Fullerene-Amyloid Complexes as Perspective Nanocomposites: Molecular Docking Studies

V.M. Trusova; P.E. Kuznietsov; O.A. Zhytniakivska; U.K. Tarabara; K.A. Vus; G.P. Gorbenko

doi:10.15407/ujpe68.12.807

Fullerene-Amyloid Complexes as Perspective Nanocomposites: Molecular Docking Studies

Authors

V.M. Trusova Department of Medical Physics and Biomedical Nanotechnologies, V.N. Karazin Kharkiv National University
P.E. Kuznietsov O.I. Akhiezer Department for Nuclear Physics and High Energy Physics, V.N. Karazin Kharkiv National University
O.A. Zhytniakivska Department of Medical Physics and Biomedical Nanotechnologies, V.N. Karazin Kharkiv National University
U.K. Tarabara Department of Medical Physics and Biomedical Nanotechnologies, V.N. Karazin Kharkiv National University
K.A. Vus Department of Medical Physics and Biomedical Nanotechnologies, V.N. Karazin Kharkiv National University
G.P. Gorbenko Department of Medical Physics and Biomedical Nanotechnologies, V.N. Karazin Kharkiv National University

DOI:

https://doi.org/10.15407/ujpe68.12.807

Keywords:

fullerenes, amyloid fibrils, molecular docking studies, nanocomposite materials

Abstract

The molecular interactions between the amyloid fibrils from Aβ-peptide, insulin and α-synuclein and fullerenes of different sizes, including C₂₀, C₃₆, C₆₀, C₇₀, and C₈₄, have been studied using the molecular docking approach. The fullerenes are found to bind to the loop or turn region of Aβ- and α-synuclein fibrillar assemblies, but reside at the end of insulin amyloid fibers, reflecting the lower affinity of carbon nanostructures to the latter aggregated protein. For all systems studied here, the fullerene binding to amyloid fibrils is size-dependent, with larger fullerenes exhibiting a higher binding affinity and a lower total energy of complexation. The analysis of side chain contacts highlights the pivotal role of van der Waals forces, specifically, alkyl and π-alkyl interactions, in the stabilization of the fullerene-amyloid complexes. The results obtained are discussed in terms of novel nanocomposite materials based on carbon nanoparticles and fibrillar proteins, as well as of the fullerene role in anti-amyloid therapy.

References

A. Cho, S. Park. Exploring the global innovation systems perspective by applying openness index to national systems of innovation. J. Open Innov. Technol. Mark. Complex 8, 181 (2022).

https://doi.org/10.3390/joitmc8040181

P.K. Sharma, S. Dorlikar, P. Rawat, V. Malik, N. Vats, M. Sharma, J.S. Rhyee, A.K. Kaushik. Nanotechnology and its application: A review (Nanotechnology in Cancer Management, 2021).

https://doi.org/10.1016/B978-0-12-818154-6.00010-X

H. Mobeen, M. Safdar, A. Fatima, S. Afzal, H. Zaman, Z. Mehdi. Emerging applications of nanotechnology in context to immunology: A comprehensive review. Front. Bioeng. Biotechnol. 10, 1 (2022).

https://doi.org/10.3389/fbioe.2022.1024871

A.D. Goswami, D.H. Trivedi, N.L. Jadhav, D.V. Pinjari. Sustainable and green synthesis of carbon nanomaterials: A review. J. Environ. Chem. Engineer. 9, 106118 (2021).

https://doi.org/10.1016/j.jece.2021.106118

R. Sridharan, B. Monisha, P.S. Kumar, K.V. Gayathri. Carbon nanomaterials and its applications in pharmaceuticals: A brief review. Chemosphere 294, 133731 (2022).

https://doi.org/10.1016/j.chemosphere.2022.133731

R.B. Onyancha, K.E. Ukhurebor, U.O. Aigbe, O.A. Osibote, H.S. Kusuma, H. Darmokoesoemo. A methodical review on carbon-based nanomaterials in energy-related applications. Ads. Sci. Technol. 2022, 4438286 (2022).

https://doi.org/10.1155/2022/4438286

P. Harris. Fullerene polymers: A brief review. J. Carbon Res. 6, 71 (2020).

https://doi.org/10.3390/c6040071

M. Paukov, C. Kramberger, I. Begichev, M. Kharlamova, M. Burdanova. Functionalized fullerenes and their applications in electrochemistry, solar cells, and nanoelectronics. Materials 16, 1276 (2023).

https://doi.org/10.3390/ma16031276

R. Bakry, R.M. Vallant, M. Najam-ul-Haq, M. Rainer, Z. Szabo, C.W. Huck, G.K. Bonn. Medicinal applications of fullerenes. Int. J. Nanomedicine 2, 639 (2007).

H. Kazemzadeh, M. Mozafari. Fullerene-based delivery systems. Drug Discovery Today 24, 898 (2019).

https://doi.org/10.1016/j.drudis.2019.01.013

N. Malhotra, G. Audira, A.L. Castillo, P. Siregar, J. Ruallo, M.J. Roldan, J.-R. Chen, J.-S. Lee, T.-R. Ger, C.-D. Hsiao. An update report on the biosafety and potential toxicity of fullerene-based nanomaterials toward aquatic animals. Oxid. Med. Cell Longev. 2021, 7995223 (2021).

https://doi.org/10.1155/2021/7995223

C. Li, R. Mezzenga. The interplay between carbon nanomaterials and amyloid fibrils in bio-nanotechnology. Nanoscale 5, 6207 (2013).

https://doi.org/10.1039/c3nr01644g

P.C. Ke, R. Zhou, L.C. Serpell, R. Riek, T.P.J. Knowles, H.A. Lashuel, E. Gazit, I.W. Hamley, T.P. Davis, M. Fandrich, D.E. Otzen, M.R. Chapman, C.M. Dobson, D.S. Eisenberg, R. Mezzenga. Half a century of amyloids: past, present and future. Chem. Soc. Rev. 49, 5473 (2020).

https://doi.org/10.1039/C9CS00199A

B. Choi, T. Kim, S.W. Lee, K. Eom. Nanomechanical characterization of amyloid fibrils using single-molecule experiments and computational simulations. Nanoscale Biol. Mater. 2016, 5873695 (2016).

https://doi.org/10.1155/2016/5873695

C. Li, R. Mezzenga. Functionalization of multiwalled carbon nanotubes and their pH-responsive hydrogels with amyloid fibrils. Langmuir 28, 10142 (2012).

https://doi.org/10.1021/la301541d

J. Majoroˇsova, M.A. Schroer, N. Tomaˇsoviˇcov'a, M. Batkov'a, P.-S. Hu, M. Kubovˇc'ıkov'a, D.I. Svergun, P. Kopˇcansk'y. Effect of the concentration of protein and nanoparticles on the structure of biohybrid nanocomposites. Biopolymers 111, e23342 (2020).

https://doi.org/10.1002/bip.23342

C. Li, J. Adamcik, R. Mezzenga. Biodegradable nanocomposites of amyloid fibrils and graphene with shape-memory and enzyme-sensing properties. Nat. Nanotechnol. 7, 421 (2012).

https://doi.org/10.1038/nnano.2012.62

K. Siposova, V.I. Petrenko, O.I. Ivankov, A. Musatov, L.A. Bulavin, M.V. Avdeev, O.A. Kyzyma. Fullerenes as an effective amyloid fibrils disaggregating nanomaterial. ACS Appl. Mater. Interfaces 12, 29 (2020).

https://doi.org/10.1021/acsami.0c07964

Z. Liu, Y. Zou, Q. Zhang, P. Chen, Y. Liu, Z. Qian. Distinct binding dynamics, sites and interactions of fullerene and fullerenols with amyloid-β peptides revealed by molecular dynamics simulations. Int. J. Mol. Sci. 20, 2048 (2019).

https://doi.org/10.3390/ijms20082048

C. Bai, Z. Lao, Y. Chen, Y. Tang, G. Wei. Pristine and hydroxylated fullerenes prevent the aggregation of human islet amyloid polypeptide and display different inhibitory mechanisms. Front. Chem. 8, 51 (2020).

https://doi.org/10.3389/fchem.2020.00051

E. Pettersen, T. Goddard, C. Huang, G. Couch, D. Greenblatt, E. Meng, T. Ferrin. UCSF Chimera - a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605 (2004).

https://doi.org/10.1002/jcc.20084

I. Guedes, A.M.S. Barreto, D. Marinho, E. Krempser, M.A. Kuenemann, O. Sperandio, L.E. Dardenne, M.A. Miteva. New machine learning and physics-based scoring functions for drug discovery. Sci. Rep. 11, 3198 (2021).

https://doi.org/10.1038/s41598-021-82410-1

Y. Yan, D. Zhang, P. Zhou, B. Li, S.-Y. Huang. HDOCK: A web server for protein-protein and protein-DNA/RNA docking based on a hybrid strategy. Nucl. Acids Res. 45, W365 (2017).

https://doi.org/10.1093/nar/gkx407

M. Karplus, H. J. Kolker. Van der Waals forces in atoms and molecules. J. Chem. Phys. 41, 3955 (1964).

https://doi.org/10.1063/1.1725842

R. Macovez. Physical properties of organic fullerene cocrystals. Front. Mater. 4, 46 (2018).

https://doi.org/10.3389/fmats.2017.00046

J. Ribas, E. Cubero, F. Luque, M. Orozco. Theoretical study of alkyl-π and aryl-π interactions. Reconciling theory and experiment. J. Org. Chem. 67, 7057 (2002).

https://doi.org/10.1021/jo0201225

Y. Li, C. Zhao, F. Luo, Z. Liu, X. Gui, Z. Luo, X. Zhang, D. Li, C. Liu, X. Li. Amyloid fibril structure of α-synuclein determined by cryo-electron microscopy. Cell Res. 28, 897 (2018).

https://doi.org/10.1038/s41422-018-0075-x

P. Huy, M. Li. Binding of fullerenes to amyloid beta fibrils: size matters. Phys. Chem. Chem. Phys. 16, 20030 (2014).

https://doi.org/10.1039/C4CP02348J

Downloads

Published

2024-01-06

How to Cite

Trusova, V., Kuznietsov, P., Zhytniakivska, O., Tarabara, U., Vus, K., & Gorbenko, G. (2024). Fullerene-Amyloid Complexes as Perspective Nanocomposites: Molecular Docking Studies. Ukrainian Journal of Physics, 68(12), 807. https://doi.org/10.15407/ujpe68.12.807

Download Citation

Issue

Vol. 68 No. 12 (2023)

Section

Physics of liquids and liquid systems, biophysics and medical physics

License

Copyright Agreement
License to Publish the Paper
Kyiv, Ukraine

The corresponding author and the co-authors (hereon referred to as the Author(s)) of the paper being submitted to the Ukrainian Journal of Physics (hereon referred to as the Paper) from one side and the Bogolyubov Institute for Theoretical Physics, National Academy of Sciences of Ukraine, represented by its Director (hereon referred to as the Publisher) from the other side have come to the following Agreement:

1. Subject of the Agreement.
The Author(s) grant(s) the Publisher the free non-exclusive right to use the Paper (of scientific, technical, or any other content) according to the terms and conditions defined by this Agreement.

2. The ways of using the Paper.
2.1. The Author(s) grant(s) the Publisher the right to use the Paper as follows.
2.1.1. To publish the Paper in the Ukrainian Journal of Physics (hereon referred to as the Journal) in original language and translated into English (the copy of the Paper approved by the Author(s) and the Publisher and accepted for publication is a constitutive part of this License Agreement).
2.1.2. To edit, adapt, and correct the Paper by approval of the Author(s).
2.1.3. To translate the Paper in the case when the Paper is written in a language different from that adopted in the Journal.
2.2. If the Author(s) has(ve) an intent to use the Paper in any other way, e.g., to publish the translated version of the Paper (except for the case defined by Section 2.1.3 of this Agreement), to post the full Paper or any its part on the web, to publish the Paper in any other editions, to include the Paper or any its part in other collections, anthologies, encyclopaedias, etc., the Author(s) should get a written permission from the Publisher.

3. License territory.
The Author(s) grant(s) the Publisher the right to use the Paper as regulated by sections 2.1.1–2.1.3 of this Agreement on the territory of Ukraine and to distribute the Paper as indispensable part of the Journal on the territory of Ukraine and other countries by means of subscription, sales, and free transfer to a third party.

4. Duration.
4.1. This Agreement is valid starting from the date of signature and acts for the entire period of the existence of the Journal.

5. Loyalty.
5.1. The Author(s) warrant(s) the Publisher that:
– he/she is the true author (co-author) of the Paper;
– copyright on the Paper was not transferred to any other party;
– the Paper has never been published before and will not be published in any other media before it is published by the Publisher (see also section 2.2);
– the Author(s) do(es) not violate any intellectual property right of other parties. If the Paper includes some materials of other parties, except for citations whose length is regulated by the scientific, informational, or critical character of the Paper, the use of such materials is in compliance with the regulations of the international law and the law of Ukraine.

6. Requisites and signatures of the Parties.
Publisher: Bogolyubov Institute for Theoretical Physics, National Academy of Sciences of Ukraine.
Address: Ukraine, Kyiv, Metrolohichna Str. 14-b.
Author: Electronic signature on behalf and with endorsement of all co-authors.