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Kehrein J, Sotriffer C. Molecular Dynamics Simulations for Rationalizing Polymer Bioconjugation Strategies: Challenges, Recent Developments, and Future Opportunities. ACS Biomater Sci Eng 2024; 10:51-74. [PMID: 37466304 DOI: 10.1021/acsbiomaterials.3c00636] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
The covalent modification of proteins with polymers is a well-established method for improving the pharmacokinetic properties of therapeutically valuable biologics. The conjugated polymer chains of the resulting hybrid represent highly flexible macromolecular structures. As the dynamics of such systems remain rather elusive for established experimental techniques from the field of protein structure elucidation, molecular dynamics simulations have proven as a valuable tool for studying such conjugates at an atomistic level, thereby complementing experimental studies. With a focus on new developments, this review aims to provide researchers from the polymer bioconjugation field with a concise and up to date overview of such approaches. After introducing basic principles of molecular dynamics simulations, as well as methods for and potential pitfalls in modeling bioconjugates, the review illustrates how these computational techniques have contributed to the understanding of bioconjugates and bioconjugation strategies in the recent past and how they may lead to a more rational design of novel bioconjugates in the future.
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Affiliation(s)
- Josef Kehrein
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Würzburg 97074, Germany
| | - Christoph Sotriffer
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Würzburg 97074, Germany
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2
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Cavallazzi Sebold B, Li J, Ni G, Fu Q, Li H, Liu X, Wang T. Going Beyond Host Defence Peptides: Horizons of Chemically Engineered Peptides for Multidrug-Resistant Bacteria. BioDrugs 2023; 37:607-623. [PMID: 37300748 PMCID: PMC10432368 DOI: 10.1007/s40259-023-00608-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2023] [Indexed: 06/12/2023]
Abstract
Multidrug-resistant (MDR) bacteria are considered a health threat worldwide, and this problem is set to increase over the decades. The ESKAPE, a group of six pathogens including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp. is the major source of concern due to their high death incidence and nosocomial acquired infection. Host defence peptides (HDPs) are a class of ribosomally synthesised peptides that have shown promising results in combating MDR, including the ESKAPE group, in- and outside bacterial biofilms. However, their poor pharmacokinetics in physiological mediums may impede HDPs from becoming viable clinical candidates. To circumvent this problem, chemical engineering of HDPs has been seen as an emergent approach to not only improve their pharmacokinetics but also their efficacy against pathogens. In this review, we explore several chemical modifications of HDPs that have shown promising results, especially against ESKAPE pathogens, and provide an overview of the current findings with respect to each modification.
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Affiliation(s)
- Bernardo Cavallazzi Sebold
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore BC, QLD, 4558, Australia
- School of Science, Engineering and Technology, University of the Sunshine Coast, Maroochydore BC, QLD, 4558, Australia
| | - Junjie Li
- The First Affiliated Hospital/Clinical Medical School, Guangdong Pharmaceutical University, Guangzhou, 510080, Guangdong, China
| | - Guoying Ni
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore BC, QLD, 4558, Australia
- The First Affiliated Hospital/Clinical Medical School, Guangdong Pharmaceutical University, Guangzhou, 510080, Guangdong, China
- Cancer Research Institute, First People's Hospital of Foshan, Foshan, 528000, Guangdong, China
| | - Quanlan Fu
- The First Affiliated Hospital/Clinical Medical School, Guangdong Pharmaceutical University, Guangzhou, 510080, Guangdong, China
| | - Hejie Li
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore BC, QLD, 4558, Australia
- School of Science, Engineering and Technology, University of the Sunshine Coast, Maroochydore BC, QLD, 4558, Australia
| | - Xiaosong Liu
- The First Affiliated Hospital/Clinical Medical School, Guangdong Pharmaceutical University, Guangzhou, 510080, Guangdong, China.
- Cancer Research Institute, First People's Hospital of Foshan, Foshan, 528000, Guangdong, China.
| | - Tianfang Wang
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore BC, QLD, 4558, Australia.
- School of Science, Engineering and Technology, University of the Sunshine Coast, Maroochydore BC, QLD, 4558, Australia.
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3
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PEGylation enhances the antibacterial and therapeutic potential of amphibian host defence peptides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2022; 1864:183806. [PMID: 34656552 DOI: 10.1016/j.bbamem.2021.183806] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 09/24/2021] [Accepted: 10/10/2021] [Indexed: 11/20/2022]
Abstract
Aurein 2.1, aurein 2.6 and aurein 3.1 are amphibian host defence peptides that kill bacteria via the use of lytic amphiphilic α-helical structures. The C-terminal PEGylation of these peptides led to decreased antibacterial activity (Minimum Lethal Concentration (MLCs) ↓ circa one and a half to threefold), reduced levels of amphiphilic α-helical structure in solvents (α-helicity ↓ circa 15.0%) and lower surface activity (Δπ ↓ > 1.5 mN m-1). This PEGylation of aureins also led to decreased levels of amphiphilic α-helical structure in the presence of anionic membranes and zwitterionic membranes (α-helicity↓ > 10.0%) as well as reduced levels of penetration (Δπ ↓ > 3.0 mN m-1) and lysis (lysis ↓ > 10.0%) of these membranes. Based on these data, it was proposed that the antibacterial action of PEGylated aureins involved the adoption of α-helical structures that promote the lysis of bacterial membranes, but with lower efficacy than their native counterparts. However, PEGylation also reduced the haemolytic activity of native aureins to negligible levels (haemolysis ↓ from circa 10% to 3% or less) and improved their relative therapeutic indices (RTIs ↑ circa three to sixfold). Based on these data, it is proposed that PEGylated aureins possess the potential for therapeutic development; for example, to combat infections due to multi-drug resistant strains of S. aureus, designated as high priority by the World Health Organization.
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Mollazadeh S, Sahebkar A, Shahlaei M, Moradi S. Nano drug delivery systems: Molecular dynamic simulation. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115823] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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5
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Heterodimer and pore formation of magainin 2 and PGLa: The anchoring and tilting of peptides in lipid bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183305. [DOI: 10.1016/j.bbamem.2020.183305] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/30/2020] [Accepted: 04/07/2020] [Indexed: 01/13/2023]
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6
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Lee H. Molecular Simulations of PEGylated Biomolecules, Liposomes, and Nanoparticles for Drug Delivery Applications. Pharmaceutics 2020; 12:E533. [PMID: 32531886 PMCID: PMC7355693 DOI: 10.3390/pharmaceutics12060533] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 06/04/2020] [Accepted: 06/08/2020] [Indexed: 12/17/2022] Open
Abstract
Since the first polyethylene glycol (PEG)ylated protein was approved by the FDA in 1990, PEGylation has been successfully applied to develop drug delivery systems through experiments, but these experimental results are not always easy to interpret at the atomic level because of the limited resolution of experimental techniques. To determine the optimal size, structure, and density of PEG for drug delivery, the structure and dynamics of PEGylated drug carriers need to be understood close to the atomic scale, as can be done using molecular dynamics simulations, assuming that these simulations can be validated by successful comparisons to experiments. Starting with the development of all-atom and coarse-grained PEG models in 1990s, PEGylated drug carriers have been widely simulated. In particular, recent advances in computer performance and simulation methodologies have allowed for molecular simulations of large complexes of PEGylated drug carriers interacting with other molecules such as anticancer drugs, plasma proteins, membranes, and receptors, which makes it possible to interpret experimental observations at a nearly atomistic resolution, as well as help in the rational design of drug delivery systems for applications in nanomedicine. Here, simulation studies on the following PEGylated drug topics will be reviewed: proteins and peptides, liposomes, and nanoparticles such as dendrimers and carbon nanotubes.
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Affiliation(s)
- Hwankyu Lee
- Department of Chemical Engineering, Dankook University, Yongin 16890, Korea
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7
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Lorenzon EN, Piccoli JP, Santos-Filho NA, Cilli EM. Dimerization of Antimicrobial Peptides: A Promising Strategy to Enhance Antimicrobial Peptide Activity. Protein Pept Lett 2019; 26:98-107. [PMID: 30605048 PMCID: PMC6416459 DOI: 10.2174/0929866526666190102125304] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/11/2018] [Accepted: 12/26/2018] [Indexed: 01/10/2023]
Abstract
Antimicrobial resistance is a global health problem with strong social and economic impacts. The development of new antimicrobial agents is considered an urgent challenge. In this regard, Antimicrobial Peptides (AMPs) appear to be novel candidates to overcome this problem. The mechanism of action of AMPs involves intracellular targets and membrane disruption. Although the exact mechanism of action of AMPs remains controversial, most AMPs act through membrane disruption of the target cell. Several strategies have been used to improve AMP activity, such as peptide dimerization. In this review, we focus on AMP dimerization, showing many examples of dimerized peptides and their effects on biological activity. Although more studies are necessary to elucidate the relationship between peptide properties and the dimerization effect on antimicrobial activity, dimerization constitutes a promising strategy to improve the effectiveness of AMPs.
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Affiliation(s)
- Esteban N Lorenzon
- Unidade Academica Especial da Saude, Universidade Federal de Jatai, Jatai-GO, Brazil
| | - Julia P Piccoli
- Instituto de Quimica, UNESP- Universidade Estadual Paulista, Araraquara-SP, Brazil
| | - Norival A Santos-Filho
- UNESP- Universidade Estadual Paulista, Campus Experimental de Registro, Registro, Sao Paulo, Brazil
| | - Eduardo M Cilli
- Instituto de Quimica, UNESP- Universidade Estadual Paulista, Araraquara-SP, Brazil
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8
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Jafari M, Doustdar F, Mehrnejad F. Molecular Self-Assembly Strategy for Encapsulation of an Amphipathic α-Helical Antimicrobial Peptide into the Different Polymeric and Copolymeric Nanoparticles. J Chem Inf Model 2018; 59:550-563. [PMID: 30475620 DOI: 10.1021/acs.jcim.8b00641] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Encapsulation of peptide and protein-based drugs in polymeric nanoparticles is one of the fundamental fields in controlled-release drug delivery systems. The molecular mechanisms of absorption of peptides to the polymeric nanoparticles are still unknown, and there is no precise molecular data on the encapsulation process of peptide and protein-based drugs. Herein, the self-assembly of different polymers and block copolymers with combinations of the various molecular weight of blocks and the effects of resultant polymer and copolymer nanomicelles on the stability of magainin2, an α-helical antimicrobial peptide, were investigated by means of all-atom molecular dynamics (MD) simulation. The micelle forming, morphology of micellar aggregations and changes in the first hydration shell of the micelles during micelles formation were explored as well. The results showed that the peptide binds to the polymer and copolymer micelles and never detaches during the MD simulation time. In general, all polymers and copolymers simultaneously encapsulated the peptide during micelles formation and had the ability to maintain the helical structure of the peptide, whereas the first hydration shell of the peptide remained unchanged. Among the micelles, the polyethylene glycol (PEG) micelles completely encapsulated magainin2 and, surprisingly, the NMR structure of the peptide was perfectly kept during the encapsulation process. The MD results also indicated that the aromatic and basic residues of the peptide strongly interact with polymers/copolymers and play important roles in the encapsulation mechanism. This research will provide a good opportunity in the design of polymer surfaces for drug delivery applications such as controlled-release peptide delivery systems.
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Affiliation(s)
- Majid Jafari
- Infectious Diseases and Tropical Medicine Research Center , Shahid Beheshti University of Medical Sciences , P.O. Box 1985717443, Tehran , Iran.,Department of Life Science Engineering, Faculty of New Sciences and Technologies , University of Tehran , P.O. Box 14395-1561, Tehran , Iran
| | - Farahnoosh Doustdar
- Infectious Diseases and Tropical Medicine Research Center , Shahid Beheshti University of Medical Sciences , P.O. Box 1985717443, Tehran , Iran.,Department of Microbiology, Faculty of Medicine , Shahid Beheshti University of Medical Sciences , P.O. Box 19839-63113 Tehran , Iran
| | - Faramarz Mehrnejad
- Department of Life Science Engineering, Faculty of New Sciences and Technologies , University of Tehran , P.O. Box 14395-1561, Tehran , Iran
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9
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Sousa SF, Peres J, Coelho M, Vieira TF. Analyzing PEGylation through Molecular Dynamics Simulations. ChemistrySelect 2018. [DOI: 10.1002/slct.201800855] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Sérgio F. Sousa
- UCIBIO@REQUIMTE; BioSIM; Departamento de Biomedicina; Faculdade de Medicina da Universidade do Porto, Alameda Professor Hernâni Monteiro; 4200-319, Porto Portugal
| | - Joana Peres
- LEPABE; Faculdade de Engenharia; Universidade do Porto, Porto; Portugal
| | - Manuel Coelho
- LEPABE; Faculdade de Engenharia; Universidade do Porto, Porto; Portugal
| | - Tatiana F. Vieira
- LEPABE; Faculdade de Engenharia; Universidade do Porto, Porto; Portugal
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10
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Lorenzón EN, Nobre TM, Caseli L, Cilli EM, da Hora GC, Soares TA, Oliveira ON. The “pre-assembled state” of magainin 2 lysine-linked dimer determines its enhanced antimicrobial activity. Colloids Surf B Biointerfaces 2018; 167:432-440. [DOI: 10.1016/j.colsurfb.2018.04.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/09/2018] [Accepted: 04/16/2018] [Indexed: 11/25/2022]
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11
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Liu C, Qi J, Shan B, Ma Y. Tachyplesin Causes Membrane Instability That Kills Multidrug-Resistant Bacteria by Inhibiting the 3-Ketoacyl Carrier Protein Reductase FabG. Front Microbiol 2018; 9:825. [PMID: 29765362 PMCID: PMC5938390 DOI: 10.3389/fmicb.2018.00825] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/11/2018] [Indexed: 12/19/2022] Open
Abstract
Tachyplesin is a type of cationic β-hairpin antimicrobial peptide discovered in horseshoe crab approximately 30 years ago that is well known for both its potential antimicrobial activities against multidrug-resistant bacteria and its cytotoxicity to mammalian cells. Though its physical interactions with artificial membranes have been well studied, details of its physiological mechanism of action the physiological consequences of its action remain limited. By using the DNA-binding fluorescent dye propidium iodide to monitor membrane integrity, confocal microscopy to assess the intracellular location of FITC-tagged tachyplesin, and RNA sequencing of the differentially expressed genes in four Gram-negative bacteria (Escherichia coli, Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa) treated with lethal or sublethal concentrations of tachyplesin, we found that compared with levofloxacin-treated bacteria, tachyplesin-treated bacteria showed significant effects on the pathways underlying unsaturated fatty acid biosynthesis. Notably, RNA levels of the conserved and essential 3-ketoacyl carrier protein reductase in this pathway (gene FabG) were elevated in all of the four bacteria after tachyplesin treatment. In vitro tests including surface plasmon resonance and enzyme activity assays showed that tachyplesin could bind and inhibit 3-ketoacyl carrier protein reductase, which was consistent with molecular docking prediction results. As unsaturated fatty acids are important for membrane fluidity, our results provided one possible mechanism to explain how tachyplesin kills bacteria and causes cytotoxicity by targeting membranes, which may be helpful for designing more specific and safer antibiotics based on the function of tachyplesin.
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Affiliation(s)
- Cunbao Liu
- Laboratory of Molecular Immunology, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Jialong Qi
- Laboratory of Molecular Immunology, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Bin Shan
- Department of Clinical Laboratory, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yanbing Ma
- Laboratory of Molecular Immunology, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
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12
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Interaction of drugs amlodipine and paroxetine with the metabolizing enzyme CYP2B4: a molecular dynamics simulation study. J Mol Model 2018; 24:67. [DOI: 10.1007/s00894-018-3617-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 02/08/2018] [Indexed: 12/26/2022]
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13
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Wu X, Wei PH, Zhu X, Wirth MJ, Bhunia A, Narsimhan G. Effect of immobilization on the antimicrobial activity of a cysteine-terminated antimicrobial Peptide Cecropin P1 tethered to silica nanoparticle against E. coli O157:H7 EDL933. Colloids Surf B Biointerfaces 2017; 156:305-312. [PMID: 28544962 DOI: 10.1016/j.colsurfb.2017.05.047] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 05/15/2017] [Accepted: 05/16/2017] [Indexed: 01/08/2023]
Abstract
Antimicrobial peptides (AMPs) have the ability to penetrate the cell membrane, form pores which eventually lead to cell death. Immobilization of AMP on nanoparticles can play a major role in antimicrobial materials, biosensors for pathogen detection and in food safety. The minimum inhibitory concentration (MIC) of free Cecropin P1 (CP1, sequence SWLSTAKKLENSAKKRLSEGIAIAIQGGPR) and adsorbed on silica nanoparticle against E. coli O157:H7 EDL933 were 0.78μg/ml. This was found to be consistent with preservation of α-helical secondary structure of CP1 upon adsorption as indicated by circular dichroism (CD). Cysteine-terminus modified Cecropin P1 (CP1C, sequence SWLSTAKKLENSAKKRLSEGIAIAIQGGPRC) was chemically immobilized onto silica nanoparticles with maleimide-PEG-NHS ester cross-linkers of different PEG chain lengths. The antimicrobial activity of CP1C in solution and adsorbed on silica nanoparticles against E. coli O157:H7 EDL933 were found to be the same as those for CP1. However, tethered CP1C exhibited much higher MIC of 24.38, 37.55 and 109.82μg/ml for (PEG)20, (PEG)6 and (PEG)2 linkers respectively. The antimicrobial activity of CP1C tethered to silica nanoparticles with (PEG)20 linker was found to be lower for lower surface coverage with MIC values being 86.06, 36.89, 24.38 and 17.84μg/ml for surface coverage of 12.3%, 24.4%, 52.8% and 83.8% respectively. All atom MD simulation of 1:3 DOPG/DOPC mixed membrane interacting with free and PEGlyated CP1C indicated that presence of PEG linker prevented CP1C from interacting with the bilayer which may explain the loss of antimicrobial activity of tethered CP1C.
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Affiliation(s)
- Xi Wu
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, United States
| | - Pei-Hsun Wei
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, United States
| | - Xiao Zhu
- Department of Research Computing, Purdue University, West Lafayette, IN 47907, United States
| | - Mary J Wirth
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, United States
| | - Arun Bhunia
- Department of Food Science, Purdue University, West Lafayette, IN 47907, United States
| | - Ganesan Narsimhan
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, United States.
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14
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Yousefpour A, Modarress H, Goharpey F, Amjad-Iranagh S. Combination of anti-hypertensive drugs: a molecular dynamics simulation study. J Mol Model 2017; 23:158. [DOI: 10.1007/s00894-017-3333-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 03/27/2017] [Indexed: 01/03/2023]
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15
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Shriver-Lake LC, Anderson GP, Taitt CR. Effect of Linker Length on Cell Capture by Poly(ethylene glycol)-Immobilized Antimicrobial Peptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:2878-2884. [PMID: 28253616 DOI: 10.1021/acs.langmuir.6b04481] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Development of antimicrobial peptide (AMP)-functionalized materials has renewed interest in using poly(ethylene glycol) (PEG)-mediated linking to minimize unwanted interactions while engendering the peptides with sufficient flexibility and freedom of movement to interact with the targeted cell types. While PEG-based linkers have been used in many AMP-based materials, the role of the tether length has been minimally explored. Here, we assess the impact of varying the length of PEG-based linkers on the binding of bacterial cells by surface-immobilized AMPs. While higher surface densities of immobilized AMPs were observed using shorter PEG linkers, the increased density was insufficient to fully account for the increased binding activity of peptides. Furthermore, effects were specific to both the peptide and cell type tested. These results suggest that simple alterations in linking strategies-such as changing tether length-may result in large differences in the surface properties of the immobilized AMPs that are not easily predictable.
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Affiliation(s)
- Lisa C Shriver-Lake
- Center for Biomolecular Science & Engineering, Naval Research Laboratory , 4555 Overlook Avenue, SW, Washington, DC 20375, United States
| | - George P Anderson
- Center for Biomolecular Science & Engineering, Naval Research Laboratory , 4555 Overlook Avenue, SW, Washington, DC 20375, United States
| | - Chris Rowe Taitt
- Center for Biomolecular Science & Engineering, Naval Research Laboratory , 4555 Overlook Avenue, SW, Washington, DC 20375, United States
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16
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Gao Q, Yu M, Su Y, Xie M, Zhao X, Li P, Ma PX. Rationally designed dual functional block copolymers for bottlebrush-like coatings: In vitro and in vivo antimicrobial, antibiofilm, and antifouling properties. Acta Biomater 2017; 51:112-124. [PMID: 28131941 DOI: 10.1016/j.actbio.2017.01.061] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Revised: 01/09/2017] [Accepted: 01/23/2017] [Indexed: 12/15/2022]
Abstract
Numerous antimicrobial coatings have been developed for biomedical devices/implants, but few can simultaneously fulfill the requirements for antimicrobial and antifouling ability and biocompatibility. In this study, to develop an antimicrobial and antibiofilm surface coating, diblock amphiphilic molecules with antimicrobial and antifouling segments in a single chain were rationally designed and synthesized. Cationic antimicrobial polypeptides (AMP) were first synthesized by N-carboxyanhydride ring-opening polymerization (NCA-ROP). Heterofunctionalized poly(ethylene glycol) with different lengths (methacrylate-PEGn-tosyl, n=10/45/90) was synthesized and site-specifically conjugated with polypeptides to form diblock amphiphiles. Along with increased PEG chain length, hemolytic activity was considerably improved, and broad-spectrum antimicrobial activity is retained. Three MA-PEGn-b-AMP copolymers were further grafted onto the surface of silicone rubber (a commonly used catheter material) via plasma/UV-induced surface polymerizations to form a bottlebrush-like coating with excellent antimicrobial activity against several pathogenic bacteria (Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus), and effectively prevent biofilm formation. This bottlebrush coating also greatly reduced protein adsorption and platelet adhesion, indicating its excellent antifouling ability. An in vitro cytotoxicity study also demonstrated that this coating is biocompatible with mammalian cells. After subcutaneous implantation of the materials in rats, we demonstrated that the g-PEG45-b-AMP bottlebrush coating exhibits significant anti-infective activity in vivo. Thus, this facilely synthesized PEGylated AMP bottlebrush coating is a feasible method to prevent biomedical devices-associated infections. STATEMENT OF SIGNIFICANCE Current antimicrobial coatings are often associated with concerns such as antibiotic resistance, environmental pollution, short-time antimicrobial activity, biofouling, poor blood compatibility and cytotoxicity, etc. To overcome these drawbacks, a robust PEGylated cationic amphiphilic peptides-based bottlebrush-like surface coating is demonstrated here, which fulfil the requirements of antimicrobial and antifouling as well as biocompatibility in the meantime. Briefly, the rational designed g-PEGn-b-AMP block copolymers (n=10/45/90) were synthesized and grafted on silicone surface. This bottlebrush-like coating efficiently kill the contacted bacteria and prevent the biofilm formation, greatly reduced protein and platelet adhesion. It also exhibits excellent blood compatibility and low cytotoxicity in vitro. In particular, g-PEG45-b-AMP coating exhibits significant anti-infection effect in vivo. This coating offering an effective strategy for combating biomedical devices-associated infections.
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17
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Wu R, Qiu X, Shi Y, Deng M. Molecular dynamics simulation of the atomistic monolayer structures of N-acyl amino acid-based surfactants. MOLECULAR SIMULATION 2016. [DOI: 10.1080/08927022.2016.1261289] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Rongliang Wu
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Material Science and Engineering, Donghua University, Shanghai, P.R.China
| | - Xinlong Qiu
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Material Science and Engineering, Donghua University, Shanghai, P.R.China
| | - Yiqin Shi
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Material Science and Engineering, Donghua University, Shanghai, P.R.China
| | - Manli Deng
- Key Laboratory of Colloid and Interface Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, P.R.China
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18
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Woo SY, Lee H. All-atom simulations and free-energy calculations of coiled-coil peptides with lipid bilayers: binding strength, structural transition, and effect on lipid dynamics. Sci Rep 2016; 6:22299. [PMID: 26926570 PMCID: PMC4772085 DOI: 10.1038/srep22299] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 02/11/2016] [Indexed: 01/04/2023] Open
Abstract
Peptides E and K, which are synthetic coiled-coil peptides for membrane fusion, were simulated with lipid bilayers composed of lipids and cholesterols at different ratios using all-atom models. We first calculated free energies of binding from umbrella sampling simulations, showing that both E and K peptides tend to adsorb onto the bilayer surface, which occurs more strongly in the bilayer composed of smaller lipid headgroups. Then, unrestrained simulations show that K peptides more deeply insert into the bilayer with partially retaining the helical structure, while E peptides less insert and predominantly become random coils, indicating the structural transition from helices to random coils, in quantitative agreement with experiments. This is because K peptides electrostatically interact with lipid phosphates, as well as because hydrocarbons of lysines of K peptide are longer than those of glutamic acids of E peptide and thus form stronger hydrophobic interactions with lipid tails. This deeper insertion of K peptide increases the bilayer dynamics and a vacancy below the peptide, leading to the rearrangement of smaller lipids. These findings help explain the experimentally observed or proposed differences in the insertion depth, binding strength, and structural transition of E and K peptides, and support the snorkeling effect.
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Affiliation(s)
- Sun Young Woo
- Department of Chemical Engineering, Dankook University, Yongin, 448-701, South Korea
| | - Hwankyu Lee
- Department of Chemical Engineering, Dankook University, Yongin, 448-701, South Korea
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Yousefpour A, Modarress H, Goharpey F, Amjad-Iranagh S. Interaction of PEGylated anti-hypertensive drugs, amlodipine, atenolol and lisinopril with lipid bilayer membrane: A molecular dynamics simulation study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1687-98. [DOI: 10.1016/j.bbamem.2015.04.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 03/09/2015] [Accepted: 04/10/2015] [Indexed: 12/12/2022]
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Han E, Lee H. Structural effects of tachyplesin I and its linear derivative on their aggregation and mobility in lipid bilayers. J Mol Graph Model 2015; 59:123-8. [DOI: 10.1016/j.jmgm.2015.04.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 04/09/2015] [Accepted: 04/17/2015] [Indexed: 10/23/2022]
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Han E, Lee H. Synergistic effects of magainin 2 and PGLa on their heterodimer formation, aggregation, and insertion into the bilayer. RSC Adv 2015. [DOI: 10.1039/c4ra08480b] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We performed coarse-grained molecular dynamics simulations of antimicrobial peptides PGLa and magainin 2 in lipid bilayers.
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Affiliation(s)
- Eol Han
- Department of Chemical Engineering
- Dankook University
- Yongin
- South Korea
| | - Hwankyu Lee
- Department of Chemical Engineering
- Dankook University
- Yongin
- South Korea
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Woo SY, Lee H. Molecular dynamics studies of PEGylated α-helical coiled coils and their self-assembled micelles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:8848-8855. [PMID: 25000284 DOI: 10.1021/la501973w] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We performed coarse-grained (CG) molecular dynamics simulations of trimeric α-helical coiled coils grafted with poly(ethylene glycol) (PEG) of different sizes and conjugate positions and the self-assembled micelle of amphiphilic trimers. The CG model for the trimeric coiled coil is verified by comparing the α-helical structure and interhelical distance with those calculated from all-atom simulations. In CG simulations of PEGylated trimers, the end-to-end distances and radii of gyration of PEGs grafted to the sides of peptides become shorter than those of free PEGs in water, which agrees with experiments. This shorter size of the grafted PEGs is also confirmed by calculating the thickness of the PEG layer, which is less than the size of the mushroom. These indicate the adsorption of PEG chains onto coiled coils since hydrophobic residues in the exterior sites of coiled coils tend to be less exposed to water and thus interact with PEGs, leading to the compact conformation of adsorbed PEGs. Simulations of the self-assembly of amphiphilic trimers show that the randomly distributed trimers self-assemble to micelles. The outer radius and hydrodynamic radius of the micelle, which were calculated respectively from radial densities and diffusion coefficients, are ∼7 nm, in agreement with the experimental value of ∼7.5 nm, while the aggregation number of amphiphilic molecules per micelle is lower than the experimentally proposed value. These simulations predict the experimentally measured size of PEGs grafted to the trimeric coiled coils and their self-assembled amphiphilic micelles and suggest that the aggregation number of the micelle may be lower, which needs to be confirmed by experiments.
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Affiliation(s)
- Sun Young Woo
- Department of Chemical Engineering, Dankook University , Yongin 448-701, South Korea
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23
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Molecular Modeling of PEGylated Peptides, Dendrimers, and Single-Walled Carbon Nanotubes for Biomedical Applications. Polymers (Basel) 2014. [DOI: 10.3390/polym6030776] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
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