Novel bioengineered MBenes for the treatment of Alzheimer's disease: An in-Sillico study

References

• Abedi, M., Abolmaali, S. S., Abedanzadeh, M., Borandeh, S., Samani, S. M., & Tamaddon, A. M. (2019). Citric acid functionalized silane coupling versus post-grafting strategy for dual pH and saline responsive delivery of cisplatin by Fe3O4/carboxyl functionalized mesoporous SiO2 hybrid nanoparticles: A-synthesis, physicochemical and biological characterization. Materials Science and Engineering: C, 104, 109922.
   PubMed Web of Science ®Google Scholar
• Akbarialiabad, H., Dahroud, M. D., Khazaei, M. M., Razmeh, S., & Zarshenas, M. M. (2021). Green tea, a medicinal food with promising neurological benefits. Current Neuropharmacology, 19(3), 349–359. https://doi.org/10.2174/1570159X18666200529152625
   PubMed Web of Science ®Google Scholar
• Alimohammadi, E., Maleki, R., Akbarialiabad, H., & Dahri, M. (2021). Novel pH-responsive nanohybrid for simultaneous delivery of doxorubicin and paclitaxel: An in-silico insight. BMC Chemistry, 15(1), 1–11. https://doi.org/10.1186/s13065-021-00735-4
   PubMed Web of Science ®Google Scholar
• Alimohammadi, E., Nikzad, A., Khedri, M., Rezaian, M., Jahromi, A. M., Rezaei, N., & Maleki, R. (2021). Potential treatment of Parkinson’s disease using new-generation carbon nanotubes: A biomolecular in silico study. Nanomedicine (London, England), 16(3), 189–204. https://doi.org/10.2217/nnm-2020-0372
   PubMed Web of Science ®Google Scholar
• Atri, A., Frölich, L., Ballard, C., Tariot, P. N., Molinuevo, J. L., Boneva, N., Windfeld, K., Raket, L. L., & Cummings, J. L. (2018). Effect of idalopirdine as adjunct to cholinesterase inhibitors on change in cognition in patients with Alzheimer disease: Three randomized clinical trials. JAMA, 319(2), 130–142. https://doi.org/10.1001/jama.2017.20373
   PubMed Web of Science ®Google Scholar
• Beck, D. A., & Daggett, V. (2004). Methods for molecular dynamics simulations of protein folding/unfolding in solution. Methods (San Diego, Calif.), 34(1), 112–120. https://doi.org/10.1016/j.ymeth.2004.03.008
   PubMed Web of Science ®Google Scholar
• Bieschke, J., Russ, J., Friedrich, R. P., Ehrnhoefer, D. E., Wobst, H., Neugebauer, K., & Wanker, E. E. (2010). EGCG remodels mature alpha-synuclein and amyloid-beta fibrils and reduces cellular toxicity . Proceedings of the National Academy of Sciences of the United States of America, 107(17), 7710–7715. https://doi.org/10.1073/pnas.0910723107
   PubMed Web of Science ®Google Scholar
• Chen, Z., Krause, G., & Reif, B. (2005). Structure and orientation of peptide inhibitors bound to beta-amyloid fibrils. Journal of Molecular Biology, 354(4), 760–776. https://doi.org/10.1016/j.jmb.2005.09.055
   PubMed Web of Science ®Google Scholar
• Chen, Y., Wang, L., & Shi, J. (2016). Two-dimensional non-carbonaceous materials-enabled efficient photothermal cancer therapy. Nano Today, 11(3), 292–308. https://doi.org/10.1016/j.nantod.2016.05.009
   Web of Science ®Google Scholar
• Chimene, D., Alge, D. L., & Gaharwar, A. K. (2015). Two-dimensional nanomaterials for biomedical applications: Emerging trends and future prospects . Advanced Materials (Deerfield Beach, Fla.), 27(45), 7261–7284. https://doi.org/10.1002/adma.201502422
   PubMed Web of Science ®Google Scholar
• Chiti, F., & Dobson, C. M. (2006). Protein misfolding, functional amyloid, and human disease. Annual Review of Biochemistry, 75, 333–366. https://doi.org/10.1146/annurev.biochem.75.101304.123901
   PubMed Web of Science ®Google Scholar
• Coric, V., Salloway, S., van Dyck, C. H., Dubois, B., Andreasen, N., Brody, M., Curtis, C., Soininen, H., Thein, S., Shiovitz, T., Pilcher, G., Ferris, S., Colby, S., Kerselaers, W., Dockens, R., Soares, H., Kaplita, S., Luo, F., Pachai, C., … Berman, R. M. (2015). Targeting prodromal Alzheimer disease with avagacestat: A randomized clinical trial. JAMA Neurology, 72(11), 1324–1333. https://doi.org/10.1001/jamaneurol.2015.0607
   PubMed Web of Science ®Google Scholar
• da Silva, J. A., Meneghetti, M. R., & Netz, P. A. (2020). Molecular dynamics simulations of the structural arrangement and density of alkylamine surfactants on copper surfaces: Implications for anisotropic growth of copper nanowires. ACS Applied Nano Materials, 3(6), 5343–5350. https://doi.org/10.1021/acsanm.0c00708
   Web of Science ®Google Scholar
• DeVos, S. L., Corjuc, B. T., Commins, C., Dujardin, S., Bannon, R. N., Corjuc, D., Moore, B. D., Bennett, R. E., Jorfi, M., Gonzales, J. A., Dooley, P. M., Roe, A. D., Pitstick, R., Irimia, D., Frosch, M. P., Carlson, G. A., & Hyman, B. T. (2018). Tau reduction in the presence of amyloid-β prevents tau pathology and neuronal death in vivo. Brain : A Journal of Neurology, 141(7), 2194–2212. https://doi.org/10.1093/brain/awy117
   PubMedGoogle Scholar
• Dhayabaran, D., Florance, E. J., Nandakumar, K., Shanmugarathinam, A., & Puratchikody, A. (2014). Anticonvulsant activity of fraction isolated from ethanolic extract of heartwood of Cedrus deodara. Journal of Natural Medicines, 68(2), 310–315. https://doi.org/10.1007/s11418-013-0798-4
   PubMed Web of Science ®Google Scholar
• Doody, R. S., Thomas, R. G., Farlow, M., Iwatsubo, T., Vellas, B., Joffe, S., Kieburtz, K., Raman, R., Sun, X., Aisen, P. S., Siemers, E., Liu-Seifert, H., & Mohs, R. (2014). Phase 3 trials of solanezumab for mild-to-moderate Alzheimer's disease. The New England Journal of Medicine, 370(4), 311–321. https://doi.org/10.1056/NEJMoa1312889
   PubMed Web of Science ®Google Scholar
• Egan, M. F., Kost, J., Tariot, P. N., Aisen, P. S., Cummings, J. L., Vellas, B., Sur, C., Mukai, Y., Voss, T., Furtek, C., Mahoney, E., Harper Mozley, L., Vandenberghe, R., Mo, Y., & Michelson, D. (2018). Randomized trial of verubecestat for mild-to-moderate Alzheimer's disease. The New England Journal of Medicine, 378(18), 1691–1703. https://doi.org/10.1056/NEJMoa1706441
   PubMed Web of Science ®Google Scholar
• Estrada, L., & Soto, C. (2007). Disrupting beta-amyloid aggregation for Alzheimer disease treatment . Current Topics in Medicinal Chemistry, 7(1), 115–126. https://doi.org/10.2174/156802607779318262
   PubMed Web of Science ®Google Scholar
• Hajipour, M. J., Santoso, M. R., Rezaee, F., Aghaverdi, H., Mahmoudi, M., & Perry, G. (2017). Advances in Alzheimer's diagnosis and therapy: The implications of nanotechnology. Trends in Biotechnology, 35(10), 937–953. https://doi.org/10.1016/j.tibtech.2017.06.002
   PubMed Web of Science ®Google Scholar
• Hanwell, M. D., Curtis, D. E., Lonie, D. C., Vandermeersch, T., Zurek, E., & Hutchison, G. R. (2012). Avogadro: An advanced semantic chemical editor, visualization, and analysis platform. Journal of Cheminformatics, 4(1), 1–17. https://doi.org/10.1186/1758-2946-4-17
   PubMedGoogle Scholar
• Harrington, C. R. (2012). The molecular pathology of Alzheimer's disease. Neuroimaging Clinics of North America, 22(1), 11–22. https://doi.org/10.1016/j.nic.2011.11.003
   PubMed Web of Science ®Google Scholar
• Hollingsworth, S. A., & Dror, R. O. (2018). Molecular dynamics simulation for all. Neuron, 99(6), 1129–1143. https://doi.org/10.1016/j.neuron.2018.08.011
   PubMed Web of Science ®Google Scholar
• Karlawish, J., & Grill, J. D. (2021). The approval of Aduhelm risks eroding public trust in Alzheimer research and the FDA. Nature Reviews Neurology, 1–2.
   PubMed Web of Science ®Google Scholar
• Kaushik, A. C., & Sahi, S. (2017). Molecular modeling and molecular dynamics simulation-based structural analysis of GPR3. Network Modeling Analysis in Health Informatics and Bioinformatics, 6(1), 9. https://doi.org/10.1007/s13721-017-0150-0
   Web of Science ®Google Scholar
• Kühne, T. D., Iannuzzi, M., Del Ben, M., Rybkin, V. V., Seewald, P., Stein, F., Laino, T., Khaliullin, R. Z., Schütt, O., Schiffmann, F., Golze, D., Wilhelm, J., Chulkov, S., Bani-Hashemian, M. H., Weber, V., Borštnik, U., Taillefumier, M., Jakobovits, A. S., Lazzaro, A., … Hutter, J. (2020). CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations. The Journal of Chemical Physics, 152(19), 194103. https://doi.org/10.1063/5.0007045
   PubMed Web of Science ®Google Scholar
• LaFerla, F. M., Green, K. N., & Oddo, S. (2007). Intracellular amyloid-beta in Alzheimer's disease . Nature Reviews. Neuroscience, 8(7), 499–509. https://doi.org/10.1038/nrn2168
   PubMed Web of Science ®Google Scholar
• Lasagna-Reeves, C., Gonzalez-Romero, D., Barria, M. A., Olmedo, I., Clos, A., Sadagopa Ramanujam, V. M., Urayama, A., Vergara, L., Kogan, M. J., & Soto, C. (2010). Bioaccumulation and toxicity of gold nanoparticles after repeated administration in mice. Biochemical and Biophysical Research Communications, 393(4), 649–655. https://doi.org/10.1016/j.bbrc.2010.02.046
   PubMed Web of Science ®Google Scholar
• Lau, D., Jian, W., Yu, Z., & Hui, D. (2018). Nano-engineering of construction materials using molecular dynamics simulations: Prospects and challenges. Composites Part B: Engineering, 143, 282–291. https://doi.org/10.1016/j.compositesb.2018.01.014
   Web of Science ®Google Scholar
• Lee, C., & Ham, S. (2011). Characterizing amyloid-beta protein misfolding from molecular dynamics simulations with explicit water . Journal of Computational Chemistry, 32(2), 349–355. https://doi.org/10.1002/jcc.21628
   PubMed Web of Science ®Google Scholar
• Lemkul, J. A., & Bevan, D. R. (2010). Assessing the stability of Alzheimer's amyloid protofibrils using molecular dynamics. The Journal of Physical Chemistry. B, 114(4), 1652–1660. https://doi.org/10.1021/jp9110794
   PubMed Web of Science ®Google Scholar
• Lobanov, M. Y., Bogatyreva, N., & Galzitskaya, O. (2008). Radius of gyration as an indicator of protein structure compactness. Molecular Biology, 42(4), 623–628. https://doi.org/10.1134/S0026893308040195
   Web of Science ®Google Scholar
• Maleki, R., Khedri, M., Malekahmadi, D., Mohaghegh, S., Jahromi, A. M., & Shahbazi, M.-A. (2021). Simultaneous doxorubicin encapsulation and in-situ microfluidic micellization of bio-targeted polymeric nanohybrids using dichalcogenide monolayers: A molecular in-silico study. Materials Today Communications, 26, 101948. https://doi.org/10.1016/j.mtcomm.2020.101948
   Web of Science ®Google Scholar
• Maleki, R., Khedri, M., Rezvantalab, S., Afsharchi, F., Musaie, K., Shafiee, S., & Shahbazi, M.-A. (2021). β‐Amyloid targeting with two‐dimensional covalent organic frameworks: Multi‐scale in‐silico dissection of nano‐biointerface. Chembiochem : A European Journal of Chemical Biology, 22(13), 2306–2318. https://doi.org/10.1002/cbic.202100075
   PubMedGoogle Scholar
• Malik, G. A., & Robertson, N. P. (2017). Treatments in Alzheimer's disease. Journal of Neurology, 264(2), 416–418. https://doi.org/10.1007/s00415-017-8395-1
   PubMed Web of Science ®Google Scholar
• Matubayasi, N. (2017). Free-energy analysis of protein solvation with all-atom molecular dynamics simulation combined with a theory of solutions. Current Opinion in Structural Biology, 43, 45–54. https://doi.org/10.1016/j.sbi.2016.10.005
   PubMed Web of Science ®Google Scholar
• Minati, L., Edginton, T., Grazia Bruzzone, M., & Giaccone, G. (2009). Reviews: Current concepts in Alzheimer's disease: A multidisciplinary review. American Journal of Alzheimer's Disease & Other Dementias®, 24(2), 95–121. https://doi.org/10.1177/1533317508328602
   PubMed Web of Science ®Google Scholar
• Moon, M. (2016). The MIND Diet: A scientific approach to enhancing brain function and helping prevent Alzheimer's and dementia. Simon and Schuster.
   Google Scholar
• Nguyen, P. H., Ramamoorthy, A., Sahoo, B. R., Zheng, J., Faller, P., Straub, J. E., Dominguez, L., Shea, J.-E., Dokholyan, N. V., De Simone, A., Ma, B., Nussinov, R., Najafi, S., Ngo, S. T., Loquet, A., Chiricotto, M., Ganguly, P., McCarty, J., Li, M. S., … Derreumaux, P. (2021). Amyloid oligomers: A joint experimental/computational perspective on Alzheimer's disease, Parkinson's disease, type II diabetes, and amyotrophic lateral sclerosis. Chemical Reviews, 121(4), 2545–2647. https://doi.org/10.1021/acs.chemrev.0c01122
   PubMed Web of Science ®Google Scholar
• Ostrowitzki, S., Lasser, R. A., Dorflinger, E., Scheltens, P., Barkhof, F., Nikolcheva, T., Ashford, E., Retout, S., Hofmann, C., Delmar, P., Klein, G., Andjelkovic, M., Dubois, B., Boada, M., Blennow, K., Santarelli, L., & Fontoura, P. (2017). A phase III randomized trial of gantenerumab in prodromal Alzheimer's disease. Alzheimer's Research & Therapy, 9(1), 95 https://doi.org/10.1186/s13195-017-0318-y
   PubMedGoogle Scholar
• Perricone, U., Gulotta, M. R., Lombino, J., Parrino, B., Cascioferro, S., Diana, P., Cirrincione, G., & Padova, A. (2018). An overview of recent molecular dynamics applications as medicinal chemistry tools for the undruggable site challenge. MedChemComm, 9(6), 920–936. https://doi.org/10.1039/c8md00166a
   PubMed Web of Science ®Google Scholar
• Pitschke, M., Prior, R., Haupt, M., & Riesner, D. (1998). Detection of single amyloid beta-protein aggregates in the cerebrospinal fluid of Alzheimer's patients by fluorescence correlation spectroscopy. Nature Medicine, 4(7), 832–834. https://doi.org/10.1038/nm0798-832
   PubMed Web of Science ®Google Scholar
• Quezada, G. R., Rozas, R. E., & Toledo, P. G. (2019). Ab initio calculations of partial charges at kaolinite edge sites and molecular dynamics simulations of cation adsorption in saline solutions at and above the pH of zero charge. The Journal of Physical Chemistry C, 123(37), 22971–22980. https://doi.org/10.1021/acs.jpcc.9b05339
   Web of Science ®Google Scholar
• Salloway, S., Sperling, R., Fox, N. C., Blennow, K., Klunk, W., Raskind, M., Sabbagh, M., Honig, L. S., Porsteinsson, A. P., Ferris, S., Reichert, M., Ketter, N., Nejadnik, B., Guenzler, V., Miloslavsky, M., Wang, D., Lu, Y., Lull, J., Tudor, I. C., … Brashear, H. R. (2014). Two phase 3 trials of bapineuzumab in mild-to-moderate Alzheimer's disease. The New England Journal of Medicine, 370(4), 322–333. https://doi.org/10.1056/NEJMoa1304839
   PubMed Web of Science ®Google Scholar
• Sun, Y., Xi, W., & Wei, G. (2015). Atomic-level study of the effects of O4 molecules on the structural properties of protofibrillar Aβ trimer: β-sheet stabilization, salt bridge protection, and binding mechanism. The Journal of Physical Chemistry. B, 119(7), 2786–2794. https://doi.org/10.1021/jp508122t
   PubMed Web of Science ®Google Scholar
• Takahashi, T., & Mihara, H. (2008). Peptide and protein mimetics inhibiting amyloid beta-peptide aggregation. Accounts of Chemical Research, 41(10), 1309–1318. https://doi.org/10.1021/ar8000475
   PubMed Web of Science ®Google Scholar
• Tan, C., Cao, X., Wu, X.-J., He, Q., Yang, J., Zhang, X., Chen, J., Zhao, W., Han, S., Nam, G.-H., Sindoro, M., & Zhang, H. (2017). Recent advances in ultrathin two-dimensional nanomaterials. Chemical Reviews, 117(9), 6225–6331. https://doi.org/10.1021/acs.chemrev.6b00558
   PubMed Web of Science ®Google Scholar
• Tay, W. M., Huang, D., Rosenberry, T. L., & Paravastu, A. K. (2013). The Alzheimer's amyloid-β(1-42) peptide forms off-pathway oligomers and fibrils that are distinguished structurally by intermolecular organization . Journal of Molecular Biology, 425(14), 2494–2508. https://doi.org/10.1016/j.jmb.2013.04.003
   PubMed Web of Science ®Google Scholar
• Thijssen, E. H., Verberk, I. M. W., Vanbrabant, J., Koelewijn, A., Heijst, H., Scheltens, P., van der Flier, W., Vanderstichele, H., Stoops, E., & Teunissen, C. E. (2021). Highly specific and ultrasensitive plasma test detects Abeta(1-42) and Abeta(1-40) in Alzheimer's disease. Scientific Reports, 11(1), 9710–9736. https://doi.org/10.1038/s41598-021-89004-x
   PubMed Web of Science ®Google Scholar
• Xiao, Y., Ma, B., McElheny, D., Parthasarathy, S., Long, F., Hoshi, M., Nussinov, R., & Ishii, Y. (2015). Aβ(1-42) fibril structure illuminates self-recognition and replication of amyloid in Alzheimer's disease . Nature Structural & Molecular Biology, 22(6), 499–505. https://doi.org/10.1038/nsmb.2991
   PubMed Web of Science ®Google Scholar
• Xie, J., Shen, Z., Anraku, Y., Kataoka, K., & Chen, X. (2019). Nanomaterial-based blood-brain-barrier (BBB) crossing strategies. Biomaterials, 224, 119491. https://doi.org/10.1016/j.biomaterials.2019.119491
   PubMed Web of Science ®Google Scholar