Molecular modeling study of natural products as potential bioactive compounds against SARS-CoV-2
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F62690094%3A18470%2F23%3A50020441" target="_blank" >RIV/62690094:18470/23:50020441 - isvavai.cz</a>
Result on the web
<a href="https://link.springer.com/article/10.1007/s00894-023-05586-5" target="_blank" >https://link.springer.com/article/10.1007/s00894-023-05586-5</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1007/s00894-023-05586-5" target="_blank" >10.1007/s00894-023-05586-5</a>
Alternative languages
Result language
angličtina
Original language name
Molecular modeling study of natural products as potential bioactive compounds against SARS-CoV-2
Original language description
Context: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the COVID-19 infection and responsible for millions of victims worldwide, remains a significant threat to public health. Even after the development of vaccines, research interest in the emergence of new variants is still prominent. Currently, the focus is on the search for effective and safe drugs, given the limitations and side effects observed for the synthetic drugs administered so far. In this sense, bioactive natural products that are widely used in the pharmaceutical industry due to their effectiveness and low toxicity have emerged as potential options in the search for safe drugs against COVID-19. Following this line, we screened 10 bioactive compounds derived from cholesterol for molecules capable of interacting with the receptor-binding domain (RBD) of the spike protein from SARS-CoV-2 (SC2Spike), responsible for the virus’s invasion of human cells. Rounds of docking followed by molecular dynamics simulations and binding energy calculations enabled the selection of three compounds worth being experimentally evaluated against SARS-CoV-2. Methods: The 3D structures of the cholesterol derivatives were prepared and optimized using the Spartan 08 software with the semi-empirical method PM3. They were then exported to the Molegro Virtual Docking (MVD®) software, where they were docked onto the RBD of a 3D structure of the SC2Spike protein that was imported from the Protein Data Bank (PDB). The best poses obtained from MVD® were subjected to rounds of molecular dynamics simulations using the GROMACS software, with the OPLS/AA force field. Frames from the MD simulation trajectories were used to calculate the ligand’s free binding energies using the molecular mechanics – Poisson-Boltzmann surface area (MM-PBSA) method. All results were analyzed using the xmgrace and Visual Molecular Dynamics (VMD) software. © 2023, The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10406 - Analytical chemistry
Result continuities
Project
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Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2023
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Journal of Molecular Modeling
ISSN
1610-2940
e-ISSN
0948-5023
Volume of the periodical
29
Issue of the periodical within the volume
6
Country of publishing house
US - UNITED STATES
Number of pages
9
Pages from-to
"Article number: 183"
UT code for WoS article
000992796900001
EID of the result in the Scopus database
2-s2.0-85159758419