Bioinformatics Study of Sea Cucumber Peptides as Antibreast Cancer Through Inhibiting the Activity of Overexpressed Protein (EGFR, PI3K, AKT1, and CDK4)
Breast cancer is the most common type of cancer in women globally. The overexpressed proteins, including EGFR, PI3K, AKT1, and CDK4, have a role in the growth of breast cancer cells. The 3D peptide structure of sea cucumber Cucumaria frondosa was modeled and then docked with EGFR, PI3K, AKT1, and CD...
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ftpubmed:oai:pubmedcentral.nih.gov:8283226 2023-05-15T15:59:38+02:00 Bioinformatics Study of Sea Cucumber Peptides as Antibreast Cancer Through Inhibiting the Activity of Overexpressed Protein (EGFR, PI3K, AKT1, and CDK4) Wargasetia, Teresa Liliana Ratnawati, Hana Widodo, Nashi Widyananda, Muhammad Hermawan 2021-07-13 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8283226/ http://www.ncbi.nlm.nih.gov/pubmed/34345161 https://doi.org/10.1177/11769351211031864 en eng SAGE Publications http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8283226/ http://www.ncbi.nlm.nih.gov/pubmed/34345161 http://dx.doi.org/10.1177/11769351211031864 © The Author(s) 2021 https://creativecommons.org/licenses/by-nc/4.0/This article is distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 License (https://creativecommons.org/licenses/by-nc/4.0/) which permits non-commercial use, reproduction and distribution of the work without further permission provided the original work is attributed as specified on the SAGE and Open Access pages (https://us.sagepub.com/en-us/nam/open-access-at-sage). CC-BY-NC Cancer Inform Original Research Text 2021 ftpubmed https://doi.org/10.1177/11769351211031864 2021-08-08T00:36:26Z Breast cancer is the most common type of cancer in women globally. The overexpressed proteins, including EGFR, PI3K, AKT1, and CDK4, have a role in the growth of breast cancer cells. The 3D peptide structure of sea cucumber Cucumaria frondosa was modeled and then docked with EGFR, PI3K, AKT1, and CDK4 proteins using AutoDock Vina software. The docking result, which has the best binding affinity value, is continued with molecular dynamics simulation. The docking results showed that all peptides bind to the active sites of the four proteins. WPPNYQW and YDWRF peptides bind to proteins with lower binding affinity values than positive controls. The four proteins were in a stable state when complexed with the WPPNYQW peptide, which was seen from the RMSD and RMSF value. PI3K-YDWRF and AKT1-YDWRF complexes are stable, characterized by high RMSD values and increased volatility in several amino acids. WPPNYQW peptide has high potential as an antibreast cancer agent because it binds to the active sites of the four proteins with low binding affinity values and stable interactions. Meanwhile, the YDWRF peptide interacts with the four proteins with low binding affinity values, but the interaction is only stable on PI3K and AKT1 proteins. Text Cucumaria frondosa PubMed Central (PMC) Vina ENVELOPE(23.433,23.433,69.833,69.833) Cancer Informatics 20 117693512110318 |
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Original Research Wargasetia, Teresa Liliana Ratnawati, Hana Widodo, Nashi Widyananda, Muhammad Hermawan Bioinformatics Study of Sea Cucumber Peptides as Antibreast Cancer Through Inhibiting the Activity of Overexpressed Protein (EGFR, PI3K, AKT1, and CDK4) |
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Original Research |
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Breast cancer is the most common type of cancer in women globally. The overexpressed proteins, including EGFR, PI3K, AKT1, and CDK4, have a role in the growth of breast cancer cells. The 3D peptide structure of sea cucumber Cucumaria frondosa was modeled and then docked with EGFR, PI3K, AKT1, and CDK4 proteins using AutoDock Vina software. The docking result, which has the best binding affinity value, is continued with molecular dynamics simulation. The docking results showed that all peptides bind to the active sites of the four proteins. WPPNYQW and YDWRF peptides bind to proteins with lower binding affinity values than positive controls. The four proteins were in a stable state when complexed with the WPPNYQW peptide, which was seen from the RMSD and RMSF value. PI3K-YDWRF and AKT1-YDWRF complexes are stable, characterized by high RMSD values and increased volatility in several amino acids. WPPNYQW peptide has high potential as an antibreast cancer agent because it binds to the active sites of the four proteins with low binding affinity values and stable interactions. Meanwhile, the YDWRF peptide interacts with the four proteins with low binding affinity values, but the interaction is only stable on PI3K and AKT1 proteins. |
format |
Text |
author |
Wargasetia, Teresa Liliana Ratnawati, Hana Widodo, Nashi Widyananda, Muhammad Hermawan |
author_facet |
Wargasetia, Teresa Liliana Ratnawati, Hana Widodo, Nashi Widyananda, Muhammad Hermawan |
author_sort |
Wargasetia, Teresa Liliana |
title |
Bioinformatics Study of Sea Cucumber Peptides as Antibreast Cancer Through Inhibiting the Activity of Overexpressed Protein (EGFR, PI3K, AKT1, and CDK4) |
title_short |
Bioinformatics Study of Sea Cucumber Peptides as Antibreast Cancer Through Inhibiting the Activity of Overexpressed Protein (EGFR, PI3K, AKT1, and CDK4) |
title_full |
Bioinformatics Study of Sea Cucumber Peptides as Antibreast Cancer Through Inhibiting the Activity of Overexpressed Protein (EGFR, PI3K, AKT1, and CDK4) |
title_fullStr |
Bioinformatics Study of Sea Cucumber Peptides as Antibreast Cancer Through Inhibiting the Activity of Overexpressed Protein (EGFR, PI3K, AKT1, and CDK4) |
title_full_unstemmed |
Bioinformatics Study of Sea Cucumber Peptides as Antibreast Cancer Through Inhibiting the Activity of Overexpressed Protein (EGFR, PI3K, AKT1, and CDK4) |
title_sort |
bioinformatics study of sea cucumber peptides as antibreast cancer through inhibiting the activity of overexpressed protein (egfr, pi3k, akt1, and cdk4) |
publisher |
SAGE Publications |
publishDate |
2021 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8283226/ http://www.ncbi.nlm.nih.gov/pubmed/34345161 https://doi.org/10.1177/11769351211031864 |
long_lat |
ENVELOPE(23.433,23.433,69.833,69.833) |
geographic |
Vina |
geographic_facet |
Vina |
genre |
Cucumaria frondosa |
genre_facet |
Cucumaria frondosa |
op_source |
Cancer Inform |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8283226/ http://www.ncbi.nlm.nih.gov/pubmed/34345161 http://dx.doi.org/10.1177/11769351211031864 |
op_rights |
© The Author(s) 2021 https://creativecommons.org/licenses/by-nc/4.0/This article is distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 License (https://creativecommons.org/licenses/by-nc/4.0/) which permits non-commercial use, reproduction and distribution of the work without further permission provided the original work is attributed as specified on the SAGE and Open Access pages (https://us.sagepub.com/en-us/nam/open-access-at-sage). |
op_rightsnorm |
CC-BY-NC |
op_doi |
https://doi.org/10.1177/11769351211031864 |
container_title |
Cancer Informatics |
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20 |
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117693512110318 |
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1766395570567512064 |