Computer Simulation of Antimicrobial Peptides

Mátyus, Edit; Kandt, Christian; Tieleman, D. Peter

doi:10.2174/092986707782360105

Cited by 95 publications

(73 citation statements)

References 128 publications

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“…Simulations and structural bioinformatic approaches can help to focus experimental work that, in turn, will eventually guide and verify simulations (Matyus et al 2007). Classical molecular dynamics simulations have been proven useful in describing elements of the mechanism of action of AMPs, including the binding of peptides to the bilayer surface, the properties of surface-bound complexes, peptide insertion, structural modifications of lipid bilayers, and the structure of model pores constructed from AMPs and lipids (Matyus et al 2007).…”

Section: Design Of Antimicrobial Peptidesmentioning

confidence: 99%

“…Classical molecular dynamics simulations have been proven useful in describing elements of the mechanism of action of AMPs, including the binding of peptides to the bilayer surface, the properties of surface-bound complexes, peptide insertion, structural modifications of lipid bilayers, and the structure of model pores constructed from AMPs and lipids (Matyus et al 2007). For example, new synthetic cationic peptides with two LPS-and lipid A (LA)-binding sites, similar to AMPs such as protegrin 1, thanatin, and androctonin, were synthesized de novo based on molecular modeling simulation and quantitative structure-activity relationship (QSAR) analysis (Frecer et al 2004).…”

Section: Design Of Antimicrobial Peptidesmentioning

confidence: 99%

See 1 more Smart Citation

New trends in peptide-based anti-biofilm strategies: a review of recent achievements and bioinformatic approaches

2012

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Antimicrobial peptides (AMPs) have a broad spectrum of activity and unspecific mechanisms of action. Therefore, they are seen as valid alternatives to overcome clinically relevant biofilms and reduce the chance of acquired resistance. This paper reviews AMPs and anti-biofilm AMP-based strategies and discusses ongoing and future work. Recent studies report successful AMP-based prophylactic and therapeutic strategies, several databases catalogue AMP information and analysis tools, and novel bioinformatics tools are supporting AMP discovery and design. However, most AMP studies are performed with planktonic cultures, and most studies on sessile cells test AMPs on growing rather than mature biofilms. Promising preliminary synergistic studies have to be consubstantiated and the study of functionalized coatings with AMPs must be further explored. Standardized operating protocols, to enforce the repeatability and reproducibility of AMP anti-biofilm tests, and automated means of screening and processing the ever-expanding literature are still missing.

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Section: Design Of Antimicrobial Peptidesmentioning

confidence: 99%

Section: Design Of Antimicrobial Peptidesmentioning

confidence: 99%

New trends in peptide-based anti-biofilm strategies: a review of recent achievements and bioinformatic approaches

2012

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“…From a computational point of view, an attractive alternative to bilayers is represented by micelles, which are computationally less demanding and are also often used in NMR experiments [86,87]. However, it is debatable whether they represent a good model of bilayer membranes [50].…”

Section: Membrane Modelsmentioning

confidence: 99%

“…Several good reviews have been published over the years on specific topics regarding the application of fluorescence methods [29][30][31][32][33][34][35][36][37][38][39][40][41][42][43][44][45][46] and MD simulations [47][48][49][50][51][52][53][54] to studies of peptide-membrane interactions. The reader is referred to them, and to the original publications, for additional details that could not be included here because of space limitations.…”

Section: Introductionmentioning

confidence: 99%

Fluorescence spectroscopy and molecular dynamics simulations in studies on the mechanism of membrane destabilization by antimicrobial peptides

Bocchinfuso

Bobone

Meisina

et al. 2011

Cell. Mol. Life Sci.

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Since their initial discovery, 30 years ago, antimicrobial peptides (AMPs) have been intensely investigated as a possible solution to the increasing problem of drug-resistant bacteria. The interaction of antimicrobial peptides with the cellular membrane of bacteria is the key step of their mechanism of action. Fluorescence spectroscopy can provide several structural details on peptide-membrane systems, such as partition free energy, aggregation state, peptide position and orientation in the bilayer, and the effects of the peptides on the membrane order. However, these "low-resolution" structural data are hardly sufficient to define the structural requirements for the pore formation process. Molecular dynamics simulations, on the other hand, provide atomic-level information on the structure and dynamics of the peptide-membrane system, but they need to be validated experimentally. In this review we summarize the information that can be obtained by both approaches, highlighting their versatility and complementarity, suggesting that their synergistic application could lead to a new level of insight into the mechanism of membrane destabilization by AMPs.

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“…In particular, the Matsuzaki group found that the decrease in antimicrobial activity was larger in β-sheet tachyplesin I than in α-helical magainin, showing the dependence on the peptide structure [3,4]. Most simulations and theoretical studies have focused on the secondary structure of AMPs and their interactions with lipid bilayers such as the formation of toroidal pores [52][53][54]. Here, simulations of PEGylated AMPs only will be reviewed.…”

Section: Antimicrobial Peptidesmentioning

confidence: 99%

Molecular Modeling of PEGylated Peptides, Dendrimers, and Single-Walled Carbon Nanotubes for Biomedical Applications

Lee

2014

Polymers

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Polyethylene glycol (PEG) has been conjugated to many drugs or drug carriers to increase their solubility and circulating lifetime, and reduce toxicity. This has motivated many experimental studies to understand the effect of PEGylation on delivery efficiency. To complement the experimental findings and uncover the mechanism that cannot be captured by experiments, all-atom and coarse-grained molecular dynamics (MD) simulations have been performed. This has become possible, due to recent advances in simulation methodologies and computational power. Simulations of PEGylated peptides show that PEG chains wrap antimicrobial peptides and weaken their binding interactions with lipid bilayers. PEGylation also influences the helical stability and tertiary structure of coiled-coil peptides. PEGylated dendrimers and single-walled carbon nanotubes (SWNTs) were simulated, showing that the PEG size and grafting density significantly modulate the conformation and structure of the PEGylated complex, the interparticle aggregation, and the interaction with lipid bilayers. In particular, simulations predicted the structural transition between the dense core and dense shell of PEGylated dendrimers, the phase behavior of self-assembled complexes of lipids, PEGylated lipids, and SWNTs, which all favorably compared with experiments. Overall, these new findings indicate that simulations can now predict the experimentally observed structure and dynamics, as well as provide atomic-scale insights into the interactions of PEGylated complexes with other molecules.

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Computer Simulation of Antimicrobial Peptides

Cited by 95 publications

References 128 publications

New trends in peptide-based anti-biofilm strategies: a review of recent achievements and bioinformatic approaches

New trends in peptide-based anti-biofilm strategies: a review of recent achievements and bioinformatic approaches

Fluorescence spectroscopy and molecular dynamics simulations in studies on the mechanism of membrane destabilization by antimicrobial peptides

Molecular Modeling of PEGylated Peptides, Dendrimers, and Single-Walled Carbon Nanotubes for Biomedical Applications

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