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Mechanisms of action of the antibiotic ciprofloxacin on the DNA-binding protein Dps detected by molecular modeling techniques

, 
Eduard Vladimirovich Tereshkin 1
Eduard Vladimirovich Tereshkin
, 
Vladislav V Kovalenko 1
Vladislav V Kovalenko
, 
Yurii Fedorovich Krupyanskii 1
Yurii Fedorovich Krupyanskii
, 
Nataliya G Loiko 2
Nataliya G Loiko
1 N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russian Federation
2 Federal Research Centre ‘Fundamentals of Biotechnology’ of the Russian Academy of Sciences, 119071 Moscow, Russian Federation
10.71267/mencom.7567
Published 2025-02-18
Communication , Volume 35, Issue 2, 148-151
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Tereshkina K. B. et al. Mechanisms of action of the antibiotic ciprofloxacin on the DNA-binding protein Dps detected by molecular modeling techniques // Mendeleev Communications. 2025. Vol. 35. No. 2. pp. 148-151.
GOST all authors (up to 50) Copy
Tereshkina K. B., Tereshkin E. V., Kovalenko V. V., Krupyanskii Y. F., Loiko N. G. Mechanisms of action of the antibiotic ciprofloxacin on the DNA-binding protein Dps detected by molecular modeling techniques // Mendeleev Communications. 2025. Vol. 35. No. 2. pp. 148-151.
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TY - JOUR
DO - 10.71267/mencom.7567
UR - https://mendcomm.colab.ws/publications/10.71267/mencom.7567
TI - Mechanisms of action of the antibiotic ciprofloxacin on the DNA-binding protein Dps detected by molecular modeling techniques
T2 - Mendeleev Communications
AU - Tereshkina, Ksenia Borisovna
AU - Tereshkin, Eduard Vladimirovich
AU - Kovalenko, Vladislav V
AU - Krupyanskii, Yurii Fedorovich
AU - Loiko, Nataliya G
PY - 2025
DA - 2025/02/18
PB - Mendeleev Communications
SP - 148-151
IS - 2
VL - 35
ER -
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@article{2025_Tereshkina,
author = {Ksenia Borisovna Tereshkina and Eduard Vladimirovich Tereshkin and Vladislav V Kovalenko and Yurii Fedorovich Krupyanskii and Nataliya G Loiko},
title = {Mechanisms of action of the antibiotic ciprofloxacin on the DNA-binding protein Dps detected by molecular modeling techniques},
journal = {Mendeleev Communications},
year = {2025},
volume = {35},
publisher = {Mendeleev Communications},
month = {Feb},
url = {https://mendcomm.colab.ws/publications/10.71267/mencom.7567},
number = {2},
pages = {148--151},
doi = {10.71267/mencom.7567}
}
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Tereshkina, Ksenia Borisovna, et al. “Mechanisms of action of the antibiotic ciprofloxacin on the DNA-binding protein Dps detected by molecular modeling techniques.” Mendeleev Communications, vol. 35, no. 2, Feb. 2025, pp. 148-151. https://mendcomm.colab.ws/publications/10.71267/mencom.7567.

Keywords

antibiotic ciprofloxacin
classical molecular dynamics
DNA-binding protein Dps
docking
free energy.
mean force potential profiles
umbrella sampling

Abstract

A comprehensive analysis of the effect of the antibiotic ciprofloxacin on the DNA-binding protein Dps of the bacterium Escherichia coli was carried out using three molecular modeling methods: docking, umbrella sampling for calculating mean force potential profiles and classical molecular dynamics. It was shown that ciprofloxacin can penetrate into the internal cavity of the protein, as well as adsorb to the surface, reducing the ability of the N-termini to bind DNA.

Funders

Russian Science Foundation
23-24-00250

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