Inhibition of Alzheimer’s amyloid-β₄₂ peptide aggregation by a bi-functional bis-tryptoline triazole: key insights from molecular dynamics simulations

References

• Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi–level parallelism from laptops to supercomputers. SoftwareX, 1–2, 19–25. doi:10.1016/j.softx.2015.06.001
   Google Scholar
• Ahn, M., Lee, B. I., Chia, S., Habchi, J., Kumita, J. R., Vendruscolo, M., … Park, C. B. (2019). Chemical and mechanistic analysis of photodynamic inhibition of Alzheimer's β-amyloid aggregation. Chemical Communications, 55(8), 1152–1155. doi:10.1039/C8CC09288E
   PubMed Web of Science ®Google Scholar
• Amadei, A., Linssen, A. B. M., & Berendsen, H. J. C. (1993). Essential dynamics of proteins. Proteins: Structure, Function, and Genetics, 17(4), 412–425. doi:10.1002/prot.340170408
   PubMed Web of Science ®Google Scholar
• Autiero, I., Langella, E., & Saviano, M. (2013). Insights into the mechanism of interaction between trehalose-conjugated beta-sheet breaker peptides and Aβ(1–42) fibrils by molecular dynamics simulations. Molecular Biosystems, 9(11), 2835–2841. doi:10.1039/c3mb70235a
   PubMedGoogle Scholar
• Awasthi, M., Singh, S., Pandey, V. P., & Dwivedi, U. N. (2018). Modulation in the conformational and stability attributes of the Alzheimer's disease associated amyloid-beta mutants and their favorable stabilization by curcumin: Molecular dynamics simulation analysis. Journal of Biomolecular Structure and Dynamics, 36(2), 407–422. doi:10.1080/07391102.2017.1279078
   PubMed Web of Science ®Google Scholar
• Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics, 81(8), 3684–3690. doi:10.1063/1.448118
   Web of Science ®Google Scholar
• Bruce, N. J., Ganotra, G. K., Kokh, D. B., Sadiq, S. K., & Wade, R. C. (2018). New approaches for computing ligand-receptor binding kinetics. Current Opinion in Structural Biology, 49, 1–10. doi:10.1016/j.sbi.2017.10.001
   PubMed Web of Science ®Google Scholar
• Chandra, B., Halder, S., Adler, J., Korn, A., Huster, D., & Maiti, S. (2017). Emerging structural details of transient amyloid-β oligomers suggest designs for effective small molecule modulators. Chemical Physics Letters, 675, 51–55. doi:10.1016/j.cplett.2017.02.070
   Web of Science ®Google Scholar
• Chu, D., & Liu, F. (2019). Pathological changes of tau related to Alzheimer's Disease. ACS Chemical Neuroscience, 10(2), 931–944. doi:10.1021/acschemneuro.8b00457
   PubMed Web of Science ®Google Scholar
• 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. doi:10.1063/1.464397
   Web of Science ®Google Scholar
• Das, S., & Smid, S. D. (2017). Identification of dibenzyl imidazolidine and triazole acetamide derivatives through virtual screening targeting amyloid beta aggregation and neurotoxicity in PC12 cells. European Journal of Medicinal Chemistry, 130, 354–364. doi:10.1016/j.ejmech.2017.02.057
   PubMed Web of Science ®Google Scholar
• DeLano, W. L. (2002). The PyMOL molecular graphics system, 571 DeLano Scientific, San Carlos, CA.
   Google Scholar
• Dhanabalan, A. K., Kesherwani, M., Velmurugan, D., & Gunasekaran, K. (2017). Identification of new BACE1 inhibitors using pharmacophore and molecular dynamics simulations approach. Journal of Molecular Graphics and Modelling, 76, 56–69. doi:10.1016/j.jmgm.2017.06.001
   PubMed Web of Science ®Google Scholar
• Di Santo, R., Costi, R., Cuzzucoli Crucitti, G., Pescatori, L., Rosi, F., Scipione, L., … Minetti, P. (2012). Design, synthesis, and structure–activity relationship of N-arylnaphthylamine derivatives as amyloid aggregation inhibitors. Journal of Medicinal Chemistry, 55(19), 8538–8548. doi:10.1021/jm301105m
   PubMed Web of Science ®Google Scholar
• Dutta, M., & Mattaparthi, V. S. K. (2018). In silico investigation on the inhibition of Aβ42 aggregation by Aβ40 peptide by potential of mean force study. Journal of Biomolecular Structure and Dynamics, 36(3), 741–752. doi:10.1080/07391102.2017.1296783
   PubMed Web of Science ®Google Scholar
• Dyrager, C., Vieira, R. P., Nyström, S., Nilsson, K. P. R., & Storr, T. (2017). Synthesis and evaluation of benzothiazole-triazole and benzothiadiazole-triazole scaffolds as potential molecular probes for amyloid-β aggregation. New Journal of Chemistry, 41(4), 1566–1573. doi:10.1039/C6NJ01703G
   Web of Science ®Google Scholar
• Essmann, U., Perera, M. L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. The Journal of Chemical Physics, 103(19), 8577–8593. doi:10.1063/1.470117
   Web of Science ®Google Scholar
• Foloppe, N., & Hubbard, R. (2006). Towards predictive ligand design with free-energy based computational methods? Current Medicinal Chemistry, 13(29), 3583–3608.
   PubMed Web of Science ®Google Scholar
• Fraser, P. E., Nguyen, J. T., Inouye, H., Surewicz, W. K., Selkoe, D. J., Podlisny, M. B., & Kirschner, D. A. (1992). Fibril formation by primate, rodent, and Dutch-hemorrhagic analogs of Alzheimer amyloid β-protein. Biochemistry, 31(44), 10716–10723. doi:10.1021/bi00159a011
   PubMed Web of Science ®Google Scholar
• Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., … Fox, D. J. (2009). Gaussian 09, Revision E.01. Wallingford, CT: Gaussian.
   Google Scholar
• Goyal, D., Shuaib, S., Mann, S., & Goyal, B. (2017). Rationally designed peptides and peptidomimetics as inhibitors of amyloid-β (Aβ) aggregation: Potential therapeutics of Alzheimer’s disease. ACS Combinatorial Science, 19(2), 55–80. doi:10.1021/acscombsci.6b00116
   PubMed Web of Science ®Google Scholar
• Greene, J. D. W., Baddeley, A. D., & Hodges, J. R. (1996). Analysis of the episodic memory deficit in early Alzheimer's disease: Evidence from the doors and people test. Neuropsychologia, 34(6), 537–551.
   PubMed Web of Science ®Google Scholar
• Habchi, J., Chia, S., Limbocker, R., Mannini, B., Ahn, M., Perni, M., … Vendruscolo, M. (2017). Systematic development of small molecules to inhibit specific microscopic steps of Aβ42 aggregation in Alzheimer’s disease. Proceedings of the National Academy of Sciences United States of America, 114(2), E200–E208. doi:10.1073/pnas.1615613114
   PubMed Web of Science ®Google Scholar
• Halverson, K., Fraser, P. E., Kirschner, D. A., & Lansbury, P. T. (1990). Molecular determinants of amyloid deposition in Alzheimer's disease: Conformational studies of synthetic β-protein fragments. Biochemistry, 29(11), 2639–2644. doi:10.1021/bi00463a003
   PubMed Web of Science ®Google Scholar
• Hardy, J., & Selkoe, D. J. (2002). The amyloid hypothesis of Alzheimer's disease: Progress and problems on the road to therapeutics. Science, 297(5580), 353–356. doi:10.1126/science.1072994
   PubMed Web of Science ®Google Scholar
• Herrup, K. (2015). The case for rejecting the amyloid cascade hypothesis. Nature Neuroscience, 18(6), 794–799. doi:10.1038/nn.4017
   PubMed Web of Science ®Google Scholar
• Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. M. E. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. doi:10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.3.CO;2-L
   Web of Science ®Google Scholar
• Hou, L., Shao, H., Zhang, Y., Li, H., Menon, N. K., Neuhaus, E. B., … Zagorski, M. G. (2004). Solution NMR studies of the Aβ(1–40) and Aβ(1–42) peptides establish that the Met35 oxidation state affects the mechanism of amyloid formation. Journal of the American Chemical Society, 126(7), 1992–2005. doi:10.1021/ja036813f
   PubMed Web of Science ®Google Scholar
• Huey, R., Morris, G. M., Olson, A. J., & Goodsell, D. S. (2007). A semiempirical free energy force field with charge-based desolvation. Journal of Computational Chemistry, 28(6), 1145–1152. doi:10.1002/jcc.20634
   PubMed Web of Science ®Google Scholar
• Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. doi:10.1016/0263-7855(96)00018-5
   PubMedGoogle Scholar
• Iadanza, M. G., Jackson, M. P., Hewitt, E. W., Ranson, N. A., & Radford, S. E. (2018). A new era for understanding amyloid structures and disease. Nature Reviews Molecular Cell Biology, 19(12), 755–773. doi:10.1038/s41580-018-0060-8
   PubMed Web of Science ®Google Scholar
• Ichiye, T., & Karplus, M. (1991). Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations. Proteins: Structure, Function, and Genetics, 11(3), 205–217. doi:10.1002/prot.340110305
   PubMed Web of Science ®Google Scholar
• Ion, G. N. D., Mihai, D. P., Lupascu, G., & Nitulescu, G. M. (2018). Application of molecular framework-based data-mining method in the search for beta-secretase 1 inhibitors through drug repurposing. Journal of Biomolecular Structure and Dynamics, 1–12. doi:10.1080/07391102.2018.1526115
   PubMedGoogle Scholar
• Iqbal, K., Liu, F., & Gong, C.-X. (2016). Tau and neurodegenerative disease: The story so far. Nature Reviews Neurology, 12(1), 15–27. doi:10.1038/nrneurol.2015.225
   PubMed Web of Science ®Google Scholar
• Jiaranaikulwanitch, J., Govitrapong, P., Fokin, V. V., & Vajragupta, O. (2012). From BACE1 inhibitor to multifunctionality of tryptoline and tryptamine triazole derivatives for Alzheimer’s disease. Molecules, 17(7), 8312–8333. doi:10.3390/molecules17078312
   PubMed Web of Science ®Google Scholar
• Jiaranaikulwanitch, J., Tadtong, S., Govitrapong, P., Fokin, V. V., & Vajragupta, O. (2017). Neuritogenic activity of bi-functional bis-tryptoline triazole. Bioorganic & Medicinal Chemistry, 25, 1195–1201. doi:10.1016/j.bmc.2016.12.027
   PubMed Web of Science ®Google Scholar
• Jones, M. R., Mathieu, E., Dyrager, C., Faissner, S., Vaillancourt, Z., Korshavn, K. J., … Storr, T. (2017). Multi-target-directed phenol-triazole ligands as therapeutic agents for Alzheimer's disease. Chemical Science, 8(8), 5636–5643. doi:10.1039/C7SC01269A
   PubMed Web of Science ®Google Scholar
• Kabsch, W., & Sander, C. (1983). Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features. Biopolymers, 22(12), 2577–2637. doi:10.1002/bip.360221211
   PubMed Web of Science ®Google Scholar
• Kang, J., Lemaire, H.-G., Unterbeck, A., Salbaum, J. M., Masters, C. L., Grzeschik, K.-H., … Müller-Hill, B. (1987). The precursor of Alzheimer’s disease amyloid A4 protein resembles a cell-surface receptor. Nature, 325(6106), 733–736. doi:10.1038/325733a0
   PubMed Web of Science ®Google Scholar
• Kaur, A., Mann, S., Kaur, A., Priyadarshi, N., Goyal, B., Singhal, N. K., & Goyal, D. (2019). Multi-target-directed triazole derivatives as promising agents for the treatment of Alzheimer’s disease. Bioorganic Chemistry, 87, 572–584. doi:10.1016/j.bioorg.2019.03.058
   PubMed Web of Science ®Google Scholar
• Knowles, T. P. J., Vendruscolo, M., & Dobson, C. M. (2014). The amyloid state and its association with protein misfolding diseases. Nature Reviews Molecular Cell Biology, 15(6), 384–396. doi:10.1038/nrm3810
   PubMed Web of Science ®Google Scholar
• Kumar, A., Sivastava, G., Srivastava, S., Verma, S., Negi, A. S., & Sharma, A. (2017). Investigation of naphthofuran moiety as potential dual inhibitor against BACE–1 and GSK–3β: Molecular dynamics simulations, binding energy, and network analysis to identify first–in–class dual inhibitors against Alzheimer's disease. Journal of Molecular Modeling, 23, 239.
   PubMed Web of Science ®Google Scholar
• Kumar, D., Ganeshpurkar, A., Kumar, D., Modi, G., Gupta, S. K., & Singh, S. K. (2018). Secretase inhibitors for the treatment of Alzheimer's disease: Long road ahead. European Journal of Medicinal Chemistry, 148, 436–452. doi:10.1016/j.ejmech.2018.02.035
   PubMed Web of Science ®Google Scholar
• Kumari, R., Kumar, R., Open Source Drug Discovery Consortium, & Lynn, A. (2014). g_mmpbsa—A GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. doi:10.1021/ci500020m
   PubMed Web of Science ®Google Scholar
• Laskowski, R. A., & Swindells, M. B. (2011). LigPlot+: Multiple ligand–protein interaction diagrams for drug discovery. Journal of Chemical Information and Modeling, 51(10), 2778–2786. doi:10.1021/ci200227u
   PubMed Web of Science ®Google Scholar
• Lazo, N. D., Grant, M. A., Condron, M. C., Rigby, A. C., & Teplow, D. B. (2005). On the nucleation of amyloid β-protein monomer folding. Protein Science, 14(6), 1581–1596. doi:10.1110/ps.041292205
   PubMed Web of Science ®Google Scholar
• Li, Y., Zhang, X.-X., Jiang, L.-J., Yuan, L., Cao, T.-T., Li, X., … Yin, S.-F. (2015). Inhibition of acetylcholinesterase (AChE): A potential therapeutic target to treat Alzheimer's disease. Chemical Biology & Drug Design, 86, 776–782. doi:10.1111/cbdd.12550
   PubMed Web of Science ®Google Scholar
• Lin, Z., & van Gunsteren, W. F. (2013). Refinement of the application of the GROMOS 54A7 force field to β-peptides. Journal of Computational Chemistry, 34(32), 2796–2805. doi:10.1002/jcc.23459
   PubMed Web of Science ®Google Scholar
• Liu, D., Xu, Y., Feng, Y., Liu, H., Shen, X., Chen, K., … Jiang, H. (2006). Inhibitor discovery targeting the intermediate structure of β-amyloid peptide on the conformational transition pathway: Implications in the aggregation mechanism of β-amyloid peptide. Biochemistry, 45(36), 10963–10972. doi:10.1021/bi060955f
   PubMed Web of Science ®Google Scholar
• Liu, S.-Q., Meng, Z.-H., Fu, Y.-X., & Zhang, K.-Q. (2010). Insights derived from molecular dynamics simulation into the molecular motions of serine protease proteinase K. Journal of Molecular Modeling, 16(1), 17–28. doi:10.1007/s00894-009-0518-x
   PubMed Web of Science ®Google Scholar
• Mager, P. P., & Fischer, K. (2001). Simulation of the lipophilic and antigenic cores of the Aβ(1–42) peptide of Alzheimer’s disease. Molecular Simulation, 27(4), 237–242. doi:10.1080/08927020108027949
   Web of Science ®Google Scholar
• Malde, A. K., Zuo, L., Breeze, M., Stroet, M., Poger, D., Nair, P. C., … Mark, A. E. (2011). An automated force field topology builder (ATB) and repository: Version 1.0. Journal of Chemical Theory and Computation, 7(12), 4026–4037. doi:10.1021/ct200196m
   PubMed Web of Science ®Google Scholar
• Manoharan, P., & Ghoshal, N. (2018). Fragment-based virtual screening approach and molecular dynamics simulation studies for identification of BACE1 inhibitor leads. Journal of Biomolecular Structure and Dynamics, 36(7), 1878–1892. doi:10.1080/07391102.2017.1337590
   PubMed Web of Science ®Google Scholar
• Martin, L., Latypova, X., Wilson, C. M., Magnaudeix, A., Perrin, M.-L., Yardin, C., & Terro, F. (2013). Tau protein kinases: Involvement in Alzheimer's disease. Ageing Research Reviews, 12(1), 289–309. doi:10.1016/j.arr.2012.06.003
   PubMed Web of Science ®Google Scholar
• Mattson, M. P. (1997). Cellular actions of beta-amyloid precursor protein and its soluble and fibrillogenic derivatives. Physiological Reviews, 77(4), 1081–1132. doi:10.1152/physrev.1997.77.4.1081
   PubMed Web of Science ®Google Scholar
• Mills, N. (2006). ChemDraw Ultra 10.0. Journal of the American Chemical Society, 128(41), 13649–13650. doi:10.1021/ja0697875
   Web of Science ®Google Scholar
• Morris, G. M., Goodsell, D. S., Halliday, R. S., Huey, R., Hart, W. E., Belew, R. K., & Olson, A. J. (1998). Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. Journal of Computational Chemistry, 19(14), 1639–1662. doi:10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B
   Web of Science ®Google Scholar
• Narang, S. S., Shuaib, S., & Goyal, B. (2017). Molecular insights into the inhibitory mechanism of rifamycin SV against β2-microglobulin aggregation: A molecular dynamics simulation study. International Journal of Biological Macromolecules, 102, 1025–1034. doi:10.1016/j.ijbiomac.2017.04.086
   PubMed Web of Science ®Google Scholar
• Nasica-Labouze, J., Nguyen, P. H., Sterpone, F., Berthoumieu, O., Buchete, N.-V., Coté, S., … Derreumaux, P. (2015). Amyloid β protein and Alzheimer’s disease: When computer simulations complement experimental studies. Chemical Reviews, 115(9), 3518–3563. doi:10.1021/cr500638n
   PubMed Web of Science ®Google Scholar
• Neal, S., Nip, A. M., Zhang, H., & Wishart, D. S. (2003). Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts. Journal of Biomolecular NMR, 26(3), 215–240.
   PubMed Web of Science ®Google Scholar
• Nelson, R., Sawaya, M. R., Balbirnie, M., Madsen, A. Ø., Riekel, C., Grothe, R., & Eisenberg, D. (2005). Structure of the cross-β spine of amyloid-like fibrils. Nature, 435(7043), 773–778. doi:10.1038/nature03680
   PubMed Web of Science ®Google Scholar
• Neto, D. C. F., Lima, J. A., Diz de Almeida, J. S. F., França, T. C. C., do Nascimento, C. J., & Villar, J. D. F. (2018). New semicarbazones as gorge-spanning ligands of acetylcholinesterase and potential new drugs against Alzheimer’s disease: Synthesis, molecular modeling, NMR, and biological evaluation. Journal of Biomolecular Structure and Dynamics, 36, 4099–4113.
   PubMed Web of Science ®Google Scholar
• Novick, P. A., Lopes, D. H., Branson, K. M., Esteras-Chopo, A., Graef, I. A., Bitan, G., & Pande, V. S. (2012). Design of β-amyloid aggregation inhibitors from a predicted structural motif. Journal of Medicinal Chemistry, 55(7), 3002–3010. doi:10.1021/jm201332p
   PubMed Web of Science ®Google Scholar
• O’Brien, R. J., & Wong, P. C. (2011). Amyloid precursor protein processing and Alzheimer’s disease. Annual Review of Neuroscience, 34, 185–204. doi:10.1146/annurev-neuro-061010-113613
   PubMed Web of Science ®Google Scholar
• Ono, K., Condron, M. M., & Teplow, D. B. (2010). Effects of the English (H6R) and Tottori (D7N) familial Alzheimer disease mutations on amyloid β-protein assembly and toxicity. Journal of Biological Chemistry, 285(30), 23186–23197. doi:10.1074/jbc.M109.086496
   PubMed Web of Science ®Google Scholar
• Panza, F., Seripa, D., Solfrizzi, V., Imbimbo, B. P., Santamato, A., Lozupone, M., … Logroscino, G. (2016). Tau aggregation inhibitors: The future of Alzheimer's pharmacotherapy? Expert Opinion on Pharmacotherapy, 17(4), 457–461. doi:10.1517/14656566.2016.1146686
   PubMed Web of Science ®Google Scholar
• Phelan, M. M., Caamaño-Gutiérrez, E., Gant, M. S., Grosman, R. X., & Madine, J. (2017). Using an NMR metabolomics approach to investigate the pathogenicity of amyloid-beta and alpha-synuclein. Metabolomics, 13, 151.
   PubMed Web of Science ®Google Scholar
• Pickhardt, M., Neumann, T., Schwizer, D., Callaway, K., Vendruscolo, M., Schenk, D., … Toth, G. (2015). Identification of small molecule inhibitors of tau aggregation by targeting monomeric tau as a potential therapeutic approach for tauopathies. Current Alzheimer Research, 12(9), 814–828. doi:10.2174/156720501209151019104951
   PubMed Web of Science ®Google Scholar
• Piplani, P., Sharma, M., Mehta, P., & Malik, R. (2018). N-(4-Hydroxyphenyl)-3,4,5-trimethoxybenzamide derivatives as potential memory enhancers: Synthesis, biological evaluation and molecular simulation studies. Journal of Biomolecular Structure and Dynamics, 36(7), 1867–1877. doi:10.1080/07391102.2017.1336943
   PubMed Web of Science ®Google Scholar
• Plazinski, W., Plazinska, A., & Drach, M. (2016). Acyclic forms of aldohexoses and ketohexoses in aqueous and DMSO solutions: Conformational features studied using molecular dynamics simulations. Physical Chemistry Chemical Physics, 18(14), 9626–9635. doi:10.1039/c6cp00809g
   PubMed Web of Science ®Google Scholar
• Qu, G., Xue, C., Zhang, M., Liang, S., Han, Y., & Ding, W. (2016). Molecular dynamics simulation of sulfobetaine-type zwitterionic surfactants at the decane/water interface: Structure, interfacial properties. Journal of Dispersion Science and Technology, 37(12), 1710–1717. doi:10.1080/01932691.2015.1135400
   Web of Science ®Google Scholar
• Rahmani, S., Mogharizadeh, L., Attar, F., Rezayat, S. M., Mousavi, S. E., & Falahati, M. (2018). Probing the interaction of silver nanoparticles with tau protein and neuroblastoma cell line as nervous system models. Journal of Biomolecular Structure and Dynamics, 36(15), 4057–4071. doi:10.1080/07391102.2017.1407673
   PubMed Web of Science ®Google Scholar
• Saini, R. K., Shuaib, S., Goyal, D., & Goyal, B. (2017). Molecular insights into Aβ42 protofibril destabilization with a fluorinated compound D744: A molecular dynamics simulation study. Journal of Molecular Recognition, 30(12), e2656. doi:10.1002/jmr.2656
   Web of Science ®Google Scholar
• Seidler, P. M., Boyer, D. R., Rodriguez, J. A., Sawaya, M. R., Cascio, D., Murray, K., … Eisenberg, D. S. (2018). Structure-based inhibitors of tau aggregation. Nature Chemistry, 10(2), 170–176. doi:10.1038/nchem.2889
   PubMed Web of Science ®Google Scholar
• Selkoe, D. J. (2001). Alzheimer's disease: Genes, proteins, and therapy. Physiological Reviews, 81(2), 741–766. doi:10.1152/physrev.2001.81.2.741
   PubMed Web of Science ®Google Scholar
• Serpell, L. C. (2000). Alzheimer's amyloid fibrils: Structure and assembly. Biochimica et Biophysica Acta, 1502(1), 16–30.
   PubMed Web of Science ®Google Scholar
• Shuaib, S., & Goyal, B. (2018). Scrutiny of the mechanism of small molecule inhibitor preventing conformational transition of amyloid-β42 monomer: Insights from molecular dynamics simulations. Journal of Biomolecular Structure and Dynamics, 36(3), 663–678. doi:10.1080/07391102.2017.1291363
   PubMed Web of Science ®Google Scholar
• Shuaib, S., Saini, R. K., Goyal, D., & Goyal, B. (2017). Insights into the inhibitory mechanism of dicyanovinyl‐substituted J147 derivative against Aβ42 aggregation and protofibril destabilization: A molecular dynamics simulation study. ChemistrySelect, 2(4), 1645–1657. doi:10.1002/slct.201601970
   Web of Science ®Google Scholar
• Sipe, J. D., & Cohen, A. S. (2000). Review: History of the amyloid fibril. Journal of Structural Biology, 130(2–3), 88–98. doi:10.1006/jsbi.2000.4221
   PubMed Web of Science ®Google Scholar
• Solis, F. J., & Wets, J. B. (1981). Minimization by random search techniques. Mathematics of Operations Research, 6(1), 19–30. doi:10.1287/moor.6.1.19
   Web of Science ®Google Scholar
• Tjernberg, L. O., Lilliehöök, C., Callaway, D. J. E., Näslund, J., Hahne, S., Thyberg, J., … Nordstedt, C. (1997). Controlling amyloid β-peptide fibril formation with protease-stable ligands. Journal of Biological Chemistry, 272(19), 12601–12605. doi:10.1074/jbc.272.19.12601
   PubMed Web of Science ®Google Scholar
• Tomaselli, S., Esposito, V., Vangone, P., van Nuland, N. A. J., Bonvin, A. M. J. J., Guerrini, R., … Picone, D. (2006). The α‐to‐β conformational transition of Alzheimer's Aβ‐(1–42) peptide in aqueous media is reversible: A step by step conformational analysis suggests the location of β conformation seeding. ChemBioChem, 7(2), 257–267. doi:10.1002/cbic.200500223
   PubMed Web of Science ®Google Scholar
• Urbanc, B., Cruz, L., Yun, S., Buldyrev, S. V., Bitan, G., Teplow, D. B., & Stanley, H. E. (2004). In silico study of amyloid β-protein folding and oligomerization. Proceedings of the National Academy of Sciences of the United States of America, 101(50), 17345–17350. doi:10.1073/pnas.0408153101
   PubMed Web of Science ®Google Scholar
• Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. C. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718. doi:10.1002/jcc.20291
   PubMed Web of Science ®Google Scholar
• Wang, Q., Yu, X., Li, L., & Zheng, J. (2014). Inhibition of amyloid-β aggregation in Alzheimer's disease. Current Pharmaceutical Design, 20(8), 1223–1243. doi:10.2174/13816128113199990068
   PubMed Web of Science ®Google Scholar
• Xu, Q., Du, X.-G., & Geng, M.-Y. (2011). Small molecule inhibitors of amyloid β peptide aggregation as a potential therapeutic strategy for Alzheimer’s disease. Acta Pharmacologica Sinica, 32, 545–551. doi:10.1038/aps.2011.14
   PubMed Web of Science ®Google Scholar
• Yun, S., Urbanc, B., Cruz, L., Bitan, G., Teplow, D. B., & Stanley, H. E. (2007). Role of electrostatic interactions in amyloid β-protein (Aβ) oligomer formation: A discrete molecular dynamics study. Biophysical Journal, 92(11), 4064–4077. doi:10.1529/biophysj.106.097766
   PubMed Web of Science ®Google Scholar
• Zeng, H., & Wu, X. (2016). Alzheimer's disease drug development based on computer-aided drug design. European Journal of Medicinal Chemistry, 121, 851–863. doi:10.1016/j.ejmech.2015.08.039
   PubMed Web of Science ®Google Scholar
• Zheng, M., Zhao, J., Cui, C., Fu, Z., Li, X., Liu, X., … Jiang, H. (2018). Computational chemical biology and drug design: Facilitating protein structure, function, and modulation studies. Medicinal Research Reviews, 38(3), 914–950. doi:10.1002/med.21483
   PubMed Web of Science ®Google Scholar