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


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 (FCh / DOCh / LCCh)
Rafał Ślusarz,,
- Laboratory of Carbohydrate Chemistry
, Justyna Samaszko-Fiertek (FCh / DOCh / LCCh)
Justyna Samaszko-Fiertek,,
- Laboratory of Carbohydrate Chemistry
, Barbara Dmochowska (FCh / DOCh / LCCh)
Barbara Dmochowska,,
- Laboratory of Carbohydrate Chemistry
, Janusz Madaj (FCh / DOCh / LCCh)
Janusz Madaj,,
- Laboratory of Carbohydrate Chemistry
Other language title versions
Journal seriesJournal of Carbohydrate Chemistry, ISSN 0732-8303, (A 20 pkt)
Issue year2017
Publication size in sheets0.65
Keywords in Englishvancomycin, vancomycin derivatives, molecular dynamics, root mean square deviation, conformational analysis
ASJC Classification1605 Organic Chemistry; 1303 Biochemistry
Languageen angielski
Score (nominal)20
ScoreMinisterial score = 20.0, 24-07-2019, ArticleFromJournal
Publication indicators WoS Citations = 0; Scopus SNIP (Source Normalised Impact per Paper): 2017 = 0.362; WoS Impact Factor: 2017 = 0.629 (2) - 2017=0.983 (5)
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* presented citation count is obtained through Internet information analysis and it is close to the number calculated by the Publish or Perish system.