Molecular Docking of Monomethine Cyanine Dyes to Lysozyme Amyloid Fibrils
Protein aggregation into highly ordered supramolecular aggregates is the hallmark of many degenerative diseases including the neurological disorders (Parkinson’s, Alzheimer’s, and Huntington’s diseases), type II diabetes, systemic amyloidosis, spongiform encephalopathies, etc. One of the simplest an...
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| Format: | Article |
| Language: | English |
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V.N. Karazin Kharkiv National University Publishing
2022-09-01
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| Series: | East European Journal of Physics |
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| Online Access: | https://periodicals.karazin.ua/eejp/article/view/18846 |
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| author | Olga Zhytniakivska Uliana Tarabara Atanas Kurutos Kateryna Vus Valeriya Trusova Galyna Gorbenko |
| author_facet | Olga Zhytniakivska Uliana Tarabara Atanas Kurutos Kateryna Vus Valeriya Trusova Galyna Gorbenko |
| author_sort | Olga Zhytniakivska |
| collection | DOAJ |
| description | Protein aggregation into highly ordered supramolecular aggregates is the hallmark of many degenerative diseases including the neurological disorders (Parkinson’s, Alzheimer’s, and Huntington’s diseases), type II diabetes, systemic amyloidosis, spongiform encephalopathies, etc. One of the simplest and effective methods for the identification and characterization of amyloid fibrils in vitro and the visualization of amyloid inclusions in vivo is based on the use of probes sensitive to the beta-pleated motifs. In the attempt to design new amyloid-sensing dyes or to optimization the existing molecules, it is crucial to have the sufficient knowledge of the molecular and atomic levels interactions in the binding sites. Among the especially useful methods available to provide the atomic-level insights into the mechanisms of various types of biomolecular interactions is molecular docking technique. In the present study, the molecular docking tool has been employed to investigate the interactions between the monomethine cyanine dyes and the lysozyme amyloid fibrils constructed from the K-peptide of lysozyme, GILQINSRW (residues 54–62 of the wild-type protein). Using the AutoDOCK and the protein-ligand interaction profiler PLIP it was found: i) monomethines interact with the fibril surface (with the aromatic residues on the top of β-sheet or with the edges of the β-sheet); ii) the dye binding is governed by the hydrophobic interactions, salt bridges and the hydrogen bonds between the aliphatic substituents on the nitrogen atom of benzothiazole part of dye molecules and the lysozyme amyloid fibril; iii) the variations in the cyanine structure and in the lysozyme amiloid twisting didn’t insert significant effect on the binding mode of cyanines. |
| first_indexed | 2024-04-09T15:50:06Z |
| format | Article |
| id | doaj.art-be73e05f6fb342e7a67e6c230d31de58 |
| institution | Directory Open Access Journal |
| issn | 2312-4334 2312-4539 |
| language | English |
| last_indexed | 2024-04-09T15:50:06Z |
| publishDate | 2022-09-01 |
| publisher | V.N. Karazin Kharkiv National University Publishing |
| record_format | Article |
| series | East European Journal of Physics |
| spelling | doaj.art-be73e05f6fb342e7a67e6c230d31de582023-04-26T11:52:16ZengV.N. Karazin Kharkiv National University PublishingEast European Journal of Physics2312-43342312-45392022-09-01314214810.26565/2312-4334-2022-3-1818846Molecular Docking of Monomethine Cyanine Dyes to Lysozyme Amyloid FibrilsOlga Zhytniakivska0Uliana Tarabara1Atanas Kurutos2Kateryna Vus3Valeriya Trusova4Galyna Gorbenko5Department of Medical Physics and Biomedical Nanotechnologies, V.N. Karazin Kharkiv National University, Kharkiv, Ukraine Department of Medical Physics and Biomedical Nanotechnologies, V.N. Karazin Kharkiv National University, Kharkiv, UkraineInstitute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Sofia, Bulgaria; Department of Pharmaceutical and Applied Organic Chemistry, Faculty of Chemistry and Pharmacy Sofia University, Sofia, BulgariaDepartment of Medical Physics and Biomedical Nanotechnologies, V.N. Karazin Kharkiv National University, Kharkiv, UkraineDepartment of Medical Physics and Biomedical Nanotechnologies, V.N. Karazin Kharkiv National University, Kharkiv, UkraineDepartment of Medical Physics and Biomedical Nanotechnologies, V.N. Karazin Kharkiv National University, Kharkiv, UkraineProtein aggregation into highly ordered supramolecular aggregates is the hallmark of many degenerative diseases including the neurological disorders (Parkinson’s, Alzheimer’s, and Huntington’s diseases), type II diabetes, systemic amyloidosis, spongiform encephalopathies, etc. One of the simplest and effective methods for the identification and characterization of amyloid fibrils in vitro and the visualization of amyloid inclusions in vivo is based on the use of probes sensitive to the beta-pleated motifs. In the attempt to design new amyloid-sensing dyes or to optimization the existing molecules, it is crucial to have the sufficient knowledge of the molecular and atomic levels interactions in the binding sites. Among the especially useful methods available to provide the atomic-level insights into the mechanisms of various types of biomolecular interactions is molecular docking technique. In the present study, the molecular docking tool has been employed to investigate the interactions between the monomethine cyanine dyes and the lysozyme amyloid fibrils constructed from the K-peptide of lysozyme, GILQINSRW (residues 54–62 of the wild-type protein). Using the AutoDOCK and the protein-ligand interaction profiler PLIP it was found: i) monomethines interact with the fibril surface (with the aromatic residues on the top of β-sheet or with the edges of the β-sheet); ii) the dye binding is governed by the hydrophobic interactions, salt bridges and the hydrogen bonds between the aliphatic substituents on the nitrogen atom of benzothiazole part of dye molecules and the lysozyme amyloid fibril; iii) the variations in the cyanine structure and in the lysozyme amiloid twisting didn’t insert significant effect on the binding mode of cyanines.https://periodicals.karazin.ua/eejp/article/view/18846monomethine cyanine dyeslysozyme amyloid fibrilsmolecular docking |
| spellingShingle | Olga Zhytniakivska Uliana Tarabara Atanas Kurutos Kateryna Vus Valeriya Trusova Galyna Gorbenko Molecular Docking of Monomethine Cyanine Dyes to Lysozyme Amyloid Fibrils East European Journal of Physics monomethine cyanine dyes lysozyme amyloid fibrils molecular docking |
| title | Molecular Docking of Monomethine Cyanine Dyes to Lysozyme Amyloid Fibrils |
| title_full | Molecular Docking of Monomethine Cyanine Dyes to Lysozyme Amyloid Fibrils |
| title_fullStr | Molecular Docking of Monomethine Cyanine Dyes to Lysozyme Amyloid Fibrils |
| title_full_unstemmed | Molecular Docking of Monomethine Cyanine Dyes to Lysozyme Amyloid Fibrils |
| title_short | Molecular Docking of Monomethine Cyanine Dyes to Lysozyme Amyloid Fibrils |
| title_sort | molecular docking of monomethine cyanine dyes to lysozyme amyloid fibrils |
| topic | monomethine cyanine dyes lysozyme amyloid fibrils molecular docking |
| url | https://periodicals.karazin.ua/eejp/article/view/18846 |
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