of both the vancomycin and teicoplanin aglycone scaffolds. Kinetic analysis indicated the 2-, 3-, 4-, and 6-amino-glucoses were transferred by GtfE with only a 4- to 30-fold drop in k(cat) and no effect on K(m) compared to the native substrate, UDP/TDP-glucose, suggesting preparative utility. The next enzyme, GtfD, could utilize the variant glucosyl-peptides as substrates for transfer of L-4-epi-vancosamine. The aminosugar moieties in these variant glycopeptides introduce sites for acylation or reductive alkylation.
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Affiliation(s)
- Heather C Losey
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
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38
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Kaplan J, Korty BD, Axelsen PH, Loll PJ. The role of sugar residues in molecular recognition by vancomycin. J Med Chem 2001; 44:1837-40. [PMID: 11356118 DOI: 10.1021/jm0005306] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The sugar residues of the glycopeptide antibiotic vancomycin contribute to the cooperativity of ligand binding, thereby increasing ligand affinity and enhancing antimicrobial activity. To assess the structural basis for these effects, we determined a 0.98 A X-ray crystal structure of the vancomycin aglycon and compared it to structures of several intact vancomycin:ligand complexes. The crystal structure reveals that the aglycon binds acetate anions and forms back-to-back dimeric complexes in a manner similar to that of intact vancomycin. However, the four independent copies of the aglycon in each asymmetric unit of the crystal exhibit a high degree of conformational heterogeneity. These results suggest that the sugar residues, in addition to enlarging and strengthening the dimer interface, provide steric constraints that limit the vancomycin molecule to a relatively small number of productive conformations.
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Affiliation(s)
- J Kaplan
- Department of Pharmacology, University of Pennsylvania, 3620 Hamilton Walk, Philadelphia, Pennsylvania 19104, USA
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39
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Hall DG, Manku S, Wang F. Solution- and solid-phase strategies for the design, synthesis, and screening of libraries based on natural product templates: a comprehensive survey. JOURNAL OF COMBINATORIAL CHEMISTRY 2001; 3:125-50. [PMID: 11300852 DOI: 10.1021/cc0001001] [Citation(s) in RCA: 140] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- D G Hall
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2 Canada.
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40
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Adamczyk M, Grote J, Moore JA, Rege SD, Yu Z. Binding interactions of vancomycin tracers with a bacterial cell wall peptidoglycan analogue. Bioorg Med Chem Lett 2000; 10:1613-5. [PMID: 10915064 DOI: 10.1016/s0960-894x(00)00298-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Binding interactions between several vancomycin tracers and (N,N'-diacetyl)KDADA in solution were evaluated in a competition format using a surface plasmon resonance instrument. Tracers derivatized from the carboxy terminus or the N-vancosaminyl sugar moiety of vancomycin bind the peptide with an affinity similar to that of underivatized vancomycin. In contrast, N-methylleucyl derivatized vancomycin tracers bind the peptide with a reduced affinity relative to vancomycin.
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Affiliation(s)
- M Adamczyk
- Department of Chemistry, Abbott Laboratories, Abbott Park, IL 60064-6016, USA.
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41
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Rao J, Lahiri J, Weis RM, Whitesides GM. Design, Synthesis, and Characterization of a High-Affinity Trivalent System Derived from Vancomycin and l-Lys-d-Ala-d-Ala. J Am Chem Soc 2000. [DOI: 10.1021/ja992648l] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jianghong Rao
- Contribution from the Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - Joydeep Lahiri
- Contribution from the Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - Robert M. Weis
- Contribution from the Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - George M. Whitesides
- Contribution from the Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
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42
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Kiselyov AS, Smith L, Tempest P. Solid support synthesis of 14- and 17-membered macrocycles via the SNAr methodology. Tetrahedron 1999. [DOI: 10.1016/s0040-4020(99)00900-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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43
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Goldberg M, Smith L, Tamayo N, Kiselyov AS. Solid support synthesis of 14-membered macrocycles containing 4-hydroxyproline structural unit via SNAr methodology. Tetrahedron 1999. [DOI: 10.1016/s0040-4020(99)00842-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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44
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Xu R, Greiveldinger G, Marenus LE, Cooper A, Ellman JA. Combinatorial Library Approach for the Identification of Synthetic Receptors Targeting Vancomycin-Resistant Bacteria. J Am Chem Soc 1999. [DOI: 10.1021/ja990240i] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ruo Xu
- Department of Chemistry, University of California Berkeley, California 94720 Department of Chemistry, University of Glasgow Glasgow G12 8QQ, Scotland, UK
| | - Guy Greiveldinger
- Department of Chemistry, University of California Berkeley, California 94720 Department of Chemistry, University of Glasgow Glasgow G12 8QQ, Scotland, UK
| | - Linda E. Marenus
- Department of Chemistry, University of California Berkeley, California 94720 Department of Chemistry, University of Glasgow Glasgow G12 8QQ, Scotland, UK
| | - Alan Cooper
- Department of Chemistry, University of California Berkeley, California 94720 Department of Chemistry, University of Glasgow Glasgow G12 8QQ, Scotland, UK
| | - Jonathan A. Ellman
- Department of Chemistry, University of California Berkeley, California 94720 Department of Chemistry, University of Glasgow Glasgow G12 8QQ, Scotland, UK
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45
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Adamczyk M, Grote J, Moore JA, Rege SD, Yu Z. Structure-binding relationships for the interaction between a vancomycin monoclonal antibody Fab fragment and a library of vancomycin analogues and tracers. Bioconjug Chem 1999; 10:176-85. [PMID: 10077465 DOI: 10.1021/bc980135i] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A series of vancomycin analogues and tracers were synthesized, and their binding interactions with an anti-vancomycin Fab fragment were evaluated under mass transport limiting conditions using surface plasmon resonance detection. Differences observed in binding interactions were utilized to define the vancomycin structural elements critical for antibody recognition. Major structural regions of vancomycin shown to play an important role in anti-vancomycin Fab fragment recognition include two sugar moieties and one chlorinated phenyl ring. The N-methylleucyl residue, the carboxy terminal residue, and residues in the peptide-binding region of vancomycin have minimal impact on the anti-vancomycin Fab fragment/vancomycin binding interaction. The selection of an antibody with such binding properties plays a critical role in the development of a vancomycin immunoassay that employs stable calibrators and controls.
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Affiliation(s)
- M Adamczyk
- Diagnostics Division Organic Chemistry (9-NM), Abbott Laboratories, Building AP 20, 100 Abbott Park Road, Abbott Park, Illinois, 60064,
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46
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Jørgensen TJD, Roepstorff P, Heck AJR. Direct Determination of Solution Binding Constants for Noncovalent Complexes between Bacterial Cell Wall Peptide Analogues and Vancomycin Group Antibiotics by Electrospray Ionization Mass Spectrometry. Anal Chem 1998. [DOI: 10.1021/ac980563h] [Citation(s) in RCA: 173] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Thomas J. D. Jørgensen
- Department of Molecular Biology, Odense University, Campusvej 55, DK-5230 Odense M, Denmark
| | - Peter Roepstorff
- Department of Molecular Biology, Odense University, Campusvej 55, DK-5230 Odense M, Denmark
| | - Albert J. R. Heck
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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47
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Yan H, Cheng X, He B. Calculation of concentrations of equilibrium components in an in vitro activity test of vancomycin antibiotics and the possible mode of action. Biophys Chem 1998; 74:107-15. [PMID: 9760722 DOI: 10.1016/s0301-4622(98)00172-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The vancomycin group of antibiotics is considered to act by binding the bacterial cell wall mucopeptide precursor terminating in -L-Lys-D-Ala-D-Ala. The dimerization of these antibiotics is also believed to play a role in the action. In this paper, we analyzed the equilibria in the in vitro antibacterial activity test of the vancomycin antibiotics both with and without the cell wall precursor analogue di-acetyl-L-Lys-D-Ala-D-Ala (DALAA). Based on the equilibria and concentration balance, we obtained 10 equations (seven quadratic equations and three linear equations) containing 10 equilibrium concentrations which relate to the antibiotic, cell wall precursor and DALAA. A computer program was written to solve these equations from known dimerization constant and the binding constants (both monomer and dimer) with DALAA of the antibiotic. The concentrations in the test for vancomycin and eremomycin were obtained. The antibiotic activity of these antibiotics may be quantitatively correlated with their dimerization constants and the binding constants through the calculation. By analyzing the calculated results, we concluded that the cell wall-bound dimer may be the major contributor to the antibiotic activity in the case of eremomycin, while the cell wall-bound monomer is possibly the determinant for the activity of vancomycin.
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Affiliation(s)
- H Yan
- Institute of Polymer Chemistry, State Key Laboratory of Functional Polymer Materials for Adsorption and Separation, Nankai University, Tianjin, People's Republic of China
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48
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49
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Grdadolnik SG, Pristovsek P, Mierke DF. Vancomycin: conformational consequences of the sugar substituent. J Med Chem 1998; 41:2090-9. [PMID: 9622550 DOI: 10.1021/jm9705972] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
High-resolution, three-dimensional structures of vancomycin and aglyco-vancomycin in DMSO were determined by nuclear magnetic resonance, metric matrix distance geometry, and molecular dynamics calculations. Conformational flexibility fast on the NMR time scale was examined by ensemble-based calculations which apply the experimentally derived restraints as an ensemble average. Two families of conformations of vancomycin, differing in the positioning of the vancosamine substituent, were observed. In contrast, the aglyco-vancomycin adopts only one conformation in solution. The conformations of vancomycin and the aglyco-vancomycin differ in the alignment of the amide protons which participate in the hydrogen-bonding network with the cell-wall precursor and orientation of the aromatic rings relative to the backbone. Therefore, the high-resolution structural characterization provides insight into a possible role of glycosylation on the activity of this important family of antibiotics.
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Affiliation(s)
- S G Grdadolnik
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
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50
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Adamczyk M, Grote J, Rege S. Chemo-enzymatic transformations in sensitive systems: lipase mediated hydrolysis of vancomycin esters. Bioorg Med Chem Lett 1998; 8:885-90. [PMID: 9871506 DOI: 10.1016/s0960-894x(98)00109-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Recently, an interest in the development of new vancomycin derivatives has been demonstrated. Here, the feasibility of using lipases, particularly those from Pseudomonas sp., for the hydrolysis of vancomycin alkyl esters is demonstrated. Benzyl ester derivatives were more easily cleavable than methyl ester derivatives, resulting in good yields of vancomycin acids without degradation.
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Affiliation(s)
- M Adamczyk
- Department of Chemistry, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, IL 60064-3500, USA
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