Molecular dynamics study on the influence of C-terminal sugar substitution on dynamics and conformation of vancomycin derivatives

Rafał Ślusarz , Justyna Samaszko-Fiertek , Barbara Dmochowska , Janusz Madaj

Abstract

Computational investigations were performed to examine the effects of the addition of 2-acetamido-2-deoxy-β-D-galactopyranosylamine or 1-amino-1-deoxy-D-glucitol connected to the C-terminus of vancomycin with different linkers. The purpose of this modification was to find more effective vancomycin derivatives by providing alternative interactions between vancomycin moiety and the peptidoglycan precursor. Each prepared vancomycin–peptidoglycan complex was optimized and submitted to the molecular dynamics study and analysis. The analysis of overall root mean square deviation, changes in position and interactions involving modified part of vancomycin as well as cluster analysis were carried out. One of the proposed vancomycin analogues seems to be efficient vancomycin substitute.
Author Rafał Ślusarz PChC
Rafał Ślusarz,,
- Laboratory of Carbohydrate Chemistry
, Justyna Samaszko-Fiertek PChC
Justyna Samaszko-Fiertek,,
- Laboratory of Carbohydrate Chemistry
, Barbara Dmochowska PChC
Barbara Dmochowska,,
- Laboratory of Carbohydrate Chemistry
, Janusz Madaj PChC
Janusz Madaj,,
- Laboratory of Carbohydrate Chemistry
Other language title versions
Journal seriesJournal of Carbohydrate Chemistry, ISSN 0732-8303
Issue year2017
Vol36
No1
Pages45-58
Publication size in sheets0.65
Keywords in Englishvancomycin, vancomycin derivatives, molecular dynamics, root mean square deviation, conformational analysis
DOIDOI:10.1080/07328303.2017.1347669
Languageen angielski
Score (nominal)20
ScoreMinisterial score = 20.0, 20-12-2017, ArticleFromJournal
Ministerial score (2013-2016) = 20.0, 20-12-2017, ArticleFromJournal
Publication indicators WoS Impact Factor: 2016 = 0.671 (2) - 2016=0.962 (5)
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