scholarly journals Polymyxin B1 within the E. coli cell envelope: insights from molecular dynamics simulations

2021 ◽  
Author(s):  
Dhanushka Weerakoon ◽  
Kamen Petrov ◽  
Conrado Pedebos ◽  
Syma Khalid
Keyword(s):  
Molecular Dynamics ◽  
Antibiotic Resistance ◽  
Molecular Dynamics Simulations ◽  
Molecular Level ◽  
Cell Envelope ◽  
Mechanisms Of Action ◽  
Coli Cell ◽  
Complementary Technique ◽  
E Coli ◽  
Dynamics Simulations

Abstract Polymyxins are used as last-resort antibiotics, where other treatments have been ineffectual due to antibiotic resistance. However, resistance to polymyxins has also been now reported, therefore it is instructive to characterise at the molecular level, the mechanisms of action of polymyxins. Here we review insights into these mechanisms from molecular dynamics simulations and discuss the utility of simulations as a complementary technique to  experimental methodologies.

scholarly journals Molecular Dynamics Simulations of the Predicted E. Coli FtsB-FtsL Tetrameric Complex

2017 ◽  
Vol 112 (3) ◽  
pp. 501a
Author(s):  
Gladys Diaz Vazquez ◽  
Samson Condon ◽  
Qiang Cui ◽  
Alessandro Senes
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
E Coli ◽  
Dynamics Simulations ◽  
Tetrameric Complex

Molecular Dynamics Simulations to Elucidate Translocation and Permeation of Active from Lipid Nanoparticle to Skin: Complemented with Experiments

Nanoscale ◽  
2021 ◽  
Author(s):  
Krishna M. Gupta ◽  
Surajit Das ◽  
Pui Shan Chow
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Level ◽  
Skin Layer ◽  
Lipid Nanoparticle ◽  
Dynamics Simulations

One of the most realistic approaches that could deliver actives (pharmaceuticals/cosmetics) deep into skin layer is encapsulation into nanoparticles (NP). Nonetheless, molecular-level understanding into the mechanism of active delivery from...

scholarly journals Molecular Dynamics Simulations of E. coli Lipopolysaccharide Bilayers

2013 ◽  
Vol 104 (2) ◽  
pp. 586a ◽  
Author(s):  
Emilia L. Wu ◽  
Olof Engstrom ◽  
Sunhwan Jo ◽  
Dani Stuhlsatz ◽  
Goran Wildmalm ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
E Coli ◽  
Dynamics Simulations

scholarly journals IDENTIFICATION OF POTENTIAL SALMONELLA TYPHI BETA-LACTAMASE TEM 1 INHIBITORS USING PEPTIDOMIMETICS, VIRTUAL SCREENING, AND MOLECULAR DYNAMICS SIMULATIONS

2018 ◽  
Vol 10 (1) ◽  
pp. 91
Author(s):  
Rakesh K. R. Pandit ◽  
Dinesh Gupta ◽  
Tapan K. Mukherjee
Keyword(s):  
Molecular Dynamics ◽  
Antibiotic Resistance ◽  
Virtual Screening ◽  
Molecular Dynamics Simulations ◽  
Active Site ◽  
Beta Lactamase ◽  
Ramachandran Plot ◽  
Small Peptide ◽  
In Silico Docking ◽  
Dynamics Simulations

Objective: The purpose of this study was to identify a potential peptidomimetic S. typhi Beta-lactamase TEM 1 inhibitor to tackle the antibiotic resistance among S. typhi.Methods: The potential peptidomimetic inhibitor was identified by in silico docking of the small peptide WFRKQLKW with S. typhi Beta-lactamase TEM 1. The 3D coordinate geometry of the residues of small peptide interacting with the active site of the receptor was generated and mimics were identified using PEP: MMs: MIMIC server. All the identified mimics were docked at the active site of the receptor using Autodock 4.2 and the best-docked complex was selected on the basis of binding energy and number of H-bonds. The complex was then subjected to molecular dynamics simulations of 30 ns using AMBER 12 software package. The stereochemical stability of the Beta-lactamase TEM 1-WFRKQLKW complex was estimated with the help of Ramachandran plot using PROCHECK tool.Results: In the present study, a new potential peptidomimetic inhibitor (ZINC05839264) of Beta-lactamase TEM 1 has been identified based on antimicrobial peptide WFRKQLKW by virtual screening of the MMsINC database. The docking and molecular simulation studies revealed that the mimic binds more tightly to the active site of the receptor than the peptide. The Ramachandran plot also shows that the Beta-lactamase TEM 1-mimic complex is stereo chemically more stable than Beta-lactamase TEM 1-WFRKQLKW complex as more number of residues (93.6%) are falling under the core region of the plot in case of the former.Conclusion: The study shows that the peptidomimetic compound can act as a potential inhibitor of S. typhi Beta-lactamase TEM 1 and further it can be developed into more effective therapeutic to tackle the problem of antibiotic resistance.

scholarly journals Insights into mechanochemical reactions at the molecular level: simulated indentations of aspirin and meloxicam crystals

2019 ◽  
Vol 10 (10) ◽  
pp. 2924-2929 ◽  
Author(s):  
Michael Ferguson ◽  
M. Silvina Moyano ◽  
Gareth A. Tribello ◽  
Deborah E. Crawford ◽  
Eduardo M. Bringa ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Level ◽  
Molecular Crystals ◽  
Classical Molecular Dynamics ◽  
Dynamics Simulations ◽  
Mechanochemical Reactions

Working towards a fundamental description of mechanochemical reactions through the use of classical molecular dynamics simulations. Capturing the transfer of molecules between two non-volatile molecular crystals during mechanochemical events.

scholarly journals Molecular Level Understanding of Chemical Erosion on Graphite Surface using Molecular Dynamics Simulations

2015 ◽  
Vol 19 (6) ◽  
pp. 54-63
Author(s):  
Ramki Murugesan ◽  
Gyoung Lark Park ◽  
Valery I. Levitas ◽  
Heesung Yang ◽  
Jae Hyun Park ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Level ◽  
Graphite Surface ◽  
Chemical Erosion ◽  
Dynamics Simulations

scholarly journals Evidence from molecular dynamics simulations of conformational preorganization in the ribonuclease H active site

F1000Research ◽  
2014 ◽  
Vol 3 ◽  
pp. 67 ◽  
Author(s):  
Kate A. Stafford ◽  
Arthur G. Palmer III
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Active Site ◽  
Extensive Study ◽  
Rnase H ◽  
Dynamic Feature ◽  
Magnesium Ions ◽  
E Coli ◽  
Domains Of Life ◽  
Dynamics Simulations

Ribonuclease H1 (RNase H) enzymes are well-conserved endonucleases that are present in all domains of life and are particularly important in the life cycle of retroviruses as domains within reverse transcriptase. Despite extensive study, especially of the E. coli homolog, the interaction of the highly negatively charged active site with catalytically required magnesium ions remains poorly understood. In this work, we describe molecular dynamics simulations of the E. coli homolog in complex with magnesium ions, as well as simulations of other homologs in their apo states. Collectively, these results suggest that the active site is highly rigid in the apo state of all homologs studied and is conformationally preorganized to favor the binding of a magnesium ion. Notably, representatives of bacterial, eukaryotic, and retroviral RNases H all exhibit similar active-site rigidity, suggesting that this dynamic feature is only subtly modulated by amino acid sequence and is primarily imposed by the distinctive RNase H protein fold.

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