Modeling approaches to investigate the interaction between Fullerene and β-Amyloid
DOI:
https://doi.org/10.33448/rsd-v10i11.19585Keywords:
Alzheimer's disease; β-amyloid; Inhibitors; Nanoparticle; Fullerene.Abstract
Alzheimer's disease is the progressive loss of mental function, characterized by degeneration of brain tissue, including the loss of nerve cells, the accumulation of an abnormal protein called β-amyloid, and the development of neurofibrillary tangles. β-amyloid aggregation is a physiological feature of Alzheimer's disease and is closely related to neurodegeneration caused by Alzheimer's. Recently, new therapies are looking for promising compounds capable of breaking down β-amyloid. Nanoparticles (NPs) are highly promising candidates for several important biological applications such as gene delivery, cell imaging and tumor therapy. Among numerous types of nanomaterials, carbon NPs have attracted particular interests, such as: zero-dimensional fullerene, one-dimensional (1D) carbon nanotubes and two-dimensional (2D) graphene. Because of this, we used molecular docking to investigate the interaction capacity of the fullerene nanoparticle with the β-amyloid aggregate. The docking results showed that the main interactions established were hydrophobic. The System had an affinity energy of -41.04 Kcal, obtained with the MM-GBSA method.
References
Ahmed, L., Rasulev, B., Turabekova, M., Leszczynska, D., & Leszczynski, J. (2013). Receptor- and ligand-based study of fullerene analogues: Comprehensive computational approach including quantum-chemical, QSAR and molecular docking simulations. Organic and Biomolecular Chemistry, 11(35), 5798–5808. https://doi.org/10.1039/c3ob40878g
Araújo, P. H. F., Ramos, R. S., da Cruz, J. N., Silva, S. G., Ferreira, E. F. B., de Lima, L. R., Macêdo, W. J. C., Espejo-Román, J. M., Campos, J. M., & Santos, C. B. R. (2020). Identification of potential COX-2 inhibitors for the treatment of inflammatory diseases using molecular modeling approaches. Molecules, 25(18), 4183. https://doi.org/10.3390/molecules25184183
Benyamini, H., Shulman-Peleg, A., Wolfson, H. J., Belgorodsky, B., Fadeev, L., & Gozin, M. (2006). Interaction of C60-fullerene and carboxyfullerene with proteins: Docking and binding site alignment. Bioconjugate Chemistry, 17(2), 378–386. https://doi.org/10.1021/bc050299g
Cascaes, M. M., Silva, S. G., Cruz, J. N., Santana de Oliveira, M., Oliveira, J., Moraes, A. A. B. de, Costa, F. A. M. da, da Costa, K. S., Diniz do Nascimento, L., & Helena de Aguiar Andrade, E. (2021). First report on the Annona exsucca DC. Essential oil and in silico identification of potential biological targets of its major compounds. Natural Product Research. https://doi.org/10.1080/14786419.2021.1893724
Castro, A. L. G., Cruz, J. N., Sodré, D. F., Correa-Barbosa, J., Azonsivo, R., de Oliveira, M. S., de Sousa Siqueira, J. E., da Rocha Galucio, N. C., de Oliveira Bahia, M., Burbano, R. M. R., do Rosário Marinho, A. M., Percário, S., Dolabela, M. F., & Vale, V. V. (2021). Evaluation of the genotoxicity and mutagenicity of isoeleutherin and eleutherin isolated from Eleutherine plicata herb. using bioassays and in silico approaches. Arabian Journal of Chemistry, 14(4), 103084. https://doi.org/10.1016/j.arabjc.2021.103084
Cheung, J., Gary, E. N., Shiomi, K., & Rosenberry, T. L. (2013). Structures of human acetylcholinesterase bound to dihydrotanshinone i and territrem B show peripheral site flexibility. ACS Medicinal Chemistry Letters, 4(11), 1091–1096. https://doi.org/10.1021/ml400304w
Colvin, M. T., Silvers, R., Ni, Q. Z., Can, T. V., Sergeyev, I., Rosay, M., Donovan, K. J., Michael, B., Wall, J., Linse, S., & Griffin, R. G. (2016). Atomic Resolution Structure of Monomorphic Aβ42 Amyloid Fibrils. Journal of the American Chemical Society, 138(30), 9663–9674. https://doi.org/10.1021/jacs.6b05129
Costa, E. B. B., Silva, R. C. C., Espejo-Román, J. M. M., Neto, M. F. de A. F. d. A., Cruz, J. N. N., Leite, F. H. A. H. A., Silva, C. H. T. P. H. T. P., Pinheiro, J. C. C., Macêdo, W. J. C. J. C., & Santos, C. B. R. B. R. (2020). Chemometric methods in antimalarial drug design from 1,2,4,5-tetraoxanes analogues. SAR and QSAR in Environmental Research, 31(9), 1–19. https://doi.org/10.1080/1062936X.2020.1803961
Costa, R. A., Cruz, J. N., Nascimento, F. C. A., Silva, S. O. S. G., Silva, S. O. S. G., Martelli, M. C., Carvalho, S. M. L., Santos, C. B. R., Neto, A. M. J. C., & Brasil, D. S. B. (2019). Studies of NMR, molecular docking, and molecular dynamics simulation of new promising inhibitors of cruzaine from the parasite Trypanosoma cruzi. Medicinal Chemistry Research, 28(3), 246–259. https://doi.org/10.1007/s00044-018-2280-z
Coupé, P., Manjón, J. V., Lanuza, E., & Catheline, G. (2019). Lifespan Changes of the Human Brain In Alzheimer’s Disease. Scientific Reports, 9(1), 1–12. https://doi.org/10.1038/s41598-019-39809-8
da Silva Costa, A. C., Carvalho, S. C., de Farias Silva, N., do Nascimento-Júnior, A. E. S., Cruz, J. N., de Jesus Chaves Neto, A. M., do Socorro Barros Brasil, D., Silva-Júnior, J. O. C., & Ribeiro-Costa, R. M. (2020). Effect of chitosan/albendazole nanocarriers’ solvation by molecular dynamics. Theoretical Chemistry Accounts, 139(7), 1–15. https://doi.org/10.1007/s00214-020-02620-0
Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98(12), 10089–10092. https://doi.org/10.1063/1.464397
De Castro Souza, I., & Da Silva Gonçalvesa, A. (2019). Computational studies of fullerene derivatives as pesticide captors. Orbital, 11(1), 10–17. https://doi.org/10.17807/orbital.v11i1.1215
Dennington, R., Keith, T., & Millam, J. (2009). GaussView, Version 5. In Semichem Inc. , Shawnee Mission, KS (p. Semichem Inc).
Deture, M. A., & Dickson, D. W. (2019). The neuropathological diagnosis of Alzheimer’s disease. In Molecular Neurodegeneration (Vol. 14, Issue 1, pp. 1–18). BioMed Central Ltd. https://doi.org/10.1186/s13024-019-0333-5
Durdagi, S., Mavromoustakos, T., Chronakis, N., & Papadopoulos, M. G. (2008). Computational design of novel fullerene analogues as potential HIV-1 PR inhibitors: Analysis of the binding interactions between fullerene inhibitors and HIV-1 PR residues using 3D QSAR, molecular docking and molecular dynamics simulations. Bioorganic and Medicinal Chemistry, 16(23), 9957–9974. https://doi.org/10.1016/j.bmc.2008.10.039
Frozza, R. L., Lourenco, M. V., & de Felice, F. G. (2018). Challenges for Alzheimer’s disease therapy: Insights from novel mechanisms beyond memory defects. In Frontiers in Neuroscience (Vol. 12, Issue FEB, p. 37). Frontiers Media S.A. https://doi.org/10.3389/fnins.2018.00037
Hess, B., Kutzner, C., Van Der Spoel, D., & Lindahl, E. (2008). GRGMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 4(3), 435–447. https://doi.org/10.1021/ct700301q
Hu, T., Chen, C., Huang, G., & Yang, X. (2016). Antibody modified-silver nanoparticles for colorimetric immuno sensing of Aβ(1-40/1-42) based on the interaction between β-amyloid and Cu2+. Sensors and Actuators, B: Chemical, 234, 63–69. https://doi.org/10.1016/j.snb.2016.04.159
Hu, T., Lu, S., Chen, C., Sun, J., & Yang, X. (2017). Colorimetric sandwich immunosensor for Aβ(1-42) based on dual antibody-modified gold nanoparticles. Sensors and Actuators, B: Chemical, 243, 792–799. https://doi.org/10.1016/j.snb.2016.12.052
Khan, I., Saeed, K., & Khan, I. (2019). Nanoparticles: Properties, applications and toxicities. In Arabian Journal of Chemistry (Vol. 12, Issue 7, pp. 908–931). Elsevier B.V. https://doi.org/10.1016/j.arabjc.2017.05.011
Leão, R. P., Cruz, J. V. J. N., da Costa, G. V., Cruz, J. V. J. N., Ferreira, E. F. B., Silva, R. C., de Lima, L. R., Borges, R. S., Dos Santos, G. B., & Santos, C. B. R. (2020). Identification of new rofecoxib-based cyclooxygenase-2 inhibitors: A bioinformatics approach. Pharmaceuticals, 13(9), 1–26. https://doi.org/10.3390/ph13090209
Leonis, G., Avramopoulos, A., Papavasileiou, K. D., Reis, H., Steinbrecher, T., & Papadopoulos, M. G. (2015). A Comprehensive Computational Study of the Interaction between Human Serum Albumin and Fullerenes. Journal of Physical Chemistry B, 119(48), 14971–14985. https://doi.org/10.1021/acs.jpcb.5b05998
Lima, A. R. J. A. de M., Siqueira, A. S., Möller, M. L. S., Souza, R. C. de, Cruz, J. N., Lima, A. R. J. A. de M., Silva, R. C. da, Aguiar, D. C. F., Junior, J. L. da S. G. V., & Gonçalves, E. C. (2020). In silico improvement of the cyanobacterial lectin microvirin and mannose interaction. Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2020.1821782
Mankar, S., Anoop, A., Sen, S., & Maji, S. K. (2011). Nanomaterials: amyloids reflect their brighter side. Nano Reviews, 2(1), 6032. https://doi.org/10.3402/nano.v2i0.6032
Mohajeri, M., Behnam, B., Barreto, G. E., & Sahebkar, A. (2019). Carbon nanomaterials and amyloid-beta interactions: potentials for the detection and treatment of Alzheimer’s disease? In Pharmacological Research (Vol. 143, pp. 186–203). Academic Press. https://doi.org/10.1016/j.phrs.2019.03.023
Neto, R. de A. M. M., Santos, C. B. R. R., Henriques, S. V. C. C., Machado, L. de O., Cruz, J. N., da Silva, C. H. T. d. P. T. de P., Federico, L. B., Oliveira, E. H. C. d. C. de, de Souza, M. P. C. C., da Silva, P. N. B. B., Taft, C. A., Ferreira, I. M., & Gomes, M. R. F. F. (2020). Novel chalcones derivatives with potential antineoplastic activity investigated by docking and molecular dynamics simulations. Journal of Biomolecular Structure and Dynamics, 1–13. https://doi.org/10.1080/07391102.2020.1839562
Qian, M., Shan, Y., Guan, S., Zhang, H., Wang, S., & Han, W. (2016). Structural Basis of Fullerene Derivatives as Novel Potent Inhibitors of Protein Tyrosine Phosphatase 1B: Insight into the Inhibitory Mechanism through Molecular Modeling Studies. Journal of Chemical Information and Modeling, 56(10), 2024–2034. https://doi.org/10.1021/acs.jcim.6b00482
Santana de Oliveira, M., Neves da Cruz, J., Almeida da Costa, W., Silva, S. G., da Paz Brito, M., Fernandes de Menezes, S. A., de Jesus Chaves Neto, A. M., de Aguiar Andrade, E. H., de Carvalho, R. N., da Cruz, J. N., Almeida da Costa, W., Silva, S. G., Brito, M. da P., de Menezes, S. A. F., de Jesus Chaves Neto, A. M., de Aguiar Andrade, E. H., de Carvalho Junior, R. N., Oliveira, M. S. De, Neves, J., & de Carvalho, R. N. (2020). Chemical Composition, Antimicrobial Properties of Siparuna guianensis Essential Oil and a Molecular Docking and Dynamics Molecular Study of its Major Chemical Constituent. Molecules, 25(17), 3852. https://doi.org/Manuscript accepted
Santana de Oliveira, M., Pereira da Silva, V. M., Cantão Freitas, L., Gomes Silva, S., Nevez Cruz, J., & de Aguiar Andrade, E. H. (2021). Extraction Yield, Chemical Composition, Preliminary Toxicity of Bignonia nocturna (Bignoniaceae) Essential Oil and in Silico Evaluation of the Interaction. Chemistry and Biodiversity, cbdv.202000982. https://doi.org/10.1002/cbdv.202000982
Santos, C. B. R., Santos, K. L. B., Cruz, J. N., Leite, F. H. A., Borges, R. S., Taft, C. A., Campos, J. M., & Silva, C. H. T. P. (2020). Molecular modeling approaches of selective adenosine receptor type 2A agonists as potential anti-inflammatory drugs. Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2020.1761878
Tzoupis, H., Leonis, G., Durdagi, S., Mouchlis, V., Mavromoustakos, T., & Papadopoulos, M. G. (2011). Binding of novel fullerene inhibitors to HIV-1 protease: Insight through molecular dynamics and molecular mechanics Poisson-Boltzmann surface area calculations. Journal of Computer-Aided Molecular Design, 25(10), 959–976. https://doi.org/10.1007/s10822-011-9475-4
Wang, J., Gu, B. J., Masters, C. L., & Wang, Y. J. (2017). A systemic view of Alzheimer disease - Insights from amyloid-β metabolism beyond the brain. In Nature Reviews Neurology (Vol. 13, Issue 10, pp. 612–623). Nature Publishing Group. https://doi.org/10.1038/nrneurol.2017.111
Yu, Y., Sun, H., Hou, T., Wang, S., & Li, Y. (2018). Fullerene derivatives act as inhibitors of leukocyte common antigen based on molecular dynamics simulations. RSC Advances, 8(25), 13997–14008. https://doi.org/10.1039/c7ra13543b
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Copyright (c) 2021 Felipe Magno da Cruz Junior; Jorddy Neves da Cruz; Fabrine Silva Alves; Isaque Gemaque de Medeiros; Gleice Vasconcelos da Silva Pereira; Luciano Augusto de Sousa; Adria Evellin Godinho de Vilhena; Luciane do Socorro Nunes dos Santos Brasil; José de Arimatéia Rodrigues do Rego; Davi do Socorro Barros Brasil
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