1
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Sheridan MS, Pandey P, Hansmann UHE. In Bacterial Membranes Lipid II Changes the Stability of Pores Formed by the Antimicrobial Peptide Nisin. J Phys Chem B 2024; 128:4741-4750. [PMID: 38696215 PMCID: PMC11104519 DOI: 10.1021/acs.jpcb.4c01249] [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] [Indexed: 05/22/2024]
Abstract
Resistance to available antibiotics poses a growing challenge to modern medicine, as this often disallows infections to be controlled. This problem can only be alleviated by the development of new drugs. Nisin, a natural lantibiotic with broad antimicrobial activity, has shown promise as a potential candidate for combating antibiotic-resistant bacteria. However, nisin is poorly soluble and barely stable at physiological pH, which despite attempts to address these issues through mutant design has restricted its use as an antibacterial drug. Therefore, gaining a deeper understanding of the antimicrobial effectiveness, which relies in part on its ability to form pores, is crucial for finding innovative ways to manage infections caused by resistant bacteria. Using large-scale molecular dynamics simulations, we find that the bacterial membrane-specific lipid II increases the stability of pores formed by nisin and that the interplay of nisin and lipid II reduces the overall integrity of bacterial membranes by changing the local thickness and viscosity.
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Affiliation(s)
- Miranda S. Sheridan
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Preeti Pandey
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Ulrich H. E. Hansmann
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, OK 73019, USA
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2
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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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3
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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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4
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Wang J, Li P, Wang N, Wang J, Xing D. Antibacterial features of material surface: strong enough to serve as antibiotics? J Mater Chem B 2023; 11:280-302. [PMID: 36533438 DOI: 10.1039/d2tb02139k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bacteria are small but need big efforts to control. The use of antibiotics not only produces superbugs that are increasingly difficult to inactivate, but also raises environmental concerns with the growing consumption. It is now believed that the antibacterial task can count on some physiochemical features of material surfaces, which can be anti-adhesive or bactericidal without releasing toxicants. It is necessary to evaluate to what extent can we rely on the surface design since the actual application scenarios will need the antibacterial performance to be sharp, robust, environmentally friendly, and long-lasting. Herein, we review the recent laboratory advances that have been classified based on the specific surface features, including hydrophobicity, charge potential, micromorphology, stiffness and viscosity, and photoactivity, and the antibacterial mechanisms of each feature are included to provide a basic rationale for future design. The significance of anti-biofilms is also introduced, given the big role of biofilms in bacteria-caused damage. A perspective on the potential wide application of antibacterial surface features as a substitute or supplement to antibiotics is then discussed. Surface design is no doubt a solution worthy to explore, and future success will be a result of further progress in multiple directions, including mechanism study and material preparation.
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Affiliation(s)
- Jie Wang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, China. .,CAS Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Institute of Oceanology, China Academy of Sciences, Qingdao 266071, China.
| | - Ping Li
- School of Rehabilitation Sciences and Engineering, University of Health and Rehabilitation Sciences, Qingdao 266071, China
| | - Ning Wang
- CAS Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Institute of Oceanology, China Academy of Sciences, Qingdao 266071, China.
| | - Jing Wang
- CAS Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Institute of Oceanology, China Academy of Sciences, Qingdao 266071, China.
| | - Dongming Xing
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, China.
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5
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Sikder A, Pearce AK, Kumar CMS, O'Reilly RK. Elucidating the role of multivalency, shape, size and functional group density on antibacterial activity of diversified supramolecular nanostructures enabled by templated assembly. MATERIALS HORIZONS 2023; 10:171-178. [PMID: 36321619 PMCID: PMC9810103 DOI: 10.1039/d2mh01117d] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
With the increased prevalence of antibiotic-resistant infections, there is an urgent need to develop novel antibacterial materials. In addition, gaining a complete understanding of the structural features that impart activity toward target microorganisms is essential to enable materials optimisation. Here we have reported a rational design to fabricate antibacterial supramolecular nanoparticles with variable shape, size and cationic group density, by exploiting noncovalent interactions between a shape determining template amphiphile and a cationic amphiphile to introduce charge on the nanoparticle surface. We have shown that the monomeric cationic amphiphile alone showed poor antibacterial activity, whereas nanostructures formed by co-assembling the complementary units showed significantly enhanced antibacterial efficiency. Further, the systematic variation of several structural parameters such as shape, spacing between the cationic groups and size of these nanostructures allowed us to elicit the role of each parameter on the overall antibacterial properties. Finally, we investigated the origin of the differing antibacterial activity of these nanoparticles having different shape and size but with the same molecular composition, by comparing the thermodynamic parameters of their binding interactions with a bacterial membrane mimic.
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Affiliation(s)
- Amrita Sikder
- School of Chemistry, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Amanda K Pearce
- School of Chemistry, University of Birmingham, Birmingham, B15 2TT, UK.
| | - C M Santosh Kumar
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Rachel K O'Reilly
- School of Chemistry, University of Birmingham, Birmingham, B15 2TT, UK.
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6
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Stachurski O, Neubauer D, Walewska A, Iłowska E, Bauer M, Bartoszewska S, Sikora K, Hać A, Wyrzykowski D, Prahl A, Kamysz W, Sikorska E. Understanding the Role of Self-Assembly and Interaction with Biological Membranes of Short Cationic Lipopeptides in the Effective Design of New Antibiotics. Antibiotics (Basel) 2022; 11:1491. [PMID: 36358146 PMCID: PMC9686977 DOI: 10.3390/antibiotics11111491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 10/22/2023] Open
Abstract
This study investigates short cationic antimicrobial lipopeptides composed of 2-4 amino acid residues and C12-C18 fatty acids attached to the N-terminal part of the peptides. The findings were discussed in the context of the relationship among biological activity, self-assembly, stability, and membrane interactions. All the lipopeptides showed the ability to self-assemble in PBS solution. In most cases, the critical aggregation concentration (CAC) much surpassed the minimal inhibitory concentration (MIC) values, suggesting that monomers are the main active form of lipopeptides. The introduction of β-alanine into the peptide sequence resulted in a compound with a high propensity to fibrillate, which increased the peptide stability and activity against S. epidermidis and C. albicans and reduced the cytotoxicity against human keratinocytes. The results of our study indicated that the target of action of lipopeptides is the bacterial membrane. Interestingly, the type of peptide counterion may affect the degree of penetration of the lipid bilayer. In addition, the binding of the lipopeptide to the membrane of Gram-negative bacteria may lead to the release of calcium ions necessary for stabilization of the lipopolysaccharide layer.
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Affiliation(s)
- Oktawian Stachurski
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Damian Neubauer
- Faculty of Pharmacy, Medicinal University of Gdansk, Al. Gen. J. Hallera 107, 80-416 Gdansk, Poland
| | - Aleksandra Walewska
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Emilia Iłowska
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Marta Bauer
- Faculty of Pharmacy, Medicinal University of Gdansk, Al. Gen. J. Hallera 107, 80-416 Gdansk, Poland
| | - Sylwia Bartoszewska
- Faculty of Pharmacy, Medicinal University of Gdansk, Al. Gen. J. Hallera 107, 80-416 Gdansk, Poland
| | - Karol Sikora
- Faculty of Pharmacy, Medicinal University of Gdansk, Al. Gen. J. Hallera 107, 80-416 Gdansk, Poland
| | - Aleksandra Hać
- Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Dariusz Wyrzykowski
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Adam Prahl
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Wojciech Kamysz
- Faculty of Pharmacy, Medicinal University of Gdansk, Al. Gen. J. Hallera 107, 80-416 Gdansk, Poland
| | - Emilia Sikorska
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
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7
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Giacometti SI, MacRae MR, Dancel-Manning K, Bhabha G, Ekiert DC. Lipid Transport Across Bacterial Membranes. Annu Rev Cell Dev Biol 2022; 38:125-153. [PMID: 35850151 DOI: 10.1146/annurev-cellbio-120420-022914] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The movement of lipids within and between membranes in bacteria is essential for building and maintaining the bacterial cell envelope. Moving lipids to their final destination is often energetically unfavorable and does not readily occur spontaneously. Bacteria have evolved several protein-mediated transport systems that bind specific lipid substrates and catalyze the transport of lipids across membranes and from one membrane to another. Specific protein flippases act in translocating lipids across the plasma membrane, overcoming the obstacle of moving relatively large and chemically diverse lipids between leaflets of the bilayer. Active transporters found in double-membraned bacteria have evolved sophisticated mechanisms to traffic lipids between the two membranes, including assembling to form large, multiprotein complexes that resemble bridges, shuttles, and tunnels, shielding lipids from the hydrophilic environment of the periplasm during transport. In this review, we explore our current understanding of the mechanisms thought to drive bacterial lipid transport.
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Affiliation(s)
- Sabrina I Giacometti
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA; , , ,
| | - Mark R MacRae
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA; , , ,
| | - Kristen Dancel-Manning
- Office of Science and Research, New York University School of Medicine, New York, NY, USA;
| | - Gira Bhabha
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA; , , ,
| | - Damian C Ekiert
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA; , , ,
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
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8
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Pokhrel R, Shakya R, Baral P, Chapagain P. Molecular Modeling and Simulation of the Peptidoglycan Layer of Gram-Positive Bacteria Staphylococcus aureus. J Chem Inf Model 2022; 62:4955-4962. [PMID: 35981320 DOI: 10.1021/acs.jcim.2c00437] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The peptidoglycan (PG) layer is a vital component of the bacterial cell wall that protects the cell from rupturing due to internal pressure. Its ubiquity across the bacterial kingdom but not animals has made it the target of drug discovery efforts. The PG layer composed of cross-linked PG strands is porous enough to allow the diffusion of molecules through the PG mesh and into the cell. The lack of an accurate atomistic model of the PG mesh has limited the computational investigations of drug diffusion in Gram-positive bacteria, which lack the outer membrane but consist of a much thicker PG layer compared to Gram-negative bacteria. In this work, we built an atomistic model of the Staphylococcus aureus PG layer architecture with horizontally aligned PG strands and performed molecular dynamics simulations of the diffusion of curcumin molecules through the PG mesh. An accurate model of the Gram-positive bacterial cell wall may aid in developing novel antibiotics to tackle the threat posed by antibiotic resistance.
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Affiliation(s)
- Rudramani Pokhrel
- Department of Physics, Florida International University, Miami, Florida 33199, United States
| | - Rojesh Shakya
- Department of Physics, Florida International University, Miami, Florida 33199, United States
| | - Prabin Baral
- Department of Physics, Florida International University, Miami, Florida 33199, United States
| | - Prem Chapagain
- Department of Physics, Florida International University, Miami, Florida 33199, United States.,Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
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9
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Bacterial Membranes Are More Perturbed by the Asymmetric Versus Symmetric Loading of Amphiphilic Molecules. MEMBRANES 2022; 12:membranes12040350. [PMID: 35448320 PMCID: PMC9032087 DOI: 10.3390/membranes12040350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/11/2022] [Accepted: 03/16/2022] [Indexed: 02/01/2023]
Abstract
Characterizing the biophysical properties of bacterial membranes is critical for understanding the protective nature of the microbial envelope, interaction of biological membranes with exogenous materials, and designing new antibacterial agents. Presented here are molecular dynamics simulations for two cationic quaternary ammonium compounds, and the anionic and nonionic form of a fatty acid molecule interacting with a Staphylococcus aureus bacterial inner membrane. The effect of the tested materials on the properties of the model membranes are evaluated with respect to various structural properties such as the lateral pressure profile, lipid tail order parameter, and the bilayer’s electrostatic potential. Conducting asymmetric loading of molecules in only one leaflet, it was observed that anionic and cationic amphiphiles have a large impact on the Staphylococcus aureus membrane’s electrostatic potential and lateral pressure profile as compared to a symmetric distribution. Nonintuitively, we find that the cationic and anionic molecules induce a similar change in the electrostatic potential, which points to the complexity of membrane interfaces, and how asymmetry can induce biophysical consequences. Finally, we link changes in membrane structure to the rate of electroporation for the membranes, and again find a crucial impact of introducing asymmetry to the system. Understanding these physical mechanisms provides critical insights and viable pathways for the rational design of membrane-active molecules, where controlling the localization is key.
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10
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11
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Antimicrobial Bacillus: Metabolites and Their Mode of Action. Antibiotics (Basel) 2022; 11:antibiotics11010088. [PMID: 35052965 PMCID: PMC8772736 DOI: 10.3390/antibiotics11010088] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/07/2022] [Accepted: 01/08/2022] [Indexed: 12/12/2022] Open
Abstract
The agricultural industry utilizes antibiotic growth promoters to promote livestock growth and health. However, the World Health Organization has raised concerns over the ongoing spread of antibiotic resistance transmission in the populace, leading to its subsequent ban in several countries, especially in the European Union. These restrictions have translated into an increase in pathogenic outbreaks in the agricultural industry, highlighting the need for an economically viable, non-toxic, and renewable alternative to antibiotics in livestock. Probiotics inhibit pathogen growth, promote a beneficial microbiota, regulate the immune response of its host, enhance feed conversion to nutrients, and form biofilms that block further infection. Commonly used lactic acid bacteria probiotics are vulnerable to the harsh conditions of the upper gastrointestinal system, leading to novel research using spore-forming bacteria from the genus Bacillus. However, the exact mechanisms behind Bacillus probiotics remain unexplored. This review tackles this issue, by reporting antimicrobial compounds produced from Bacillus strains, their proposed mechanisms of action, and any gaps in the mechanism studies of these compounds. Lastly, this paper explores omics approaches to clarify the mechanisms behind Bacillus probiotics.
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12
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Pokhrel R, Bhattarai N, Baral P, Gerstman BS, Park JH, Handfield M, Chapagain PP. Lipid II Binding and Transmembrane Properties of Various Antimicrobial Lanthipeptides. J Chem Theory Comput 2021; 18:516-525. [PMID: 34874159 DOI: 10.1021/acs.jctc.1c00666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
There has been an alarming rise in antibacterial resistant infections in recent years due to the widespread use of antibiotics, and there is a dire need for the development of new antibiotics utilizing novel modes of action. Lantibiotics are promising candidates to engage in the fight against resistant strains of bacteria due to their unique modes of action, including interference with cell wall synthesis by binding to lipid II and creating pores in bacterial membranes. In this study, we use atomic-scale molecular dynamics computational studies to compare both the lipid II binding ability and the membrane interactions of five lanthipeptides that are commonly used in antimicrobial research: nisin, Mutacin 1140 (MU1140), gallidermin, NVB302, and NAI107. Among the five peptides investigated, nisin is found to be the most efficient at forming water channels through a membrane, whereas gallidermin and MU1140 are found to be better at binding the lipid II molecules. Nisin's effectiveness in facilitating water transport across the membrane is due to the creation of several different water trajectories along with no significant water delay points along the paths. The shorter peptide deoxyactagardine B (NVB302) was found to not form a water channel. These detailed observations provide insights into the dual mechanisms of the action of lantibiotic peptides and can facilitate the design and development of novel lanthipeptides by strategic placement of different residues.
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Affiliation(s)
| | | | | | | | - Jae H Park
- Oragenics Inc., Alachua, Florida 32615, United States
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13
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Kosikowska-Adamus P, Sikorska E, Wyrzykowski D, Walewska A, Golda A, Deptuła M, Obuchowski M, Prahl A, Pikuła M, Lesner A. Lipidation of Temporin-1CEb Derivatives as a Tool for Activity Improvement, Pros and Cons of the Approach. Int J Mol Sci 2021; 22:ijms22136679. [PMID: 34206444 PMCID: PMC8269107 DOI: 10.3390/ijms22136679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 11/16/2022] Open
Abstract
The alarming raise of multi-drug resistance among human microbial pathogens makes the development of novel therapeutics a priority task. In contrast to conventional antibiotics, antimicrobial peptides (AMPs), besides evoking a broad spectrum of activity against microorganisms, could offer additional benefits, such as the ability to neutralize toxins, modulate inflammatory response, eradicate bacterial and fungal biofilms or prevent their development. The latter properties are of special interest, as most antibiotics available on the market have limited ability to diffuse through rigid structures of biofilms. Lipidation of AMPs is considered as an effective approach for enhancement of their antimicrobial potential and in vivo stability; however, it could also have undesired impact on selectivity, solubility or the aggregation state of the modified peptides. In the present work, we describe the results of structural modifications of compounds designed based on cationic antimicrobial peptides DK5 and CAR-PEG-DK5, derivatized at their N-terminal part with fatty acids with different lengths of carbon chain. The proposed modifications substantially improved antimicrobial properties of the final compounds and their effectiveness in inhibition of biofilm development as well as eradication of pre-formed 24 h old biofilms of Candida albicans and Staphylococcus aureus. The most active compounds (C5-DK5, C12-DK5 and C12-CAR-PEG-DK5) were also potent against multi-drug resistant Staphylococcus aureus USA300 strain and clinical isolates of Pseudomonas aeruginosa. Both experimental and in silico methods revealed strong correlation between the length of fatty acid attached to the peptides and their final membranolytic properties, tendency to self-assemble and cytotoxicity.
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Affiliation(s)
- Paulina Kosikowska-Adamus
- Faculty of Chemistry, University of Gdansk, 80-309 Gdańsk, Poland; (E.S.); (D.W.); (A.W.); (A.P.); (A.L.)
- Correspondence:
| | - Emilia Sikorska
- Faculty of Chemistry, University of Gdansk, 80-309 Gdańsk, Poland; (E.S.); (D.W.); (A.W.); (A.P.); (A.L.)
| | - Dariusz Wyrzykowski
- Faculty of Chemistry, University of Gdansk, 80-309 Gdańsk, Poland; (E.S.); (D.W.); (A.W.); (A.P.); (A.L.)
| | - Aleksandra Walewska
- Faculty of Chemistry, University of Gdansk, 80-309 Gdańsk, Poland; (E.S.); (D.W.); (A.W.); (A.P.); (A.L.)
| | - Anna Golda
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland;
| | - Milena Deptuła
- Laboratory of Tissue Engineering and Regenerative Medicine, Department of Embryology, Medical University of Gdansk, 80-210 Gdańsk, Poland; (M.D.); (M.P.)
| | - Michał Obuchowski
- Department of Medical Biotechnology, Intercollegiate Faculty of Biotechnology UG-MUG, Medical University of Gdansk, 80-210 Gdańsk, Poland;
| | - Adam Prahl
- Faculty of Chemistry, University of Gdansk, 80-309 Gdańsk, Poland; (E.S.); (D.W.); (A.W.); (A.P.); (A.L.)
| | - Michał Pikuła
- Laboratory of Tissue Engineering and Regenerative Medicine, Department of Embryology, Medical University of Gdansk, 80-210 Gdańsk, Poland; (M.D.); (M.P.)
| | - Adam Lesner
- Faculty of Chemistry, University of Gdansk, 80-309 Gdańsk, Poland; (E.S.); (D.W.); (A.W.); (A.P.); (A.L.)
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14
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Lone A, Mottawea W, Mehdi Y, Hammami R. Bacteriocinogenic probiotics as an integrated alternative to antibiotics in chicken production - why and how? Crit Rev Food Sci Nutr 2021; 62:8744-8760. [PMID: 34060404 DOI: 10.1080/10408398.2021.1932722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The misuse of antibiotics in the livestock industry has played an important role in the spread of resistant superbugs with severe health implications for humans. With the recent ban on the use of antibiotics in poultry and poultry feed in Canada and the USA, poultry farmers will have to rely on the use of alternatives to antibiotics (such as feed acidifiers, antibodies, bacteriophages, antimicrobial peptides, prebiotics, and probiotics) to maintain the same productivity and health of their livestock. Of particular interest are bacteriocinogenic probiotics, that is, bacterial strains capable of producing bacteriocins that confer health benefits on the host. These bacterial strains have multiple promising features, such as the ability to attach to the host mucosa, colonize, proliferate, and produce advantageous products such as bacteriocins and short-chain fatty acids. These not only affect pathogenic colonization but improve poultry phenotype as well. Bacteriocins are antimicrobial peptides with multiple promising features such as being non-harmful for human and animal consumption, non-disruptive to the host microbiota eubiosis, non-cytotoxic, and non-carcinogenic. Therefore, bacteriocinogenic probiotics are at the forefront to be excellent candidates for effective replacements to antibiotics. While evidence of their safety and effectiveness is accumulating in vitro and in vivo in inhibiting pathogens while promoting animal health, their safety and history of use in livestock remains unclear and requires additional investigations. In the present paper, we review the safety assessment regulations and commercialization policies on existing and novel bacteriocinogenic and bacteriocin products intended to be used in poultry feed as an alternative to antibiotics.
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Affiliation(s)
- Ayesha Lone
- GUT Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Walid Mottawea
- GUT Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada.,Faculty of Pharmacy, Department of Microbiology and Immunology, Mansoura University, Mansoura, Egypt
| | - Youcef Mehdi
- Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, Canada
| | - Riadh Hammami
- GUT Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
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15
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Pokorny A, Almeida PF. The Antibiotic Peptide Daptomycin Functions by Reorganizing the Membrane. J Membr Biol 2021; 254:97-108. [DOI: 10.1007/s00232-021-00175-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 01/21/2021] [Indexed: 10/22/2022]
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16
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Liu L, Zhao L, Liu L, Yue S, Wang J, Cao Z. Influence of Different Aromatic Hydrophobic Residues on the Antimicrobial Activity and Membrane Selectivity of BRBR-NH 2 Tetrapeptide. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:15331-15342. [PMID: 33295774 DOI: 10.1021/acs.langmuir.0c02777] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The ultrashort linear antimicrobial tetrapeptide BRBR-NH2 with an unnatural residue biphenylalanine (B) has potent and rapid antimethicillin-resistant Staphylococcus aureus (MRSA) activity but lacks hemolytic activity. The anti-MRSA activity of BRBR-NH2 is 8-fold more potent than that of WRWR-NH2 and 16-fold more potent than that of FRFR-NH2. However, how to influence their antimicrobial activities and mechanisms through the substitution of different aromatic hydrophobic residues is still unclear. In this work, to study the effects of varying hydrophobic interactions and membrane selectivities of BRBR-NH2, we performed multiple long-time (1000 ns) molecular dynamics (MD) simulations to investigate the interactions of a red blood cell (RBC) membrane and a Gram-positive bacterial cell membrane with three different tetrapeptides (BRBR-NH2, WRWR-NH2, and FRFR-NH2) under different ratios of peptides and lipids and also explored the changes in the membrane and structural characteristics of peptides. The binding energy results show that BRBR-NH2 interacts weakly with the RBC membrane, while not all BRBR-NH2 can be adsorbed to the RBC membrane surface. The MD simulation results produced significant local membrane thinning of multiBRBR-NH2 peptides in the Gram-positive bacterial cell membrane. An in-depth analysis of structural features and peptide-membrane interactions suggests that the aggregation of BRBR-NH2 on the membrane surface plays a crucial role in the destruction of the cell membrane. Taken together with the observed local membrane thinning, the in-depth analysis demonstrated that the interactions between the lipid bilayer and the BRBR-NH2 aggregation surface result in a local disturbance of the membrane structure. It can be concluded that the high anti-MRSA activity of BRBR-NH2 is attributed to the aggregation of BRBR-NH2 on the membrane surface. On the other hand, WRWR-NH2 and FRFR-NH2 peptides tend to bind with the membrane surface in a monomeric form and cover the membrane surface in a carpet-like manner. Therefore, these results provide an advanced microscopic understanding of how hydrophobic interactions or hydrophobic residues affect the antimicrobial activity and mechanism of antimicrobial peptides (AMPs).
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Affiliation(s)
- Lei Liu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Liling Zhao
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Lixia Liu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Shizhong Yue
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Jihua Wang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Zanxia Cao
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
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17
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Małuch I, Stachurski O, Kosikowska-Adamus P, Makowska M, Bauer M, Wyrzykowski D, Hać A, Kamysz W, Deptuła M, Pikuła M, Sikorska E. Double-Headed Cationic Lipopeptides: An Emerging Class of Antimicrobials. Int J Mol Sci 2020; 21:ijms21238944. [PMID: 33255674 PMCID: PMC7728077 DOI: 10.3390/ijms21238944] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 11/19/2020] [Accepted: 11/21/2020] [Indexed: 12/17/2022] Open
Abstract
Antimicrobial peptides (AMPs) constitute a promising tool in the development of novel therapeutic agents useful in a wide range of bacterial and fungal infections. Among the modifications improving pharmacokinetic and pharmacodynamic characteristics of natural AMPs, an important role is played by lipidation. This study focuses on the newly designed and synthesized lipopeptides containing multiple Lys residues or their shorter homologues with palmitic acid (C16) attached to the side chain of a residue located in the center of the peptide sequence. The approach resulted in the development of lipopeptides representing a model of surfactants with two polar headgroups. The aim of this study is to explain how variations in the length of the peptide chain or the hydrocarbon side chain of an amino acid residue modified with C16, affect biological functions of lipopeptides, their self-assembling propensity, and their mode of action.
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Affiliation(s)
- Izabela Małuch
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (I.M.); (O.S.); (P.K.-A.); (M.M.); (D.W.)
| | - Oktawian Stachurski
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (I.M.); (O.S.); (P.K.-A.); (M.M.); (D.W.)
| | - Paulina Kosikowska-Adamus
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (I.M.); (O.S.); (P.K.-A.); (M.M.); (D.W.)
| | - Marta Makowska
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (I.M.); (O.S.); (P.K.-A.); (M.M.); (D.W.)
| | - Marta Bauer
- Faculty of Pharmacy, Medicinal University of Gdansk, Al. Gen. J. Hallera 107, 80-416 Gdansk, Poland; (M.B.); (W.K.)
| | - Dariusz Wyrzykowski
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (I.M.); (O.S.); (P.K.-A.); (M.M.); (D.W.)
| | - Aleksandra Hać
- Faculty of Biology, University of Gdansk, Str. 59, 80-308 Gdansk, Poland;
| | - Wojciech Kamysz
- Faculty of Pharmacy, Medicinal University of Gdansk, Al. Gen. J. Hallera 107, 80-416 Gdansk, Poland; (M.B.); (W.K.)
| | - Milena Deptuła
- Laboratory of Tissue Engineering and Regenerative Medicine, Department of Embryology, Faculty of Medicine, Medical University of Gdansk, Dębinki 1, 80-211 Gdańsk, Poland; (M.D.); (M.P.)
| | - Michał Pikuła
- Laboratory of Tissue Engineering and Regenerative Medicine, Department of Embryology, Faculty of Medicine, Medical University of Gdansk, Dębinki 1, 80-211 Gdańsk, Poland; (M.D.); (M.P.)
| | - Emilia Sikorska
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (I.M.); (O.S.); (P.K.-A.); (M.M.); (D.W.)
- Correspondence:
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18
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Chandrashekar S, Vijayakumar R, Chelliah R, Oh DH. Identification and Purification of Potential Bioactive Peptide of Moringa oleifera Seed Extracts. PLANTS 2020; 9:plants9111445. [PMID: 33120901 PMCID: PMC7716235 DOI: 10.3390/plants9111445] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/21/2020] [Accepted: 10/24/2020] [Indexed: 11/16/2022]
Abstract
The aim of the study was to investigate the antibacterial and anticoagulant activity of Moringa (Moringa oleifera) seed extracts and coagulant protein for their potential application in water treatment. Pathogenic microorganisms were obtained from Ramachandra Hospital, Chennai, India. Bacterial cell aggregation and growth kinetics studies were employed for six bacterial strains with different concentrations of seed extracts and coagulant protein. Moringa seed extract and coagulant protein showed cell aggregation against six bacterial strains, whereas seed extract alone showed growth inhibition of all six bacterial strains for up to 6 h, compared to that of control. Escherichia coli and Salmonella para typhi B did not develop resistance against coagulant protein. The results imply that Moringa oleifera is likely an efficient low-molecular bioactive peptide (with <7.5 kDa plant-based coagulant and antimicrobial peptides, confirmed by applying amino acid sequences), using liquid chromatography–mass spectrometry and HPLC, with the corresponding sequences from Napin-1A peptide posing different degrees of antibacterial activity against different pathogenic organisms.
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Affiliation(s)
- Sangeeta Chandrashekar
- Department of Food Science and Biotechnology, College of Agriculture and Life Science, Kangwon National University, Chuncheon 24341, Korea;
- Department of Physiology, Bharath Institute of Higher Education and Research, Chennai 600 073, India
| | - Raman Vijayakumar
- Department of Physiology, Bharath Institute of Higher Education and Research, Chennai 600 073, India
- Correspondence: (R.V.); (R.C.); (D.-H.O.); Tel.: +82-33-250-6457 (D.-H.O.)
| | - Ramachandran Chelliah
- Department of Food Science and Biotechnology, College of Agriculture and Life Science, Kangwon National University, Chuncheon 24341, Korea;
- Correspondence: (R.V.); (R.C.); (D.-H.O.); Tel.: +82-33-250-6457 (D.-H.O.)
| | - Deog-Hwan Oh
- Department of Food Science and Biotechnology, College of Agriculture and Life Science, Kangwon National University, Chuncheon 24341, Korea;
- Correspondence: (R.V.); (R.C.); (D.-H.O.); Tel.: +82-33-250-6457 (D.-H.O.)
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19
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Neubauer D, Jaśkiewicz M, Sikorska E, Bartoszewska S, Bauer M, Kapusta M, Narajczyk M, Kamysz W. Effect of Disulfide Cyclization of Ultrashort Cationic Lipopeptides on Antimicrobial Activity and Cytotoxicity. Int J Mol Sci 2020; 21:E7208. [PMID: 33003569 PMCID: PMC7582905 DOI: 10.3390/ijms21197208] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 12/20/2022] Open
Abstract
Ultrashort cationic lipopeptides (USCLs) are considered to be a promising class of antimicrobials with high activity against a broad-spectrum of microorganisms. However, the majority of these compounds are characterized by significant toxicity toward human cells, which hinders their potential application. To overcome those limitations, several approaches have been advanced. One of these is disulfide cyclization that has been shown to improve drug-like characteristics of peptides. In this article the effect of disulfide cyclization of the polar head of N-palmitoylated USCLs on in vitro biological activity has been studied. Lipopeptides used in this study consisted of three or four basic amino acids (lysine and arginine) and cystine in a cyclic peptide. In general, disulfide cyclization of the lipopeptides resulted in peptides with reduced cytotoxicity. Disulfide-cyclized USCLs exhibited improved selectivity between Candida sp., Gram-positive strains and normal cells in contrast to their linear counterparts. Interactions between selected USCLs and membranes were studied by molecular dynamics simulations using a coarse-grained force field. Moreover, membrane permeabilization properties and kinetics were examined. Fluorescence and transmission electron microscopy revealed damage to Candida cell membrane and organelles. Concluding, USCLs are strong membrane disruptors and disulfide cyclization of polar head can have a beneficial effect on its in vitro selectivity between Candida sp. and normal human cells.
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Affiliation(s)
- Damian Neubauer
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, 80-416 Gdańsk, Poland; (M.J.); (S.B.); (M.B.); (W.K.)
| | - Maciej Jaśkiewicz
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, 80-416 Gdańsk, Poland; (M.J.); (S.B.); (M.B.); (W.K.)
| | - Emilia Sikorska
- Department of Organic Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland;
| | - Sylwia Bartoszewska
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, 80-416 Gdańsk, Poland; (M.J.); (S.B.); (M.B.); (W.K.)
| | - Marta Bauer
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, 80-416 Gdańsk, Poland; (M.J.); (S.B.); (M.B.); (W.K.)
| | - Małgorzata Kapusta
- Department of Plant Cytology and Embryology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland;
| | - Magdalena Narajczyk
- Laboratory of Electron Microscopy, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland;
| | - Wojciech Kamysz
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, 80-416 Gdańsk, Poland; (M.J.); (S.B.); (M.B.); (W.K.)
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20
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Tavares TD, Antunes JC, Padrão J, Ribeiro AI, Zille A, Amorim MTP, Ferreira F, Felgueiras HP. Activity of Specialized Biomolecules against Gram-Positive and Gram-Negative Bacteria. Antibiotics (Basel) 2020; 9:E314. [PMID: 32526972 PMCID: PMC7344598 DOI: 10.3390/antibiotics9060314] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/01/2020] [Accepted: 06/08/2020] [Indexed: 11/24/2022] Open
Abstract
The increased resistance of bacteria against conventional pharmaceutical solutions, the antibiotics, has raised serious health concerns. This has stimulated interest in the development of bio-based therapeutics with limited resistance, namely, essential oils (EOs) or antimicrobial peptides (AMPs). This study envisaged the evaluation of the antimicrobial efficacy of selected biomolecules, namely LL37, pexiganan, tea tree oil (TTO), cinnamon leaf oil (CLO) and niaouli oil (NO), against four bacteria commonly associated to nosocomial infections: Staphylococcus aureus, Staphylococcus epidermidis, Escherichia coli and Pseudomonas aeruginosa. The antibiotic vancomycin and silver nanoparticles (AgNPs) were used as control compounds for comparison purposes. The biomolecules were initially screened for their antibacterial efficacy using the agar-diffusion test, followed by the determination of minimal inhibitory concentrations (MICs), kill-time kinetics and the evaluation of the cell morphology upon 24 h exposure. All agents were effective against the selected bacteria. Interestingly, the AgNPs required a higher concentration (4000-1250 µg/mL) to induce the same effects as the AMPs (500-7.8 µg/mL) or EOs (365.2-19.7 µg/mL). Pexiganan and CLO were the most effective biomolecules, requiring lower concentrations to kill both Gram-positive and Gram-negative bacteria (62.5-7.8 µg/mL and 39.3-19.7 µg/mL, respectively), within a short period of time (averaging 2 h 15 min for all bacteria). Most biomolecules apparently disrupted the bacteria membrane stability due to the observed cell morphology deformation and by effecting on the intracellular space. AMPs were observed to induce morphological deformations and cellular content release, while EOs were seen to split and completely envelope bacteria. Data unraveled more of the potential of these new biomolecules as replacements for the conventional antibiotics and allowed us to take a step forward in the understanding of their mechanisms of action against infection-related bacteria.
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Affiliation(s)
| | | | | | | | | | | | | | - Helena P. Felgueiras
- Centre for Textile Science and Technology (2C2T), Department of Textile Engineering, University of Minho, Campus of Azurém, 4800-058 Guimarães, Portugal; (T.D.T.); (J.C.A.); (J.P.); (A.I.R.); (A.Z.); (M.T.P.A.); (F.F.)
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21
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Panina I, Krylov N, Nolde D, Efremov R, Chugunov A. Environmental and dynamic effects explain how nisin captures membrane-bound lipid II. Sci Rep 2020; 10:8821. [PMID: 32483218 PMCID: PMC7264305 DOI: 10.1038/s41598-020-65522-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 05/01/2020] [Indexed: 11/09/2022] Open
Abstract
Antibiotics (AB) resistance is a major threat to global health, thus the development of novel AB classes is urgently needed. Lantibiotics (i.e. nisin) are natural compounds that effectively control bacterial populations, yet their clinical potential is very limited. Nisin targets membrane-embedded cell wall precursor - lipid II - via capturing its pyrophosphate group (PPi), which is unlikely to evolve, and thus represents a promising pharmaceutical target. Understanding of exact molecular mechanism of initial stages of membrane-bound lipid II recognition by water-soluble nisin is indispensable. Here, using molecular simulations, we demonstrate that the structure of lipid II is determined to a large extent by the surrounding water-lipid milieu. In contrast to the bulk solvent, in the bilayer only two conformational states remain capable of nisin binding. In these states PPi manifests a unique arrangement of hydrogen bond acceptors on the bilayer surface. Such a "pyrophosphate pharmacophore" cannot be formed by phospholipids, which explains high selectivity of nisin/lipid II recognition. Similarly, the "recognition module" of nisin, being rather flexible in water, adopts the only stable conformation in the presence of PPi analogue (which mimics the lipid II molecule). We establish the "energy of the pyrophosphate pharmacophore" approach, which effectively distinguishes nisin conformations that can form a complex with PPi. Finally, we propose a molecular model of nisin recognition module/lipid II complex in the bacterial membrane. These results will be employed for further study of lipid II targeting by antimicrobial (poly)cyclic peptides and for design of novel AB prototypes.
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Affiliation(s)
- Irina Panina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., Moscow, 117997, Russia.,National Research University Higher School of Economics, Moscow, 101000, Russia
| | - Nikolay Krylov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., Moscow, 117997, Russia.,National Research University Higher School of Economics, Moscow, 101000, Russia
| | - Dmitry Nolde
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., Moscow, 117997, Russia.,National Research University Higher School of Economics, Moscow, 101000, Russia
| | - Roman Efremov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., Moscow, 117997, Russia. .,National Research University Higher School of Economics, Moscow, 101000, Russia. .,Moscow Institute of Physics and Technology (State University), Dolgoprudny, 141701, Moscow, Oblast, Russia.
| | - Anton Chugunov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., Moscow, 117997, Russia.,National Research University Higher School of Economics, Moscow, 101000, Russia.,Moscow Institute of Physics and Technology (State University), Dolgoprudny, 141701, Moscow, Oblast, Russia
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22
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Leonard A, Möhlis K, Schlüter R, Taylor E, Lalk M, Methling K. Exploring metabolic adaptation of Streptococcus pneumoniae to antibiotics. J Antibiot (Tokyo) 2020; 73:441-454. [PMID: 32210362 PMCID: PMC7292801 DOI: 10.1038/s41429-020-0296-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 01/31/2020] [Accepted: 02/09/2020] [Indexed: 02/07/2023]
Abstract
The Gram-positive bacterium Streptococcus pneumoniae is one of the common causes of community acquired pneumonia, meningitis, and otitis media. Analyzing the metabolic adaptation toward environmental stress conditions improves our understanding of its pathophysiology and its dependency on host-derived nutrients. In this study, extra- and intracellular metabolic profiles were evaluated to investigate the impact of antimicrobial compounds targeting different pathways of the metabolome of S. pneumoniae TIGR4Δcps. For the metabolomics approach, we analyzed the complex variety of metabolites by using 1H NMR, HPLC-MS, and GC–MS as different analytical techniques. Through this combination, we detected nearly 120 metabolites. For each antimicrobial compound, individual metabolic effects were detected that often comprised global biosynthetic pathways. Cefotaxime altered amino acids metabolism and carbon metabolism. The purine and pyrimidine metabolic pathways were mostly affected by moxifloxacin treatment. The combination of cefotaxime and azithromycin intensified the stress response compared with the use of the single antibiotic. However, we observed that three cell wall metabolites were altered only by treatment with the combination of the two antibiotics. Only moxifloxacin stress-induced alternation in CDP-ribitol concentration. Teixobactin-Arg10 resulted in global changes of pneumococcal metabolism. To meet the growing requirements for new antibiotics, our metabolomics approach has shown to be a promising complement to other OMICs investigations allowing insights into the mode of action of novel antimicrobial compounds.
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Affiliation(s)
- Anne Leonard
- Institute for Biochemistry, Metabolomics, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Kevin Möhlis
- Institute for Biochemistry, Metabolomics, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Rabea Schlüter
- Imaging Center of the Department of Biology, University of Greifswald, F.-L-Jahn-Str. 15, 17489, Greifswald, Germany
| | - Edward Taylor
- University of Lincoln, School of Life Sciences, Green Lane, LN67DL, Lincoln, England, United Kingdom
| | - Michael Lalk
- Institute for Biochemistry, Metabolomics, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Karen Methling
- Institute for Biochemistry, Metabolomics, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany.
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23
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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: 116] [Impact Index Per Article: 29.0] [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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24
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Rončević T, Puizina J, Tossi A. Antimicrobial Peptides as Anti-Infective Agents in Pre-Post-Antibiotic Era? Int J Mol Sci 2019; 20:E5713. [PMID: 31739573 PMCID: PMC6887943 DOI: 10.3390/ijms20225713] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/08/2019] [Accepted: 11/11/2019] [Indexed: 02/06/2023] Open
Abstract
Resistance to antibiotics is one of the main current threats to human health and every year multi-drug resistant bacteria are infecting millions of people worldwide, with many dying as a result. Ever since their discovery, some 40 years ago, the antimicrobial peptides (AMPs) of innate defense have been hailed as a potential alternative to conventional antibiotics due to their relatively low potential to elicit resistance. Despite continued effort by both academia and start-ups, currently there are still no antibiotics based on AMPs in use. In this study, we discuss what we know and what we do not know about these agents, and what we need to know to successfully translate discovery to application. Understanding the complex mechanics of action of these peptides is the main prerequisite for identifying and/or designing or redesigning novel molecules with potent biological activity. However, other aspects also need to be well elucidated, i.e., the (bio)synthetic processes, physiological and pathological contexts of their activity, and a quantitative understanding of how physico-chemical properties affect activity. Research groups worldwide are using biological, biophysical, and algorithmic techniques to develop models aimed at designing molecules with the necessary blend of antimicrobial potency and low toxicity. Shedding light on some open questions may contribute toward improving this process.
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Affiliation(s)
- Tomislav Rončević
- Department of Biology, Faculty of Science, University of Split, 21000 Split, Croatia;
- Laboratory for Aquaculture, Institute of Oceanography and Fisheries, 21000 Split, Croatia
| | - Jasna Puizina
- Department of Biology, Faculty of Science, University of Split, 21000 Split, Croatia;
| | - Alessandro Tossi
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy;
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25
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Bai X, Chen X. Rational design, conformational analysis and membrane-penetrating dynamics study of Bac2A-derived antimicrobial peptides against gram-positive clinical strains isolated from pyemia. J Theor Biol 2019; 473:44-51. [DOI: 10.1016/j.jtbi.2019.03.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/17/2019] [Accepted: 03/23/2019] [Indexed: 10/27/2022]
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26
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Chauhan J, Kwasny SM, Fletcher S, Opperman TJ, de Leeuw EPH. Optimization of a small-molecule Lipid II binder. Bioorg Med Chem Lett 2019; 29:1849-1853. [PMID: 31126852 DOI: 10.1016/j.bmcl.2019.04.046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 04/23/2019] [Accepted: 04/26/2019] [Indexed: 11/16/2022]
Abstract
Lipid II is an essential precursor of bacterial cell wall biosynthesis and an attractive target for antibiotics. Lipid II is comprised of specialized lipid (bactoprenol) linked to a hydrophilic head group consisting of a peptidoglycan subunit (N-acetylglucosamine (GlcNAc)-N-acetylmuramic acid (MurNAc) disaccharide coupled to a short pentapeptide moiety) via a pyrophosphate. We previously identified a (E)-2,4-bis(4-bromophenyl)-6-(4-(dimethylamino)styryl)pyrylium boron tetrafluoride salt, termed 6jc48-1, that interacts with the MurNAc moiety, the phosphate cage and the isoprenyl tail of Lipid II. Here, we report on the structure-activity relationship of 6jc48-1 derivatives obtained by de novo chemical synthesis. Our results indicate that bacterial killing is positively driven by bi-phenyl stacking with peptidoglycan units. Replacement of bromides by fluorides resulted in activity against S. aureus without affecting Lipid II binding and cytotoxicity. Antibacterial activity was affected negatively by extended interaction of the scaffold with Lipid II isoprenyl units.
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Affiliation(s)
- Jay Chauhan
- Institute of Human Virology & Department of Biochemistry and Molecular Biology of the University of Maryland Baltimore School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Steven M Kwasny
- Microbiotix, Inc., One Innovation Drive, Worcester, MA 01605, USA
| | - Steven Fletcher
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, 20 Penn Street, Baltimore, MD 21201, USA
| | | | - Erik P H de Leeuw
- Institute of Human Virology & Department of Biochemistry and Molecular Biology of the University of Maryland Baltimore School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA.
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Preclinical evaluation of the maximum tolerated dose and toxicokinetics of enteric-coated lantibiotic OG253 capsules. Toxicol Appl Pharmacol 2019; 374:32-40. [PMID: 31034929 DOI: 10.1016/j.taap.2019.04.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 04/22/2019] [Accepted: 04/25/2019] [Indexed: 11/23/2022]
Abstract
Clostridium difficile associated disease (CDAD) is the leading infectious cause of antibiotic-associated diarrhea and colitis in the United States. Both the incidence and severity of CDAD have been increased over the past two decades. We evaluated the maximum tolerated dose (MTD) and toxicokinetics of OG253, a novel lantibiotic in development for the treatment of CDAD. OG253 was orally administered to Wistar Han rats as enteric-coated capsules in a one-day dose escalation study, followed by a seven-day repeated dose toxicokinetics study. All three doses of OG253 (6.75, 27 and 108 mg/day) were generally well-tolerated with no treatment-related clinical signs, alterations in body weight or food consumption in both one-day acute tolerability and seven-days repeated dose tolerability and toxicokinetics study. OG253 capsule administration neither significantly alter the weight of organs nor affect the hematology, coagulation, clinical biochemistry parameters and urine pH compared to placebo capsule administered rats. LC-MS/MS analysis did not detect OG253 in the plasma, indicating that OG253 is not absorbed into the blood from the rat gastrointestinal tract. Glandular atrophy of the rectal mucosa was noticed in two out of six rats administered with a high dose of OG253. Surprisingly, we found that OG253 treatment significantly lowered both serum cholesterol and triglyceride levels in both sexes of rats. Overall, there was a 29.8 and 61.38% decrease in the serum cholesterol and triglyceride levels, respectively as compared to placebo-treated rats. The well-tolerated high dose of OG253 (425.7 mg/kg/day) is recommended as the MTD for safety and efficacy studies. Further preclinical study is needed to evaluate the safety profile of OG253 under longer exposure.
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Calvez P, Jouhet J, Vié V, Durmort C, Zapun A. Lipid Phases and Cell Geometry During the Cell Cycle of Streptococcus pneumoniae. Front Microbiol 2019; 10:351. [PMID: 30936851 PMCID: PMC6432855 DOI: 10.3389/fmicb.2019.00351] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 02/11/2019] [Indexed: 01/31/2023] Open
Abstract
The coexistence of different lipid phases is well-known in vitro, but evidence for their presence and function in cellular membranes remains scarce. Using a combination of fluorescent lipid probes, we observe segregation of domains that suggests the coexistence of liquid and gel phases in the membrane of Streptococcus pneumoniae, where they are localized to minimize bending stress in the ellipsoid geometry defined by the cell wall. Gel phase lipids with high bending rigidity would be spontaneously organized at the equator where curvature is minimal, thus marking the future division site, while liquid phase membrane maps onto the oblong hemispheres. In addition, the membrane-bound cell wall precursor with its particular dynamic acyl chain localizes at the division site where the membrane is highly curved. We propose a complete “chicken-and-egg” model where cell geometry determines the localization of lipid phases that positions the cell division machinery, which in turn alters the localization of lamellar phases by assembling the cell wall with a specific geometry.
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Affiliation(s)
| | - Juliette Jouhet
- UMR 5168 CNRS, CEA, INRA, CEA Grenoble, Laboratoire de Physiologie Cellulaire Végétale, Bioscience and Biotechnologies Institute of Grenoble, Université Grenoble Alpes, Grenoble, France
| | - Véronique Vié
- Univ Rennes, CNRS, IPR-UMR 6251, ScanMat-UMS2001, Rennes, France
| | | | - André Zapun
- Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
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29
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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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30
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Pokhrel R, Bhattarai N, Baral P, Gerstman BS, Park JH, Handfield M, Chapagain PP. Molecular mechanisms of pore formation and membrane disruption by the antimicrobial lantibiotic peptide Mutacin 1140. Phys Chem Chem Phys 2019; 21:12530-12539. [DOI: 10.1039/c9cp01558b] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The emergence of antibiotic-resistance is a major concern to global human health and identification of novel antibiotics is critical to mitigate the threat.
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Affiliation(s)
| | - Nisha Bhattarai
- Department of Physics
- Florida International University
- Miami
- USA
| | - Prabin Baral
- Department of Physics
- Florida International University
- Miami
- USA
| | - Bernard S. Gerstman
- Department of Physics
- Florida International University
- Miami
- USA
- Biomolecular Sciences Institute
| | | | | | - Prem P. Chapagain
- Department of Physics
- Florida International University
- Miami
- USA
- Biomolecular Sciences Institute
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31
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Greber KE, Zielińska J, Nierzwicki Ł, Ciura K, Kawczak P, Nowakowska J, Bączek T, Sawicki W. Are the short cationic lipopeptides bacterial membrane disruptors? Structure-Activity Relationship and molecular dynamic evaluation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1861:93-99. [PMID: 30463703 DOI: 10.1016/j.bbamem.2018.08.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 08/22/2018] [Accepted: 08/23/2018] [Indexed: 12/21/2022]
Abstract
Short cationic lipopeptides are amphiphilic molecules that exhibit antimicrobial activity mainly against Gram-positives. These compounds bind to bacterial membranes and disrupt their integrity. Here we examine the structure-activity relation (SAR) of lysine-based lipopeptides, with a prospect to rationally design more active compounds. The presented study aims to explain how antimicrobial activity of lipopeptides is affected by the charge of lipopeptide headgroup and the length of lipopeptide acyl chain. The obtained SAR models suggest that the lipophilicity of short synthetic cationic lipopeptides is the major factor that determines their antimicrobial activities. In order to link the differences in antimicrobial activity to the mechanism of action of lipopeptides containing one and two hydrophobic chains, we additionally performed molecular dynamic (MD) simulations. By using combined coarse-grained and all-atom simulations we also show that these compounds neither affect the organization of the membrane lipids nor aggregate to form separate phases. These results, along with the onset of antimicrobial activity of lipopeptides well below the critical micelle concentration (CMC), indicate that lipopeptides do not act in a simple detergent-like manner.
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Affiliation(s)
- Katarzyna E Greber
- Medical University of Gdańsk, Faculty of Pharmacy, Department of Physical Chemistry, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland.
| | - Joanna Zielińska
- Medical University of Gdańsk, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland
| | - Łukasz Nierzwicki
- Gdańsk University of Technology, Faculty of Chemistry, Department of Physical Chemistry, ul. Gabriela Narutowicza 11/12, 80-233 Gdańsk, Poland.
| | - Krzesimir Ciura
- Medical University of Gdańsk, Faculty of Pharmacy, Department of Physical Chemistry, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland
| | - Piotr Kawczak
- Medical University of Gdańsk, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland
| | - Joanna Nowakowska
- Medical University of Gdańsk, Faculty of Pharmacy, Department of Physical Chemistry, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland
| | - Tomasz Bączek
- Medical University of Gdańsk, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland
| | - Wiesław Sawicki
- Medical University of Gdańsk, Faculty of Pharmacy, Department of Physical Chemistry, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland
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Kers JA, Sharp RE, Muley S, Mayo M, Colbeck J, Zhu Y, DeFusco AW, Park JH, Handfield M. Blueprints for the rational design of therapeutic mutacin 1140 variants. Chem Biol Drug Des 2018; 92:1940-1953. [DOI: 10.1111/cbdd.13365] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 06/12/2018] [Accepted: 07/09/2018] [Indexed: 12/27/2022]
Affiliation(s)
- Johan A. Kers
- Intrexon Corp.; Industrial Products Division; South San Francisco California
| | - R. Eryl Sharp
- Intrexon Corp.; Industrial Products Division; South San Francisco California
| | - Sheela Muley
- Intrexon Corp.; Industrial Products Division; South San Francisco California
| | - Melissa Mayo
- Intrexon Corp.; Industrial Products Division; South San Francisco California
| | - Jeffrey Colbeck
- Intrexon Corp.; Industrial Products Division; South San Francisco California
| | - Yihui Zhu
- Intrexon Corp.; Industrial Products Division; South San Francisco California
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Punekar AS, Samsudin F, Lloyd AJ, Dowson CG, Scott DJ, Khalid S, Roper DI. The role of the jaw subdomain of peptidoglycan glycosyltransferases for lipid II polymerization. Cell Surf 2018; 2:54-66. [PMID: 30046666 PMCID: PMC6053601 DOI: 10.1016/j.tcsw.2018.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 06/12/2018] [Accepted: 06/12/2018] [Indexed: 12/27/2022] Open
Abstract
Bacterial peptidoglycan glycosyltransferases (PGT) catalyse the essential polymerization of lipid II into linear glycan chains required for peptidoglycan biosynthesis. The PGT domain is composed of a large head subdomain and a smaller jaw subdomain and can be potently inhibited by the antibiotic moenomycin A (MoeA). We present an X-ray structure of the MoeA-bound Staphylococcus aureus monofunctional PGT enzyme, revealing electron density for a second MoeA bound to the jaw subdomain as well as the PGT donor site. Isothermal titration calorimetry confirms two drug-binding sites with markedly different affinities and positive cooperativity. Hydrophobic cluster analysis suggests that the membrane-interacting surface of the jaw subdomain has structural and physicochemical properties similar to amphipathic cationic α -helical antimicrobial peptides for lipid II recognition and binding. Furthermore, molecular dynamics simulations of the drug-free and -bound forms of the enzyme demonstrate the importance of the jaw subdomain movement for lipid II selection and polymerization process and provide molecular-level insights into the mechanism of peptidoglycan biosynthesis by PGTs.
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Affiliation(s)
- Avinash S. Punekar
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Firdaus Samsudin
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Adrian J. Lloyd
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | | | - David J. Scott
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
- ISIS Neutron and Muon Spallation Source and Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire, United Kingdom
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - David I. Roper
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
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34
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Yang R, Zhang G, Zhang F, Li Z, Huang C. Membrane permeabilization design of antimicrobial peptides based on chikungunya virus fusion domain scaffold and its antibacterial activity against gram-positive Streptococcus pneumoniae in respiratory infection. Biochimie 2018; 146:139-147. [DOI: 10.1016/j.biochi.2017.12.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 12/18/2017] [Indexed: 01/08/2023]
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Franzoi M, van Heuvel Y, Thomann S, Schürch N, Kallio PT, Venier P, Essig A. Structural Insights into the Mode of Action of the Peptide Antibiotic Copsin. Biochemistry 2017; 56:4992-5001. [PMID: 28825809 DOI: 10.1021/acs.biochem.7b00697] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Defensins make up a class of cysteine-rich antimicrobial peptides, expressed by virtually all eukaryotes as part of their innate immune response. Because of their unique mode of action and rapid killing of pathogenic microbes, defensins are considered promising alternatives to clinically applied antibiotics. Copsin is a defensin-like peptide, previously identified in the mushroom Coprinopsis cinerea. It exerts its activity against a range of Gram-positive bacteria by binding to the peptidoglycan precursor lipid II and prevention of proper cell wall formation. In this study, we present a new workflow for the generation, production, and activity-driven selection of copsin derivatives, based on their expression in Pichia pastoris. One hundred fifty-two single-amino acid mutants and combinations thereof allowed the identification of k-copsin, a peptide variant exhibiting significantly enhanced activity against Bacillus subtilis and Staphylococcus aureus. Furthermore, we performed in silico characterizations of membrane interactions of copsin and k-copsin, in the presence and absence of lipid II. The molecular dynamics data highlighted a high variability in lipid II binding, with a preference for the MurNAc moiety with 47 and 35% of the total contacts for copsin and k-copsin, respectively. Mutated amino acids were located in loop regions of k-copsin and shown to be crucial in the perturbation of the bacterial membrane. These structural studies provide a better understanding of how defensins can be developed toward antibacterial therapies less prone to resistance issues.
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Affiliation(s)
- Marco Franzoi
- Department of Biology, University of Padova , Via Ugo Bassi 58/B, Padova 35131, Italy
| | - Yasemin van Heuvel
- Institute of Microbiology, Swiss Federal Institute of Technology, ETH Zurich , CH-8093 Zurich, Switzerland
| | - Susanne Thomann
- Biology Division, Spiez Laboratory, Federal Office for Civil Protection , CH-3700 Spiez, Switzerland
| | - Nadia Schürch
- Biology Division, Spiez Laboratory, Federal Office for Civil Protection , CH-3700 Spiez, Switzerland
| | - Pauli T Kallio
- Institute of Microbiology, Swiss Federal Institute of Technology, ETH Zurich , CH-8093 Zurich, Switzerland
| | - Paola Venier
- Department of Biology, University of Padova , Via Ugo Bassi 58/B, Padova 35131, Italy
| | - Andreas Essig
- Institute of Microbiology, Swiss Federal Institute of Technology, ETH Zurich , CH-8093 Zurich, Switzerland
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36
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Müller A, Klöckner A, Schneider T. Targeting a cell wall biosynthesis hot spot. Nat Prod Rep 2017; 34:909-932. [PMID: 28675405 DOI: 10.1039/c7np00012j] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Covering: up to 2017History points to the bacterial cell wall biosynthetic network as a very effective target for antibiotic intervention, and numerous natural product inhibitors have been discovered. In addition to the inhibition of enzymes involved in the multistep synthesis of the macromolecular layer, in particular, interference with membrane-bound substrates and intermediates essential for the biosynthetic reactions has proven a valuable antibacterial strategy. A prominent target within the peptidoglycan biosynthetic pathway is lipid II, which represents a particular "Achilles' heel" for antibiotic attack, as it is readily accessible on the outside of the cytoplasmic membrane. Lipid II is a unique non-protein target that is one of the structurally most conserved molecules in bacterial cells. Notably, lipid II is more than just a target molecule, since sequestration of the cell wall precursor may be combined with additional antibiotic activities, such as the disruption of membrane integrity or disintegration of membrane-bound multi-enzyme machineries. Within the membrane bilayer lipid II is likely organized in specific anionic phospholipid patches that form a particular "landing platform" for antibiotics. Nature has invented a variety of different "lipid II binders" of at least 5 chemical classes, and their antibiotic activities can vary substantially depending on the compounds' physicochemical properties, such as amphiphilicity and charge, and thus trigger diverse cellular effects that are decisive for antibiotic activity.
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Affiliation(s)
- Anna Müller
- Institute of Pharmaceutical Microbiology, University of Bonn, Bonn, Germany.
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37
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Vukomanović M, Žunič V, Kunej Š, Jančar B, Jeverica S, Podlipec R, Suvorov D. Nano-engineering the Antimicrobial Spectrum of Lantibiotics: Activity of Nisin against Gram Negative Bacteria. Sci Rep 2017; 7:4324. [PMID: 28659619 PMCID: PMC5489483 DOI: 10.1038/s41598-017-04670-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 05/18/2017] [Indexed: 11/22/2022] Open
Abstract
Lantibiotics, bacteria-sourced antimicrobial peptides, are very good candidates for effective and safe food additives. Among them, nisin is already approved by the EU and FDA, and has been used in food preservation for the past 40 years. Now, there is a possibility and strong interest to extend its applicability to biomedicine for designing innovative alternatives to antibiotics. The main obstacle is, however, its naturally narrow spectrum of antimicrobial activity, focused on Gram positive bacteria. Here we demonstrate broadening nisin's spectrum to Gram negative bacteria using a nano-engineering approach. After binding nisin molecules to the surface of gold nano-features, uniformly deposited on spherical carbon templates, we created a nanocomposite with a high density of positively charged groups. Before assembly, none of the components of the nanocomposite showed any activity against bacterial growth, which was changed after assembly in the form of the nanocomposite. For the first time we showed that this type of structure enables interactions capable of disintegrating the wall of Gram negative bacteria. As confirmed by the nisin model, the developed approach opens up new horizons for the use of lantibiotics in designing post-antibiotic drugs.
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Affiliation(s)
- Marija Vukomanović
- Advanced Materials Department, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia.
| | - Vojka Žunič
- Advanced Materials Department, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia
| | - Špela Kunej
- Advanced Materials Department, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia
| | - Boštjan Jančar
- Advanced Materials Department, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia
| | - Samo Jeverica
- Institute for Microbiology and Immunology, Medical Faculty, University of Ljubljana, Zaloška 4, 1000, Ljubljana, Slovenia
| | - Rok Podlipec
- Laboratory of Biophysics, Condensed Matter Physics Department, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia
| | - Danilo Suvorov
- Advanced Materials Department, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia
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38
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Ng V, Chan WC. New Found Hope for Antibiotic Discovery: Lipid II Inhibitors. Chemistry 2016; 22:12606-16. [PMID: 27388768 DOI: 10.1002/chem.201601315] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Indexed: 12/14/2022]
Abstract
Research into antibacterial agents has recently gathered pace in light of the disturbing crisis of antimicrobial resistance. The development of modern tools offers the opportunity of reviving the fallen era of antibacterial discovery through uncovering novel lead compounds that target vital bacterial cell components, such as lipid II. This paper provides a summary of the role of lipid II as well as an overview and insight into the structural features of macrocyclic peptides that inhibit this bacterial cell wall component. The recent discovery of teixobactin, a new class of lipid II inhibitor has generated substantial research interests. As such, the significant progress that has been achieved towards its development as a promising antibacterial agent is discussed.
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Affiliation(s)
- Vivian Ng
- School of Pharmacy, Centre of Biomolecular Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Weng C Chan
- School of Pharmacy, Centre of Biomolecular Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
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39
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Sachdeva S, Kolimi N, Nair SA, Rathinavelan T. Key diffusion mechanisms involved in regulating bidirectional water permeation across E. coli outer membrane lectin. Sci Rep 2016; 6:28157. [PMID: 27320406 PMCID: PMC4913347 DOI: 10.1038/srep28157] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 05/31/2016] [Indexed: 12/27/2022] Open
Abstract
Capsular polysaccharides (CPSs) are major bacterial virulent determinants that facilitate host immune evasion. E. coli group1 K30CPS is noncovalently attached to bacterial surface by Wzi, a lectin. Intriguingly, structure based phylogenetic analysis indicates that Wzi falls into porin superfamily. Molecular dynamics (MD) simulations further shed light on dual role of Wzi as it also functions as a bidirectional passive water specific porin. Such a functional role of Wzi was not realized earlier, due to the occluded pore. While five water specific entry points distributed across extracellular & periplasmic faces regulate the water diffusion involving different mechanisms, a luminal hydrophobic plug governs water permeation across the channel. Coincidently, MD observed open state structure of “YQF” triad is seen in sugar-binding site of sodium-galactose cotransporters, implicating its involvement in K30CPS surface anchorage. Importance of Loop 5 (L5) in membrane insertion is yet another highlight. Change in water diffusion pattern of periplasmic substitution mutants suggests Wzi’s role in osmoregulation by aiding in K30CPS hydration, corroborating earlier functional studies. Water molecules located inside β-barrel of Wzi crystal structure further strengthens the role of Wzi in osmoregulation. Thus, interrupting water diffusion or L5 insertion may reduce bacterial virulence.
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Affiliation(s)
- Shivangi Sachdeva
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana State 502285, India
| | - Narendar Kolimi
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana State 502285, India
| | - Sanjana Anilkumar Nair
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana State 502285, India
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40
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Witzke S, Petersen M, Carpenter TS, Khalid S. Molecular Dynamics Simulations Reveal the Conformational Flexibility of Lipid II and Its Loose Association with the Defensin Plectasin in the Staphylococcus aureus Membrane. Biochemistry 2016; 55:3303-14. [PMID: 27158738 DOI: 10.1021/acs.biochem.5b01315] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lipid II is critical for peptidoglycan synthesis, which is the main component of the bacterial cell wall. Lipid II is a relatively conserved and important part of the cell wall biosynthesis pathway and is targeted by antibiotics such as the lantibiotics, which achieve their function by disrupting the biosynthesis of the cell wall. Given the urgent need for development of novel antibiotics to counter the growing threat of bacterial infection resistance, it is imperative that a thorough molecular-level characterization of the molecules targeted by antibiotics be achieved. To this end, we present a molecular dynamics simulation study of the conformational dynamics of Lipid II within a detailed model of the Staphylococcus aureus cell membrane. We show that Lipid II is able to adopt a range of conformations, even within the packed lipidic environment of the membrane. Our simulations also reveal dimerization of Lipid II mediated by cations. In the presence of the defensin peptide plectasin, the conformational lability of Lipid II allows it to form loose complexes with the protein, via a number of different binding modes.
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Affiliation(s)
- Sarah Witzke
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Odense, Denmark.,School of Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, U.K
| | - Michael Petersen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Odense, Denmark
| | - Timothy S Carpenter
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory , 7000 East Avenue, Livermore, California 94550, United States
| | - Syma Khalid
- School of Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, U.K
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41
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Docking and molecular dynamics simulations of the ternary complex nisin2:lipid II. Sci Rep 2016; 6:21185. [PMID: 26888784 PMCID: PMC4758073 DOI: 10.1038/srep21185] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 01/18/2016] [Indexed: 11/30/2022] Open
Abstract
Lanthionine antibiotics are an important class of naturally-occurring antimicrobial peptides. The best-known, nisin, is a commercial food preservative. However, structural and mechanistic details on nisin-lipid II membrane complexes are currently lacking. Recently, we have developed empirical force-field parameters to model lantibiotics. Docking and molecular dynamics (MD) simulations have been used to study the nisin2:lipid II complex in bacterial membranes, which has been put forward as the building block of nisin/lipid II binary membrane pores. An Ile1Trp mutation of the N-terminus of nisin has been modelled and docked onto lipid II models; the computed binding affinity increased compared to wild-type. Wild-type nisin was also docked onto three different lipid II structures and a stable 2:1 nisin:lipid II complex formed. This complex was inserted into a membrane. Six independent MD simulations revealed key interactions in the complex, specifically the N-terminal engagement of nisin with lipid II at the pyrophosphate and C-terminus of the pentapeptide chain. Nisin2 inserts into the membrane and we propose this as the first step in pore formation, mediated by the nisin N-terminus–lipid II pentapeptide hydrogen bond. The lipid II undecaprenyl chain adopted different conformations in the presence of nisin, which may also have implications for pore formation.
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42
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References. Antibiotics (Basel) 2015. [DOI: 10.1128/9781555819316.refs] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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43
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Pluhackova K, Böckmann RA. Biomembranes in atomistic and coarse-grained simulations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015. [PMID: 26194872 DOI: 10.1088/0953-8984/27/32/323103] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The architecture of biological membranes is tightly coupled to the localization, organization, and function of membrane proteins. The organelle-specific distribution of lipids allows for the formation of functional microdomains (also called rafts) that facilitate the segregation and aggregation of membrane proteins and thus shape their function. Molecular dynamics simulations enable to directly access the formation, structure, and dynamics of membrane microdomains at the molecular scale and the specific interactions among lipids and proteins on timescales from picoseconds to microseconds. This review focuses on the latest developments of biomembrane force fields for both atomistic and coarse-grained molecular dynamics (MD) simulations, and the different levels of coarsening of biomolecular structures. It also briefly introduces scale-bridging methods applicable to biomembrane studies, and highlights selected recent applications.
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Affiliation(s)
- Kristyna Pluhackova
- Computational Biology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg, Staudtstr. 5, 91058 Erlangen, Germany
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Kern NR, Lee HS, Wu EL, Park S, Vanommeslaeghe K, MacKerell AD, Klauda JB, Jo S, Im W. Lipid-linked oligosaccharides in membranes sample conformations that facilitate binding to oligosaccharyltransferase. Biophys J 2015; 107:1885-1895. [PMID: 25418169 DOI: 10.1016/j.bpj.2014.09.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 09/05/2014] [Accepted: 09/09/2014] [Indexed: 01/21/2023] Open
Abstract
Lipid-linked oligosaccharides (LLOs) are the substrates of oligosaccharyltransferase (OST), the enzyme that catalyzes the en bloc transfer of the oligosaccharide onto the acceptor asparagine of nascent proteins during the process of N-glycosylation. To explore LLOs' preferred location, orientation, structure, and dynamics in membrane bilayers of three different lipid types (dilauroylphosphatidylcholine, dimyristoylphosphatidylcholine, and dioleoylphosphatidylcholine), we have modeled and simulated both eukaryotic (Glc3-Man9-GlcNAc2-PP-Dolichol) and bacterial (Glc1-GalNAc5-Bac1-PP-Undecaprenol) LLOs, which are composed of an isoprenoid moiety and an oligosaccharide, linked by pyrophosphate. The simulations show no strong impact of different bilayer hydrophobic thicknesses on the overall orientation, structure, and dynamics of the isoprenoid moiety and the oligosaccharide. The pyrophosphate group stays in the bilayer head group region. The isoprenoid moiety shows high flexibility inside the bilayer hydrophobic core, suggesting its potential role as a tentacle to search for OST. The oligosaccharide conformation and dynamics are similar to those in solution, but there are preferred interactions between the oligosaccharide and the bilayer interface, which leads to LLO sugar orientations parallel to the bilayer surface. Molecular docking of the bacterial LLO to a bacterial OST suggests that such orientations can enhance binding of LLOs to OST.
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Affiliation(s)
- Nathan R Kern
- Department of Molecular Biosciences and Center for Bioinformatics, University of Kansas, Lawrence, Kansas
| | - Hui Sun Lee
- Department of Molecular Biosciences and Center for Bioinformatics, University of Kansas, Lawrence, Kansas
| | - Emilia L Wu
- Department of Molecular Biosciences and Center for Bioinformatics, University of Kansas, Lawrence, Kansas
| | - Soohyung Park
- Department of Molecular Biosciences and Center for Bioinformatics, University of Kansas, Lawrence, Kansas
| | - Kenno Vanommeslaeghe
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering and Biophysics Program, University of Maryland, College Park, Maryland
| | - Sunhwan Jo
- Department of Molecular Biosciences and Center for Bioinformatics, University of Kansas, Lawrence, Kansas
| | - Wonpil Im
- Department of Molecular Biosciences and Center for Bioinformatics, University of Kansas, Lawrence, Kansas.
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von Nussbaum F, Süssmuth RD. Multiple Attack on Bacteria by the New Antibiotic Teixobactin. Angew Chem Int Ed Engl 2015; 54:6684-6. [DOI: 10.1002/anie.201501440] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Indexed: 11/07/2022]
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von Nussbaum F, Süssmuth RD. Multipler Angriff auf Bakterien durch das neue Antibiotikum Teixobactin. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201501440] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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47
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Turpin ER, Mulholland S, Teale AM, Bonev BB, Hirst JD. New CHARMM force field parameters for dehydrated amino acid residues, the key to lantibiotic molecular dynamics simulations. RSC Adv 2014. [DOI: 10.1039/c4ra09897h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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48
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Structural dynamics of the cell wall precursor lipid II in the presence and absence of the lantibiotic nisin. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:3061-8. [PMID: 25128154 DOI: 10.1016/j.bbamem.2014.07.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 07/23/2014] [Accepted: 07/25/2014] [Indexed: 01/06/2023]
Abstract
Representing a physiological "Achilles' heel", the cell wall precursor lipid II (LII) is a prime target for various classes of antibiotics. Over the years LII-binding agents have been recognized as promising candidates and templates in the search for new antibacterial compounds to complement or replace existing drugs. To elucidate the molecular structural basis underlying LII functional mechanism and to better understand if and how lantibiotic binding alters the molecular behavior of LII, we performed molecular dynamics (MD) simulations of phospholipid membrane-embedded LII in the absence and presence of the LII-binding lantibiotic nisin. In a series of 2×4 independent, unbiased 100ns MD simulations we sampled the conformational dynamics of nine LII as well as nine LII-nisin complexes embedded in an aqueous 150mM NaCl/POPC phospholipid membrane environment. We found that nisin binding to LII induces a reduction of LII mobility and flexibility, an outward shift of the LII pentapeptide, an inward movement of the LII disaccharide section, and an overall deeper insertion of the LII tail group into the membrane. The latter effect might indicate an initial step in adopting a stabilizing, scaffold-like structure in the process of nisin-induced membrane leakage. At the same time nisin conformation and LII interaction remain similar to the 1WCO LII-nisin NMR solution structure.
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Sikorska E, Dawgul M, Greber K, Iłowska E, Pogorzelska A, Kamysz W. Self-assembly and interactions of short antimicrobial cationic lipopeptides with membrane lipids: ITC, FTIR and molecular dynamics studies. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:2625-34. [PMID: 24978107 DOI: 10.1016/j.bbamem.2014.06.016] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 05/13/2014] [Accepted: 06/23/2014] [Indexed: 11/28/2022]
Abstract
In this work, the self-organization and the behavior of the surfactant-like peptides in the presence of biological membrane models were studied. The studies were focused on synthetic palmitic acid-containing lipopeptides, C16-KK-NH2 (I), C16-KGK-NH2 (II) and C16-KKKK-NH2 (III). The self-assembly was explored by molecular dynamics simulations using a coarse-grained force field. The critical micellar concentration was estimated by the surface tension measurements. The thermodynamics of the peptides binding to the anionic and zwitterionic lipids were established using isothermal titration calorimetry (ITC). The influence of the peptides on the lipid acyl chain ordering was determined using FTIR spectroscopy. The compounds studied show surface-active properties with a distinct CMC over the millimolar range. An increase in the steric and electrostatic repulsion between polar head groups shifts the CMC toward higher values and reduces the aggregation number. An analysis of the peptide-membrane binding revealed a unique interplay between the initial electrostatic and the subsequent hydrophobic interactions enabling the lipopeptides to interact with the lipid bilayer. In the case of C16-KKKK-NH2 (III), compensation of the electrostatic and hydrophobic interactions upon binding to the anionic membrane has been suggested and consequently no overall binding effects were noticed in ITC thermograms and FTIR spectra.
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Affiliation(s)
- Emilia Sikorska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland.
| | - Małgorzata Dawgul
- Faculty of Pharmacy with Subfaculty of Laboratory Medicine, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland
| | - Katarzyna Greber
- Faculty of Pharmacy with Subfaculty of Laboratory Medicine, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland
| | - Emilia Iłowska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Aneta Pogorzelska
- Faculty of Pharmacy with Subfaculty of Laboratory Medicine, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland
| | - Wojciech Kamysz
- Faculty of Pharmacy with Subfaculty of Laboratory Medicine, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland
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The sentinel role of peptidoglycan recycling in the β-lactam resistance of the Gram-negative Enterobacteriaceae and Pseudomonas aeruginosa. Bioorg Chem 2014; 56:41-8. [PMID: 24955547 DOI: 10.1016/j.bioorg.2014.05.011] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 05/21/2014] [Accepted: 05/22/2014] [Indexed: 01/16/2023]
Abstract
The peptidoglycan is the structural polymer of the bacterial cell envelope. In contrast to an expectation of a structural stasis for this polymer, during the growth of the Gram-negative bacterium this polymer is in a constant state of remodeling and extension. Our current understanding of this peptidoglycan "turnover" intertwines with the deeply related phenomena of the liberation of small peptidoglycan segments (muropeptides) during turnover, the presence of dedicated recycling pathways for reuse of these muropeptides, β-lactam inactivation of specific penicillin-binding proteins as a mechanism for the perturbation of the muropeptide pool, and this perturbation as a controlling mechanism for signal transduction leading to the expression of β-lactamase(s) as a key resistance mechanism against the β-lactam antibiotics. The nexus for many of these events is the control of the AmpR transcription factor by the composition of the muropeptide pool generated during peptidoglycan recycling. In this review we connect the seminal observations of the past decades to new observations that resolve some, but certainly not all, of the key structures and mechanisms that connect to AmpR.
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