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Computational Prediction of the Mode of Binding of Antitumor Lankacidin C to Tubulin

[Image: see text] Lankacidin C, which is an antibiotic produced by the organism Streptomyces rochei, shows considerable antitumor activity. The mechanism of its antitumor activity remained elusive for decades until it was recently shown to overstabilize microtubules by binding at the taxol binding s...

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Autores principales: Ayoub, Ahmed Taha, Elrefaiy, Mohamed Ali, Arakawa, Kenji
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2019
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6648929/
https://www.ncbi.nlm.nih.gov/pubmed/31459641
http://dx.doi.org/10.1021/acsomega.8b03470
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author Ayoub, Ahmed Taha
Elrefaiy, Mohamed Ali
Arakawa, Kenji
author_facet Ayoub, Ahmed Taha
Elrefaiy, Mohamed Ali
Arakawa, Kenji
author_sort Ayoub, Ahmed Taha
collection PubMed
description [Image: see text] Lankacidin C, which is an antibiotic produced by the organism Streptomyces rochei, shows considerable antitumor activity. The mechanism of its antitumor activity remained elusive for decades until it was recently shown to overstabilize microtubules by binding at the taxol binding site of tubulin, causing mitotic arrest followed by apoptosis. However, the exact binding mode of lankacidin C inside the tubulin binding pocket remains unknown, an issue that impedes proper structure-based design, modification, and optimization of the drug. Here, we have used computational methods to predict the most likely binding mode of lankacidin C to tubulin. We employed ensemble-based docking in different software packages, supplemented with molecular dynamics simulation and subsequent binding-energy prediction. The molecular dynamics simulations performed on lankacidin C were collectively 1.1 μs long. Also, a multiple-trajectory approach was performed to assess the stability of different potential binding modes. The identified binding mode could serve as an ideal starting point for structural modification and optimization of lankacidin C to enhance its affinity to the tubulin binding site and therefore improve its antitumor activity.
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spelling pubmed-66489292019-08-27 Computational Prediction of the Mode of Binding of Antitumor Lankacidin C to Tubulin Ayoub, Ahmed Taha Elrefaiy, Mohamed Ali Arakawa, Kenji ACS Omega [Image: see text] Lankacidin C, which is an antibiotic produced by the organism Streptomyces rochei, shows considerable antitumor activity. The mechanism of its antitumor activity remained elusive for decades until it was recently shown to overstabilize microtubules by binding at the taxol binding site of tubulin, causing mitotic arrest followed by apoptosis. However, the exact binding mode of lankacidin C inside the tubulin binding pocket remains unknown, an issue that impedes proper structure-based design, modification, and optimization of the drug. Here, we have used computational methods to predict the most likely binding mode of lankacidin C to tubulin. We employed ensemble-based docking in different software packages, supplemented with molecular dynamics simulation and subsequent binding-energy prediction. The molecular dynamics simulations performed on lankacidin C were collectively 1.1 μs long. Also, a multiple-trajectory approach was performed to assess the stability of different potential binding modes. The identified binding mode could serve as an ideal starting point for structural modification and optimization of lankacidin C to enhance its affinity to the tubulin binding site and therefore improve its antitumor activity. American Chemical Society 2019-02-28 /pmc/articles/PMC6648929/ /pubmed/31459641 http://dx.doi.org/10.1021/acsomega.8b03470 Text en Copyright © 2019 American Chemical Society This is an open access article published under an ACS AuthorChoice License (http://pubs.acs.org/page/policy/authorchoice_termsofuse.html) , which permits copying and redistribution of the article or any adaptations for non-commercial purposes.
spellingShingle Ayoub, Ahmed Taha
Elrefaiy, Mohamed Ali
Arakawa, Kenji
Computational Prediction of the Mode of Binding of Antitumor Lankacidin C to Tubulin
title Computational Prediction of the Mode of Binding of Antitumor Lankacidin C to Tubulin
title_full Computational Prediction of the Mode of Binding of Antitumor Lankacidin C to Tubulin
title_fullStr Computational Prediction of the Mode of Binding of Antitumor Lankacidin C to Tubulin
title_full_unstemmed Computational Prediction of the Mode of Binding of Antitumor Lankacidin C to Tubulin
title_short Computational Prediction of the Mode of Binding of Antitumor Lankacidin C to Tubulin
title_sort computational prediction of the mode of binding of antitumor lankacidin c to tubulin
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6648929/
https://www.ncbi.nlm.nih.gov/pubmed/31459641
http://dx.doi.org/10.1021/acsomega.8b03470
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