2022
DOI: 10.1101/2022.07.15.500204
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Differentiating interactions of antimicrobials with Gram-negative and Gram-positive bacterial cell walls using molecular dynamics simulations

Abstract: Developing molecular models to capture the complex physicochemical architecture of the bacterial cell wall and to study the interaction with antibacterial molecules is an important aspect of assessing and developing novel antimicrobial molecules. We carried out molecular dynamics simulations using an atomistic model of peptidoglycan (PGN) to represent the architecture for Gram-positive Staphylococcus aureus. The model is developed to capture various structural features of the staphylococcal cell wall, such as… Show more

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Cited by 2 publications
(3 citation statements)
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“…Later, Torres et al 102 Molecular dynamics can capture the physical interactions of AMP with a model bacterial membrane where compositions of the biological membrane can be explicitly modeled given a set membrane composition. 96 Sharma et al 103 applied MD simulation to compare the difference in binding, orientation, and penetration of melittin (AMP) in the presence of a peptidoglycan layer for membrane simulation representative of E. coli (Gram-negative) and S. aureus (Gram-positive). However, such simulations are still computationally expensive and is difficult to scale up to large data sets.…”
Section: Applicationsmentioning
confidence: 99%
“…Later, Torres et al 102 Molecular dynamics can capture the physical interactions of AMP with a model bacterial membrane where compositions of the biological membrane can be explicitly modeled given a set membrane composition. 96 Sharma et al 103 applied MD simulation to compare the difference in binding, orientation, and penetration of melittin (AMP) in the presence of a peptidoglycan layer for membrane simulation representative of E. coli (Gram-negative) and S. aureus (Gram-positive). However, such simulations are still computationally expensive and is difficult to scale up to large data sets.…”
Section: Applicationsmentioning
confidence: 99%
“…MD simulations have provided a molecular understanding of the barriers offered by different regions of the complex OM, ,, highlighting the asymmetric free-energy landscape for molecular translocation, which is quite distinct from the inner membrane . The barrier properties of the peptidoglycan layer have recently been investigated in our laboratory. , Molecular dynamics simulations of surfactants and fatty acids have been widely used to capture properties like self-assembly and partitioning of surfactants , and also used for investigating the interactions of surfactants with mammalian membrane models. , However, owing to the complex architecture of the bacterial cell envelope, MD simulations of interactions with surfactants are yet to be reported. A molecular view of surfactant interactions with the cell envelope and subsequent action is only partially understood.…”
Section: Introductionmentioning
confidence: 99%
“…15 The barrier properties of the peptidoglycan layer have recently been investigated in our laboratory. 24,25 Molecular dynamics simulations of surfactants and fatty acids have been widely used to capture properties like self-assembly and partitioning of surfactants 26,27 and also used for investigating the interactions of surfactants with mammalian membrane models. 28,29 However, owing to the complex architecture of the bacterial cell envelope, MD simulations of interactions with surfactants are yet to be reported.…”
Section: ■ Introductionmentioning
confidence: 99%