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Torabi M, Nazaruk E, Bilewicz R. Alignment of lyotropic liquid crystals using magnetic nanoparticles improves ionic transport through built-in peptide ion channels. J Colloid Interface Sci 2024; 674:982-992. [PMID: 38964002 DOI: 10.1016/j.jcis.2024.06.227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 06/28/2024] [Accepted: 06/28/2024] [Indexed: 07/06/2024]
Abstract
HYPOTHESIS We hypothesize that simultaneous incorporation of ion channel peptides (in this case, potassium channel as a model) and hydrophobic magnetite Fe3O4 nanoparticles (hFe3O4NPs) within lipidic hexagonal mesophases, and aligning them using an external magnetic field can significantly enhance ion transport through lipid membranes. EXPERIMENTS In this study, we successfully characterized the incorporation of gramicidin membrane ion channels and hFe3O4NPs in the lipidic hexagonal structure using SAXS and cryo-TEM methods. Additionally, we thoroughly investigated the conductive characteristics of freestanding films of lipidic hexagonal mesophases, both with and without gramicidin potassium channels, utilizing a range of electrochemical techniques, including impedance spectroscopy, normal pulse voltammetry, and chronoamperometry. FINDINGS Our research reveals a state-of-the-art breakthrough in enhancing ion transport in lyotropic liquid crystals as matrices for integral proteins and peptides. We demonstrate the remarkable efficacy of membranes composed of hexagonal lipid mesophases embedded with K+ transporting peptides. This enhancement is achieved through doping with hFe3O4NPs and exposure to a magnetic field. We investigate the intricate interplay between the conductive properties of the lipidic hexagonal structure, hFe3O4NPs, gramicidin incorporation, and the influence of Ca2+ on K+ channels. Furthermore, our study unveils a new direction in ion channel studies and biomimetic membrane investigations, presenting a versatile model for biomimetic membranes with unprecedented ion transport capabilities under an appropriately oriented magnetic field. These findings hold promise for advancing membrane technology and various biotechnological and biomedical applications of membrane proteins.
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Affiliation(s)
- Mostafa Torabi
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02093 Warsaw, Poland
| | - Ewa Nazaruk
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02093 Warsaw, Poland
| | - Renata Bilewicz
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02093 Warsaw, Poland; Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02089 Warsaw, Poland.
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2
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Dey S, Patel A, Haloi N, Srimayee S, Paul S, Barik GK, Akhtar N, Shaw D, Hazarika G, Prusty BM, Kumar M, Santra MK, Tajkhorshid E, Bhattacharjee S, Manna D. Quinoline Thiourea-Based Zinc Ionophores with Antibacterial Activity. J Med Chem 2023; 66:11078-11093. [PMID: 37466499 DOI: 10.1021/acs.jmedchem.3c00368] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
The increasing resistance of bacteria to commercially available antibiotics threatens patient safety in healthcare settings. Perturbation of ion homeostasis has emerged as a potential therapeutic strategy to fight against antibacterial resistance and other channelopathies. This study reports the development of 8-aminoquinoline (QN) derivatives and their transmembrane Zn2+ transport activities. Our findings showed that a potent QN-based Zn2+ transporter exhibits promising antibacterial properties against Gram-positive bacteria with reduced hemolytic activity and cytotoxicity to mammalian cells. Furthermore, this combination showed excellent in vivo efficacy against Staphylococcus aureus. Interestingly, this combination prevented bacterial resistance and restored susceptibility of gentamicin and methicillin-resistant S. aureus to commercially available β-lactam and other antibiotics that had lost their activity against the drug-resistant bacterial strain. Our findings suggest that the transmembrane transport of Zn2+ by QN derivatives could be a promising strategy to combat bacterial infections and restore the activity of other antibiotics.
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Affiliation(s)
- Subhasis Dey
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Anjali Patel
- Centre for Environment, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Nandan Haloi
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Soumya Srimayee
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Suman Paul
- Department of Molecular Biology and Bioinformatics, Tripura University (A Central University), Suryamaninagar, Tripura 799022, India
| | | | - Nasim Akhtar
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Dipanjan Shaw
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Gunanka Hazarika
- Centre for Environment, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Biswa Mohan Prusty
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Mohit Kumar
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | | | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Surajit Bhattacharjee
- Department of Molecular Biology and Bioinformatics, Tripura University (A Central University), Suryamaninagar, Tripura 799022, India
| | - Debasis Manna
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
- Centre for Environment, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
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3
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Yang F, Zhao F. Mechanism of visible light enhances microbial degradation of Bisphenol A. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130214. [PMID: 36327837 DOI: 10.1016/j.jhazmat.2022.130214] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
Bisphenol A (BPA) is a toxic endocrine disruptor detected in various environments. Microbial metabolic/enzymatic degradation has been thought to be the main pathway for BPA attenuation in natural environments. In this study, we found that under visible light conditions, superoxide produced by bacteria was the main reason for the rapid removal of BPA, accounting for 57 % of the total removal rate. With visible light, the bacteria degraded BPA at a rate of 0.22 mg/L/d, and the total removal within 8 days reached 85 %, which is 4.7 times compared with that of dark culture. The intermediate product 4-iso-propenylphenol, which was considered as an end-product of microbial degradation of BPA in previous reports, was detected in large quantities at 24 h in culture but gradually decreased in our experiment. Community analysis suggested bacteria with aromatic hydrocarbon degradation ability were more enriched under light incubation. Moreover, the bacteria showed well degradation ability to various pharmaceutically active but nonbiodegradable compounds including diclofenac and fluoxetine, with a removal rate of 88 % and 20 %, respectively. Our study revealed the organic pollutant transformation pathway under the combined action of light and microorganisms, providing new insights into the microbial treatment of aromatic hydrocarbon pollutants.
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Affiliation(s)
- Fan Yang
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Feng Zhao
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China.
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4
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Fang ST, Huang SH, Yang CH, Liou JW, Mani H, Chen YC. Effects of Calcium Ions on the Antimicrobial Activity of Gramicidin A. Biomolecules 2022; 12:biom12121799. [PMID: 36551225 PMCID: PMC9775247 DOI: 10.3390/biom12121799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/04/2022] Open
Abstract
Gramicidin A (gA) is a linear antimicrobial peptide that can form a channel and specifically conduct monovalent cations such as H+ across the lipid membrane. The antimicrobial activity of gA is associated with the formation of hydroxyl free radicals and the imbalance of NADH metabolism, possibly a consequence caused by the conductance of cations. The ion conductivity of gramicidin A can be blocked by Ca2+ ions. However, the effect of Ca2+ ions on the antimicrobial activity of gA is unclear. To unveil the role of Ca2+ ions, we examined the effect of Ca2+ ions on the antimicrobial activity of gramicidin A against Staphylococcus aureus (S. aureus). Results showed that the antimicrobial mechanism of gA and antimicrobial activity by Ca2+ ions are concentration-dependent. At the low gA concentration (≤1 μM), the antimicrobial mechanism of gA is mainly associated with the hydroxyl free radical formation and NADH metabolic imbalance. Under this mode, Ca2+ ions can significantly inhibit the hydroxyl free radical formation and NADH metabolic imbalance. On the other hand, at high gA concentration (≥5 μM), gramicidin A acts more likely as a detergent. Gramicidin A not only causes an increase in hydroxyl free radical levels and NAD+/NADH ratios but also induces the destruction of the lipid membrane composition. At this condition, Ca2+ ions can no longer reduce the gA antimicrobial activity but rather enhance the bacterial killing ability of gramicidin A.
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Affiliation(s)
- Shang-Ting Fang
- Department of Medicine, MacKay Medical College, New Taipei City 252, Taiwan
| | - Shu-Hsiang Huang
- Department of Medicine, MacKay Medical College, New Taipei City 252, Taiwan
| | - Chin-Hao Yang
- Department of Biochemistry, School of Medicine, Tzu Chi University, Hualien City 97004, Taiwan
| | - Jen-Wen Liou
- Department of Biochemistry, School of Medicine, Tzu Chi University, Hualien City 97004, Taiwan
| | - Hemalatha Mani
- Department of Biochemistry, School of Medicine, Tzu Chi University, Hualien City 97004, Taiwan
| | - Yi-Cheng Chen
- Department of Medicine, MacKay Medical College, New Taipei City 252, Taiwan
- Correspondence:
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5
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Defeat undefeatable: ionic liquids as novel antimicrobial agents. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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6
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Wang L, Liu L, Liu Y, Wang F, Zhou X. Antimicrobial performance of novel glutathione-conjugated silver nanoclusters (GSH@AgNCs) against Escherichia coli and Staphylococcus aureus by membrane-damage and biofilm-inhibition mechanisms. Food Res Int 2022; 160:111680. [DOI: 10.1016/j.foodres.2022.111680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 07/06/2022] [Accepted: 07/11/2022] [Indexed: 11/16/2022]
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7
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Han P, Chen Z, Liu Y, Ma A, Li S, Jia Y. An accurate strategy for pointing the key biocatalytic sites of bre2691A protein for modification of the brevilaterin from Brevibacillus laterosporus. Microb Cell Fact 2022; 21:196. [PMID: 36123650 PMCID: PMC9484153 DOI: 10.1186/s12934-022-01918-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/05/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Brevilaterin A-E, a novel class of multi-component cationic antimicrobial lipopeptides, were biosynthesized by a non-ribosomal peptides synthetase (NRPS) in Brevibacillus laterosporus. However, the antimicrobial abilities of different brevilaterin components varied greatly, and this multi-component form was impeding the scale production of the excellent component, and a little information about the brevilaterin biosynthesis mechanism was available to apply in brevilaterin design modification. In this study, we used an accurate strategy that revealed the reason for producing multi-component was the substrate selectivity of bre2691A protein being not enough specific and pinpointed the key design sites to make the specificity of bre2691A enhanced. RESULTS Bioinformatic analysis revealed that the biocatalytic site of bre2691A, which was an adenylation domain catalyzed and recognized methionine, leucine, valine and isoleucine and thus introduced them into brevilaterins and caused different components (brevilaterin A-E), was consisted of A1 ~ A10 residues named specificity-conferring code. Coupling molecular docking simulations with mutation studies identified A2 and A7 as critical residues, where determined substrate-specificity and impacted activity. The in virto activity assay showed that the A2 mutant (G193A) would lose activity against methionine and have no effect on the other three amino acids, the A7 mutant (G285C) would enhance the catalytic activity against four substrates, especially against leucine at almost a double activity. When the A2 and A7 residues were synchronously mutated, this mutant would be more focused on recognizing leucine. CONCLUSIONS An accurate strategy that combined with bioinformatics and site-directed mutation techniques revealed the pivotal site A2 and A7 positions of bre2691A protein that could be used to design and modify brevilaterins, thus further providing a reasonable direction of genetic engineering for Brevibacillus laterosporus. A deeper understanding of the function of crucial residues in the adenylation domain would make it get more accurate and highly efficient design and more fully utilized. Furthermore, it would contribute to biotechnological applications, namely for the large centralized synthesis of antimicrobial peptides, or for the optimization of their production.
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Affiliation(s)
- Panpan Han
- School of Food and Health, Beijing Technology and Business University, No.33 Fucheng Road, Haidian District, Beijing, 100048, China
| | - Zhou Chen
- School of Food and Health, Beijing Technology and Business University, No.33 Fucheng Road, Haidian District, Beijing, 100048, China
| | - Yangliu Liu
- School of Food and Health, Beijing Technology and Business University, No.33 Fucheng Road, Haidian District, Beijing, 100048, China
| | - Aijin Ma
- School of Food and Health, Beijing Technology and Business University, No.33 Fucheng Road, Haidian District, Beijing, 100048, China
| | - Siting Li
- School of Food and Health, Beijing Technology and Business University, No.33 Fucheng Road, Haidian District, Beijing, 100048, China
| | - Yingmin Jia
- School of Food and Health, Beijing Technology and Business University, No.33 Fucheng Road, Haidian District, Beijing, 100048, China.
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8
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Khan NA, Kaur N, Owens P, Thomas OP, Boyd A. Bis-Indole Alkaloids Isolated from the Sponge Spongosorites calcicola Disrupt Cell Membranes of MRSA. Int J Mol Sci 2022; 23:ijms23041991. [PMID: 35216106 PMCID: PMC8874442 DOI: 10.3390/ijms23041991] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/06/2022] [Accepted: 02/08/2022] [Indexed: 02/01/2023] Open
Abstract
Antimicrobial resistance (AMR) is a global health challenge with methicillin resistant Staphylococcus aureus (MRSA), a leading cause of nosocomial infection. In the search for novel antibiotics, marine sponges have become model organisms as they produce diverse bioactive compounds. We investigated and compared the antibacterial potential of 3 bis-indole alkaloids—bromodeoxytopsentin, bromotopsentin and spongotine A—isolated from the Northeastern Atlantic sponge Spongosorites calcicola. Antimicrobial activity was determined by MIC and time-kill assays. The mechanism of action of bis-indoles was assessed using bacterial cytological profiling via fluorescence microscopy. Finally, we investigated the ability of bis-indole alkaloids to decrease the cytotoxicity of pathogens upon co-incubation with HeLa cells through the measurement of mammalian cell lysis. The bis-indoles were bactericidal to clinically relevant Gram-positive pathogens including MRSA and to the Gram-negative gastroenteric pathogen Vibrio parahaemolyticus. Furthermore, the alkaloids were synergistic in combination with conventional antibiotics. Antimicrobial activity of the bis-indole alkaloids was due to rapid disruption and permeabilization of the bacterial cell membrane. Significantly, the bis-indoles reduced pathogen cytotoxicity toward mammalian cells, indicating their ability to prevent bacterial virulence. In conclusion, sponge bis-indole alkaloids are membrane-permeabilizing agents that represent good antibiotic candidates because of their potency against Gram-positive and Gram-negative bacterial pathogens.
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Affiliation(s)
- Neyaz A. Khan
- Discipline of Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway, H91 TK33 Galway, Ireland;
| | - Navdeep Kaur
- Discipline of Chemistry, School of Biological and Chemical Science and Ryan Institute, National University of Ireland Galway, H91 TK33 Galway, Ireland; (N.K.); (O.P.T.)
| | - Peter Owens
- Centre for Microscopy and Imaging, National University of Ireland, Galway, H91 TK33 Galway, Ireland;
| | - Olivier P. Thomas
- Discipline of Chemistry, School of Biological and Chemical Science and Ryan Institute, National University of Ireland Galway, H91 TK33 Galway, Ireland; (N.K.); (O.P.T.)
| | - Aoife Boyd
- Discipline of Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway, H91 TK33 Galway, Ireland;
- Correspondence: ; Tel.: +353-(0)91-492404
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9
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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: 30] [Impact Index Per Article: 15.0] [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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10
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A Review of Antimicrobial Peptides: Its Function, Mode of Action and Therapeutic Potential. Int J Pept Res Ther 2022. [DOI: 10.1007/s10989-021-10325-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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11
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Qiu M, Kuang F, Chen Y, Shan W, Li Y, Bao X, Gao X, An D. Biomimetic FeCo@PDA nanozyme platform with Fenton catalytic activity as efficient antibacterial agent. J Mater Chem B 2022; 10:5582-5593. [DOI: 10.1039/d2tb00588c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The multidrug resistance of bacteria caused by the abuse of traditional antibiotics poses a great threat to public health security, so it is urgent to develop effective antibacterial agents to...
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12
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The antimicrobial and immunomodulatory effects of Ionophores for the treatment of human infection. J Inorg Biochem 2021; 227:111661. [PMID: 34896767 DOI: 10.1016/j.jinorgbio.2021.111661] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/27/2021] [Accepted: 11/03/2021] [Indexed: 12/18/2022]
Abstract
Ionophores are a diverse class of synthetic and naturally occurring ion transporter compounds which demonstrate both direct and in-direct antimicrobial properties against a broad panel of bacterial, fungal, viral and parasitic pathogens. In addition, ionophores can regulate the host-immune response during communicable and non-communicable disease states. Although the clinical use of ionophores such as Amphotericin B, Bedaquiline and Ivermectin highlight the utility of ionophores in modern medicine, for many other ionophore compounds issues surrounding toxicity, bioavailability or lack of in vivo efficacy studies have hindered clinical development. The antimicrobial and immunomodulating properties of a range of compounds with characteristics of ionophores remain largely unexplored. As such, ionophores remain a latent therapeutic avenue to address both the global burden of antimicrobial resistance, and the unmet clinical need for new antimicrobial therapies. This review will provide an overview of the broad-spectrum antimicrobial and immunomodulatory properties of ionophores, and their potential uses in clinical medicine for combatting infection.
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13
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Weng C, Shen L, Teo JW, Lim ZC, Loh BS, Ang WH. Targeted Antibacterial Strategy Based on Reactive Oxygen Species Generated from Dioxygen Reduction Using an Organoruthenium Complex. JACS AU 2021; 1:1348-1354. [PMID: 34604844 PMCID: PMC8479771 DOI: 10.1021/jacsau.1c00262] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Indexed: 06/13/2023]
Abstract
Pathogenic microorganisms pose a serious threat to global public health due to their persistent adaptation and growing resistance to antibiotics. Alternative therapeutic strategies are required to address this growing threat. Bactericidal antibiotics that are routinely prescribed to treat infections rely on hydroxyl radical formation for their therapeutic efficacies. We developed a redox approach to target bacteria using organotransition metal complexes to mediate the reduction of cellular O2 to H2O2, as a precursor for hydroxyl radicals via Fenton reaction. We prepared a library of 480 unique organoruthenium Schiff-base complexes using a coordination-driven three-component assembly strategy and identified the lead organoruthenium complex Ru1 capable of selectively invoking oxidative stress in Gram-positive bacteria, in particular methicillin-resistant Staphylococcus aureus, via transfer hydrogenation reaction and/or single electron transfer on O2. This strategy paves the way for a targeted antimicrobial approach leveraging on the redox chemistry of organotransition metal complexes to combat drug resistance.
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Affiliation(s)
- Cheng Weng
- Department
of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore 117544, Singapore
| | - Linghui Shen
- Department
of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore 117544, Singapore
| | - Jin Wei Teo
- Department
of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore 117544, Singapore
| | - Zhi Chiaw Lim
- Department
of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore 117544, Singapore
| | - Boon Shing Loh
- Department
of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore 117544, Singapore
| | - Wee Han Ang
- Department
of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore 117544, Singapore
- NUS
Graduate School - Integrative Sciences and Engineering Programme, National University of Singapore, 21 Lower Kent Ridge Road, Singapore 119077, Singapore
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14
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Haoyang WW, Xiao Q, Ye Z, Fu Y, Zhang DW, Li J, Xiao L, Li ZT, Hou JL. Gramicidin A-based unimolecular channel: cancer cell-targeting behavior and ion transport-induced apoptosis. Chem Commun (Camb) 2021; 57:1097-1100. [PMID: 33443269 DOI: 10.1039/d0cc08073j] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of glycoside-peptide conjugates were prepared by engineering at the N-terminus of the natural peptide gramicidin A. The conjugate containing galactose moiety formed a unimolecular transmembrane channel and mediated ion transport to induce apoptosis of cancer cells. More importantly, it exhibited liver cancer cell-targeting behavior due to the galactose-asialoglycoprotein receptor recognition.
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Affiliation(s)
- Wei-Wei Haoyang
- Department of Chemistry, Fudan University, 220 Handan Road, Shanghai 200433, China.
| | - Qi Xiao
- Department of Chemistry, Fudan University, 220 Handan Road, Shanghai 200433, China.
| | - Zhongju Ye
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry Nankai University, China.
| | - Yonghong Fu
- Department of Chemistry, Fudan University, 220 Handan Road, Shanghai 200433, China.
| | - Dan-Wei Zhang
- Department of Chemistry, Fudan University, 220 Handan Road, Shanghai 200433, China.
| | - Jian Li
- Clinical Laboratory Center, Children's Hospital of Fudan University, No. 399 Wanyuan Road, Shanghai 201102, China.
| | - Lehui Xiao
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry Nankai University, China.
| | - Zhan-Ting Li
- Department of Chemistry, Fudan University, 220 Handan Road, Shanghai 200433, China.
| | - Jun-Li Hou
- Department of Chemistry, Fudan University, 220 Handan Road, Shanghai 200433, China.
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15
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Sun D, He S, Bennett WFD, Bilodeau CL, Andersen OS, Lightstone FC, Ingólfsson HI. Atomistic Characterization of Gramicidin Channel Formation. J Chem Theory Comput 2021; 17:7-12. [PMID: 33378617 PMCID: PMC7808174 DOI: 10.1021/acs.jctc.0c00989] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Indexed: 01/09/2023]
Abstract
We investigated gramicidin A (gA) subunit dimerization in lipid bilayers using microsecond-long replica-exchange umbrella sampling simulations, millisecond-long unbiased molecular dynamics simulations, and machine learning. Our simulations led to a dimer structure that is indistinguishable from the experimentally determined gA channel structures, with the two gA subunits joined by six hydrogen bonds (6HB). The simulations also uncovered two additional dimer structures, with different gA-gA stacking orientations that were stabilized by four or two hydrogen bonds (4HB or 2HB). When examining the temporal evolution of the dimerization, we found that two bilayer-inserted gA subunits can form the 6HB dimer directly, with no discernible intermediate states, as well as through paths that involve the 2HB and 4HB dimers.
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Affiliation(s)
- Delin Sun
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore
National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Stewart He
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore
National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - W. F. Drew Bennett
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore
National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Camille L. Bilodeau
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore
National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
- Howard
P. Isermann Department of Chemical and Biological Engineering and
Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Olaf S. Andersen
- Department
of Physiology and Biophysics, Weill Cornell
Medicine, New York, New York 10065, United States
| | - Felice C. Lightstone
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore
National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Helgi I. Ingólfsson
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore
National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
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16
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Abel S, Marchi M. Deciphering the Structure of the Gramicidin A Channel in the Presence of AOT Reverse Micelles in Pentane Using Molecular Dynamics Simulations. J Phys Chem B 2020; 124:11802-11818. [PMID: 33346653 DOI: 10.1021/acs.jpcb.0c08902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structural studies of proteins and, in particular, integral membrane proteins (IMPs) using solution NMR spectroscopy approaches are challenging due to not only their inherent structural complexities but also the fact that they need to be solubilized in biomimetic environments (such as micelles), which enhances the slow molecular reorientation. To deal with these difficulties and increase the effective rate of molecular reorientation, the encapsulation of IMPs in the aqueous core of the reverse micelle (RM) dissolved in a low-viscosity solvent has been proven to be a viable approach. However, the effect of the reverse micelle (RM) environment on the IMP structure and function is little known. To gain insight into these aspects, this article presents a series of atomistic unconstrained molecular dynamics (MD) of a model ion channel (gramicidin A, gA) with RMs formed with anionic surfactant diacyl chain bis(2-ethylhexyl) sodium succinate (AOT) in pentane at a water-to-surfactant molar ratio (W0) of 6. The simulations were carried out with different protocols and starting conditions for a total of 2.4 μs and were compared with other MDs used with the gA channel inserted in models of the SDS micelle or the DMPC membrane. We show here that in the presence of AOT RMs the gA dimer did not look like the "dumbbell-like" model anticipated by experiments, where the C-terminal parts of the gA are capped with two RMs and the rest of the dimer is protected from the oil solvent by the AOT acyl chains. In contrast, the MD simulations reveal that the AOT, Na+, and water formed two well-defined and elongated RMs attached to the C-terminal ends of the gA dimer, while the rest is in direct contact with the pentane. The initial β6.3 secondary structure of the gA is well conserved and filled with 6-9 waters, as in SDS micelles or the DMPC membrane. Finally, the water movement inside the gA is strongly affected by the presence of RMs at each extremity, and no passage of water molecules through the gA channel is observed even after a long simulation period, whereas the opposite was found for gA in SDS and DMPC.
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Affiliation(s)
- Stéphane Abel
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Massimo Marchi
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, 91198 Gif-sur-Yvette, France
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17
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The Effect of Calcium and Halide Ions on the Gramicidin A Molecular State and Antimicrobial Activity. Int J Mol Sci 2020; 21:ijms21176177. [PMID: 32867026 PMCID: PMC7503548 DOI: 10.3390/ijms21176177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/12/2020] [Accepted: 08/24/2020] [Indexed: 11/23/2022] Open
Abstract
Gramicidin A (gA) forms several convertible conformations in different environments. In this study, we investigated the effect of calcium halides on the molecular state and antimicrobial activity of gramicidin A. The molecular state of gramicidin A is highly affected by the concentration of calcium salt and the type of halide anion. Gramicidin A can exist in two states that can be characterized by circular dichroism (CD), mass, nuclear magnetic resonance (NMR) and fluorescence spectroscopy. In State 1, the main molecular state of gramicidin A is as a dimer, and the addition of calcium salt can convert a mixture of four species into a single species, which is possibly a left-handed parallel double helix. In State 2, the addition of calcium halides drives gramicidin A dissociation and denaturation from a structured dimer into a rapid equilibrium of structured/unstructured monomer. We found that the abilities of dissociation and denaturation were highly dependent on the type of halide anion. The dissociation ability of calcium halides may play a vital role in the antimicrobial activity, as the structured monomeric form had the highest antimicrobial activity. Herein, our study demonstrated that the molecular state was correlated with the antimicrobial activity.
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18
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Hammond K, Ryadnov MG, Hoogenboom BW. Atomic force microscopy to elucidate how peptides disrupt membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183447. [PMID: 32835656 DOI: 10.1016/j.bbamem.2020.183447] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/30/2020] [Accepted: 08/13/2020] [Indexed: 12/24/2022]
Abstract
Atomic force microscopy is an increasingly attractive tool to study how peptides disrupt membranes. Often performed on reconstituted lipid bilayers, it provides access to time and length scales that allow dynamic investigations with nanometre resolution. Over the last decade, AFM studies have enabled visualisation of membrane disruption mechanisms by antimicrobial or host defence peptides, including peptides that target malignant cells and biofilms. Moreover, the emergence of high-speed modalities of the technique broadens the scope of investigations to antimicrobial kinetics as well as the imaging of peptide action on live cells in real time. This review describes how methodological advances in AFM facilitate new insights into membrane disruption mechanisms.
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Affiliation(s)
- Katharine Hammond
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, UK; London Centre for Nanotechnology, University College London, London WC1H 0AH, UK; Department of Physics & Astronomy, University College London, London WC1E 6BT, UK.
| | - Maxim G Ryadnov
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, UK; Department of Physics, King's College London, Strand Lane, London WC2R 2LS, UK.
| | - Bart W Hoogenboom
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK; Department of Physics & Astronomy, University College London, London WC1E 6BT, UK.
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19
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Magana M, Pushpanathan M, Santos AL, Leanse L, Fernandez M, Ioannidis A, Giulianotti MA, Apidianakis Y, Bradfute S, Ferguson AL, Cherkasov A, Seleem MN, Pinilla C, de la Fuente-Nunez C, Lazaridis T, Dai T, Houghten RA, Hancock REW, Tegos GP. The value of antimicrobial peptides in the age of resistance. THE LANCET. INFECTIOUS DISEASES 2020; 20:e216-e230. [PMID: 32653070 DOI: 10.1016/s1473-3099(20)30327-3] [Citation(s) in RCA: 514] [Impact Index Per Article: 128.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 03/29/2020] [Accepted: 04/16/2020] [Indexed: 12/20/2022]
Abstract
Accelerating growth and global expansion of antimicrobial resistance has deepened the need for discovery of novel antimicrobial agents. Antimicrobial peptides have clear advantages over conventional antibiotics which include slower emergence of resistance, broad-spectrum antibiofilm activity, and the ability to favourably modulate the host immune response. Broad bacterial susceptibility to antimicrobial peptides offers an additional tool to expand knowledge about the evolution of antimicrobial resistance. Structural and functional limitations, combined with a stricter regulatory environment, have hampered the clinical translation of antimicrobial peptides as potential therapeutic agents. Existing computational and experimental tools attempt to ease the preclinical and clinical development of antimicrobial peptides as novel therapeutics. This Review identifies the benefits, challenges, and opportunities of using antimicrobial peptides against multidrug-resistant pathogens, highlights advances in the deployment of novel promising antimicrobial peptides, and underlines the needs and priorities in designing focused development strategies taking into account the most advanced tools available.
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Affiliation(s)
- Maria Magana
- Department of Biopathology and Clinical Microbiology, Aeginition Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Ana L Santos
- Department of Chemistry, Rice University, Houston, TX, USA; Investigación Sanitaria de las Islas Baleares, Palma, Spain
| | - Leon Leanse
- Department of Dermatology, Harvard Medical School, Boston, MA, USA; Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, USA
| | - Michael Fernandez
- Department of Urologic Sciences, Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | | | | | | | - Steven Bradfute
- Department of Internal Medicine, Center for Global Health, University of New Mexico, Albuquerque, NM, USA
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Artem Cherkasov
- Department of Urologic Sciences, Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Mohamed N Seleem
- Department of Comparative Pathobiology, Purdue University College of Veterinary Medicine, West Lafayette, IN, USA
| | - Clemencia Pinilla
- Torrey Pines Institute for Molecular Studies, Port St Lucie, FL, USA
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, Penn Institute for Computational Science, and Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Themis Lazaridis
- Department of Chemistry, The City College of New York, New York, NY, USA; Graduate Programs in Chemistry, Biochemistry, and Physics, The Graduate Center, City University of New York, NY, USA
| | - Tianhong Dai
- Department of Dermatology, Harvard Medical School, Boston, MA, USA; Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Robert E W Hancock
- Department of Microbiology and Immunology, Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - George P Tegos
- Reading Hospital, Tower Health, West Reading, PA, USA; Micromoria, Venture X Marlborough, Marlborough, MA, USA.
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20
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Ren X, Zou L, Holmgren A. Targeting Bacterial Antioxidant Systems for Antibiotics Development. Curr Med Chem 2020; 27:1922-1939. [PMID: 31589114 DOI: 10.2174/0929867326666191007163654] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 09/18/2018] [Accepted: 12/13/2018] [Indexed: 12/15/2022]
Abstract
The emergence of multidrug-resistant bacteria has become an urgent issue in modern medicine which requires novel strategies to develop antibiotics. Recent studies have supported the hypothesis that antibiotic-induced bacterial cell death is mediated by Reactive Oxygen Species (ROS). The hypothesis also highlighted the importance of antioxidant systems, the defense mechanism which contributes to antibiotic resistance. Thioredoxin and glutathione systems are the two major thiol-dependent systems which not only provide antioxidant capacity but also participate in various biological events in bacteria, such as DNA synthesis and protein folding. The biological importance makes them promising targets for novel antibiotics development. Based on the idea, ebselen and auranofin, two bacterial thioredoxin reductase inhibitors, have been found to inhibit the growth of bacteria lacking the GSH efficiently. A recent study combining ebselen and silver exhibited a strong synergistic effect against Multidrug-Resistant (MDR) Gram-negative bacteria which possess both thioredoxin and glutathione systems. These drug-repurposing studies are promising for quick clinical usage due to their well-known profile.
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Affiliation(s)
- Xiaoyuan Ren
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Lili Zou
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden.,Translational Neuroscience & Neural Regeneration and Repair Institute/ Institute of Cell Therapy, The First Hospital of Yichang, Three Gorges University, 443000 Yichang, China
| | - Arne Holmgren
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
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21
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Yang Y, Wu D, Wang C, Shan A, Bi C, Li Y, Gan W. Hybridization with Insect Cecropin A (1-8) Improve the Stability and Selectivity of Naturally Occurring Peptides. Int J Mol Sci 2020; 21:ijms21041470. [PMID: 32098142 PMCID: PMC7073140 DOI: 10.3390/ijms21041470] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 02/19/2020] [Accepted: 02/19/2020] [Indexed: 12/15/2022] Open
Abstract
Antimicrobial peptides (AMPs) offer great hope and a promising opportunity to overcome the rapid development of drug-resistant pathogenic microbes. However, AMPs often lack the stability required for a successful systemic drug. Hybridizing different AMPs is a simple and effective strategy to obtain novel peptides. N-terminal fragment of cecropin A (CA (1-8)) is often used to hybridize with other AMPs to reduce cytotoxicity. However, hybridizing with CA (1-8) in improving the stability of AMPs is not clear. Therefore, a series of peptides were designed by combining with CA (1–8) and their antibacterial activity and stability in the presence of salts and human serum were evaluated. The resultant α-helical hybrid peptide CA-FO composed of CA (1-8) and the most potent region of Fowlicidin-2 (FO (1–15)) exhibited excellent antibacterial activity (2-8 μM) and cell selectivity toward bacterial over mammalian cells. Moreover, CA-FO still retained vigorous antimicrobial activity in the presence of human serum and salts at physiological concentrations. CA-FO exhibited effective antibacterial activity by increasing membrane permeability and damaging membrane integrity. In conclusion, these results indicated the success of hybridization in designing and optimizing AMPs with improved stability and selectivity and the peptide CA-FO can be further evaluated as peptide-therapy to treat bacterial infections.
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Affiliation(s)
- Yang Yang
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China; (Y.Y.); (D.W.); (C.W.); (C.B.)
| | - Di Wu
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China; (Y.Y.); (D.W.); (C.W.); (C.B.)
| | - Chenxi Wang
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China; (Y.Y.); (D.W.); (C.W.); (C.B.)
| | - Anshan Shan
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China; (Y.Y.); (D.W.); (C.W.); (C.B.)
- Correspondence: ; Tel.: +86-451-5519-0685
| | - Chongpeng Bi
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China; (Y.Y.); (D.W.); (C.W.); (C.B.)
| | - Yanbing Li
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China;
| | - Wenping Gan
- Institute of Animal Husbandry and Veterinary Medicine, Heilongjiang Academy of Land Reclamation Sciences, Harbin 150038, China;
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22
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Antimicrobial activity of resveratrol-derived monomers and dimers against foodborne pathogens. Sci Rep 2019; 9:19525. [PMID: 31862939 PMCID: PMC6925292 DOI: 10.1038/s41598-019-55975-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 12/04/2019] [Indexed: 01/10/2023] Open
Abstract
Plant polyphenolic compounds are considered a promising source for new antibacterial agents. In this study, we evaluated the antimicrobial activity of a collection of resveratrol-derived monomers and dimers screened as single molecules against a panel of nine foodborne pathogens. The results demonstrated that two monomers (i.e., pterostilbene 2 and (E)-3-hydroxy-4′,5-dimethoxystilbene 9) and three dimers (i.e., δ-viniferin 10, viniferifuran 14 and dehydro-δ-viniferin 15) were endowed with significant antibacterial activity against gram-positive bacteria. The exposure of gram-positive foodborne pathogens to 100 µg/mL of 2, 9 and 15 induced severe cell membrane damage, resulting in the disruption of the phospholipid bilayer. The most promising dimeric compound, dehydro-δ-viniferin 15, was tested against Listeria monocytogenes, resulting in a loss of cultivability, viability and cell membrane potential. TEM analysis revealed grave morphological modifications on the cell membrane and leakage of intracellular content, confirming that the cell membrane was the principal biological target of the tested derivative.
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23
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Kumar N, Sood D, Tomar R, Chandra R. Antimicrobial Peptide Designing and Optimization Employing Large-Scale Flexibility Analysis of Protein-Peptide Fragments. ACS OMEGA 2019; 4:21370-21380. [PMID: 31867532 PMCID: PMC6921640 DOI: 10.1021/acsomega.9b03035] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 11/15/2019] [Indexed: 05/24/2023]
Abstract
The mankind relies on the use of antibiotics for a healthy life. The epidemic-like emergence of drug-resistant bacterial strains is increasingly becoming one of the leading causes of morbidity and mortality, which gives rise to design a potential antimicrobial peptide (AMP). Here, we have designed the potential AMP using the extensive dynamics simulation since protein-peptide interactions are linked to large conformational changes. Therefore, we have employed the advanced computational avenue CABS molecular docking method that enabled the flexible peptide-protein molecular docking with a large-scale rearrangement of the protein. Lead AMP was investigated against the wild-type (WT) and mutant-PBP5 (MT-PBP5) proteins (antiresistance property). AMP20 showed strong interactions with wtPBP5 and mtPBP5 and involvement of a large number of elements in interactions determined through an atomic model study. Full flexibility analysis showed the stable interaction of AMP20 with both the wild-type and mutant form of PBP5 with root-mean-square deviation (RMSD) values of ∼4.51 and 4.85 Å, respectively. Moreover, peptide dynamics showed involvement of all residues of AMP20 through contact map analysis, and extensive simulation confirmed the stable interaction of AMP20, with lower values of RMSD, radius of gyration, and root-mean-square fluctuation. This study paves the way for a potential approach to design the AMP with amino acid walking and large-scale conformational rearrangements of amino acids.
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24
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Aguayo S, Schuh CMAP, Vicente B, Aguayo LG. Association between Alzheimer's Disease and Oral and Gut Microbiota: Are Pore Forming Proteins the Missing Link? J Alzheimers Dis 2019; 65:29-46. [PMID: 30040725 DOI: 10.3233/jad-180319] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Alzheimer's disease (AD) is a neurodegenerative condition affecting millions of people worldwide. It is associated with cerebral amyloid-β (Aβ) plaque deposition in the brain, synaptic disconnection, and subsequent progressive neuronal death. Although considerable progress has been made to elucidate the pathogenesis of AD, the specific causes of the disease remain highly unknown. Recent research has suggested a potential association between certain infectious diseases and dementia, either directly due to bacterial brain invasion and toxin production, or indirectly by modulating the immune response. Therefore, in the present review we focus on the emerging issues of bacterial infection and AD, including the existence of antimicrobial peptides having pore-forming properties that act in a similar way to pores formed by Aβ in a variety of cell membranes. Special focus is placed on oral bacteria and biofilms, and on the potential mechanisms associating bacterial infection and toxin production in AD. The role of bacterial outer membrane vesicles on the transport and delivery of toxins as well as porins to the brain is also discussed. Aβ has shown to possess antimicrobial activity against several bacteria, and therefore could be upregulated as a response to bacteria and bacterial toxins in the brain. Although further research is needed, we believe that the control of biofilm-mediated diseases could be an important potential prevention mechanism for AD development.
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25
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Nair RR, Sharan D, Sebastian J, Swaminath S, Ajitkumar P. Heterogeneity of ROS levels in antibiotic-exposed mycobacterial subpopulations confers differential susceptibility. MICROBIOLOGY-SGM 2019; 165:668-682. [PMID: 31091187 DOI: 10.1099/mic.0.000797] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Phenotypically heterogeneous but genetically identical mycobacterial subpopulations exist in in vitro cultures, in vitro-infected macrophages, infected animal models and tuberculosis patients. In this regard, we recently reported the presence of two subpopulations of cells, which are phenotypically different in length and buoyant density, in mycobacterial cultures. These are the low-buoyant-density short-sized cells (SCs), which constitute ~10-20 % of the population, and the high-buoyant-density normal/long-sized cells (NCs), which form ~80-90 % of the population. The SCs were found to be significantly more susceptible to rifampicin (RIF), isoniazid (INH), H2O2 and acidified nitrite than the NCs. Here we report that the RIF-/INH-/H2O2-exposed SCs showed significantly higher levels of oxidative stress and therefore higher susceptibility than the equivalent number of exposed NCs. Significantly higher levels of hydroxyl radical and superoxide were found in the antibiotic-exposed SCs than in the equivalently exposed NCs. Different proportions of the subpopulation of SCs were found to have different levels of reactive oxygen species (ROS). The hydroxyl radical quencher, thiourea, and the superoxide dismutase mimic, TEMPOL, significantly reduced hydroxyl radical and superoxide levels, respectively, in the antibiotic-exposed SCs and NCs and thereby decreased their differential susceptibility to antibiotics. Thus, the present study shows that the heterogeneity of the reactive oxygen species (ROS) levels in these mycobacterial subpopulations confers differential susceptibility to antibiotics. We have discussed the possible mechanisms that can generate differential ROS levels in the antibiotic-exposed SCs and NCs. The present study advances our current understanding of the molecular mechanisms underlying antibiotic tolerance in mycobacteria.
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Affiliation(s)
- Rashmi Ravindran Nair
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore - 560012, Karnataka, India
| | - Deepti Sharan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore - 560012, Karnataka, India
| | - Jees Sebastian
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore - 560012, Karnataka, India
| | - Sharmada Swaminath
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore - 560012, Karnataka, India
| | - Parthasarathi Ajitkumar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore - 560012, Karnataka, India
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26
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Sugár IP, Bonanno AP, Chong PLG. Gramicidin Lateral Distribution in Phospholipid Membranes: Fluorescence Phasor Plots and Statistical Mechanical Model. Int J Mol Sci 2018; 19:E3690. [PMID: 30469389 PMCID: PMC6274966 DOI: 10.3390/ijms19113690] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 11/14/2018] [Accepted: 11/15/2018] [Indexed: 11/16/2022] Open
Abstract
When using small mole fraction increments to study gramicidins in phospholipid membranes, we found that the phasor dots of intrinsic fluorescence of gramicidin D and gramicidin A in dimyristoyl-sn-glycero-3-phosphocholine (DMPC) unilamellar and multilamellar vesicles exhibit a biphasic change with peptide content at 0.143 gramicidin mole fraction. To understand this phenomenon, we developed a statistical mechanical model of gramicidin/DMPC mixtures. Our model assumes a sludge-like mixture of fluid phase and aggregates of rigid clusters. In the fluid phase, gramicidin monomers are randomly distributed. A rigid cluster is formed by a gramicidin dimer and DMPC molecules that are condensed to the dimer, following particular stoichiometries (critical gramicidin mole fractions, Xcr including 0.143). Rigid clusters form aggregates in which gramicidin dimers are regularly distributed, in some cases, even to superlattices. At Xcr, the size of cluster aggregates and regular distributions reach a local maximum. Before a similar model was developed for cholesterol/DMPC mixtures (Sugar and Chong (2012) J. Am. Chem. Soc. 134, 1164⁻1171) and here the similarities and differences are discussed between these two models.
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Affiliation(s)
- István P Sugár
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Alexander P Bonanno
- Department of Medical Genetics and Molecular Biochemistry, The Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA.
| | - Parkson Lee-Gau Chong
- Department of Medical Genetics and Molecular Biochemistry, The Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA.
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27
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Ganesan P, Ramalingam R. Investigation of structural stability and functionality of homodimeric gramicidin towards peptide‐based drug: a molecular simulation approach. J Cell Biochem 2018; 120:4903-4911. [DOI: 10.1002/jcb.27765] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 09/06/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Pavithrra Ganesan
- Bioinformatics Lab, Department of Biotechnology, School of Biosciences and Technology Vellore Institute of Technology (VIT) Vellore India
| | - Rajasekaran Ramalingam
- Bioinformatics Lab, Department of Biotechnology, School of Biosciences and Technology Vellore Institute of Technology (VIT) Vellore India
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28
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Yang CH, Chen YC, Peng SY, Tsai APY, Lee TJF, Yen JH, Liou JW. An engineered arginine-rich α-helical antimicrobial peptide exhibits broad-spectrum bactericidal activity against pathogenic bacteria and reduces bacterial infections in mice. Sci Rep 2018; 8:14602. [PMID: 30279591 PMCID: PMC6168480 DOI: 10.1038/s41598-018-32981-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 09/20/2018] [Indexed: 12/05/2022] Open
Abstract
The increase in the prevalence of antibiotic-resistant bacteria has become a major public health concern. Antimicrobial peptides (AMPs) are emerging as promising candidates addressing this issue. In this study, we designed several AMPs by increasing α-helical contents and positive charges and optimizing hydrophobicity and amphipathicity in the Sushi 1 peptide from horseshoe crabs. A neural network–based bioinformatic prediction tool was used for the first stage evaluations of peptide properties. Among the peptides designed, Sushi-replacement peptide (SRP)-2, an arginine-rich and highly α-helical peptide, showed broad-spectrum bactericidal activity against both Gram-positive and Gram-negative bacteria, including methicillin-resistant Staphylococcus aureus and multidrug-resistant Acinetobacter baumannii; nevertheless, it showed little hemolytic and cytotoxic activity against mammalian cells. Atomic force microscopy results indicated that SRP-2 should interact directly with cell membrane components, resulting in bacterial cell death. SRP-2 also neutralized LPS-induced macrophage activation. Moreover, in an intraperitoneal multidrug-resistant A. baumannii infection mouse model, SRP-2 successfully reduced the bacterial number in ascitic fluid and tumor necrosis factor-α production. Our study findings demonstrate that bioinformatic calculations can be powerful tools to help design potent AMPs and that arginine is superior to lysine for providing positive charges for AMPs to exhibit better bactericidal activity and selectivity against bacterial cells.
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Affiliation(s)
- Chin-Hao Yang
- Institute of Medical Sciences, Tzu Chi University, Hualien, Taiwan
| | - Yi-Cheng Chen
- Department of Medicine, Mackay Medical College, New Taipei, Taiwan
| | - Shih-Yi Peng
- Department of Biochemistry, School of Medicine, Tzu Chi University, Hualien, Taiwan
| | - Andy Po-Yi Tsai
- Ph.D. Program in Translational Medicine, Tzu Chi University/Academia Sinica, Taipei, Taiwan
| | - Tony Jer-Fu Lee
- Department of Medical Research, Buddhist Tzu Chi General Hospital, Hualien, Taiwan.,Department of Pharmacology, Southern Illinois University School of Medicine, Springfield, IL, USA
| | - Jui-Hung Yen
- Department of Molecular Biology and Human Genetics, Tzu Chi University, Hualien, Taiwan
| | - Je-Wen Liou
- Institute of Medical Sciences, Tzu Chi University, Hualien, Taiwan. .,Department of Biochemistry, School of Medicine, Tzu Chi University, Hualien, Taiwan.
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29
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Identification of Effective Dimeric Gramicidin-D Peptide as Antimicrobial Therapeutics over Drug Resistance: In-Silico Approach. Interdiscip Sci 2018; 11:575-583. [PMID: 30182355 DOI: 10.1007/s12539-018-0304-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 07/25/2018] [Accepted: 08/28/2018] [Indexed: 10/28/2022]
Abstract
Discovering and developing the antimicrobial peptides are recently focused on pharmaceutical firm, since they serve as complementary to antibiotics in prevailing over drug resistance by eliciting the disruption of microbial membrane. Still, there are lots of challenges to bring up the structurally stable and functionally efficient antimicrobial peptides. It is well known that gramicidin D is the prominent antimicrobial peptide that exists as g-AB, g-BC, and g-AC. This study analyzes the structural stability and the functional activity of hetero-dimeric double-stranded gramicidin-D peptides, thereby demonstrating its potent antimicrobial activity against antibiotic-resistant micro-organisms. To investigate the structural stability and functionality of gramicidin D, we performed static and dynamic analysis. Initially, we observed a maximum number of intermolecular interactions and membrane penetration in g-AB as compared to g-BC and g-AC. To substantiate further, the geometrical and thermodynamic parameters revealed the retention of maximum stability in g-AB than g-AC and g-BC. Thus, the conformational free energy and the binding free energy showed the variation among gramicidin-D peptides for the prediction of increased stability and functionality. In conclusion, g-AB peptide has definitely demonstrated adequate structural stability and functionality and this work will need to be considered in peptide-based drug discovery.
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Pitsalidis C, Pappa AM, Porel M, Artim CM, Faria GC, Duong DD, Alabi CA, Daniel S, Salleo A, Owens RM. Biomimetic Electronic Devices for Measuring Bacterial Membrane Disruption. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1803130. [PMID: 30117203 DOI: 10.1002/adma.201803130] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 06/28/2018] [Indexed: 06/08/2023]
Abstract
Antibiotic discovery has experienced a severe slowdown in terms of discovery of new candidates. In vitro screening methods using phospholipids to model the bacterial membrane provide a route to identify molecules that specifically disrupt bacterial membranes causing cell death. Thanks to the electrically insulating properties of the major component of the cell membrane, phospholipids, electronic devices are highly suitable transducers of membrane disruption. The organic electrochemical transistor (OECT) is a highly sensitive ion-to-electron converter. Here, the OECT is used as a transducer of the permeability of a lipid monolayer (ML) at a liquid:liquid interface, designed to read out changes in ion flux caused by compounds that interact with, and disrupt, lipid assembly. This concept is illustrated using the well-documented antibiotic Polymixin B and the highly sensitive quantitation of permeability of the lipid ML induced by two novel recently described antibacterial amine-based oligothioetheramides is shown, highlighting molecular scale differences in their disruption capabilities. It is anticipated that this platform has the potential to play a role in front-line antimicrobial compound design and characterization thanks to the compatibility of semiconductor microfabrication technology with high-throughput readouts.
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Affiliation(s)
- Charalampos Pitsalidis
- Department of Chemical Engineering and Biotechnology, Philippa Fawcett Drive, CB30AS, Cambridge, UK
| | - Anna-Maria Pappa
- Department of Chemical Engineering and Biotechnology, Philippa Fawcett Drive, CB30AS, Cambridge, UK
| | - Mintu Porel
- Department of Chemical and Biomolecular Engineering, Olin hall, Ithaca, NY, 14850, USA
| | - Christine M Artim
- Department of Chemical and Biomolecular Engineering, Olin hall, Ithaca, NY, 14850, USA
| | - Gregorio C Faria
- Department of Materials Science and Engineering, Stanford University, 496 Lomita Mall, Stanford, CA, 94305, USA
| | - Duc D Duong
- Department of Materials Science and Engineering, Stanford University, 496 Lomita Mall, Stanford, CA, 94305, USA
| | - Christopher A Alabi
- Department of Chemical and Biomolecular Engineering, Olin hall, Ithaca, NY, 14850, USA
| | - Susan Daniel
- Department of Chemical and Biomolecular Engineering, Olin hall, Ithaca, NY, 14850, USA
| | - Alberto Salleo
- Department of Materials Science and Engineering, Stanford University, 496 Lomita Mall, Stanford, CA, 94305, USA
| | - Róisín M Owens
- Department of Chemical Engineering and Biotechnology, Philippa Fawcett Drive, CB30AS, Cambridge, UK
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31
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Karash S, Kwon YM. Iron-dependent essential genes in Salmonella Typhimurium. BMC Genomics 2018; 19:610. [PMID: 30107784 PMCID: PMC6092869 DOI: 10.1186/s12864-018-4986-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 07/31/2018] [Indexed: 12/17/2022] Open
Abstract
Background The molecular mechanisms underlying bacterial cell death due to stresses or bactericidal antibiotics are complex and remain puzzling. Due to the current crisis of antibiotic resistance, development of effective antibiotics is urgently required. Previously, it has been shown that iron is required for effective killing of bacterial cells by numerous bactericidal antibiotics. Results We investigated the death or growth inhibition of S. Typhimurium under iron-restricted conditions, following disruption of essential genes, by transposon mutagenesis using transposon sequencing (Tn-seq). Our high-resolution Tn-seq analysis revealed that transposon mutants of S. Typhimurium with insertions in essential genes escaped immediate killing or growth inhibition under iron-restricted conditions for approximately one-third of all previously known essential genes. Based on this result, we classified all essential genes into two categories, iron-dependent essential genes, for which the insertion mutants can grow slowly if iron is restricted, and iron-independent essential genes, for which the mutants become nonviable regardless of iron concentration. The iron-dependency of the iron-dependent essential genes was further validated by the fact that the relative abundance of these essential gene mutants increased further with more severe iron restrictions. Our unexpected observation can be explained well by the common killing mechanisms of bactericidal antibiotics via production of reactive oxygen species (ROS). In this model, iron restriction would inhibit production of ROS, leading to reduced killing activity following blocking of essential gene functions. Interestingly, the targets of most antibiotics currently in use clinically are iron-dependent essential genes. Conclusions Our result suggests that targeting iron-independent essential genes may be a better strategy for future antibiotic development, because blocking their essential gene functions would lead to immediate cell death regardless of the iron concentration. This work expands our knowledge on the role of iron to a broad range of essential functions and pathways, providing novel insights for development of more effective antibiotics. Electronic supplementary material The online version of this article (10.1186/s12864-018-4986-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sardar Karash
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, USA.,Department of Biology, College of Education, Salahaddin University, Erbil, Kurdistan, Iraq
| | - Young Min Kwon
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, USA. .,Department of Poultry Science, University of Arkansas, Fayetteville, AR, 72701, USA.
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Reddy DN, Singh S, Ho CMW, Patel J, Schlesinger P, Rodgers S, Doctor A, Marshall GR. Design, synthesis, and biological evaluation of stable β 6.3-Helices: Discovery of non-hemolytic antibacterial peptides. Eur J Med Chem 2018; 149:193-210. [PMID: 29501941 DOI: 10.1016/j.ejmech.2018.02.057] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 01/26/2018] [Accepted: 02/16/2018] [Indexed: 11/25/2022]
Abstract
Gramicidin A, a topical antibiotic made from alternating L and D amino acids, is characterized by its wide central pore; upon insertion into membranes, it forms channels that disrupts ion gradients. We present helical peptidomimetics with this characteristic wide central pore that have been designed to mimic gramicidin A channels. Mimetics were designed using molecular modeling focused on oligomers of heterochiral dipeptides of proline analogs, in particular azaproline (AzPro). Molecular Dynamics simulations in water confirmed the stability of the designed helices. A sixteen-residue Formyl-(AzPro-Pro)8-NHCH2CH2OH helix was synthesized as well as a full thirty-two residue Cbz-(AzPro-Pro)16-OtBu channels. No liposomal lysis activity was observed suggesting lack of channel formation, possibly due to inappropriate hydrogen-bonding interactions in the membrane. These peptidomimetics also did not hemolyze red blood cells, unlike gramicidin A.
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Affiliation(s)
- Damodara N Reddy
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Sukrit Singh
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chris M W Ho
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Janki Patel
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Paul Schlesinger
- Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Stephen Rodgers
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Allan Doctor
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Garland R Marshall
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.
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Zhou M, Liu F, Yang X, Jin J, Dong X, Zeng KW, Liu D, Zhang Y, Ma M, Yang D. Bacillibactin and Bacillomycin Analogues with Cytotoxicities against Human Cancer Cell Lines from Marine Bacillus sp. PKU-MA00093 and PKU-MA00092. Mar Drugs 2018; 16:E22. [PMID: 29320403 PMCID: PMC5793070 DOI: 10.3390/md16010022] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 12/21/2017] [Accepted: 01/05/2018] [Indexed: 12/12/2022] Open
Abstract
Nonribosomal peptides from marine Bacillus strains have received considerable attention for their complex structures and potent bioactivities. In this study, we carried out PCR-based genome mining for potential nonribosomal peptides producers from our marine bacterial library. Twenty-one "positive" strains were screened out from 180 marine bacterial strains, and subsequent small-scale fermentation, HPLC and phylogenetic analysis afforded Bacillus sp. PKU-MA00092 and PKU-MA00093 as two candidates for large-scale fermentation and isolation. Ten nonribosomal peptides, including four bacillibactin analogues (1-4) and six bacillomycin D analogues (5-10) were discovered from Bacillus sp. PKU-MA00093 and PKU-MA00092, respectively. Compounds 1 and 2 are two new compounds and the ¹H NMR and 13C NMR data of compounds 7 and 9 is first provided. All compounds 1-10 were assayed for their cytotoxicities against human cancer cell lines HepG2 and MCF7, and the bacillomycin D analogues 7-10 showed moderate cytotoxicities with IC50 values from 2.9 ± 0.1 to 8.2 ± 0.2 µM. The discovery of 5-10 with different fatty acid moieties gave us the opportunity to reveal the structure-activity relationships of bacillomycin analogues against these human cancer cell lines. These results enrich the structural diversity and bioactivity properties of nonribosomal peptides from marine Bacillus strains.
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Affiliation(s)
- Mengjie Zhou
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China.
| | - Fawang Liu
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China.
| | - Xiaoyan Yang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China.
| | - Jing Jin
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China.
| | - Xin Dong
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China.
| | - Ke-Wu Zeng
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China.
| | - Dong Liu
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China.
| | - Yingtao Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China.
| | - Ming Ma
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China.
| | - Donghui Yang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China.
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34
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Antimicrobial Electrospun Fibers of Polyester Loaded with Engineered Cyclic Gramicidin Analogues. FIBERS 2017. [DOI: 10.3390/fib5030034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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35
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Nagra S, Kumar D, Bhattacharyya R, Banerjee D, Mukherjee T. Designing of a penta-peptide against drug resistant E. coli. Bioinformation 2017; 13:192-195. [PMID: 28729761 PMCID: PMC5512857 DOI: 10.6026/97320630013192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 05/05/2017] [Accepted: 06/05/2017] [Indexed: 01/21/2023] Open
Abstract
Drug resistant pathogens are vibrant global problem. Penicillin binding protein 5 (PBP5) plays important role in bacterial cell wall biosynthesis. Mutation in PBP5 is a well-known mechanism for development of drug resistant strain of bacteria. In this context we have designed a peptide that fits better at the ligand-binding site of mutant PBP5 compared to wild type PBP5. It is expected that the designed peptide will halt the growth of drug resistant pathogen harboring mutant variety of PBP5. We have recommended experimental validation of the above concept.
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Affiliation(s)
- Sachin Nagra
- Department of Biotechnology, Maharishi Markandeshwar University, Mullana, Ambala, haryana 133207
| | - Deepak Kumar
- Department of Experimental Medicine and Biotechnology, Postgraduate Institute of Medical Education and Research, Chandigarh 160012
| | - Rajasri Bhattacharyya
- past: Department of Biotechnology, Maharishi Markandeshwar University, Mullana, Ambala, haryana 133207; present: Department of Experimental Medicine and Biotechnology, Postgraduate Institute of Medical Education and Research, Chandigarh 160012
| | - Dibyajyoti Banerjee
- Department of Experimental Medicine and Biotechnology, Postgraduate Institute of Medical Education and Research, Chandigarh 160012
| | - Tapan Mukherjee
- Department of Biotechnology, Maharishi Markandeshwar University, Mullana, Ambala, haryana 133207
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36
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Van Acker H, Coenye T. The Role of Reactive Oxygen Species in Antibiotic-Mediated Killing of Bacteria. Trends Microbiol 2017; 25:456-466. [PMID: 28089288 DOI: 10.1016/j.tim.2016.12.008] [Citation(s) in RCA: 339] [Impact Index Per Article: 48.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/09/2016] [Accepted: 12/15/2016] [Indexed: 11/26/2022]
Abstract
Recently, it was proposed that there is a common mechanism behind the activity of bactericidal antibiotics, involving the production of reactive oxygen species (ROS). However, the involvement of ROS in antibiotic-mediated killing has become the subject of much debate. In the present review, we provide an overview of the data supporting the ROS hypothesis; we also present data that explain the contradictory results often obtained when studying antibiotic-induced ROS production. For this latter aspect we will focus on the importance of taking the experimental setup into consideration and on the importance of some technical aspects of the assays typically used. Finally, we discuss the link between ROS production and toxin-antitoxin modules, and present an overview of implications for treatment.
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Affiliation(s)
- Heleen Van Acker
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium.
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37
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Jadhav KB, Stein C, Makarewicz O, Pradel G, Lichtenecker RJ, Sack H, Heinemann SH, Arndt HD. Bioactivity of topologically confined gramicidin A dimers. Bioorg Med Chem 2016; 25:261-268. [PMID: 27865644 DOI: 10.1016/j.bmc.2016.10.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 10/21/2016] [Accepted: 10/27/2016] [Indexed: 10/20/2022]
Abstract
The d-/l-peptide gramicidin A (gA) is well known as a pivotal ion channel model and shows a broad spectrum of bioactivities such as antibiosis, antimalarial activity, as well as hemolysis. We applied inter-chain disulfide bonds to constrain the conformational freedom of gA into parallel and antiparallel dimeric topologies. Albeit the constructs were not found to be monoconformational, CD- and IR-spectroscopic studies suggested that this strategy indeed restricted the conformational space of the d-/l-peptide construct, and that β-helical secondary structures prevail. Correlative testing of gA dimers in antimicrobial, antimalarial, and ion conduction assays suggested that the tail-to-tail antiparallel single stranded β6.3 helix dominantly mediates the bioactivity of gA. Other conformers are unlikely to contribute to these activities. From these investigations, only weakly ion conducting gA dimers were identified that retained nM antimalarial activity.
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Affiliation(s)
- Kirtikumar B Jadhav
- Friedrich Schiller University Jena, Institute of Organic Chemistry and Macromolecular Chemistry, Humboldtstr. 10, D-07743 Jena, Germany
| | - Claudia Stein
- Center for Infectious Diseases and Infection Control, Jena University Hospital, Erlanger Allee 101, D-07747 Jena, Germany
| | - Oliwia Makarewicz
- Center for Infectious Diseases and Infection Control, Jena University Hospital, Erlanger Allee 101, D-07747 Jena, Germany
| | - Gabriele Pradel
- RWTH Aachen University, Division of Cellular and Applied Infection Biology, Worringerweg 1, D-52074 Aachen, Germany
| | - Roman J Lichtenecker
- Friedrich Schiller University Jena, Institute of Organic Chemistry and Macromolecular Chemistry, Humboldtstr. 10, D-07743 Jena, Germany
| | - Holger Sack
- Center for Molecular Biomedicine, Department of Biophysics, Friedrich Schiller University Jena and Jena University Hospital, Hans-Knöll-Str. 2, D-07745 Jena, Germany
| | - Stefan H Heinemann
- Center for Molecular Biomedicine, Department of Biophysics, Friedrich Schiller University Jena and Jena University Hospital, Hans-Knöll-Str. 2, D-07745 Jena, Germany
| | - Hans-Dieter Arndt
- Friedrich Schiller University Jena, Institute of Organic Chemistry and Macromolecular Chemistry, Humboldtstr. 10, D-07743 Jena, Germany.
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38
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Tangerina MMP, Correa H, Haltli B, Vilegas W, Kerr RG. Bioprospecting from cultivable bacterial communities of marine sediment and invertebrates from the underexplored Ubatuba region of Brazil. Arch Microbiol 2016; 199:155-169. [PMID: 27644133 DOI: 10.1007/s00203-016-1290-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 07/28/2016] [Accepted: 09/09/2016] [Indexed: 11/26/2022]
Abstract
Shrimp fisheries along the Brazilian coast have significant environmental impact due to high by-catch rates (21 kg per kilogram of shrimp). Typically discarded, by-catch contains many invertebrates that may host a great variety of bacterial genera, some of which may produce bioactive natural products with biotechnological applications. Therefore, to utilize by-catch that is usually discarded we explored the biotechnological potential of culturable bacteria of two abundant by-catch invertebrate species, the snail Olivancillaria urceus and the sea star Luidia senegalensis. Sediment from the collection area was also investigated. Utilizing multiple isolation approaches, 134 isolates were obtained from the invertebrates and sediment. Small-subunit rRNA (16S) gene sequencing revealed that the isolates belonged to Proteobacteria, Firmicutes and Actinobacteria phyla and were distributed among 28 genera. Several genera known for their capacity to produce bioactive natural products (Micromonospora, Streptomyces, Serinicoccus and Verrucosispora) were retrieved from the invertebrate samples. To query the bacterial isolates for their ability to produce bioactive metabolites, all strains were fermented and fermentation extracts profiled by UP LC-HRMS and tested for antimicrobial activity. Four strains exhibited antimicrobial activity against methicillin-resistant Staphylococcus aureus (MRSA) and Staphylococcus warneri.
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Affiliation(s)
- Marcelo M P Tangerina
- Biosciences Institute, São Paulo State University - UNESP, Coastal Campus, Praça Infante Dom Henrique s/n, São Vicente, SP, P.O. Box 73601, 11380-972, Brazil
- Chemistry Institute, São Paulo State University - UNESP, Araraquara Campus. Prof. Francisco Degni, 55, Araraquara, SP, 14800-060, Brazil
| | - Hebelin Correa
- Department of Chemistry, University of Prince Edward Island, 550 University Avenue, Charlottetown, PE C1A 4P3, Canada
| | - Brad Haltli
- Department of Chemistry, University of Prince Edward Island, 550 University Avenue, Charlottetown, PE C1A 4P3, Canada
- Department of Biomedical Sciences, Atlantic Veterinary College, University of Prince Edward Island, 550 University Avenue, Charlottetown, PE C1A 4P3, Canada
| | - Wagner Vilegas
- Biosciences Institute, São Paulo State University - UNESP, Coastal Campus, Praça Infante Dom Henrique s/n, São Vicente, SP, P.O. Box 73601, 11380-972, Brazil
| | - Russell G Kerr
- Department of Chemistry, University of Prince Edward Island, 550 University Avenue, Charlottetown, PE C1A 4P3, Canada.
- Department of Biomedical Sciences, Atlantic Veterinary College, University of Prince Edward Island, 550 University Avenue, Charlottetown, PE C1A 4P3, Canada.
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39
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Shavrina M, Zimin A, Molochkov N, Chernyshov S, Machulin A, Mikoulinskaia G. In vitro
study of the antibacterial effect of the bacteriophage T5 thermostable endolysin on Escherichia coli
cells. J Appl Microbiol 2016; 121:1282-1290. [DOI: 10.1111/jam.13251] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 07/26/2016] [Accepted: 08/03/2016] [Indexed: 01/07/2023]
Affiliation(s)
- M.S. Shavrina
- Branch of Shemyakin & Ovchinnikov's Institute of Bioorganic Chemistry RAS; Pushchino Moscow Russia
| | - A.A. Zimin
- Skryabin's Institute of Biochemistry and Physiology of Micro-organisms RAS; Pushchino Moscow Russia
| | - N.V. Molochkov
- Institute of Theoretical and Experimental Biophysics RAS; Pushchino Moscow Russia
| | - S.V. Chernyshov
- Branch of Shemyakin & Ovchinnikov's Institute of Bioorganic Chemistry RAS; Pushchino Moscow Russia
| | - A.V. Machulin
- Skryabin's Institute of Biochemistry and Physiology of Micro-organisms RAS; Pushchino Moscow Russia
| | - G.V. Mikoulinskaia
- Branch of Shemyakin & Ovchinnikov's Institute of Bioorganic Chemistry RAS; Pushchino Moscow Russia
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40
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Ramalingam B, Parandhaman T, Das SK. Antibacterial Effects of Biosynthesized Silver Nanoparticles on Surface Ultrastructure and Nanomechanical Properties of Gram-Negative Bacteria viz. Escherichia coli and Pseudomonas aeruginosa. ACS APPLIED MATERIALS & INTERFACES 2016; 8:4963-4976. [PMID: 26829373 DOI: 10.1021/acsami.6b00161] [Citation(s) in RCA: 258] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Understanding the interactions of silver nanoparticles (AgNPs) with the cell surface is crucial for the evaluation of bactericidal activity and for advanced biomedical and environmental applications. Biosynthesis of AgNPs was carried out through in situ reduction of silver nitrate (AgNO3) by cell free protein of Rhizopus oryzae and the synthesized AgNPs was characterized by UV-vis spectroscopy, high resolution transmission electron microscopy (HRTEM), dynamic light scattering (DLS), ζ-potential analysis, and FTIR spectroscopy. The HRTEM measurement confirmed the formation of 7.1 ± 1.2 nm AgNPs, whereas DLS study demonstrated average hydrodynamic size of AgNPs as 9.1 ± 1.6 nm. The antibacterial activity of the biosynthesized AgNPs (ζ = -17.1 ± 1.2 mV) was evaluated against Gram-negative bacteria such as Escherichia coli and Pseudomonas aeruginosa. The results showed that AgNPs exhibited concentration dependent antibacterial activity and 100% killing of E. coli and P. aeruginosa achieved when the cells were treated with 4.5 and 2.7 μg/mL AgNPs, respectively for 4 h. Furthermore, the intracellular reactive oxygen species (ROS) production suppressed the antioxidant defense and exerted mechanical damage to the membrane. AgNPs also induced surface charge neutralization and altered of the cell membrane permeability causing nonviability of the cells. Atomic force microscopy (AFM) studies depicted alteration of ultrastructural and nanomechanical properties of the cell surface following interaction with AgNPs, whereas FTIR spectroscopic analysis demonstrated that cell membrane of the treated cells underwent an order-to-disorder transition during the killing process and chemical composition of the cell membrane including fatty acids, proteins, and carbohydrates was decomposed following interaction with AgNPs.
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Affiliation(s)
- Baskaran Ramalingam
- Bioproducts Laboratory, Council of Scientific and Industrial Research (CSIR)-Central Leather Research Institute (CLRI) , Chennai 600020, India
| | - Thanusu Parandhaman
- Bioproducts Laboratory, Council of Scientific and Industrial Research (CSIR)-Central Leather Research Institute (CLRI) , Chennai 600020, India
- Academy of Scientific and Innovative Research (AcSIR) , New Delhi 110001, India
| | - Sujoy K Das
- Bioproducts Laboratory, Council of Scientific and Industrial Research (CSIR)-Central Leather Research Institute (CLRI) , Chennai 600020, India
- Academy of Scientific and Innovative Research (AcSIR) , New Delhi 110001, India
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41
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Maione S, del Valle LJ, Pérez-Madrigal MM, Cativiela C, Puiggalí J, Alemán C. Electrospray loading and release of hydrophobic gramicidin in polyester microparticles. RSC Adv 2016. [DOI: 10.1039/c6ra11056h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Gramicidin, a pentadecapeptide with well-known antimicrobial properties and recently identified therapeutic activity against different carcinomas, has been loaded by electrospraying in biodegradable and biocompatible poly(tetramethylene succinate).
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Affiliation(s)
- Silvana Maione
- Department of Chemical Engineering
- ETSEIB
- Universitat Politècnica de Catalunya
- Barcelona 08028
- Spain
| | - Luis J. del Valle
- Department of Chemical Engineering
- ETSEIB
- Universitat Politècnica de Catalunya
- Barcelona 08028
- Spain
| | - Maria M. Pérez-Madrigal
- Department of Chemical Engineering
- ETSEIB
- Universitat Politècnica de Catalunya
- Barcelona 08028
- Spain
| | - Carlos Cativiela
- Departamento de Química Orgánica
- Instituto de Síntesis Química y Catálisis Homogénea-ISQCH
- CSIC-Universidad de Zaragoza
- 50009 Zaragoza
- Spain
| | - Jordi Puiggalí
- Department of Chemical Engineering
- ETSEIB
- Universitat Politècnica de Catalunya
- Barcelona 08028
- Spain
| | - Carlos Alemán
- Department of Chemical Engineering
- ETSEIB
- Universitat Politècnica de Catalunya
- Barcelona 08028
- Spain
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