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Ottonello A, Wyllie JA, Yahiaoui O, Sun S, Koelln RA, Homer JA, Johnson RM, Murray E, Williams P, Bolla JR, Robinson CV, Fallon T, Soares da Costa TP, Moses JE. Shapeshifting bullvalene-linked vancomycin dimers as effective antibiotics against multidrug-resistant gram-positive bacteria. Proc Natl Acad Sci U S A 2023; 120:e2208737120. [PMID: 37011186 PMCID: PMC10104512 DOI: 10.1073/pnas.2208737120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 02/24/2023] [Indexed: 04/05/2023] Open
Abstract
The alarming rise in superbugs that are resistant to drugs of last resort, including vancomycin-resistant enterococci and staphylococci, has become a significant global health hazard. Here, we report the click chemistry synthesis of an unprecedented class of shapeshifting vancomycin dimers (SVDs) that display potent activity against bacteria that are resistant to the parent drug, including the ESKAPE pathogens, vancomycin-resistant Enterococcus (VRE), methicillin-resistant Staphylococcus aureus (MRSA), as well as vancomycin-resistant S. aureus (VRSA). The shapeshifting modality of the dimers is powered by a triazole-linked bullvalene core, exploiting the dynamic covalent rearrangements of the fluxional carbon cage and creating ligands with the capacity to inhibit bacterial cell wall biosynthesis. The new shapeshifting antibiotics are not disadvantaged by the common mechanism of vancomycin resistance resulting from the alteration of the C-terminal dipeptide with the corresponding d-Ala-d-Lac depsipeptide. Further, evidence suggests that the shapeshifting ligands destabilize the complex formed between the flippase MurJ and lipid II, implying the potential for a new mode of action for polyvalent glycopeptides. The SVDs show little propensity for acquired resistance by enterococci, suggesting that this new class of shapeshifting antibiotic will display durable antimicrobial activity not prone to rapidly acquired clinical resistance.
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Affiliation(s)
- Alessandra Ottonello
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC3086, Australia
| | - Jessica A. Wyllie
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC3086, Australia
| | - Oussama Yahiaoui
- Department of Chemistry, School of Physical Sciences, The University of Adelaide, Adelaide, SA5005, Australia
| | - Shoujun Sun
- Cancer Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724
| | - Rebecca A. Koelln
- Cancer Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724
| | - Joshua A. Homer
- Cancer Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724
| | - Robert M. Johnson
- Cancer Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724
| | - Ewan Murray
- National Biofilms Innovation Centre, Biodiscovery Institute and School of Life Sciences, University of Nottingham, University Park, NottinghamNG7 2RD, U.K.
| | - Paul Williams
- National Biofilms Innovation Centre, Biodiscovery Institute and School of Life Sciences, University of Nottingham, University Park, NottinghamNG7 2RD, U.K.
| | - Jani R. Bolla
- Department of Biology, University of Oxford, OxfordOX1 3RB, U.K.
- The Kavli Institute for Nanoscience Discovery, University of Oxford, OxfordOX1 3QU, U.K.
| | - Carol V. Robinson
- The Kavli Institute for Nanoscience Discovery, University of Oxford, OxfordOX1 3QU, U.K.
- Physical and Theoretical Chemistry Laboratory, University of Oxford, OxfordOX1 3QZ, U.K.
| | - Thomas Fallon
- Department of Chemistry, School of Physical Sciences, The University of Adelaide, Adelaide, SA5005, Australia
| | | | - John E. Moses
- Cancer Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724
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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: 15] [Impact Index Per Article: 7.5] [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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Alternatives to Fight Vancomycin-Resistant Staphylococci and Enterococci. Antibiotics (Basel) 2021; 10:antibiotics10091116. [PMID: 34572698 PMCID: PMC8471638 DOI: 10.3390/antibiotics10091116] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 12/25/2022] Open
Abstract
Gram positive pathogens are a significant cause of healthcare-associated infections, with Staphylococci and Enterococci being the most prevalent ones. Vancomycin, a last resort glycopeptide, is used to fight these bacteria but the emergence of resistance against this drug leaves some patients with few therapeutic options. To counter this issue, new generations of antibiotics have been developed but resistance has already been reported. In this article, we review the strategies in place or in development to counter vancomycin-resistant pathogens. First, an overview of traditional antimicrobials already on the market or in the preclinical or clinical pipeline used individually or in combination is summarized. The second part focuses on the non-traditional antimicrobials, such as antimicrobial peptides, bacteriophages and nanoparticles. The conclusion is that there is hitherto no substitute equivalent to vancomycin. However, promising strategies based on drugs with multiple mechanisms of action and treatments based on bacteriophages possibly combined with conventional antibiotics are hoped to provide treatment options for vancomycin-resistant Gram-positive pathogens.
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Li W, Separovic F, O'Brien-Simpson NM, Wade JD. Chemically modified and conjugated antimicrobial peptides against superbugs. Chem Soc Rev 2021; 50:4932-4973. [PMID: 33710195 DOI: 10.1039/d0cs01026j] [Citation(s) in RCA: 184] [Impact Index Per Article: 61.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Antimicrobial resistance (AMR) is one of the greatest threats to human health that, by 2050, will lead to more deaths from bacterial infections than cancer. New antimicrobial agents, both broad-spectrum and selective, that do not induce AMR are urgently required. Antimicrobial peptides (AMPs) are a novel class of alternatives that possess potent activity against a wide range of Gram-negative and positive bacteria with little or no capacity to induce AMR. This has stimulated substantial chemical development of novel peptide-based antibiotics possessing improved therapeutic index. This review summarises recent synthetic efforts and their impact on analogue design as well as their various applications in AMP development. It includes modifications that have been reported to enhance antimicrobial activity including lipidation, glycosylation and multimerization through to the broad application of novel bio-orthogonal chemistry, as well as perspectives on the direction of future research. The subject area is primarily the development of next-generation antimicrobial agents through selective, rational chemical modification of AMPs. The review further serves as a guide toward the most promising directions in this field to stimulate broad scientific attention, and will lead to new, effective and selective solutions for the several biomedical challenges to which antimicrobial peptidomimetics are being applied.
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Affiliation(s)
- Wenyi Li
- Melbourne Dental School, Centre for Oral Health Research, University of Melbourne, VIC 3010, Australia. and Bio21 Institute, University of Melbourne, VIC 3010, Australia
| | - Frances Separovic
- Bio21 Institute, University of Melbourne, VIC 3010, Australia and School of Chemistry, University of Melbourne, VIC 3010, Australia
| | - Neil M O'Brien-Simpson
- Melbourne Dental School, Centre for Oral Health Research, University of Melbourne, VIC 3010, Australia. and Bio21 Institute, University of Melbourne, VIC 3010, Australia
| | - John D Wade
- School of Chemistry, University of Melbourne, VIC 3010, Australia and The Florey Institute of Neuroscience and Mental Health, University of Melbourne, VIC 3010, Australia.
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Abstract
![]()
Glycopeptide
antibiotics (GPAs) are a key weapon in the fight against drug resistant
bacteria, with vancomycin still a mainstream therapy against serious
Gram-positive infections more than 50 years after it was first introduced.
New, more potent semisynthetic derivatives that have entered the clinic,
such as dalbavancin and oritavancin, have superior pharmacokinetic
and target engagement profiles that enable successful treatment of
vancomycin-resistant infections. In the face of resistance development,
with multidrug resistant (MDR) S. pneumoniae and methicillin-resistant Staphylococcus aureus (MRSA) together causing 20-fold more infections than all MDR Gram-negative
infections combined, further improvements are desirable to ensure
the Gram-positive armamentarium is adequately maintained for future
generations. A range of modified glycopeptides has been generated
in the past decade via total syntheses, semisynthetic modifications
of natural products, or biological engineering. Several of these
have undergone extensive characterization with demonstrated in vivo efficacy, good PK/PD profiles, and no reported preclinical
toxicity; some may be suitable for formal preclinical development.
The natural product monobactam, cephalosporin, and β-lactam
antibiotics all spawned multiple generations of commercially and clinically
successful semisynthetic derivatives. Similarly, next-generation glycopeptides
are now technically well positioned to advance to the clinic, if sufficient
funding and market support returns to antibiotic development.
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Affiliation(s)
- Mark A. T. Blaskovich
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, Queensland 4072, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Chemistry Building 68, Cooper Road, Brisbane, Queensland 4072, Australia
| | - Karl A. Hansford
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, Queensland 4072, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Chemistry Building 68, Cooper Road, Brisbane, Queensland 4072, Australia
| | - Mark S. Butler
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, Queensland 4072, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Chemistry Building 68, Cooper Road, Brisbane, Queensland 4072, Australia
| | - ZhiGuang Jia
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, Queensland 4072, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Chemistry Building 68, Cooper Road, Brisbane, Queensland 4072, Australia
| | - Alan E. Mark
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, Queensland 4072, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Chemistry Building 68, Cooper Road, Brisbane, Queensland 4072, Australia
| | - Matthew A. Cooper
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, Queensland 4072, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Chemistry Building 68, Cooper Road, Brisbane, Queensland 4072, Australia
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Bowden S, Joseph C, Tang S, Cannon J, Francis E, Zhou M, Baker JR, Choi SK. Oritavancin Retains a High Affinity for a Vancomycin-Resistant Cell-Wall Precursor via Its Bivalent Motifs of Interaction. Biochemistry 2018; 57:2723-2732. [PMID: 29651842 DOI: 10.1021/acs.biochem.8b00187] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Despite its potent antibacterial activities against drug-resistant Gram-positive pathogens, oritavancin remains partially understood with respect to its primary mode of hydrogen bond interaction with a cell-wall peptide regarding the role of its lipophilic 4'-chlorobiphenyl moiety. Here we report a surface plasmon resonance (SPR) study performed in two cell-wall model surfaces, each prepared by immobilization with a vancomycin-susceptible Lys-d-Ala-d-Ala or vancomycin-resistant Lys-d-Ala-d-Lac peptide. Analysis of binding kinetics performed on the peptide surface showed that oritavancin bound ∼100-1000-fold more tightly than vancomycin on each model surface. Ligand competition experiments conducted by SPR and fluorescence spectroscopy provided evidence that such affinity enhancement can be attributed to its 4'-chlorobiphenyl moiety, possibly through a hydrophobic interaction that led to a gain of free energy with a contribution from enthalpy as suggested by a variable-temperature SPR experiment. On the basis of these findings, we propose a model for the bivalent motifs of interaction of oritavancin with cell-wall peptides, by which the drug molecule can retain a strong interaction even with the vancomycin-resistant peptide. In summary, this study advances our understanding of oritavancin and offers new insight into the significance of bivalent motifs in the design of glycopeptide antibiotics.
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Silverman SM, Moses JE, Sharpless KB. Reengineering Antibiotics to Combat Bacterial Resistance: Click Chemistry [1,2,3]-Triazole Vancomycin Dimers with Potent Activity against MRSA and VRE. Chemistry 2016; 23:79-83. [PMID: 27747932 DOI: 10.1002/chem.201604765] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Indexed: 01/22/2023]
Abstract
Vancomycin has long been considered a drug of last resort. Its efficiency in treating multiple drug-resistant bacterial infections, particularly methicillin-resistant Staphylococcus aureus (MRSA), has had a profound effect on the treatment of life-threatening infections. However, the emergence of resistance to vancomycin is a cause for significant worldwide concern, prompting the urgent development of new effective treatments for antibiotic resistant bacterial infections. Harnessing the benefits of multivalency and cooperativity against vancomycin-resistant strains, we report a Click Chemistry approach towards reengineered vancomycin derivatives and the synthesis of a number of dimers with increased potency against MRSA and vancomycin resistant Enterococci (VRE; VanB). These semi-synthetic dimeric ligands were linked together with great efficiency using the powerful CuAAC reaction, demonstrating high levels of selectivity and purity.
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Affiliation(s)
- Steven M Silverman
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - John E Moses
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.,School of Chemistry, University of Nottingham, Nottingham, NG7 2RD, UK
| | - K Barry Sharpless
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
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Yarlagadda V, Sarkar P, Manjunath GB, Haldar J. Lipophilic vancomycin aglycon dimer with high activity against vancomycin-resistant bacteria. Bioorg Med Chem Lett 2015; 25:5477-80. [PMID: 26525861 DOI: 10.1016/j.bmcl.2015.10.083] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 10/27/2015] [Indexed: 10/22/2022]
Abstract
Antibiotic-resistant superbugs such as vancomycin-resistant Enterococci (VRE) and Staphylococci have become a major global health hazard. To address this issue, we synthesized vancomycin aglycon dimers to systematically probe the impact of a linker on biological activity. A dimer having a pendant lipophilic moiety in the linker showed ∼300-fold more activity than vancomycin against VRE. The high activity of the compound is attributed to its enhanced binding affinity to target peptides which resulted in improved peptidoglycan (cell wall) biosynthesis inhibition. Therefore, our studies suggest that these compounds, prepared by using facile synthetic methodology, can be used to combat vancomycin-resistant bacterial infections.
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Affiliation(s)
- Venkateswarlu Yarlagadda
- Chemical Biology and Medicinal Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur PO, Bengaluru 560064, Karnataka, India
| | - Paramita Sarkar
- Chemical Biology and Medicinal Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur PO, Bengaluru 560064, Karnataka, India
| | - Goutham B Manjunath
- Chemical Biology and Medicinal Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur PO, Bengaluru 560064, Karnataka, India
| | - Jayanta Haldar
- Chemical Biology and Medicinal Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur PO, Bengaluru 560064, Karnataka, India.
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Okano A, Nakayama A, Wu K, Lindsey EA, Schammel AW, Feng Y, Collins KC, Boger DL. Total syntheses and initial evaluation of [Ψ[C(═S)NH]Tpg⁴]vancomycin, [Ψ[C(═NH)NH]Tpg⁴]vancomycin, [Ψ[CH₂NH]Tpg⁴]vancomycin, and their (4-chlorobiphenyl)methyl derivatives: synergistic binding pocket and peripheral modifications for the glycopeptide antibiotics. J Am Chem Soc 2015; 137:3693-704. [PMID: 25750995 PMCID: PMC4376669 DOI: 10.1021/jacs.5b01008] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Full details of studies are disclosed on the total syntheses of binding pocket analogues of vancomycin bearing the peripheral L-vancosaminyl-1,2-D-glucosyl disaccharide that contain changes to a key single atom in the residue-4 amide (residue-4 carbonyl O → S, NH, H2) designed to directly address the underlying molecular basis of resistance to vancomycin. Also disclosed are studies piloting the late-stage transformations conducted on the synthetically more accessible C-terminus hydroxymethyl aglycon derivatives and full details of the peripheral chlorobiphenyl functionalization of all of the binding-pocket-modified vancomycin analogues designed for dual D-Ala-D-Ala/D-Ala-D-Lac binding. Their collective assessment indicates that combined binding pocket and chlorobiphenyl peripherally modified analogues exhibit a remarkable spectrum of antimicrobial activity (VSSA, MRSA, and VanA and VanB VRE) and impressive potencies against both vancomycin-sensitive and vancomycin-resistant bacteria (MICs = 0.06-0.005 and 0.5-0.06 μg/mL for the amidine and methylene analogues, respectively) and likely benefit from two independent and synergistic mechanisms of action, only one of which is dependent on D-Ala-D-Ala/D-Ala-D-Lac binding. Such analogues are likely to display especially durable antibiotic activity that is not prone to rapidly acquired clinical resistance.
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Affiliation(s)
- Akinori Okano
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Atsushi Nakayama
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Kejia Wu
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Erick A. Lindsey
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Alex W. Schammel
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yiqing Feng
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Karen C. Collins
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Dale L. Boger
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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Kinouchi H, Arimoto H, Nishiguchi K, Oka M, Maki H, Kitagawa H, Kamimori H. Binding properties of antimicrobial agents to dipeptide terminal of lipid II using surface plasmon resonance. Anal Biochem 2014; 452:67-75. [PMID: 24556247 DOI: 10.1016/j.ab.2014.02.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 02/05/2014] [Accepted: 02/07/2014] [Indexed: 10/25/2022]
Abstract
We developed a surface plasmon resonance (SPR) assay to estimate the interactions of antimicrobial agents with the dipeptide terminal of lipid II (D-alanyl-D-alanine) and its analogous dipeptides (L-alanyl-L-alanine and D-alanyl-D-lactate) as ligands. The established SPR method showed the reproducible immobilization of ligands on sensor chip and analysis of binding kinetics of antimicrobial agents to ligands. The ligand-immobilized chip could be used repeatedly for at least 200 times for the binding assay of antimicrobial agents, indicating that the ligand-immobilized chip is sufficiently robust for the analysis of binding kinetics. In this SPR system, the selective and specific binding characteristics of vancomycin and its analogs to the ligands were estimated and the kinetic parameters were calculated. The kinetic parameters revealed that one of the remarkable binding characteristics was the specific interaction of vancomycin to only the D-alanyl-D-alanine ligand. In addition, the kinetic binding data of SPR showed close correlation with the antimicrobial activity. The SPR data of other antimicrobial agents (e.g., teicoplanin) to the ligands showed correlation with the antimicrobial activity on the basis of the therapeutic mechanism. Our SPR method could be a valuable tool for predicting the binding characteristics of antimicrobial agents to the dipeptide terminal of lipid II.
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Affiliation(s)
- Hiroki Kinouchi
- Pharmaceutical Research Division, Shionogi & Co., Ltd., Toyonaka, Osaka 561-0825, Japan.
| | - Hirokazu Arimoto
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8577, Japan
| | - Kenzo Nishiguchi
- Pharmaceutical Research Division, Shionogi & Co., Ltd., Toyonaka, Osaka 561-0825, Japan
| | - Masako Oka
- Pharmaceutical Research Division, Shionogi & Co., Ltd., Toyonaka, Osaka 561-0825, Japan
| | - Hideki Maki
- Pharmaceutical Research Division, Shionogi & Co., Ltd., Toyonaka, Osaka 561-0825, Japan
| | - Hiroshi Kitagawa
- Department of Biochemistry, Kobe Pharmaceutical University, Higashinada-ku, Kobe 658-8558, Japan
| | - Hiroshi Kamimori
- Pharmaceutical Research Division, Shionogi & Co., Ltd., Toyonaka, Osaka 561-0825, Japan
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In vivo studies suggest that induction of VanS-dependent vancomycin resistance requires binding of the drug to D-Ala-D-Ala termini in the peptidoglycan cell wall. Antimicrob Agents Chemother 2013; 57:4470-80. [PMID: 23836175 DOI: 10.1128/aac.00523-13] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
VanRS two-component regulatory systems are key elements required for the transcriptional activation of inducible vancomycin resistance genes in bacteria, but the precise nature of the ligand signal that activates these systems has remained undefined. Using the resistance system in Streptomyces coelicolor as a model, we have undertaken a series of in vivo studies which indicate that the VanS sensor kinase in VanB-type resistance systems is activated by vancomycin in complex with the d-alanyl-d-alanine (d-Ala-d-Ala) termini of cell wall peptidoglycan (PG) precursors. Complementation of an essential d-Ala-d-Ala ligase activity by constitutive expression of vanA encoding a bifunctional d-Ala-d-Ala and d-alanyl-d-lactate (d-Ala-d-Lac) ligase activity allowed construction of strains that synthesized variable amounts of PG precursors containing d-Ala-d-Ala. Assays quantifying the expression of genes under VanRS control showed that the response to vancomycin in these strains correlated with the abundance of d-Ala-d-Ala-containing PG precursors; strains producing a lower proportion of PG precursors terminating in d-Ala-d-Ala consistently exhibited a lower response to vancomycin. Pretreatment of wild-type cells with vancomycin or teicoplanin to saturate and mask the d-Ala-d-Ala binding sites in nascent PG also blocked the transcriptional response to subsequent vancomycin exposure, and desleucyl vancomycin, a vancomycin analogue incapable of interacting with d-Ala-d-Ala residues, failed to induce van gene expression. Activation of resistance by a vancomycin-d-Ala-d-Ala PG complex predicts a limit to the proportion of PG that can be derived from precursors terminating in d-Ala-d-Lac, a restriction also enforced by the bifunctional activity of the VanA ligase.
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Nakamura J, Yamashiro H, Hayashi S, Yamamoto M, Miura K, Xu S, Doi T, Maki H, Yoshida O, Arimoto H. Elucidation of the Active Conformation of Vancomycin Dimers with Antibacterial Activity against Vancomycin-Resistant Bacteria. Chemistry 2012; 18:12681-9. [DOI: 10.1002/chem.201201211] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Indexed: 11/11/2022]
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Ashford PA, Bew SP. Recent advances in the synthesis of new glycopeptide antibiotics. Chem Soc Rev 2011; 41:957-78. [PMID: 21829829 DOI: 10.1039/c1cs15125h] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The vancomycin family of glycopeptide antibiotics has been inspiring research in the field of synthetic chemistry since the 1980s. Recent studies have moved away from the focus of total synthesis into new territory: the design and evaluation of novel compounds based on the natural products which exhibit improved antibacterial activity. Modern approaches to drug synthesis draw together investigations into the nature of the binding environment, and innovative synthetic methodologies which provide solutions to the challenging structural features and stereochemistry associated with this intriguing class of compounds. New analogues, derivatives and dimers of the natural products, as well as recent successes in the total synthesis of the complestatins are described in this tutorial review, covering literature from the last decade.
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Yoshida O, Nakamura J, Yamashiro H, Miura K, Hayashi S, Umetsu K, Xu S, Maki H, Arimoto H. New insight into the mode of action of vancomycin dimers in bacterial cell wall synthesis. MEDCHEMCOMM 2011. [DOI: 10.1039/c0md00230e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Szpilman AM, Carreira EM. Probing the Biology of Natural Products: Molecular Editing by Diverted Total Synthesis. Angew Chem Int Ed Engl 2010; 49:9592-628. [DOI: 10.1002/anie.200904761] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Szpilman AM, Carreira EM. Untersuchung der Biologie von Naturstoffen: systematische Strukturvariation durch umgelenkte Totalsynthese. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200904761] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Leung SSF, Tirado-Rives J, Jorgensen WL. Vancomycin analogs: Seeking improved binding of d-Ala-d-Ala and d-Ala-d-Lac peptides by side-chain and backbone modifications. Bioorg Med Chem 2009; 17:5874-86. [PMID: 19620008 PMCID: PMC2892990 DOI: 10.1016/j.bmc.2009.07.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Revised: 06/27/2009] [Accepted: 07/03/2009] [Indexed: 10/20/2022]
Abstract
In order to seek vancomycin analogs with improved performance against VanA and VanB resistant bacterial strains, extensive computational investigations have been performed to examine the effects of side-chain and backbone modifications. Changes in binding affinities for tripeptide cell-wall precursor mimics, Ac(2)-l-Lys-d-Ala-d-Ala (3) and Ac(2)-l-Lys-d-Ala-d-Lac (4), with vancomycin analogs were computed with Monte Carlo/free energy perturbation (MC/FEP) calculations. Replacements of the 3-hydroxyl group in residue 7 with small alkyl or alkoxy groups, which improve contacts with the methyl side chain of the ligands'd-Ala residue, are predicted to be the most promising to enhance binding for both ligands. The previously reported amine backbone modification as in 5 is shown to complement the hydrophobic modifications for binding monoacetylated tripeptides. In addition, replacement of the hydroxyl groups in residues 5 and 7 by fluorine is computed to have negligible impact on binding the tripeptides, though it may be pharmacologically advantageous.
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Jia Y, Ma N, Liu Z, Bois-Choussy M, Gonzalez-Zamora E, Malabarba A, Brunati C, Zhu J. Design and Synthesis of Simple Macrocycles Active Against Vancomycin-ResistantEnterococci (VRE). Chemistry 2006; 12:5334-51. [PMID: 16634107 DOI: 10.1002/chem.200600137] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
16-membered meta,para-cyclophanes mimicking the vancomycin binding pocket (D-O-E ring) were designed and synthesized. The structural key features of these biaryl ether containing macrocycles are (1) the presence of beta-amino-alpha-hydroxy acid or alpha,beta-diamino acid as the C-terminal component of the cyclopeptide and (2) the presence of a hydrophobic chain or lipidated aminoglucose at the appropriate position. Cycloetherification by an intramolecular nucleophilic aromatic substitution reaction (S(N)Ar) is used as the key step for the construction of the macrocycle. The atropselectivity of this ring-closure reaction is found to be sensitive to the peptide backbone and chemoselective cyclization (phenol versus primary amine) is achievable. Glycosylation of phenol was realized with freshly prepared 3,4,6-tri-O-acetyl-2-N-lauroyl-2-amino-2-deoxy-alpha-D-glucopyranosyl bromide under phase-transfer conditions. Minimum inhibitory concentrations for all of the derivatives are measured by using a standard microdilution assay, and potent bioactivities against both sensitive and resistant strains are found for some of these compounds (MIC (minimum inhibitory concentration) = 4 microg mL(-1) against VRE). From these preliminary SAR studies, it was anticipated that both the presence of a hydrophobic substituent and an appropriate structure of the macrocycle were required for this series of compounds to be active against VRE.
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Affiliation(s)
- Yanxing Jia
- Institut de Chimie des Substances Naturelles, CNRS, 91198 Gif-sur-Yvette Cedex, France
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Affiliation(s)
- Peter Welzel
- Institut für Organische Chemie, Universität Leipzig, Germany.
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Abstract
[reaction: see text] The rapid diversification of glycopeptides via glycorandomization reveals that significantly diverse substitutions are tolerated and suggests there may be a synergistic benefit to the construction of mechanistically related natural product core scaffold fusions. This work also further highlights the utility of chemoenzymatic approaches to diversify complex natural product architectures.
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Affiliation(s)
- Xun Fu
- Laboratory for Biosynthetic Chemistry, Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705, USA
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Jia Y, Gonzalez-Zamora E, Ma N, Liu Z, Bois-Choussy M, Malabarba A, Brunati C, Zhu J. Identification of synthetic compounds active against VRE: the role of the lipidated aminoglucose and the structure of glycopeptide binding pocket. Bioorg Med Chem Lett 2005; 15:4594-9. [PMID: 16099650 DOI: 10.1016/j.bmcl.2005.06.098] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2005] [Revised: 06/25/2005] [Accepted: 06/27/2005] [Indexed: 11/28/2022]
Abstract
A modified vancomycin binding pocket (D-O-E ring) incorporating an alpha-hydroxy-beta-amino acid at the AA4 position is designed and synthesized. Some of these compounds display potent bioactivities against both sensitive- and resistant-strains (8 microg/ml against VREF). Both the lipidated aminoglucose and the structure of the 16-membered macrocycle are found to be important for the anti-VRE activities. The polyamine appendage at the C-terminal, on the other hand, improved the activity against vancomycin-sensitive strains.
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Affiliation(s)
- Yanxing Jia
- Institut de Chimie des Substances Naturelles, CNRS, 91198 Gif-sur-Yvette Cedex, France
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24
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Affiliation(s)
- Dan Kahne
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA.
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Preobrazhenskaya MN, Olsufyeva EN. Patents on glycopeptides of the vancomycin family and their derivatives as antimicrobials: January 1999 – June 2003. Expert Opin Ther Pat 2005. [DOI: 10.1517/13543776.14.2.141] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Ma N, Jia Y, Liu Z, Gonzalez-Zamora E, Bois-Choussy M, Malabarba A, Brunati C, Zhu J. Design and synthesis of macrocycles active against vancomycin-resistant enterococci (VRE): the interplay between d-Ala-d-Lac binding and hydrophobic effect. Bioorg Med Chem Lett 2005; 15:743-6. [PMID: 15664849 DOI: 10.1016/j.bmcl.2004.11.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2004] [Revised: 10/29/2004] [Accepted: 11/04/2004] [Indexed: 11/29/2022]
Abstract
A modified vancomycin binding pocket (D-O-E ring) incorporating a CHNHCOR function at the AA4 position is designed and synthesized. Potent bioactivities against both sensitive- and resistant-strain are found for some of these compounds (MIC 4 microg/mL against VREF). From this preliminary SAR studies, it was speculated that the D-Ala-D-Ala binding was required for this series of compounds since the corresponding des-leucine derivative is inactive. The presence of long aliphatic chain was important for the desired activities and such hydrophobic effect is specific as no beneficial effect is observed when the same aliphatic chain was attached to the other part of the molecule.
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Affiliation(s)
- Nianchun Ma
- Institut de Chimie des Substances Naturelles, CNRS, 91198 Gif-sur-Yvette Cedex, France
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Abstract
The introduction of high-throughput synthesis and combinatorial chemistry has precipitated a global decline in the screening of natural products by the pharmaceutical industry. Some companies terminated their natural products program, despite the unproven success of the new technologies. This was a premature decision, as natural products have a long history of providing important medicinal agents. Furthermore, they occupy a complementary region of chemical space compared with the typical synthetic compound library. For these reasons, the interest in natural products has been rekindled. Various approaches have evolved that combine the power of natural products and organic chemistry, ranging from the combinatorial total synthesis of analogues to the exploration of natural product scaffolds and the design of completely unnatural molecules that resemble natural products in their molecular characteristics.
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Abstract
In the year 2003 there was a 17% increase in the number of publications citing work performed using optical biosensor technology compared with the previous year. We collated the 962 total papers for 2003, identified the geographical regions where the work was performed, highlighted the instrument types on which it was carried out, and segregated the papers by biological system. In this overview, we spotlight 13 papers that should be on everyone's 'must read' list for 2003 and provide examples of how to identify and interpret high-quality biosensor data. Although we still find that the literature is replete with poorly performed experiments, over-interpreted results and a general lack of understanding of data analysis, we are optimistic that these shortcomings will be addressed as biosensor technology continues to mature.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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