1
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Marinho Righetto G, Alves Santos-Filho N, Oliveira Catarin Nunes L, André C, Souza JM, Andricopulo AD, Martins Bispo PJ, Cilli EM, Camargo ILBDC. Optimizing Bothropstoxin-I-Derived Peptides: Exploring the Antibacterial Potential of p-BthW. ACS OMEGA 2024; 9:23662-23674. [PMID: 38854567 PMCID: PMC11154919 DOI: 10.1021/acsomega.4c01303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 05/06/2024] [Accepted: 05/15/2024] [Indexed: 06/11/2024]
Abstract
Antimicrobial peptides are an emerging class of antibiotics that present a series of advantageous characteristics such as wide structural variety, broad spectrum of activity, and low propensity to select for resistance. They are found in all classes of life as defense molecules. A group of peptides derived from the protein Bothropstoxin-I has been previously studied as an alternative treatment against multi-drug-resistant bacteria. The peptide p-BthTX-I (sequence: KKYRYHLKPFCKK) and its homodimer, linked by disulfide oxidation through the residues of Cys11 and the serum degradation product [sequence: (KKYRYHLKPFC)2], were evaluated and showed similar antimicrobial activity. In this study, we synthesized an analogue of p-BthTX-I that uses the strategy of Fmoc-Lys(Fmoc)-OH in the C-terminal region for dimerization and tryptophan for all aromatic amino acids to provide better membrane interactions. This analogue, named p-BthW, displayed potent antibacterial activity at lower concentrations and maintained the same hemolytic levels as the original molecule. Our assessment revealed that p-BthW has a quick in vitro bactericidal action and prolonged post-antibiotic effect, comparable to the action of polymyxin B. The mode of action of p-BthW seems to rely not only on membrane depolarization but also on necrosis-like effects, especially in Gram-negative bacteria. Overall, the remarkable results regarding the propensity to develop resistance reaffirmed the great potential of the developed molecule.
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Affiliation(s)
- Gabriela Marinho Righetto
- Laboratory
of Molecular Epidemiology and Microbiology, Department of Physics
and Interdisciplinary Science, University
of Sao Paulo, 13563-120 São Carlos, Brazil
| | - Norival Alves Santos-Filho
- Department
of Biochemistry and Organic Chemistry, Institute of Chemistry, São Paulo State University, 14800-060 Araraquara, Brazil
| | - Letícia Oliveira Catarin Nunes
- Department
of Biochemistry and Organic Chemistry, Institute of Chemistry, São Paulo State University, 14800-060 Araraquara, Brazil
| | - Camille André
- Infectious
Disease Institute, Department of Ophthalmology, Massachusetts Eye
and Ear, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Julia Medeiros Souza
- Laboratory
of Medicinal and Computational Chemistry, Department of Physics and
Interdisciplinary Science, University of
Sao Paulo, 13563-120 São Carlos, Brazil
| | - Adriano Defini Andricopulo
- Laboratory
of Medicinal and Computational Chemistry, Department of Physics and
Interdisciplinary Science, University of
Sao Paulo, 13563-120 São Carlos, Brazil
| | - Paulo José Martins Bispo
- Infectious
Disease Institute, Department of Ophthalmology, Massachusetts Eye
and Ear, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Eduardo Maffud Cilli
- Department
of Biochemistry and Organic Chemistry, Institute of Chemistry, São Paulo State University, 14800-060 Araraquara, Brazil
| | - Ilana Lopes Baratella da Cunha Camargo
- Laboratory
of Molecular Epidemiology and Microbiology, Department of Physics
and Interdisciplinary Science, University
of Sao Paulo, 13563-120 São Carlos, Brazil
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2
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Peñalver M, Paradela A, Palacios-Cuéllar C, Pucciarelli MG, García-Del Portillo F. Experimental evidence of d-glutamate racemase activity in the uncultivated bacterium Candidatus Saccharimonas aalborgensis. Environ Microbiol 2024; 26:e16621. [PMID: 38558504 DOI: 10.1111/1462-2920.16621] [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: 01/29/2024] [Accepted: 03/16/2024] [Indexed: 04/04/2024]
Abstract
The Candidate Phyla Radiation (CPR) encompasses widespread uncultivated bacteria with reduced genomes and limited metabolic capacities. Most CPR bacteria lack the minimal set of enzymes required for peptidoglycan (PG) synthesis, leaving it unclear how these bacteria produce this essential envelope component. In this study, we analysed the distribution of d-amino acid racemases that produce the universal PG components d-glutamate (d-Glu) or d-alanine (d-Ala). We also examined moonlighting enzymes that synthesize d-Glu or d-Ala. Unlike other phyla in the domain Bacteria, CPR bacteria do not exhibit these moonlighting activities and have, at most, one gene encoding either a Glu or Ala racemase. One of these 'orphan' racemases is a predicted Glu racemase (MurICPR) from the CPR bacterium Candidatus Saccharimonas aalborgenesis. The expression of MurICPR restores the growth of a Salmonella d-Glu auxotroph lacking its endogenous racemase and results in the substitution of l-Ala by serine as the first residue in a fraction of the PG stem peptides. In vitro, MurICPR exclusively racemizes Glu as a substrate. Therefore, Ca. Saccharimonas aalborgensis may couple Glu racemization to serine and d-Glu incorporation into the stem peptide. Our findings provide the first insights into the synthesis of PG by an uncultivated environmental bacterium and illustrate how to experimentally test enzymatic activities from CPR bacteria related to PG metabolism.
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Affiliation(s)
- Marcos Peñalver
- Laboratory of Intracellular Bacterial Pathogens, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
- Department of Molecular Biology, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Centro de Biologia Molecular Severo Ochoa (CBM), CSIC-UAM, Madrid, Spain
| | - Alberto Paradela
- Proteomics Facility, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
| | - César Palacios-Cuéllar
- Laboratory of Intracellular Bacterial Pathogens, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
| | - M Graciela Pucciarelli
- Laboratory of Intracellular Bacterial Pathogens, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
- Department of Molecular Biology, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Centro de Biologia Molecular Severo Ochoa (CBM), CSIC-UAM, Madrid, Spain
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3
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Braun C, Wingen LM, Menche D. Strategies and tactics for the synthesis of lipid I and II and shortened analogues: functional building blocks of bacterial cell wall biosynthesis. Nat Prod Rep 2023; 40:1718-1734. [PMID: 37492928 DOI: 10.1039/d3np00018d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Covering: the literature up to 2022This study discusses various synthetic strategies for the synthesis of lipid II, the pivotal bacterial cell wall precursor. In detail, it examines different solution phase approaches, reviews various solid phase sequences, and evaluates enzymatic ventures. The underlying rationale, scope, limitations, and perspectives of these strategies are discussed. The focus is on the tactics and strategies towards the authentic peptidoglycan compound, as well as analogues thereof with shortened side chains, which are increasingly recognized as more beneficial surrogates with more favorable physicochemical properties.
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Affiliation(s)
- Christina Braun
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, D-53121 Bonn, Germany.
| | - Lukas Martin Wingen
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, D-53121 Bonn, Germany.
| | - Dirk Menche
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, D-53121 Bonn, Germany.
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4
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Kumar G, Engle K. Natural products acting against S. aureus through membrane and cell wall disruption. Nat Prod Rep 2023; 40:1608-1646. [PMID: 37326041 DOI: 10.1039/d2np00084a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Covering: 2015 to 2022Staphylococcus aureus (S. aureus) is responsible for several community and hospital-acquired infections with life-threatening complications such as bacteraemia, endocarditis, meningitis, liver abscess, and spinal cord epidural abscess. In recent decades, the abuse and misuse of antibiotics in humans, animals, plants, and fungi and the treatment of nonmicrobial diseases have led to the rapid emergence of multidrug-resistant pathogens. The bacterial wall is a complex structure consisting of the cell membrane, peptidoglycan cell wall, and various associated polymers. The enzymes involved in bacterial cell wall synthesis are established antibiotic targets and continue to be a central focus for antibiotic development. Natural products play a vital role in drug discovery and development. Importantly, natural products provide a starting point for active/lead compounds that sometimes need modification based on structural and biological properties to meet the drug criteria. Notably, microorganisms and plant metabolites have contributed as antibiotics for noninfectious diseases. In this study, we have summarized the recent advances in understanding the activity of the drugs or agents of natural origin that directly inhibit the bacterial membrane, membrane components, and membrane biosynthetic enzymes by targeting membrane-embedded proteins. We also discussed the unique aspects of the active mechanisms of established antibiotics or new agents.
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Affiliation(s)
- Gautam Kumar
- Department of Natural Products, Chemical Sciences, National Institute of Pharmaceutical Education and Research-Hyderabad, Hyderabad, Balanagar, 500037, India.
| | - Kritika Engle
- Department of Natural Products, Chemical Sciences, National Institute of Pharmaceutical Education and Research-Hyderabad, Hyderabad, Balanagar, 500037, India.
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5
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Stojković D, Petrović J, Carević T, Soković M, Liaras K. Synthetic and Semisynthetic Compounds as Antibacterials Targeting Virulence Traits in Resistant Strains: A Narrative Updated Review. Antibiotics (Basel) 2023; 12:963. [PMID: 37370282 PMCID: PMC10295040 DOI: 10.3390/antibiotics12060963] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 05/24/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
This narrative review paper provides an up-to-date overview of the potential of novel synthetic and semisynthetic compounds as antibacterials that target virulence traits in resistant strains. The review focused on research conducted in the last five years and investigated a range of compounds including azoles, indoles, thiophenes, glycopeptides, pleuromutilin derivatives, lactone derivatives, and chalcones. The emergence and spread of antibiotic-resistant bacterial strains is a growing public health concern, and new approaches are urgently needed to combat this threat. One promising approach is to target virulence factors, which are essential for bacterial survival and pathogenesis, but not for bacterial growth. By targeting virulence factors, it may be possible to reduce the severity of bacterial infections without promoting the development of resistance. We discuss the mechanisms of action of the various compounds investigated and their potential as antibacterials. The review highlights the potential of targeting virulence factors as a promising strategy to combat antibiotic resistance and suggests that further research is needed to identify new compounds and optimize their efficacy. The findings of this review suggest that novel synthetic and semisynthetic compounds that target virulence factors have great potential as antibacterials in the fight against antibiotic resistance.
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Affiliation(s)
- Dejan Stojković
- Department of Plant Physiology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11000 Belgrade, Serbia; (D.S.); (J.P.); (T.C.); (M.S.)
| | - Jovana Petrović
- Department of Plant Physiology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11000 Belgrade, Serbia; (D.S.); (J.P.); (T.C.); (M.S.)
| | - Tamara Carević
- Department of Plant Physiology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11000 Belgrade, Serbia; (D.S.); (J.P.); (T.C.); (M.S.)
| | - Marina Soković
- Department of Plant Physiology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11000 Belgrade, Serbia; (D.S.); (J.P.); (T.C.); (M.S.)
| | - Konstantinos Liaras
- Department of Life and Health Sciences, School of Sciences and Engineering, University of Nicosia, 2417 Nicosia, Cyprus
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6
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Sidders AE, Kedziora KM, Arts M, Daniel JM, de Benedetti S, Beam JE, Bui DT, Parsons JB, Schneider T, Rowe SE, Conlon BP. Antibiotic-induced accumulation of lipid II synergizes with antimicrobial fatty acids to eradicate bacterial populations. eLife 2023; 12:80246. [PMID: 36876902 PMCID: PMC10030119 DOI: 10.7554/elife.80246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 03/05/2023] [Indexed: 03/07/2023] Open
Abstract
Antibiotic tolerance and antibiotic resistance are the two major obstacles to the efficient and reliable treatment of bacterial infections. Identifying antibiotic adjuvants that sensitize resistant and tolerant bacteria to antibiotic killing may lead to the development of superior treatments with improved outcomes. Vancomycin, a lipid II inhibitor, is a frontline antibiotic for treating methicillin-resistant Staphylococcus aureus and other Gram-positive bacterial infections. However, vancomycin use has led to the increasing prevalence of bacterial strains with reduced susceptibility to vancomycin. Here, we show that unsaturated fatty acids act as potent vancomycin adjuvants to rapidly kill a range of Gram-positive bacteria, including vancomycin-tolerant and resistant populations. The synergistic bactericidal activity relies on the accumulation of membrane-bound cell wall intermediates that generate large fluid patches in the membrane leading to protein delocalization, aberrant septal formation, and loss of membrane integrity. Our findings provide a natural therapeutic option that enhances vancomycin activity against difficult-to-treat pathogens, and the underlying mechanism may be further exploited to develop antimicrobials that target recalcitrant infection.
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Affiliation(s)
- Ashelyn E Sidders
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Katarzyna M Kedziora
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, United States
- Bioinformatics and Analytics Research Collaborative, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Melina Arts
- Institute for Pharmaceutical Microbiology, University of Bonn, Bonn, Germany
| | - Jan-Martin Daniel
- Institute for Pharmaceutical Microbiology, University of Bonn, Bonn, Germany
| | | | - Jenna E Beam
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Duyen T Bui
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Joshua B Parsons
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, United States
- Division of Infectious Diseases, Duke University, Durham, United States
| | - Tanja Schneider
- Institute for Pharmaceutical Microbiology, University of Bonn, Bonn, Germany
| | - Sarah E Rowe
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Brian P Conlon
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, United States
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, United States
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7
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Guan D, Chen F, Shi W, Lan L, Huang W. Single Modification at the N-Terminus of Norvancomycin to Combat Drug-Resistant Gram-Positive Bacteria. ChemMedChem 2023; 18:e202200708. [PMID: 36823383 DOI: 10.1002/cmdc.202200708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/20/2023] [Accepted: 02/23/2023] [Indexed: 02/25/2023]
Abstract
In the arsenal of glycopeptide antibiotics, norvancomycin, which differs from vancomycin by a single methyl group, has received much less attention. Facing the risks of serious antibiotic resistance and even the collapse of last-line defenses, we designed and synthesized 40 novel norvancomycin derivatives to combat the threat. 32 compounds are single N-terminally modified derivatives generated through simple and efficient methods. Diversity at the N-terminus was greatly enriched, mainly by lipophilic attachment and strategies for the introduction of lipo-sulfonium moieties for extensive structure-activity relationship analysis. The first incorporation of a sulfonium moiety into the norvancomycin structure gave rise to compounds that exhibited 4- to 2048-fold higher activity against vancomycin-resistant bacteria VISA and VRE. This N-terminal modification for norvancomycin provides an alternatively useful and promising strategy to restore the antibacterial activity of glycopeptide antibiotics against resistant bacteria, highlighting the same importance of the N-terminal site as well as the vancosamine position, which is worth further study and development.
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Affiliation(s)
- Dongliang Guan
- CAS Key Laboratory of Receptor Research, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai, 201203, P. R. China.,Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yanta, Shandong, 264117, P. R. China
| | - Feifei Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, P. R. China
| | - Wei Shi
- CAS Key Laboratory of Receptor Research, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai, 201203, P. R. China.,Center for Biotherapeutics Discovery Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, P. R. China
| | - Lefu Lan
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, P. R. China.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, P. R. China.,University of Chinese Academy of Sciences, No.19 A Yuquan Road, Beijing, 100049, P. R. China
| | - Wei Huang
- CAS Key Laboratory of Receptor Research, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai, 201203, P. R. China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, P. R. China.,University of Chinese Academy of Sciences, No.19 A Yuquan Road, Beijing, 100049, P. R. China.,Center for Biotherapeutics Discovery Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, P. R. China
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8
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Righetto GM, Lopes JLDS, Bispo PJM, André C, Souza JM, Andricopulo AD, Beltramini LM, Camargo ILBDC. Antimicrobial Activity of an Fmoc-Plantaricin 149 Derivative Peptide against Multidrug-Resistant Bacteria. Antibiotics (Basel) 2023; 12:antibiotics12020391. [PMID: 36830301 PMCID: PMC9952790 DOI: 10.3390/antibiotics12020391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
Antimicrobial resistance poses a major threat to public health. Given the paucity of novel antimicrobials to treat resistant infections, the emergence of multidrug-resistant bacteria renewed interest in antimicrobial peptides as potential therapeutics. This study designed a new analog of the antimicrobial peptide Plantaricin 149 (Pln149-PEP20) based on previous Fmoc-peptides. The minimal inhibitory concentrations of Pln149-PEP20 were determined for 60 bacteria of different species and resistance profiles, ranging from 1 mg/L to 128 mg/L for Gram-positive bacteria and 16 to 512 mg/L for Gram-negative. Furthermore, Pln149-PEP20 demonstrated excellent bactericidal activity within one hour. To determine the propensity to develop resistance to Pln149-PEP20, a directed-evolution in vitro experiment was performed. Whole-genome sequencing of selected mutants with increased MICs and wild-type isolates revealed that most mutations were concentrated in genes associated with membrane metabolism, indicating the most likely target of Pln149-PEP20. Synchrotron radiation circular dichroism showed how this molecule disturbs the membranes, suggesting a carpet mode of interaction. Membrane depolarization and transmission electron microscopy assays supported these two hypotheses, although a secondary intracellular mechanism of action is possible. The molecule studied in this research has the potential to be used as a novel antimicrobial therapy, although further modifications and optimization remain possible.
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Affiliation(s)
- Gabriela Marinho Righetto
- Laboratory of Molecular Epidemiology and Microbiology, Department of Physics and Interdisciplinary Science, São Carlos Institute of Physics, University of São Paulo, São Carlos 13563-120, Brazil
| | - José Luiz de Souza Lopes
- Laboratory of Applied Biophysics, Department of Applied Physics, Institute of Physics, University of São Paulo, São Paulo 05315-970, Brazil
| | - Paulo José Martins Bispo
- Department of Ophthalmology, Infectious Disease Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02115, USA
| | - Camille André
- Department of Ophthalmology, Infectious Disease Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02115, USA
| | - Julia Medeiros Souza
- Laboratory of Medicinal and Computational Chemistry, Department of Physics and Interdisciplinary Science, São Carlos Institute of Physics, University of São Paulo, São Carlos 13563-120, Brazil
| | - Adriano Defini Andricopulo
- Laboratory of Medicinal and Computational Chemistry, Department of Physics and Interdisciplinary Science, São Carlos Institute of Physics, University of São Paulo, São Carlos 13563-120, Brazil
| | - Leila Maria Beltramini
- Group of Biophysics and Structural Biology “Sérgio Mascarenhas”, Department of Physics and Interdisciplinary Science, São Carlos Institute of Physics, University of São Paulo, São Carlos 13563-120, Brazil
| | - Ilana Lopes Baratella da Cunha Camargo
- Laboratory of Molecular Epidemiology and Microbiology, Department of Physics and Interdisciplinary Science, São Carlos Institute of Physics, University of São Paulo, São Carlos 13563-120, Brazil
- Correspondence: ; Tel.: +55-(16)-3373-8654
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9
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Panina IS, Balandin SV, Tsarev AV, Chugunov AO, Tagaev AA, Finkina EI, Antoshina DV, Sheremeteva EV, Paramonov AS, Rickmeyer J, Bierbaum G, Efremov RG, Shenkarev ZO, Ovchinnikova TV. Specific Binding of the α-Component of the Lantibiotic Lichenicidin to the Peptidoglycan Precursor Lipid II Predetermines Its Antimicrobial Activity. Int J Mol Sci 2023; 24:ijms24021332. [PMID: 36674846 PMCID: PMC9863751 DOI: 10.3390/ijms24021332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/21/2022] [Accepted: 01/06/2023] [Indexed: 01/12/2023] Open
Abstract
To date, a number of lantibiotics have been shown to use lipid II-a highly conserved peptidoglycan precursor in the cytoplasmic membrane of bacteria-as their molecular target. The α-component (Lchα) of the two-component lantibiotic lichenicidin, previously isolated from the Bacillus licheniformis VK21 strain, seems to contain two putative lipid II binding sites in its N-terminal and C-terminal domains. Using NMR spectroscopy in DPC micelles, we obtained convincing evidence that the C-terminal mersacidin-like site is involved in the interaction with lipid II. These data were confirmed by the MD simulations. The contact area of lipid II includes pyrophosphate and disaccharide residues along with the first isoprene units of bactoprenol. MD also showed the potential for the formation of a stable N-terminal nisin-like complex; however, the conditions necessary for its implementation in vitro remain unknown. Overall, our results clarify the picture of two component lantibiotics mechanism of antimicrobial action.
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Affiliation(s)
- Irina S. Panina
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Sergey V. Balandin
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Correspondence: ; Tel.: +7-495-335-0900
| | - Andrey V. Tsarev
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Anton O. Chugunov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Andrey A. Tagaev
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Ekaterina I. Finkina
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Daria V. Antoshina
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Elvira V. Sheremeteva
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Alexander S. Paramonov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Jasmin Rickmeyer
- Institute of Medical Microbiology, Immunology and Parasitology, Medical Faculty, University of Bonn, 53117 Bonn, Germany
| | - Gabriele Bierbaum
- Institute of Medical Microbiology, Immunology and Parasitology, Medical Faculty, University of Bonn, 53117 Bonn, Germany
| | - Roman G. Efremov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
- Department of Applied Mathematics, National Research University Higher School of Economics, 101000 Moscow, Russia
| | - Zakhar O. Shenkarev
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Tatiana V. Ovchinnikova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
- Department of Bioorganic Chemistry, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
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10
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Enzymatic Synthesis of Vancomycin-Modified DNA. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248927. [PMID: 36558056 PMCID: PMC9782525 DOI: 10.3390/molecules27248927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/06/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022]
Abstract
Many potent antibiotics fail to treat bacterial infections due to emergence of drug-resistant strains. This surge of antimicrobial resistance (AMR) calls in for the development of alternative strategies and methods for the development of drugs with restored bactericidal activities. In this context, we surmised that identifying aptamers using nucleotides connected to antibiotics will lead to chemically modified aptameric species capable of restoring the original binding activity of the drugs and hence produce active antibiotic species that could be used to combat AMR. Here, we report the synthesis of a modified nucleoside triphosphate equipped with a vancomycin moiety on the nucleobase. We demonstrate that this nucleotide analogue is suitable for polymerase-mediated synthesis of modified DNA and, importantly, highlight its compatibility with the SELEX methodology. These results pave the way for bacterial-SELEX for the identification of vancomycin-modified aptamers.
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11
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Rütten A, Kirchner T, Musiol-Kroll EM. Overview on Strategies and Assays for Antibiotic Discovery. Pharmaceuticals (Basel) 2022; 15:1302. [PMID: 36297414 PMCID: PMC9607151 DOI: 10.3390/ph15101302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/12/2022] [Accepted: 10/14/2022] [Indexed: 11/23/2022] Open
Abstract
The increase in antibiotic resistance poses a major threat to global health. Actinomycetes, the Gram-positive bacteria of the order Actinomycetales, are fertile producers of bioactive secondary metabolites, including antibiotics. Nearly two-thirds of antibiotics that are used for the treatment of bacterial infections were originally isolated from actinomycetes strains belonging to the genus Streptomyces. This emphasizes the importance of actinomycetes in antibiotic discovery. However, the identification of a new antimicrobial compound and the exploration of its mode of action are very challenging tasks. Therefore, different approaches that enable the "detection" of an antibiotic and the characterization of the mechanisms leading to the biological activity are indispensable. Beyond bioinformatics tools facilitating the identification of biosynthetic gene clusters (BGCs), whole cell-screenings-in which cells are exposed to actinomycete-derived compounds-are a common strategy applied at the very early stage in antibiotic drug development. More recently, target-based approaches have been established. In this case, the drug candidates were tested for interactions with usually validated targets. This review focuses on the bioactivity-based screening methods and provides the readers with an overview on the most relevant assays for the identification of antibiotic activity and investigation of mechanisms of action. Moreover, the article includes examples of the successful application of these methods and suggestions for improvement.
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Affiliation(s)
- Anika Rütten
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’ (CMFI), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Teresa Kirchner
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’ (CMFI), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Ewa Maria Musiol-Kroll
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’ (CMFI), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
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12
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Qi YK, Tang X, Wei NN, Pang CJ, Du SS, Wang KW. Discovery, synthesis, and optimization of teixobactin, a novel antibiotic without detectable bacterial resistance. J Pept Sci 2022; 28:e3428. [PMID: 35610021 DOI: 10.1002/psc.3428] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 05/07/2022] [Accepted: 05/10/2022] [Indexed: 11/09/2022]
Abstract
Discovering new antibiotics with novel chemical scaffolds and antibacterial mechanisms presents a challenge for medicinal scientists worldwide as the ever-increasing bacterial resistance poses a serious threat to human health. A new cyclic peptide-based antibiotic termed teixobactin was discovered from a screen of uncultured soil bacteria through iChip technology in 2015. Teixobactin exhibits excellent antibacterial activity against all the tested gram-positive pathogens and Mycobacterium tuberculosis, including drug-resistant strains. Given that teixobactin targets the highly conserved lipid II and lipid III, which induces the simultaneous inhibition of both peptidoglycan and teichoic acid synthesis, the emergence of resistance is considered to be rather difficult. The novel structure, potent antibacterial activity, and highly conservative targets make teixobactin a promising lead compound for further antibiotic development. This review provides a comprehensive treatise on the advances of teixobactin in the areas of discovery processes, antibacterial activity, mechanisms of action, chemical synthesis, and structural optimizations. The synthetic methods for the key building block l-allo-End, natural teixobactin, representative teixobactin analogues, as well as the structure-activity relationship studies will be highlighted and discussed in details. Finally, some insights into new trends for the generation of novel teixobactin analogues and tips for future work and directions will be commented.
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Affiliation(s)
- Yun-Kun Qi
- Department of Medicinal Chemistry, School of Pharmacy, Qingdao University, Qingdao, China.,Institute of Innovative Drugs, Qingdao University, Qingdao, China.,State Key Laboratory Base for Eco-Chemical Engineering in College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Xiaowen Tang
- Department of Medicinal Chemistry, School of Pharmacy, Qingdao University, Qingdao, China
| | - Ning-Ning Wei
- Institute of Innovative Drugs, Qingdao University, Qingdao, China
| | - Cheng-Jian Pang
- The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Shan-Shan Du
- State Key Laboratory Base for Eco-Chemical Engineering in College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Ke Wei Wang
- Department of Medicinal Chemistry, School of Pharmacy, Qingdao University, Qingdao, China.,Institute of Innovative Drugs, Qingdao University, Qingdao, China
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13
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Olademehin OP, Shuford KL, Kim SJ. Molecular dynamics simulations of the secondary-binding site in disaccharide-modified glycopeptide antibiotics. Sci Rep 2022; 12:7087. [PMID: 35490171 PMCID: PMC9056522 DOI: 10.1038/s41598-022-10735-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 04/12/2022] [Indexed: 11/16/2022] Open
Abstract
Oritavancin is a semisynthetic glycopeptide antibiotic used to treat severe infections by multidrug-resistant Gram-positive pathogens. Oritavancin is known to be a thousand times more potent than vancomycin against Gram-positive bacteria due to the additional interactions with bacterial peptidoglycan (PG) facilitated by a secondary-binding site. The presence of this secondary-binding site is evident in desleucyl-oritavancin, an Edman degradation product of oritavancin, still retaining its potency against Gram-positive bacteria, whereas desleucyl-vancomycin is devoid of any antimicrobial activities. Herein, using explicit solvent molecular dynamics (MD) simulations, steered MD simulations, and umbrella sampling, we show evidence of a secondary-binding site mediated by the disaccharide-modified hydrophobic sidechain of oritavancin interactions with the pentaglycyl-bridge segment of the PG. The interactions were characterized through comparison to the interaction of PG with chloroeremomycin, vancomycin, and the desleucyl analogs of the glycopeptides. Our results show that the enhanced binding of oritavancin to PG over the binding of the other complexes studied is due to an increase in the hydrophobic effect, electrostatic and van der Waals interactions, and not the average number of hydrogen bonds. Our ranking of the binding interactions of the biomolecular complexes directly correlates with the order based on their experimental minimum inhibitory concentrations. The results of our simulations provide insight into the modification of glycopeptides to increase their antimicrobial activities or the design of novel antibiotics against pathogenic Gram-positive bacteria.
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Affiliation(s)
| | - Kevin L Shuford
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76706, USA.
| | - Sung J Kim
- Department of Chemistry, Howard University, Washington, DC, 20059, USA.
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14
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Kumar S, Mollo A, Kahne D, Ruiz N. The Bacterial Cell Wall: From Lipid II Flipping to Polymerization. Chem Rev 2022; 122:8884-8910. [PMID: 35274942 PMCID: PMC9098691 DOI: 10.1021/acs.chemrev.1c00773] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The peptidoglycan (PG) cell wall is an extra-cytoplasmic glycopeptide polymeric structure that protects bacteria from osmotic lysis and determines cellular shape. Since the cell wall surrounds the cytoplasmic membrane, bacteria must add new material to the PG matrix during cell elongation and division. The lipid-linked precursor for PG biogenesis, Lipid II, is synthesized in the inner leaflet of the cytoplasmic membrane and is subsequently translocated across the bilayer so that the PG building block can be polymerized and cross-linked by complex multiprotein machines. This review focuses on major discoveries that have significantly changed our understanding of PG biogenesis in the past decade. In particular, we highlight progress made toward understanding the translocation of Lipid II across the cytoplasmic membrane by the MurJ flippase, as well as the recent discovery of a novel class of PG polymerases, the SEDS (shape, elongation, division, and sporulation) glycosyltransferases RodA and FtsW. Since PG biogenesis is an effective target of antibiotics, these recent developments may lead to the discovery of much-needed new classes of antibiotics to fight bacterial resistance.
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Affiliation(s)
- Sujeet Kumar
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Aurelio Mollo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Natividad Ruiz
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
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15
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Gottstein J, Zaschke-Kriesche J, Unsleber S, Voitsekhovskaia I, Kulik A, Behrmann LV, Overbeck N, Stühler K, Stegmann E, Smits SHJ. New insights into the resistance mechanism for the BceAB-type transporter SaNsrFP. Sci Rep 2022; 12:4232. [PMID: 35273305 PMCID: PMC8913810 DOI: 10.1038/s41598-022-08095-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 02/23/2022] [Indexed: 11/16/2022] Open
Abstract
Treatment of bacterial infections is one of the major challenges of our time due to the evolved resistance mechanisms of pathogens against antibiotics. To circumvent this problem, it is necessary to understand the mode of action of the drug and the mechanism of resistance of the pathogen. One of the most potent antibiotic targets is peptidoglycan (PGN) biosynthesis, as this is an exclusively occurring and critical feature of bacteria. Lipid II is an essential PGN precursor synthesized in the cytosol and flipped into the outer leaflet of the membrane prior to its incorporation into nascent PGN. Antimicrobial peptides (AMPs), such as nisin and colistin, targeting PGN synthesis are considered promising weapons against multidrug-resistant bacteria. However, human pathogenic bacteria that were also resistant to these compounds evolved by the expression of an ATP-binding cassette transporter of the bacitracin efflux (BceAB) type localized in the membrane. In the human pathogen Streptococcus agalactiae, the BceAB transporter SaNsrFP is known to confer resistance to the antimicrobial peptide nisin. The exact mechanism of action for SaNsrFP is poorly understood. For a detailed characterization of the resistance mechanism, we heterologously expressed SaNsrFP in Lactococcus lactis. We demonstrated that SaNsrFP conferred resistance not only to nisin but also to a structurally diverse group of antimicrobial PGN-targeting compounds such as ramoplanin, lysobactin, or bacitracin/(Zn)-bacitracin. Growth experiments revealed that SaNsrFP-producing cells exhibited normal behavior when treated with nisin and/or bacitracin, in contrast to the nonproducing cells, for which growth was significantly reduced. We further detected the accumulation of PGN precursors in the cytoplasm after treating the cells with bacitracin. This did not appear when SaNsrFP was produced. Whole-cell proteomic protein experiments verified that the presence of SaNsrFP in L. lactis resulted in higher production of several proteins associated with cell wall modification. These included, for example, the N-acetylmuramic acid-6-phosphate etherase MurQ and UDP-glucose 4-epimerase. Analysis of components of the cell wall of SaNsrFP-producing cells implied that the transporter is involved in cell wall modification. Since we used an ATP-deficient mutant of the transporter as a comparison, we can show that SaNsrFP and its inactive mutant do not show the same phenotype, albeit expressed at similar levels, which demonstrates the ATP dependency of the mediated resistance processes. Taken together, our data agree to a target protection mechanism and imply a direct involvement of SaNsrFP in resistance by shielding the membrane-localized target of these antimicrobial peptides, resulting in modification of the cell wall.
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Affiliation(s)
- Julia Gottstein
- Institute of Biochemistry, Heinrich-Heine-University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany
| | - Julia Zaschke-Kriesche
- Institute of Biochemistry, Heinrich-Heine-University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany
| | - Sandra Unsleber
- Interfaculty Institute of Microbiology and Infection Medicin, Eberhard Karls University, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Irina Voitsekhovskaia
- Interfaculty Institute of Microbiology and Infection Medicin, Eberhard Karls University, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Andreas Kulik
- Interfaculty Institute of Microbiology and Infection Medicin, Eberhard Karls University, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Lara V Behrmann
- Institute of Biochemistry, Heinrich-Heine-University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany
| | - Nina Overbeck
- Molecular Proteomics Laboratory, Heinrich-Heine-University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany
| | - Kai Stühler
- Molecular Proteomics Laboratory, Heinrich-Heine-University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany
| | - Evi Stegmann
- Interfaculty Institute of Microbiology and Infection Medicin, Eberhard Karls University, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich-Heine-University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany.
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16
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Kim G, Xu Y, Zhang J, Sui Z, Corke H. Antibacterial Activity and Multi-Targeting Mechanism of Dehydrocorydaline From Corydalis turtschaninovii Bess. Against Listeria monocytogenes. Front Microbiol 2022; 12:799094. [PMID: 35087499 PMCID: PMC8787222 DOI: 10.3389/fmicb.2021.799094] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 11/29/2021] [Indexed: 11/13/2022] Open
Abstract
Listeria monocytogenes is a foodborne pathogen, with relatively low incidence but high case-fatality. Phytochemicals have been recognized as a promising antimicrobial agent as an alternative to synthetic chemicals due to their safety and high efficacy with multi-target sites. This study identified and characterized a novel antibacterial agent, dehydrocorydaline, in the Corydalis turschaninovii rhizome using HPLC-LTQ-Orbitrap-HRMS, and its antibacterial effect with lowest MIC (1 mg/mL) and MBC (2 mg/mL) values. In addition, an in vitro growth kinetic assay, cytoplasmic nucleic acid and protein leakage assay, and observation of morphological changes in bacterial cells supported the strong antibacterial activity. Dehydrocorydaline also displayed effective inhibitory effects on biofilm formation and bacterial motility. In order to investigate the potential antibacterial mechanism of action of dehydrocorydaline against L. monocytogenes, label-free quantitative proteomics was used, demonstrating that dehydrocorydaline has multiple targets for combating L. monocytogenes including dysregulation of carbohydrate metabolism, suppression of cell wall synthesis, and inhibition of bacterial motility. Overall, this study demonstrated that dehydrocorydaline has potential as a natural and effective antibacterial agent with multi-target sites in pathogenic bacteria, and provides the basis for development of a new class of antibacterial agent.
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Affiliation(s)
- Gowoon Kim
- Department of Food Science and Technology, Shanghai Jiao Tong University, Shanghai, China
| | - Yijuan Xu
- Department of Food Science and Technology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiarong Zhang
- Biotechnology and Food Engineering Program, Guangdong Technion - Israel Institute of Technology, Shantou, China
| | - Zhongquan Sui
- Department of Food Science and Technology, Shanghai Jiao Tong University, Shanghai, China
| | - Harold Corke
- Biotechnology and Food Engineering Program, Guangdong Technion - Israel Institute of Technology, Shantou, China.,Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
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17
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Li L, Koirala B, Hernandez Y, MacIntyre LW, Ternei MA, Russo R, Brady SF. Identification of structurally diverse menaquinone-binding antibiotics with in vivo activity against multidrug-resistant pathogens. Nat Microbiol 2022; 7:120-131. [PMID: 34949828 PMCID: PMC8732328 DOI: 10.1038/s41564-021-01013-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 10/29/2021] [Indexed: 12/14/2022]
Abstract
The emergence of multidrug-resistant bacteria poses a threat to global health and necessitates the development of additional in vivo active antibiotics with diverse modes of action. Directly targeting menaquinone (MK), which plays an important role in bacterial electron transport, is an appealing, yet underexplored, mode of action due to a dearth of MK-binding molecules. Here we combine sequence-based metagenomic mining with a motif search of bioinformatically predicted natural product structures to identify six biosynthetic gene clusters that we predicted encode MK-binding antibiotics (MBAs). Their predicted products (MBA1-6) were rapidly accessed using a synthetic bioinformatic natural product approach, which relies on bioinformatic structure prediction followed by chemical synthesis. Among these six structurally diverse MBAs, four make up two new MBA structural families. The most potent member of each new family (MBA3, MBA6) proved effective at treating methicillin-resistant Staphylococcus aureus infection in a murine peritonitis-sepsis model. The only conserved feature present in all MBAs is the sequence 'GXLXXXW', which we propose represents a minimum MK-binding motif. Notably, we found that a subset of MBAs were active against Mycobacterium tuberculosis both in vitro and in macrophages. Our findings suggest that naturally occurring MBAs are a structurally diverse and untapped class of mechanistically interesting, in vivo active antibiotics.
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Affiliation(s)
- Lei Li
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Bimal Koirala
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Yozen Hernandez
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Logan W MacIntyre
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Melinda A Ternei
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Riccardo Russo
- Department of Medicine, Center for Emerging and Re-emerging Pathogens, Rutgers University-New Jersey Medical School, Newark, NJ, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA.
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18
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Wingen LM, Braun C, Rausch M, Gross H, Schneider T, Menche D. Versatile synthesis of pathogen specific bacterial cell wall building blocks. RSC Adv 2022; 12:15046-15069. [PMID: 35702425 PMCID: PMC9115884 DOI: 10.1039/d2ra01915a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/05/2022] [Indexed: 11/21/2022] Open
Abstract
Full details on the design, strategies and tactics for development of a novel synthetic sequence to farnesyl lipid I and II analogs is reported. The modular route was based on a three coupling strategy involving an efficient solid phase synthesis of the elaborate peptide fragment, which proceeded with excellent yield and stereoselectivity and was efficiently applied for the convergent synthesis of 3-lipid I and II. Furthermore, the generality of this route was demonstrated by synthesis of 3-lipid I congeners that are characteristic for S. aureus and E. faecalis. All 3-lipid I and II building blocks were obtained in high purity revealing high spectroscopic resolution. A modular three coupling strategy involving a versatile solid phase peptide synthesis enables access to pathogen specific lipid analogs in high yield, revealing high spectroscopic resolution of these key bacterial cell wall building blocks.![]()
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Affiliation(s)
- Lukas Martin Wingen
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, D-53121 Bonn, Germany
| | - Christina Braun
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, D-53121 Bonn, Germany
| | - Marvin Rausch
- Institute for Pharmaceutical Microbiology, University Clinic Bonn, University of Bonn, D-53115 Bonn, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Germany
| | - Harald Gross
- Pharmaceutical Institute, Dept. of Pharmaceutical Biology, University of Tübingen, D-72076 Tübingen, Germany
| | - Tanja Schneider
- Institute for Pharmaceutical Microbiology, University Clinic Bonn, University of Bonn, D-53115 Bonn, Germany
| | - Dirk Menche
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, D-53121 Bonn, Germany
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19
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Jakaria SM, Budil DE, Murtagh J. Glycopeptide antibiotic drug stability in aqueous solution. AAPS OPEN 2022; 8:20. [PMCID: PMC9742044 DOI: 10.1186/s41120-022-00067-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 11/11/2022] [Indexed: 12/14/2022] Open
Abstract
Glycopeptide antimicrobials are a class of naturally occurring or semi-synthetic glycosylated products that have shown antibacterial activity against gram-positive organisms by inhibiting cell-wall synthesis. In most cases, these drugs are prepared in dry powder (lyophilized) form due to chemical and physical instability in aqueous solution; however, from an economic and practical point of view, liquid formulations are preferred. Researchers have recently found ways to formulate some glycopeptide antibiotic therapeutic drugs in aqueous solution at refrigerated or room temperature. Chemical degradation can be significantly slowed by formulating them at a defined pH with specific buffers, avoiding oxygen reactive species, and minimizing solvent exposure. Sugars, amino acids, polyols, and surfactants can reduce physical degradation by restricting glycopeptide mobility and reducing solvent interaction. This review focuses on recent studies on glycopeptide antibiotic drug stability in aqueous solution. It is organized into three sections: (i) glycopeptide antibiotic instability due to chemical and physical degradation, (ii) strategies to improve glycopeptide antibiotic stability in aqueous solution, and (iii) a survey of glycopeptide antibiotic drugs currently available in the market and their stability based on published literature and patents. Antimicrobial resistance deaths are expected to increase by 2050, making heat-stable glycopeptides in aqueous solution an important treatment option for multidrug-resistant and extensively drug-resistant pathogens. In conclusion, it should be possible to formulate heat stable glycopeptide drugs in aqueous solution by understanding the degradation mechanisms of this class of therapeutic drugs in greater detail, making them easily accessible to developing countries with a lack of cold chains.
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Affiliation(s)
- Sardar M. Jakaria
- Hikma Pharmaceuticals, Bedford, OH 44146 USA ,grid.261112.70000 0001 2173 3359Department of Chemistry and Chemical Biology, Northeastern University, MA 02115 Boston, USA
| | - David E. Budil
- grid.261112.70000 0001 2173 3359Department of Chemistry and Chemical Biology, Northeastern University, MA 02115 Boston, USA
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20
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THCz: Small molecules with antimicrobial activity that block cell wall lipid intermediates. Proc Natl Acad Sci U S A 2021; 118:2108244118. [PMID: 34785593 PMCID: PMC8617507 DOI: 10.1073/pnas.2108244118] [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] [Accepted: 10/05/2021] [Indexed: 11/18/2022] Open
Abstract
Considering the alarming emergence of resistance to most antibiotics and the need for new antibiotics, the finding here of a small-molecule class, THCz, that displayed bactericidal activity against gram-positive and selected gram-negative bacteria, is of the greatest importance. We found that THCz target the cell envelope synthesis and can easily be synthesized and modified, and resistance did not readily develop in vitro. Thus, THCz are promising scaffolds for development of bacterial cell wall inhibitors. Emerging antibiotic resistance demands identification of novel antibacterial compound classes. A bacterial whole-cell screen based on pneumococcal autolysin-mediated lysis induction was developed to identify potential bacterial cell wall synthesis inhibitors. A hit class comprising a 1-amino substituted tetrahydrocarbazole (THCz) scaffold, containing two essential amine groups, displayed bactericidal activity against a broad range of gram-positive and selected gram-negative pathogens in the low micromolar range. Mode of action studies revealed that THCz inhibit cell envelope synthesis by targeting undecaprenyl pyrophosphate–containing lipid intermediates and thus simultaneously inhibit peptidoglycan, teichoic acid, and polysaccharide capsule biosynthesis. Resistance did not readily develop in vitro, and the ease of synthesizing and modifying these small molecules, as compared to natural lipid II–binding antibiotics, makes THCz promising scaffolds for development of cell wall–targeting antimicrobials.
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21
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Tocchetti A, Iorio M, Hamid Z, Armirotti A, Reggiani A, Donadio S. Understanding the Mechanism of Action of NAI-112, a Lanthipeptide with Potent Antinociceptive Activity. Molecules 2021; 26:molecules26226764. [PMID: 34833857 PMCID: PMC8624038 DOI: 10.3390/molecules26226764] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/29/2021] [Accepted: 11/04/2021] [Indexed: 11/16/2022] Open
Abstract
NAI-112, a glycosylated, labionine-containing lanthipeptide with weak antibacterial activity, has demonstrated analgesic activity in relevant mouse models of nociceptive and neuropathic pain. However, the mechanism(s) through which NAI-112 exerts its analgesic and antibacterial activities is not known. In this study, we analyzed changes in the spinal cord lipidome resulting from treatment with NAI-112 of naive and in-pain mice. Notably, NAI-112 led to an increase in phosphatidic acid levels in both no-pain and pain models and to a decrease in lysophosphatidic acid levels in the pain model only. We also showed that NAI-112 can form complexes with dipalmitoyl-phosphatidic acid and that Staphylococcus aureus can become resistant to NAI-112 through serial passages at sub-inhibitory concentrations of the compound. The resulting resistant mutants were phenotypically and genotypically related to vancomycin-insensitive S. aureus strains, suggesting that NAI-112 binds to the peptidoglycan intermediate lipid II. Altogether, our results suggest that NAI-112 binds to phosphate-containing lipids and blocks pain sensation by decreasing levels of lysophosphatidic acid in the TRPV1 pathway.
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Affiliation(s)
| | - Marianna Iorio
- Naicons Srl, Viale Ortles 22/4, 20139 Milan, Italy; (A.T.); (S.D.)
- Correspondence:
| | - Zeeshan Hamid
- D3 Validation, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy; (Z.H.); (A.R.)
| | - Andrea Armirotti
- Analytical Chemistry Lab, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy;
| | - Angelo Reggiani
- D3 Validation, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy; (Z.H.); (A.R.)
| | - Stefano Donadio
- Naicons Srl, Viale Ortles 22/4, 20139 Milan, Italy; (A.T.); (S.D.)
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22
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Kotsogianni I, Wood TM, Alexander FM, Cochrane SA, Martin NI. Binding Studies Reveal Phospholipid Specificity and Its Role in the Calcium-Dependent Mechanism of Action of Daptomycin. ACS Infect Dis 2021; 7:2612-2619. [PMID: 34406007 PMCID: PMC8438661 DOI: 10.1021/acsinfecdis.1c00316] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Multidrug-resistant bacteria pose a serious global health threat as antibiotics are increasingly losing their clinical efficacy. A molecular level understanding of the mechanism of action of antimicrobials plays a key role in developing new agents to combat the threat of antimicrobial resistance. Daptomycin, the only clinically used calcium-dependent lipopeptide antibiotic, selectively disrupts Gram-positive bacterial membranes to illicit its bactericidal effect. In this study, we use isothermal titration calorimetry to further characterize the structural features of the target bacterial phospholipids that drive daptomycin binding. Our studies reveal that daptomycin shows a clear preference for the phosphoglycerol headgroup. Furthermore, unlike other calcium-dependent lipopeptide antibiotics, calcium binding by daptomycin is strongly dependent on the presence of phosphatidylglycerol. These investigations provide new insights into daptomycin's phospholipid specificity and calcium binding behavior.
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Affiliation(s)
- Ioli Kotsogianni
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Thomas M. Wood
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Francesca M. Alexander
- School of Chemistry and Chemical Engineering, David Keir Building, Stranmillis Road, Queen’s University Belfast, Belfast, BT9 5AG, United Kingdom
| | - Stephen A. Cochrane
- School of Chemistry and Chemical Engineering, David Keir Building, Stranmillis Road, Queen’s University Belfast, Belfast, BT9 5AG, United Kingdom
| | - Nathaniel I. Martin
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
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23
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Ogasawara Y, Dairi T. Discovery of an alternative pathway of peptidoglycan biosynthesis: A new target for pathway specific inhibitors. J Ind Microbiol Biotechnol 2021; 48:6296644. [PMID: 34114638 PMCID: PMC8788868 DOI: 10.1093/jimb/kuab038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/07/2021] [Indexed: 11/13/2022]
Abstract
Peptidoglycan in bacterial cell walls is a biopolymer consisting of sugars and amino acids and plays important role in maintaining cell integrity from the environment. Its biosynthesis is a major target for antibiotics and the genes and enzymes involved in the biosynthetic pathway have been well studied. However, we recently identified an alternative pathway in the early stage of peptidoglycan biosynthesis in Xanthomonas oryzae, a plant pathogen causing bacterial blight disease of rice. The distribution of the alternative pathway is limited to relatively few bacterial genera that contain many pathogenic species, including Xylella and Stenotrophomonas, besides Xanthomonas. Thus, the alternative pathway is an attractive target for the development of narrow spectrum antibiotics specific to pathogens. In this minireview, we summarize the discovery of the alternative pathway and identification of its specific inhibitors.
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Affiliation(s)
- Yasushi Ogasawara
- Graduate School of Engineering, Hokkaido University, N13 & W8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Tohru Dairi
- Graduate School of Engineering, Hokkaido University, N13 & W8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
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24
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Wirtz DA, Ludwig KC, Arts M, Marx CE, Krannich S, Barac P, Kehraus S, Josten M, Henrichfreise B, Müller A, König GM, Peoples AJ, Nitti A, Spoering AL, Ling LL, Lewis K, Crüsemann M, Schneider T. Biosynthesis and Mechanism of Action of the Cell Wall Targeting Antibiotic Hypeptin. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Daniel A. Wirtz
- Institute for Pharmaceutical Biology University of Bonn Nussallee 6 53115 Bonn Germany
| | - Kevin C. Ludwig
- Institute for Pharmaceutical Microbiology University of Bonn University Clinic Bonn Meckenheimer Allee 168 53115 Bonn Germany
- DZIF German Center for Infectious Research, partner site Bonn-Cologne Germany
| | - Melina Arts
- Institute for Pharmaceutical Microbiology University of Bonn University Clinic Bonn Meckenheimer Allee 168 53115 Bonn Germany
| | - Carina E. Marx
- Institute for Pharmaceutical Microbiology University of Bonn University Clinic Bonn Meckenheimer Allee 168 53115 Bonn Germany
| | - Sebastian Krannich
- Institute for Pharmaceutical Microbiology University of Bonn University Clinic Bonn Meckenheimer Allee 168 53115 Bonn Germany
| | - Paul Barac
- Institute for Pharmaceutical Biology University of Bonn Nussallee 6 53115 Bonn Germany
| | - Stefan Kehraus
- Institute for Pharmaceutical Biology University of Bonn Nussallee 6 53115 Bonn Germany
| | - Michaele Josten
- DZIF German Center for Infectious Research, partner site Bonn-Cologne Germany
- Institute for Medical Microbiology, Immunology and Parasitology University Hospital Bonn Venusberg Campus 1 53127 Bonn Germany
| | - Beate Henrichfreise
- Institute for Pharmaceutical Microbiology University of Bonn University Clinic Bonn Meckenheimer Allee 168 53115 Bonn Germany
| | - Anna Müller
- Institute for Pharmaceutical Microbiology University of Bonn University Clinic Bonn Meckenheimer Allee 168 53115 Bonn Germany
| | - Gabriele M. König
- Institute for Pharmaceutical Biology University of Bonn Nussallee 6 53115 Bonn Germany
| | | | | | | | | | - Kim Lewis
- Department of Biology Antimicrobial Discovery Center Northeastern University Boston MA 02115 USA
| | - Max Crüsemann
- Institute for Pharmaceutical Biology University of Bonn Nussallee 6 53115 Bonn Germany
| | - Tanja Schneider
- Institute for Pharmaceutical Microbiology University of Bonn University Clinic Bonn Meckenheimer Allee 168 53115 Bonn Germany
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25
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Wirtz DA, Ludwig KC, Arts M, Marx CE, Krannich S, Barac P, Kehraus S, Josten M, Henrichfreise B, Müller A, König GM, Peoples AJ, Nitti A, Spoering AL, Ling LL, Lewis K, Crüsemann M, Schneider T. Biosynthesis and Mechanism of Action of the Cell Wall Targeting Antibiotic Hypeptin. Angew Chem Int Ed Engl 2021; 60:13579-13586. [PMID: 33768646 PMCID: PMC8252469 DOI: 10.1002/anie.202102224] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/19/2021] [Indexed: 02/06/2023]
Abstract
Hypeptin is a cyclodepsipeptide antibiotic produced by Lysobacter sp. K5869, isolated from an environmental sample by the iChip technology, dedicated to the cultivation of previously uncultured microorganisms. Hypeptin shares structural features with teixobactin and exhibits potent activity against a broad spectrum of gram‐positive pathogens. Using comprehensive in vivo and in vitro analyses, we show that hypeptin blocks bacterial cell wall biosynthesis by binding to multiple undecaprenyl pyrophosphate‐containing biosynthesis intermediates, forming a stoichiometric 2:1 complex. Resistance to hypeptin did not readily develop in vitro. Analysis of the hypeptin biosynthetic gene cluster (BGC) supported a model for the synthesis of the octapeptide. Within the BGC, two hydroxylases were identified and characterized, responsible for the stereoselective β‐hydroxylation of four building blocks when bound to peptidyl carrier proteins. In vitro hydroxylation assays corroborate the biosynthetic hypothesis and lead to the proposal of a refined structure for hypeptin.
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Affiliation(s)
- Daniel A Wirtz
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| | - Kevin C Ludwig
- Institute for Pharmaceutical Microbiology, University of Bonn, University Clinic Bonn, Meckenheimer Allee 168, 53115, Bonn, Germany.,DZIF, German Center for Infectious Research, partner site Bonn-Cologne, Germany
| | - Melina Arts
- Institute for Pharmaceutical Microbiology, University of Bonn, University Clinic Bonn, Meckenheimer Allee 168, 53115, Bonn, Germany
| | - Carina E Marx
- Institute for Pharmaceutical Microbiology, University of Bonn, University Clinic Bonn, Meckenheimer Allee 168, 53115, Bonn, Germany
| | - Sebastian Krannich
- Institute for Pharmaceutical Microbiology, University of Bonn, University Clinic Bonn, Meckenheimer Allee 168, 53115, Bonn, Germany
| | - Paul Barac
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| | - Stefan Kehraus
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| | - Michaele Josten
- DZIF, German Center for Infectious Research, partner site Bonn-Cologne, Germany.,Institute for Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Venusberg Campus 1, 53127, Bonn, Germany
| | - Beate Henrichfreise
- Institute for Pharmaceutical Microbiology, University of Bonn, University Clinic Bonn, Meckenheimer Allee 168, 53115, Bonn, Germany
| | - Anna Müller
- Institute for Pharmaceutical Microbiology, University of Bonn, University Clinic Bonn, Meckenheimer Allee 168, 53115, Bonn, Germany
| | - Gabriele M König
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| | | | - Anthony Nitti
- NovoBiotic Pharmaceuticals, Cambridge, MA, 02138, USA
| | | | - Losee L Ling
- NovoBiotic Pharmaceuticals, Cambridge, MA, 02138, USA
| | - Kim Lewis
- Department of Biology, Antimicrobial Discovery Center, Northeastern University, Boston, MA, 02115, USA
| | - Max Crüsemann
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| | - Tanja Schneider
- Institute for Pharmaceutical Microbiology, University of Bonn, University Clinic Bonn, Meckenheimer Allee 168, 53115, Bonn, Germany
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26
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Wang Y, Liang Z, Zheng Y, Leung ASL, Yan SC, So PK, Leung YC, Wong WL, Wong KY. Rational structural modification of the isatin scaffold to develop new and potent antimicrobial agents targeting bacterial peptidoglycan glycosyltransferase. RSC Adv 2021; 11:18122-18130. [PMID: 35480164 PMCID: PMC9033243 DOI: 10.1039/d1ra02119b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/10/2021] [Indexed: 12/11/2022] Open
Abstract
A series of isatin derivatives bearing three different substituent groups at the N-1, C-3 and C-5 positions of the isatin scaffold were systematically designed and synthesized to study the structure-activity relationship of their inhibition of bacterial peptidoglycan glycosyltransferase (PGT) activity and antimicrobial susceptibility against S. aureus, E. coli and methicillin-resistant Staphylococcus aureus (MRSA (BAA41)) strains. The substituents at these sites are pointing towards three different directions from the isatin scaffold to interact with the amino acid residues in the binding pocket of PGT. Comparative studies of their structure-activity relationship allow us to gain better understanding of the direction of the substituents that contribute critical interactions leading to inhibition activity against the bacterial enzyme. Our results indicate that the modification of these sites is able to maximize the antimicrobial potency and inhibitory action against the bacterial enzyme. Two compounds show good antimicrobial potency (MIC = 3 μg mL-1 against S. aureus and MRSA; 12-24 μg mL-1 against E. coli). Results of the inhibition study against the bacterial enzyme (E. coli PBP 1b) reveal that some compounds are able to achieve excellent in vitro inhibitions of bacterial enzymatic activity (up to 100%). The best half maximal inhibitory concentration (IC50) observed among the new compounds is 8.9 μM.
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Affiliation(s)
- Yong Wang
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University Hunghom Kowloon Hong Kong P. R. China
| | - Zhiguang Liang
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University Hunghom Kowloon Hong Kong P. R. China
| | - Yuanyuan Zheng
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University Hunghom Kowloon Hong Kong P. R. China
| | - Alan Siu-Lun Leung
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University Hunghom Kowloon Hong Kong P. R. China
| | - Siu-Cheong Yan
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University Hunghom Kowloon Hong Kong P. R. China
| | - Pui-Kin So
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University Hunghom Kowloon Hong Kong P. R. China
| | - Yun-Chung Leung
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University Hunghom Kowloon Hong Kong P. R. China
| | - Wing-Leung Wong
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University Hunghom Kowloon Hong Kong P. R. China
| | - Kwok-Yin Wong
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University Hunghom Kowloon Hong Kong P. R. China
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27
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Panter F, Bader CD, Müller R. Synergizing the potential of bacterial genomics and metabolomics to find novel antibiotics. Chem Sci 2021; 12:5994-6010. [PMID: 33995996 PMCID: PMC8098685 DOI: 10.1039/d0sc06919a] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/22/2021] [Indexed: 12/13/2022] Open
Abstract
Antibiotic development based on natural products has faced a long lasting decline since the 1970s, while both the speed and the extent of antimicrobial resistance (AMR) development have been severely underestimated. The discovery of antimicrobial natural products of bacterial and fungal origin featuring new chemistry and previously unknown mode of actions is increasingly challenged by rediscovery issues. Natural products that are abundantly produced by the corresponding wild type organisms often featuring strong UV signals have been extensively characterized, especially the ones produced by extensively screened microbial genera such as streptomycetes. Purely synthetic chemistry approaches aiming to replace the declining supply from natural products as starting materials to develop novel antibiotics largely failed to provide significant numbers of antibiotic drug leads. To cope with this fundamental issue, microbial natural products science is being transformed from a 'grind-and-find' study to an integrated approach based on bacterial genomics and metabolomics. Novel technologies in instrumental analytics are increasingly employed to lower detection limits and expand the space of detectable substance classes, while broadening the scope of accessible and potentially bioactive natural products. Furthermore, the almost exponential increase in publicly available bacterial genome data has shown that the biosynthetic potential of the investigated strains by far exceeds the amount of detected metabolites. This can be judged by the discrepancy between the number of biosynthetic gene clusters (BGC) encoded in the genome of each microbial strain and the number of secondary metabolites actually detected, even when considering the increased sensitivity provided by novel analytical instrumentation. In silico annotation tools for biosynthetic gene cluster classification and analysis allow fast prioritization in BGC-to-compound workflows, which is highly important to be able to process the enormous underlying data volumes. BGC prioritization is currently accompanied by novel molecular biology-based approaches to access the so-called orphan BGCs not yet correlated with a secondary metabolite. Integration of metabolomics, in silico genomics and molecular biology approaches into the mainstream of natural product research will critically influence future success and impact the natural product field in pharmaceutical, nutritional and agrochemical applications and especially in anti-infective research.
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Affiliation(s)
- Fabian Panter
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy, Saarland University Campus E8 1 66123 Saarbrücken Germany
- German Centre for Infection Research (DZIF) Partner Site Hannover-Braunschweig Germany
- Helmholtz International Lab for Anti-infectives Campus E8 1 66123 Saarbrücken Germany
| | - Chantal D Bader
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy, Saarland University Campus E8 1 66123 Saarbrücken Germany
- German Centre for Infection Research (DZIF) Partner Site Hannover-Braunschweig Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy, Saarland University Campus E8 1 66123 Saarbrücken Germany
- German Centre for Infection Research (DZIF) Partner Site Hannover-Braunschweig Germany
- Helmholtz International Lab for Anti-infectives Campus E8 1 66123 Saarbrücken Germany
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28
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Fisher JF, Mobashery S. β-Lactams against the Fortress of the Gram-Positive Staphylococcus aureus Bacterium. Chem Rev 2021; 121:3412-3463. [PMID: 33373523 PMCID: PMC8653850 DOI: 10.1021/acs.chemrev.0c01010] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The biological diversity of the unicellular bacteria-whether assessed by shape, food, metabolism, or ecological niche-surely rivals (if not exceeds) that of the multicellular eukaryotes. The relationship between bacteria whose ecological niche is the eukaryote, and the eukaryote, is often symbiosis or stasis. Some bacteria, however, seek advantage in this relationship. One of the most successful-to the disadvantage of the eukaryote-is the small (less than 1 μm diameter) and nearly spherical Staphylococcus aureus bacterium. For decades, successful clinical control of its infection has been accomplished using β-lactam antibiotics such as the penicillins and the cephalosporins. Over these same decades S. aureus has perfected resistance mechanisms against these antibiotics, which are then countered by new generations of β-lactam structure. This review addresses the current breadth of biochemical and microbiological efforts to preserve the future of the β-lactam antibiotics through a better understanding of how S. aureus protects the enzyme targets of the β-lactams, the penicillin-binding proteins. The penicillin-binding proteins are essential enzyme catalysts for the biosynthesis of the cell wall, and understanding how this cell wall is integrated into the protective cell envelope of the bacterium may identify new antibacterials and new adjuvants that preserve the efficacy of the β-lactams.
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Affiliation(s)
- Jed F Fisher
- Department of Chemistry and Biochemistry, McCourtney Hall, University of Notre Dame, Notre Dame Indiana 46556, United States
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, McCourtney Hall, University of Notre Dame, Notre Dame Indiana 46556, United States
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29
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Olademehin O, Kim SJ, Shuford KL. Molecular Dynamics Simulation of Atomic Interactions in the Vancomycin Binding Site. ACS OMEGA 2021; 6:775-785. [PMID: 33458529 PMCID: PMC7808135 DOI: 10.1021/acsomega.0c05353] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 12/10/2020] [Indexed: 06/12/2023]
Abstract
Vancomycin is a glycopeptide antibiotic produced by Amycolaptopsis orientalis used to treat serious infections by Gram-positive pathogens including methicillin-resistant Staphylococcus aureus. Vancomycin inhibits cell wall biosynthesis by targeting lipid II, which is the membrane-bound peptidoglycan precursor. The heptapeptide aglycon structure of vancomycin binds to the d-Ala-d-Ala of the pentapeptide stem structure in lipid II. The third residue of vancomycin aglycon is asparagine, which is not directly involved in the dipeptide binding. Nonetheless, asparagine plays a crucial role in substrate recognition, as the vancomycin analogue with asparagine substituted by aspartic acid (VD) shows a reduction in antibacterial activities. To characterize the function of asparagine, binding of vancomycin and its aspartic-acid-substituted analogue VD to l-Lys-d-Ala-d-Ala and l-Lys-d-Ala-d-Lac was investigated using molecular dynamic simulations. Binding interactions were analyzed using root-mean-square deviation (RMSD), two-dimensional (2D) contour plots, hydrogen bond analysis, and free energy calculations of the complexes. The analysis shows that the aspartate substitution introduced a negative charge to the binding cleft of VD, which altered the aglycon conformation that minimized the repulsive lone pair interaction in the binding of a depsipeptide. Our findings provide new insight for the development of novel glycopeptide antibiotics against the emerging vancomycin-resistant pathogens by chemical modification at the third residue in vancomycin to improve its binding affinity to the d-Ala-d-Lac-terminated peptidoglycan in lipid II found in vancomycin-resistant enterococci and vancomycin-resistant S. aureus.
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Affiliation(s)
- Olatunde
P. Olademehin
- Department
of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Sung Joon Kim
- Department
of Chemistry, Howard University, Washington, District of
Columbia 20059, United
States
| | - Kevin L. Shuford
- Department
of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
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30
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Li J, Huo H, Yang F, Zhou Q, Li M, Chen ZS, Ji K. Gold( iii)-catalyzed bicyclizations of alkylidenecyclopropane-tethered ynones for divergent synthesis of indene and naphthalenone-based polycycles. Org Chem Front 2021. [DOI: 10.1039/d1qo00821h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A gold(iii)-catalyzed cascade oxidation/cyclization of alkylidenecyclopropane-tethered ynones for the assembly of indene and naphthalenone-based polycycles by employing different N-oxides is reported.
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Affiliation(s)
- Jian Li
- College of Chemistry and Pharmacy, Northwest A&F University, Shaanxi Key Laboratory of Natural Products & Chemical Biology, 3 Taicheng Road, Yangling, Shaanxi 712100, China
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Haibo Huo
- State Key Laboratory of Crop Stress Biology in Arid Area, College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fang Yang
- College of Chemistry and Pharmacy, Northwest A&F University, Shaanxi Key Laboratory of Natural Products & Chemical Biology, 3 Taicheng Road, Yangling, Shaanxi 712100, China
| | - Qianqian Zhou
- College of Chemistry and Pharmacy, Northwest A&F University, Shaanxi Key Laboratory of Natural Products & Chemical Biology, 3 Taicheng Road, Yangling, Shaanxi 712100, China
| | - Mengxue Li
- College of Chemistry and Pharmacy, Northwest A&F University, Shaanxi Key Laboratory of Natural Products & Chemical Biology, 3 Taicheng Road, Yangling, Shaanxi 712100, China
| | - Zi-Sheng Chen
- College of Chemistry and Pharmacy, Northwest A&F University, Shaanxi Key Laboratory of Natural Products & Chemical Biology, 3 Taicheng Road, Yangling, Shaanxi 712100, China
| | - Kegong Ji
- College of Chemistry and Pharmacy, Northwest A&F University, Shaanxi Key Laboratory of Natural Products & Chemical Biology, 3 Taicheng Road, Yangling, Shaanxi 712100, China
- Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
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31
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Moazzezy N, Rismani E, Rezaei M, Karam MRA, Rafati S, Bouzari S, Oloomi M. Computational evaluation of modified peptides from human neutrophil peptide 1 (HNP-1). J Biomol Struct Dyn 2020; 40:1163-1171. [PMID: 32981420 DOI: 10.1080/07391102.2020.1823249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The development of bacterial resistance toward antibiotics has been led to pay attention to the antimicrobial peptides (AMPs). The common mechanism of AMPs is disrupting the integrity of the bacterial membrane. One of the most accessible targets for α-defensins human neutrophil peptide-1 (HNP-1) is lipid II. In the present study, we performed homology modeling and geometrical validation of human neutrophil defensin 1. Then, the conformational and physicochemical properties of HNP-1 derived peptides 2Abz14S29, 2Abz23S29, and HNP1ΔC18A, as well as their interaction with lipid II were studied computationally. The overall quality of the predicted model of full protein was -5.14, where over 90% of residues were in the most favored and allowed regions in the Ramachandran plot. Although HNP-1 and HNP1ΔC18A were classified as unstable peptides, 2Abz14S29 and 2Abz23S29 were stable, based on the instability index values. Molecular docking showed similar interaction pattern of peptides and HNP-1 to lipid II. Molecular dynamic simulations revealed the overall stability of conformations, though the fluctuations of amino acids in the modified peptides were relatively higher than HNP-1. Further, the binding affinity constant (Kd) of HNP-1 and 2Abz23S29 in complex with lipid II was 10 times stronger than 2Abz14S29 and HNP1ΔC18A. Overall, computational studies of conformational and interaction patterns have signified how derived peptides could have displayed relatively similar antimicrobial results compared to HNP-1 in the reported experimental studies. Chemical modifications not only have improved the physicochemical properties of derived peptides compared to HNP-1, but also they have retained the similar pattern and binding affinity of peptides. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Neda Moazzezy
- Molecular Biology Department, Pasteur Institute of Iran, Tehran, Iran
| | - Elham Rismani
- Molecular Medicine Department, Pasteur Institute of Iran, Tehran, Iran
| | - Maryam Rezaei
- Molecular Biology Department, Pasteur Institute of Iran, Tehran, Iran
| | | | - Sima Rafati
- Immunotherapy and Leishmania Vaccine Research Department, Pasteur Institute of Iran, Tehran, Iran
| | - Saeid Bouzari
- Molecular Biology Department, Pasteur Institute of Iran, Tehran, Iran
| | - Mana Oloomi
- Molecular Biology Department, Pasteur Institute of Iran, Tehran, Iran
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32
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Fullenkamp CR, Hsu YP, Quardokus EM, Zhao G, Bewley CA, VanNieuwenhze M, Sulikowski GA. Synthesis of 9-Dechlorochrysophaentin A Enables Studies Revealing Bacterial Cell Wall Biosynthesis Inhibition Phenotype in B. subtilis. J Am Chem Soc 2020; 142:16161-16166. [PMID: 32866011 DOI: 10.1021/jacs.0c04917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chrysophaentin A is an antimicrobial natural product isolated from the marine alga C. taylori in milligram quantity. Structurally, chrysophaentin A features a macrocyclic biaryl ether core incorporating two trisubstituted chloroalkenes at its periphery. A concise synthesis of iso- and 9-dechlorochrysophaentin A enabled by a Z-selective ring-closing metathesis (RCM) cyclization followed by an oxygen to carbon ring contraction is described. Fluorescent microscopy studies revealed 9-dechlorochrysophaentins leads to inhibition of bacterial cell wall biosynthesis by disassembly of key divisome proteins, the cornerstone to bacterial cell wall biosynthesis and division.
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Affiliation(s)
| | - Yen-Pang Hsu
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States.,Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Ellen M Quardokus
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Gengxiang Zhao
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Carole A Bewley
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Michael VanNieuwenhze
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States.,Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Gary A Sulikowski
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States.,Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37235, United States.,Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
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33
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Wingen LM, Rausch M, Schneider T, Menche D. Modular Total Synthesis of Farnesyl Analogues of Cell Wall Precursors Lipid I and II Containing the Staphylococcus aureus Pentaglycine Bridge Modification. J Org Chem 2020; 85:10206-10215. [PMID: 32571025 DOI: 10.1021/acs.joc.0c01004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A scalable and modular total synthesis of 3-lipid I and 3-lipid II was accomplished by a novel route involving an efficient solid phase synthesis of the peptide fragment and an effective chemoenzymatic attachment of the second sugar moiety. The generality of this route was further documented by the synthesis of an analogue bearing the pentaglycine interpeptidic bridge modification characteristic for the human pathogen Staphylococcus aureus.
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Affiliation(s)
- Lukas M Wingen
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, 53121 Bonn, Germany
| | - Marvin Rausch
- Institute for Pharmaceutical Microbiology, University Clinic Bonn, University of Bonn, 53115 Bonn, Germany.,German Center for Infection Research (DZIF), partner site Bonn-Cologne, 53127 Bonn, Germany
| | - Tanja Schneider
- Institute for Pharmaceutical Microbiology, University Clinic Bonn, University of Bonn, 53115 Bonn, Germany
| | - Dirk Menche
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, 53121 Bonn, Germany
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34
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Ortiz‐López FJ, Carretero‐Molina D, Sánchez‐Hidalgo M, Martín J, González I, Román‐Hurtado F, Cruz M, García‐Fernández S, Reyes F, Deisinger JP, Müller A, Schneider T, Genilloud O. Cacaoidin, First Member of the New Lanthidin RiPP Family. Angew Chem Int Ed Engl 2020; 59:12654-12658. [DOI: 10.1002/anie.202005187] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Indexed: 11/05/2022]
Affiliation(s)
- Francisco Javier Ortiz‐López
- Fundación MEDINA Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía Avenida del Conocimiento 34. Parque Tecnológico de Ciencias de la Salud 18016 Armilla Granada Spain
| | - Daniel Carretero‐Molina
- Fundación MEDINA Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía Avenida del Conocimiento 34. Parque Tecnológico de Ciencias de la Salud 18016 Armilla Granada Spain
| | - Marina Sánchez‐Hidalgo
- Fundación MEDINA Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía Avenida del Conocimiento 34. Parque Tecnológico de Ciencias de la Salud 18016 Armilla Granada Spain
| | - Jesús Martín
- Fundación MEDINA Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía Avenida del Conocimiento 34. Parque Tecnológico de Ciencias de la Salud 18016 Armilla Granada Spain
| | - Ignacio González
- Fundación MEDINA Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía Avenida del Conocimiento 34. Parque Tecnológico de Ciencias de la Salud 18016 Armilla Granada Spain
| | - Fernando Román‐Hurtado
- Fundación MEDINA Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía Avenida del Conocimiento 34. Parque Tecnológico de Ciencias de la Salud 18016 Armilla Granada Spain
| | - Mercedes Cruz
- Fundación MEDINA Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía Avenida del Conocimiento 34. Parque Tecnológico de Ciencias de la Salud 18016 Armilla Granada Spain
| | | | - Fernando Reyes
- Fundación MEDINA Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía Avenida del Conocimiento 34. Parque Tecnológico de Ciencias de la Salud 18016 Armilla Granada Spain
| | - Julia Patricia Deisinger
- Institute for Pharmaceutical Microbiology University Clinic Bonn University of Bonn Meckenheimer Allee 168 53115 Bonn Germany
- DZIF German Center for Infection Research partner site Bonn-Cologne Bonn Germany
| | - Anna Müller
- Institute for Pharmaceutical Microbiology University Clinic Bonn University of Bonn Meckenheimer Allee 168 53115 Bonn Germany
| | - Tanja Schneider
- Institute for Pharmaceutical Microbiology University Clinic Bonn University of Bonn Meckenheimer Allee 168 53115 Bonn Germany
- DZIF German Center for Infection Research partner site Bonn-Cologne Bonn Germany
| | - Olga Genilloud
- Fundación MEDINA Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía Avenida del Conocimiento 34. Parque Tecnológico de Ciencias de la Salud 18016 Armilla Granada Spain
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35
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Ortiz‐López FJ, Carretero‐Molina D, Sánchez‐Hidalgo M, Martín J, González I, Román‐Hurtado F, Cruz M, García‐Fernández S, Reyes F, Deisinger JP, Müller A, Schneider T, Genilloud O. Cacaoidin, First Member of the New Lanthidin RiPP Family. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005187] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Francisco Javier Ortiz‐López
- Fundación MEDINA Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía Avenida del Conocimiento 34. Parque Tecnológico de Ciencias de la Salud 18016 Armilla Granada Spain
| | - Daniel Carretero‐Molina
- Fundación MEDINA Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía Avenida del Conocimiento 34. Parque Tecnológico de Ciencias de la Salud 18016 Armilla Granada Spain
| | - Marina Sánchez‐Hidalgo
- Fundación MEDINA Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía Avenida del Conocimiento 34. Parque Tecnológico de Ciencias de la Salud 18016 Armilla Granada Spain
| | - Jesús Martín
- Fundación MEDINA Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía Avenida del Conocimiento 34. Parque Tecnológico de Ciencias de la Salud 18016 Armilla Granada Spain
| | - Ignacio González
- Fundación MEDINA Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía Avenida del Conocimiento 34. Parque Tecnológico de Ciencias de la Salud 18016 Armilla Granada Spain
| | - Fernando Román‐Hurtado
- Fundación MEDINA Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía Avenida del Conocimiento 34. Parque Tecnológico de Ciencias de la Salud 18016 Armilla Granada Spain
| | - Mercedes Cruz
- Fundación MEDINA Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía Avenida del Conocimiento 34. Parque Tecnológico de Ciencias de la Salud 18016 Armilla Granada Spain
| | | | - Fernando Reyes
- Fundación MEDINA Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía Avenida del Conocimiento 34. Parque Tecnológico de Ciencias de la Salud 18016 Armilla Granada Spain
| | - Julia Patricia Deisinger
- Institute for Pharmaceutical Microbiology University Clinic Bonn University of Bonn Meckenheimer Allee 168 53115 Bonn Germany
- DZIF German Center for Infection Research partner site Bonn-Cologne Bonn Germany
| | - Anna Müller
- Institute for Pharmaceutical Microbiology University Clinic Bonn University of Bonn Meckenheimer Allee 168 53115 Bonn Germany
| | - Tanja Schneider
- Institute for Pharmaceutical Microbiology University Clinic Bonn University of Bonn Meckenheimer Allee 168 53115 Bonn Germany
- DZIF German Center for Infection Research partner site Bonn-Cologne Bonn Germany
| | - Olga Genilloud
- Fundación MEDINA Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía Avenida del Conocimiento 34. Parque Tecnológico de Ciencias de la Salud 18016 Armilla Granada Spain
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36
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Mode of action of teixobactins in cellular membranes. Nat Commun 2020; 11:2848. [PMID: 32503964 PMCID: PMC7275090 DOI: 10.1038/s41467-020-16600-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/12/2020] [Indexed: 12/16/2022] Open
Abstract
The natural antibiotic teixobactin kills pathogenic bacteria without detectable resistance. The difficult synthesis and unfavourable solubility of teixobactin require modifications, yet insufficient knowledge on its binding mode impedes the hunt for superior analogues. Thus far, teixobactins are assumed to kill bacteria by binding to cognate cell wall precursors (Lipid II and III). Here we present the binding mode of teixobactins in cellular membranes using solid-state NMR, microscopy, and affinity assays. We solve the structure of the complex formed by an improved teixobactin-analogue and Lipid II and reveal how teixobactins recognize a broad spectrum of targets. Unexpectedly, we find that teixobactins only weakly bind to Lipid II in cellular membranes, implying the direct interaction with cell wall precursors is not the sole killing mechanism. Our data suggest an additional mechanism affords the excellent activity of teixobactins, which can block the cell wall biosynthesis by capturing precursors in massive clusters on membranes. The natural antibiotic teixobactin kills bacteria by direct binding to their cognate cell wall precursors (Lipid II and III). Here authors use solid-state NMR to reveal the native binding mode of teixobactins and show that teixobactins only weakly bind to Lipid II in anionic cellular membranes.
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37
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Goddard TN, Patel J, Park HB, Crawford JM. Dimeric Stilbene Antibiotics Target the Bacterial Cell Wall in Drug-Resistant Gram-Positive Pathogens. Biochemistry 2020; 59:1966-1971. [PMID: 32410442 PMCID: PMC10578317 DOI: 10.1021/acs.biochem.0c00213] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The prevalence of antibiotic resistance has been increasing globally, and new antimicrobial agents are needed to address this growing problem. We previously reported that a stilbene dimer from Photorhabdus gammaproteobacteria exhibits strong activity relative to its monomer against the multidrug-resistant Gram-positive pathogens methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus faecalis. Here, we show that related dietary plant stilbene-derived dimers also have activity against these pathogens, and MRSA is unable to develop substantial resistance even after daily nonlethal exposure to the lead compound for a duration of three months. Through a systematic deduction process, we established the mode of action of the lead dimer, which targets the bacterial cell wall. Genome sequencing of modest resistance mutants, mass spectrometry analysis of cell wall precursors, and exogenous lipid II chemical complementation studies support the target as being lipid II itself or lipid II trafficking processes. Given the broad distribution of stilbenes in plants, including dietary plants, we anticipate that our mode of action studies here could be more broadly applicable to multipartite host-bacterium-plant interactions.
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Affiliation(s)
- Tyler N. Goddard
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Jaymin Patel
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Hyun Bong Park
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Jason M. Crawford
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA
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38
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Liu Y, Jia Y, Yang K, Li R, Xiao X, Wang Z. Antagonizing Vancomycin Resistance in Enterococcus by Surface Localized Antimicrobial Display-Derived Peptides. ACS Infect Dis 2020; 6:761-767. [PMID: 31505930 DOI: 10.1021/acsinfecdis.9b00164] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Decreasing the therapeutic pipeline for vancomycin-resistant Enterococci (VRE) calls for novel strategies to enhance our antibacterial arsenal. Herein, we investigated the potential applications of surface localized antimicrobial display (SLAY)-derived cationic peptides in the fight against VanA operon mediated vancomycin-resistant Enterococcus. Through determining their antibacterial spectrum, we found that SLAY peptide 1/2 displayed moderate bactericidal activity against Enterococcus with minimal inhibitory concentration (MIC) values of 2-8 μg/mL. Furthermore, we observed a significant synergistic activity between SLAY-P1 and vancomycin against VRE. Mechanistic studies demonstrated that SLAY-P1 specifically inhibits transcription of the vanRS two-component system, thereby restoring vancomycin activity and resulting in the accumulation of the cell wall precursor. Meaningfully, the combination of SLAY-P1 and vancomycin prevents the emergence of vancomycin resistance. Consistent with in vitro synergistic results, the addition of SLAY-P1 significantly enhanced the survival rates of Galleria mellonella larvae compared with vancomycin monotherapy. Taken together, these results suggested that SLAY-derived cationic peptides not only display antibacterial activity against VRE but also reverse vancomycin resistance in Enterococcus, providing promising candidates for combating vancomycin-resistant pathogens.
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Affiliation(s)
- Yuan Liu
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, No. 88 University South Road, Yangzhou, Jiangsu 225009, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, No. 88 University South Road, Yangzhou, Jiangsu 225009, China
| | - Yuqian Jia
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, No. 88 University South Road, Yangzhou, Jiangsu 225009, China
| | - Kangni Yang
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, No. 88 University South Road, Yangzhou, Jiangsu 225009, China
| | - Ruichao Li
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, No. 88 University South Road, Yangzhou, Jiangsu 225009, China
| | - Xia Xiao
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, No. 88 University South Road, Yangzhou, Jiangsu 225009, China
| | - Zhiqiang Wang
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, No. 88 University South Road, Yangzhou, Jiangsu 225009, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, No. 88 University South Road, Yangzhou, Jiangsu 225009, China
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39
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Lockey C, Edwards RJ, Roper DI, Dixon AM. The Extracellular Domain of Two-component System Sensor Kinase VanS from Streptomyces coelicolor Binds Vancomycin at a Newly Identified Binding Site. Sci Rep 2020; 10:5727. [PMID: 32235931 PMCID: PMC7109055 DOI: 10.1038/s41598-020-62557-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 03/11/2020] [Indexed: 11/24/2022] Open
Abstract
The glycopeptide antibiotic vancomycin has been widely used to treat infections of Gram-positive bacteria including Clostridium difficile and methicillin-resistant Staphylococcus aureus. However, since its introduction, high level vancomycin resistance has emerged. The genes responsible require the action of the two-component regulatory system VanSR to induce expression of resistance genes. The mechanism of detection of vancomycin by this two-component system has yet to be elucidated. Diverging evidence in the literature supports activation models in which the VanS protein binds either vancomycin, or Lipid II, to induce resistance. Here we investigated the interaction between vancomycin and VanS from Streptomyces coelicolor (VanSSC), a model Actinomycete. We demonstrate a direct interaction between vancomycin and purified VanSSC, and traced these interactions to the extracellular region of the protein, which we reveal adopts a predominantly α-helical conformation. The VanSSC-binding epitope within vancomycin was mapped to the N-terminus of the peptide chain, distinct from the binding site for Lipid II. In targeting a separate site on vancomycin, the effective VanS ligand concentration includes both free and lipid-bound molecules, facilitating VanS activation. This is the first molecular description of the VanS binding site within vancomycin, and could direct engineering of future therapeutics.
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Affiliation(s)
- Christine Lockey
- MOAC Doctoral Training Centre, University of Warwick, Coventry, CV4 7AL, UK
| | - Richard J Edwards
- Medical Research Council Doctoral Training Centre, University of Warwick, Coventry, CV4 7AL, UK
| | - David I Roper
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Ann M Dixon
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
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40
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Ca 2+-Daptomycin targets cell wall biosynthesis by forming a tripartite complex with undecaprenyl-coupled intermediates and membrane lipids. Nat Commun 2020; 11:1455. [PMID: 32193379 PMCID: PMC7081307 DOI: 10.1038/s41467-020-15257-1] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 02/25/2020] [Indexed: 11/08/2022] Open
Abstract
The lipopeptide daptomycin is used as an antibiotic to treat severe infections with gram-positive pathogens, such as methicillin resistant Staphylococcus aureus (MRSA) and drug-resistant enterococci. Its precise mechanism of action is incompletely understood, and a specific molecular target has not been identified. Here we show that Ca2+-daptomycin specifically interacts with undecaprenyl-coupled cell envelope precursors in the presence of the anionic phospholipid phosphatidylglycerol, forming a tripartite complex. We use microbiological and biochemical assays, in combination with fluorescence and optical sectioning microscopy of intact staphylococcal cells and model membrane systems. Binding primarily occurs at the staphylococcal septum and interrupts cell wall biosynthesis. This is followed by delocalisation of components of the peptidoglycan biosynthesis machinery and massive membrane rearrangements, which may account for the pleiotropic cellular events previously reported. The identification of carrier-bound cell wall precursors as specific targets explains the specificity of daptomycin for bacterial cells. Our work reconciles apparently inconsistent previous results, and supports a concise model for the mode of action of daptomycin.
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41
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Fisher JF, Mobashery S. Constructing and deconstructing the bacterial cell wall. Protein Sci 2020; 29:629-646. [PMID: 31747090 PMCID: PMC7021008 DOI: 10.1002/pro.3737] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 09/17/2019] [Accepted: 09/18/2019] [Indexed: 12/11/2022]
Abstract
The history of modern medicine cannot be written apart from the history of the antibiotics. Antibiotics are cytotoxic secondary metabolites that are isolated from Nature. The antibacterial antibiotics disproportionately target bacterial protein structure that is distinct from eukaryotic protein structure, notably within the ribosome and within the pathways for bacterial cell-wall biosynthesis (for which there is not a eukaryotic counterpart). This review focuses on a pre-eminent class of antibiotics-the β-lactams, exemplified by the penicillins and cephalosporins-from the perspective of the evolving mechanisms for bacterial resistance. The mechanism of action of the β-lactams is bacterial cell-wall destruction. In the monoderm (single membrane, Gram-positive staining) pathogen Staphylococcus aureus the dominant resistance mechanism is expression of a β-lactam-unreactive transpeptidase enzyme that functions in cell-wall construction. In the diderm (dual membrane, Gram-negative staining) pathogen Pseudomonas aeruginosa a dominant resistance mechanism (among several) is expression of a hydrolytic enzyme that destroys the critical β-lactam ring of the antibiotic. The key sensing mechanism used by P. aeruginosa is monitoring the molecular difference between cell-wall construction and cell-wall deconstruction. In both bacteria, the resistance pathways are manifested only when the bacteria detect the presence of β-lactams. This review summarizes how the β-lactams are sensed and how the resistance mechanisms are manifested, with the expectation that preventing these processes will be critical to future chemotherapeutic control of multidrug resistant bacteria.
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Affiliation(s)
- Jed F. Fisher
- Department of Chemistry and BiochemistryUniversity of Notre DameSouth BendIndiana
| | - Shahriar Mobashery
- Department of Chemistry and BiochemistryUniversity of Notre DameSouth BendIndiana
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42
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Cochrane RVK, Alexander FM, Boland C, Fetics SK, Caffrey M, Cochrane SA. From plant to probe: semi-synthesis of labelled undecaprenol analogues allows rapid access to probes for antibiotic targets. Chem Commun (Camb) 2020; 56:8603-8606. [DOI: 10.1039/d0cc03388j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Extraction of undecaprenol from bay leaves followed by synthetic modification is a convenient method to obtain novel chemical probes.
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Affiliation(s)
| | | | - Coilín Boland
- School of Medicine and School of Biochemistry and Immunology
- Trinity Biomedical Sciences Institute
- Trinity College Dublin
- Dublin 2
- Ireland
| | - Susan K. Fetics
- School of Medicine and School of Biochemistry and Immunology
- Trinity Biomedical Sciences Institute
- Trinity College Dublin
- Dublin 2
- Ireland
| | - Martin Caffrey
- School of Medicine and School of Biochemistry and Immunology
- Trinity Biomedical Sciences Institute
- Trinity College Dublin
- Dublin 2
- Ireland
| | - Stephen A. Cochrane
- School of Chemistry and Chemical Engineering
- Queen's University Belfast
- Belfast
- UK
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43
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Häfner S. Another protein in the wall. Microbes Infect 2019; 22:93-95. [PMID: 31539563 DOI: 10.1016/j.micinf.2019.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 08/28/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Sophia Häfner
- University of Copenhagen, BRIC Biotech Research & Innovation Centre, Anders Lund Group, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark.
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44
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Tan S, Moore G, Nodwell J. Put a Bow on It: Knotted Antibiotics Take Center Stage. Antibiotics (Basel) 2019; 8:antibiotics8030117. [PMID: 31405236 PMCID: PMC6784204 DOI: 10.3390/antibiotics8030117] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/06/2019] [Accepted: 08/09/2019] [Indexed: 01/15/2023] Open
Abstract
Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large class of natural products produced across all domains of life. The lasso peptides, a subclass of RiPPs with a lasso-like structure, are structurally and functionally unique compared to other known peptide antibiotics in that the linear peptide is literally "tied in a knot" during its post-translational maturation. This underexplored class of peptides brings chemical diversity and unique modes of action to the antibiotic space. To date, eight different lasso peptides have been shown to target three known molecular machines: RNA polymerase, the lipid II precursor in peptidoglycan biosynthesis, and the ClpC1 subunit of the Clp protease involved in protein homeostasis. Here, we discuss the current knowledge on lasso peptide biosynthesis as well as their antibiotic activity, molecular targets, and mechanisms of action.
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Affiliation(s)
- Stephanie Tan
- Department of Biochemistry, MaRS Discovery District, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Gaelen Moore
- Department of Biochemistry, MaRS Discovery District, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Justin Nodwell
- Department of Biochemistry, MaRS Discovery District, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada.
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45
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Medeiros‐Silva J, Jekhmane S, Breukink E, Weingarth M. Towards the Native Binding Modes of Antibiotics that Target Lipid II. Chembiochem 2019; 20:1731-1738. [PMID: 30725496 PMCID: PMC6767406 DOI: 10.1002/cbic.201800796] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Indexed: 12/22/2022]
Abstract
The alarming rise of antimicrobial resistance (AMR) imposes severe burdens on healthcare systems and the economy worldwide, urgently calling for the development of new antibiotics. Antimicrobial peptides could be ideal templates for next-generation antibiotics, due to their low propensity to cause resistance. An especially promising branch of antimicrobial peptides target lipid II, the precursor of the bacterial peptidoglycan network. To develop these peptides into clinically applicable compounds, detailed information on their pharmacologically relevant modes of action is of critical importance. Here we review the binding modes of a selection of peptides that target lipid II and highlight shortcomings in our molecular understanding that, at least partly, relate to the widespread use of artificial membrane mimics for structural studies of membrane-active antibiotics. In particular, with the example of the antimicrobial peptide nisin, we showcase how the native cellular membrane environment can be critical for understanding of the physiologically relevant binding mode.
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Affiliation(s)
- João Medeiros‐Silva
- NMR SpectroscopyBijvoet Center for Biomolecular ResearchDepartment of ChemistryFaculty of ScienceUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - Shehrazade Jekhmane
- NMR SpectroscopyBijvoet Center for Biomolecular ResearchDepartment of ChemistryFaculty of ScienceUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - Eefjan Breukink
- Membrane Biochemistry and BiophysicsBijvoet Center for Biomolecular ResearchDepartment of ChemistryFaculty of ScienceUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - Markus Weingarth
- NMR SpectroscopyBijvoet Center for Biomolecular ResearchDepartment of ChemistryFaculty of ScienceUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
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46
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Indrakumar S, Zalar M, Pohl C, Nørgaard A, Streicher W, Harris P, Golovanov AP, Peters GH. Conformational Stability Study of a Therapeutic Peptide Plectasin Using Molecular Dynamics Simulations in Combination with NMR. J Phys Chem B 2019; 123:4867-4877. [DOI: 10.1021/acs.jpcb.9b02370] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Sowmya Indrakumar
- Department of Chemistry, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Matja Zalar
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester M1 7DN, U.K
| | - Christin Pohl
- Department of Chemistry, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
- Novozymes, Krogshoejvej 36, Bagsvaerd 2880, Denmark
| | | | | | - Pernille Harris
- Department of Chemistry, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Alexander P. Golovanov
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester M1 7DN, U.K
| | - Günther H.J. Peters
- Department of Chemistry, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
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47
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Tan S, Ludwig KC, Müller A, Schneider T, Nodwell JR. The Lasso Peptide Siamycin-I Targets Lipid II at the Gram-Positive Cell Surface. ACS Chem Biol 2019; 14:966-974. [PMID: 31026131 DOI: 10.1021/acschembio.9b00157] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ribosomally synthesized post-translationally modified peptides (RiPPs) are a diverse class of biologically active molecules produced by many environmental bacteria. While thousands of these compounds have been identified, mostly through genome mining, a relatively small number has been investigated at the molecular level. One less understood class of RiPPs is the lasso peptides. These are 20-25 amino acid residue compounds bearing an N-terminal macrocyclic ring and a C-terminal tail that is threaded through the ring. We have carried out a detailed investigation on the mechanism of action of the siamycin-I lasso peptide. We demonstrate that siamycin-I interacts with lipid II, the central building block of the major cell wall component peptidoglycan, which is readily accessible on the outside of the cell. This interaction compromises cell wall biosynthesis in a manner that activates the liaI stress response. Additionally, resistance to siamycin-I can be brought about by mutations in the essential WalKR two-component system that causes thickening of the cell wall. Siamycin-I is the first lasso peptide that has been shown to inhibit cell wall biosynthesis.
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Affiliation(s)
- Stephanie Tan
- Department of Biochemistry, MaRS Discovery District, University of Toronto, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1
| | - Kevin C. Ludwig
- Institute for Pharmaceutical Microbiology, University of Bonn, Meckenheimer Allee 168, 53115 Bonn, Germany
| | - Anna Müller
- Institute for Pharmaceutical Microbiology, University of Bonn, Meckenheimer Allee 168, 53115 Bonn, Germany
- German Centre for Infection Research (DZIF), partner site Bonn-Cologne, Bonn, Germany
| | - Tanja Schneider
- Institute for Pharmaceutical Microbiology, University of Bonn, Meckenheimer Allee 168, 53115 Bonn, Germany
- German Centre for Infection Research (DZIF), partner site Bonn-Cologne, Bonn, Germany
| | - Justin R. Nodwell
- Department of Biochemistry, MaRS Discovery District, University of Toronto, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1
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48
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Irazoki O, Hernandez SB, Cava F. Peptidoglycan Muropeptides: Release, Perception, and Functions as Signaling Molecules. Front Microbiol 2019; 10:500. [PMID: 30984120 PMCID: PMC6448482 DOI: 10.3389/fmicb.2019.00500] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 02/27/2019] [Indexed: 12/12/2022] Open
Abstract
Peptidoglycan (PG) is an essential molecule for the survival of bacteria, and thus, its biosynthesis and remodeling have always been in the spotlight when it comes to the development of antibiotics. The peptidoglycan polymer provides a protective function in bacteria, but at the same time is continuously subjected to editing activities that in some cases lead to the release of peptidoglycan fragments (i.e., muropeptides) to the environment. Several soluble muropeptides have been reported to work as signaling molecules. In this review, we summarize the mechanisms involved in muropeptide release (PG breakdown and PG recycling) and describe the known PG-receptor proteins responsible for PG sensing. Furthermore, we overview the role of muropeptides as signaling molecules, focusing on the microbial responses and their functions in the host beyond their immunostimulatory activity.
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Affiliation(s)
| | | | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
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49
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Wu C, Shang Z, Lemetre C, Ternei MA, Brady SF. Cadasides, Calcium-Dependent Acidic Lipopeptides from the Soil Metagenome That Are Active against Multidrug-Resistant Bacteria. J Am Chem Soc 2019; 141:3910-3919. [PMID: 30735616 PMCID: PMC6592427 DOI: 10.1021/jacs.8b12087] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The growing threat of antibiotic resistance necessitates the discovery of antibiotics that are active against resistant pathogens. Calcium-dependent antibiotics are a small family of structurally diverse acidic lipopeptides assembled by nonribosomal peptide synthetases (NRPSs) that are known to display various modes of action against antibiotic-resistant pathogens. Here we use NRPS adenylation (AD) domain sequencing to guide the identification, recovery, and cloning of the cde biosynthetic gene cluster from a soil metagenome. Heterologous expression of the cde biosynthetic gene cluster led to the production of cadasides A (1) and B (2), a subfamily of acidic lipopeptides that is distinct from previously characterized calcium-dependent antibiotics in terms of both overall structure and acidic residue rich peptide core. The cadasides inhibit the growth of multidrug-resistant Gram-positive pathogens by disrupting cell wall biosynthesis in the presence of high concentrations of calcium. Interestingly, sequencing of AD domains from diverse soils revealed that sequences predicted to arise from cadaside-like gene clusters are predominantly found in soils containing high levels of calcium carbonate.
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Affiliation(s)
| | | | - Christophe Lemetre
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065
| | - Melinda A. Ternei
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065
| | - Sean F. Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065
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50
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Panina IS, Chugunov AO, Efremov RG. Lipid II as a Target for Novel Antibiotics: Structural and Molecular Dynamics Studies. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2019. [DOI: 10.1134/s1068162019010126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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