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Research Articles

A series of molecular modeling techniques to reveal selective mechanisms of inhibitors to β-Site amyloid precursor protein cleaving enzyme 1 (BACE1) and β-site amyloid precursor protein cleaving enzyme 2 (BACE2)

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Pages 2824-2837 | Received 04 Mar 2020, Accepted 07 Apr 2020, Published online: 20 Apr 2020

References

  • Agrahari, A. K., Doss, G. P. C., Siva, R., Magesh, R., & Zayed, H. (2019). Molecular insights of the G2019S substitution in LRRK2 kinase domain associated with Parkinson’s disease: A molecular dynamics simulation approach. Journal of Theoretical Biology, 469, 163–171. doi:10.1016/j.jtbi.2019.03.003
  • Alzheimer’s, A. s A. J. & Dementia, (2016). 2016 Alzheimer’s disease facts and figures. Alzheimers Dement, 12, 459–509.
  • Banner, D. W., Gsell, B., Benz, J., Bertschinger, J., Burger, D., Brack, S., Cuppuleri, S., Debulpaep, M., Gast, A., Grabulovski, D., Hennig, M., Hilpert, H., Huber, W., Kuglstatter, A., Kusznir, E., Laeremans, T., Matile, H., Miscenic, C., Rufer, A. C., … Ruf, A. (2013). Mapping the conformational space accessible to BACE2 using surface mutants and cocrystals with Fab fragments, Fynomers and Xaperones. Acta Crystallographica Section D Biological Crystallography, 69(6), 1124–1137. doi:10.1107/S0907444913006574
  • 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
  • Chen, J. (2018). Functional roles of magnesium binding to extracellular signal-regulated kinase 2 explored by molecular dynamics simulations and principal component analysis. Journal of Biomolecular Structure and Dynamics, 36(2), 351–361. doi:10.1080/07391102.2016.1277783
  • Chen, F., Sun, H., Wang, J., Zhu, F., Liu, H., Wang, Z., Lei, T., Li, Y., & Hou, T. (2018). Assessing the performance of MM/PBSA and MM/GBSA methods. 8. Predicting binding free energies and poses of protein-RNA complexes. Rna, 24(9), 1183–1194. doi:10.1261/rna.065896.118
  • Essmann, U., Perera, 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
  • Filser, S., Ovsepian, S. V., Masana, M., Blazquez-Llorca, L., Brandt Elvang, A., Volbracht, C., Muller, M. B., Jung, C. K., & Herms, J. (2015). Pharmacological inhibition of BACE1 impairs synaptic plasticity and cognitive functions. Biological Psychiatry, 77(8), 729–739. doi:10.1016/j.biopsych.2014.10.013
  • Genheden, S., & Ryde, U. (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on Drug Discovery, 10(5), 449–461. doi:10.1517/17460441.2015.1032936
  • Imbimbo, B. P., & Watling, M. (2019). Investigational BACE inhibitors for the treatment of Alzheimer’s disease. Expert Opinion on Investigational Drugs , 28(11), 967–975. doi:10.1080/13543784.2019.1683160
  • Izaguirre, J. A., Catarello, D. P., Wozniak, J. M., & Skeel, R. D. (2001). Langevin stabilization of molecular dynamics. The Journal of Chemical Physics, 114(5), 2090–2098. doi:10.1063/1.1332996
  • Jeppsson, F., Eketjall, S., Janson, J., Karlstrom, S., Gustavsson, S., Olsson, L. L., Radesater, A. C., Ploeger, B., Cebers, G., Kolmodin, K., Swahn, B. M., von Berg, S., Bueters, T., & Falting, J. (2012). Discovery of AZD3839, a potent and selective BACE1 inhibitor clinical candidate for the treatment of Alzheimer disease. Journal of Biological Chemistry, 287(49), 41245–41257. doi:10.1074/jbc.M112.409110
  • Johansson, P., Kaspersson, K., Gurrell, I. K., Back, E., Eketjall, S., Scott, C. W., Cebers, G., Thorne, P., McKenzie, M. J., Beaton, H., Davey, P., Kolmodin, K., Holenz, J., Duggan, M. E., Budd Haeberlein, S., & Burli, R. W. (2018). Toward beta-Secretase-1 Inhibitors with Improved Isoform Selectivity. Journal of Medicinal Chemistry, 61(8), 3491–3502. doi:10.1021/acs.jmedchem.7b01716
  • Kim, I., & Allen, T. W. (2012). Bennett’s acceptance ratio and histogram analysis methods enhanced by umbrella sampling along a reaction coordinate in configurational space. Journal of Chemical Physics, 136(16), 164103. doi:10.1063/1.3701766
  • Kong, X., Pan, P., Li, D., Tian, S., Li, Y., & Hou, T. (2015). Importance of protein flexibility in ranking inhibitor affinities: Modeling the binding mechanisms of piperidine carboxamides as Type I1/2 ALK inhibitors. Physical Chemistry Chemical Physics, 17(8), 6098–6113. doi:10.1039/C4CP05440G
  • Kräutler, V., van Gunsteren, W. F., & Hünenberger, P. H. (2001). A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations. Journal of Computational Chemistry, 22(5), 501–508. doi:10.1002/1096-987X(20010415)22:5<501::AID-JCC1021>3.0.CO;2-V
  • Kumar, S., Rosenberg, J. M., Bouzida, D., Swendsen, R. H., & Kollman, P. A. (1992). The weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method. Journal of Computational Chemistry, 13(8), 1011–1021. doi:10.1002/jcc.540130812
  • Liu, H., Han, R., Li, J., Liu, H., & Zheng, L. (2016). Molecular mechanism of R-bicalutamide switching from androgen receptor antagonist to agonist induced by amino acid mutations using molecular dynamics simulations and free energy calculation. Journal of Computer-Aided Molecular Design, 30(12), 1189–1200. doi:10.1007/s10822-016-9992-2
  • Loncharich, R. J., Brooks, B. R., & Pastor, R. W. (1992). Langevin dynamics of peptides: The frictional dependence of isomerization rates of N-acetylalanyl-N’-methylamide. Biopolymers, 32(5), 523–535. doi:10.1002/bip.360320508
  • Luo, Y., Bolon, B., Kahn, S., Bennett, B. D., Babu-Khan, S., Denis, P., Fan, W., Kha, H., Zhang, J., Gong, Y., Martin, L., Louis, J. C., Yan, Q., Richards, W. G., Citron, M., & Vassar, R. (2001). Mice deficient in BACE1, the Alzheimer’s beta-secretase, have normal phenotype and abolished beta-amyloid generation. Nature Neuroscience, 4(3), 231–232. doi:10.1038/85059
  • Maier, J. A., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser, K. E., & Simmerling, C. (2015). ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB. Journal of Chemical Theory and Computation, 11(8), 3696–3713. doi:10.1021/acs.jctc.5b00255
  • Markwick, P. R., Pierce, L. C., Goodin, D. B., & McCammon, J. A. (2011). Adaptive Accelerated Molecular Dynamics (Ad-AMD) Revealing the Molecular Plasticity of P450cam. The Journal of Physical Chemistry Letters, 2(3), 158–164. doi:10.1021/jz101462n
  • Miao, Y., Nichols, S. E., Gasper, P. M., Metzger, V. T., & McCammon, J. A. (2013). Activation and dynamic network of the M2 muscarinic receptor. Proceedings of the National Academy of Sciences, 110(27), 10982–10987. doi:10.1073/pnas.1309755110
  • Miao, Y., Sinko, W., Pierce, L., Bucher, D., Walker, R. C., & McCammon, J. A. (2014). Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation. Journal of Chemical Theory and Computation, 10(7), 2677–2689. doi:10.1021/ct500090q
  • Miller, B. R., 3rd, McGee, T. D., Jr., Swails, J. M., Homeyer, N., Gohlke, H., & Roitberg, A. E. (2012). MMPBSA.py: An Efficient Program for End-State Free Energy Calculations. Journal of Chemical Theory and Computation, 8(9), 3314–3321. doi:10.1021/ct300418h
  • Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. doi:10.1002/jcc.21256
  • Moussa-Pacha, N. M., Abdin, S. M., Omar, H. A., Alniss, H., & Al-Tel, T. H. (2020). BACE1 inhibitors: Current status and future directions in treating Alzheimer’s disease. Medicinal Research Reviews, 40(1), 339–384. doi:10.1002/med.21622
  • Onufriev, A., Bashford, D., & David, A. (2000). Modification of the generalized Born model suitable for macromolecules. The Journal of Physical Chemistry B, 104(15), 3712–3720. doi:10.1021/jp994072s
  • Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera–a visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. doi:10.1002/jcc.20084
  • Reddy, M. R., Reddy, C. R., Rathore, R. S., Erion, M. D., Aparoy, P., Reddy, R. N., & Reddanna, P. (2014). Free energy calculations to estimate ligand-binding affinities in structure-based drug design. Current Pharmaceutical Design, 20(20), 3323–3337. doi:10.2174/13816128113199990604
  • Roe, D. R., & Cheatham, T. E. 3rd (2013). PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data. Journal of Chemical Theory and Computation, 9(7), 3084–3095. doi:10.1021/ct400341p
  • Sun, H., Duan, L., Chen, F., Liu, H., Wang, Z., Pan, P., Zhu, F., Zhang, J. Z. H., & Hou, T. (2018). Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches. Physical Chemistry Chemical Physics, 20(21), 14450–14460. doi:10.1039/C7CP07623A
  • Vassar, R., Kuhn, P. H., Haass, C., Kennedy, M. E., Rajendran, L., Wong, P. C., & Lichtenthaler, S. F. (2014). Function, therapeutic potential and cell biology of BACE proteases: Current status and future prospects. Journal of Neurochemistry, 130(1), 4–28. doi:10.1111/jnc.12715
  • Wang, E., Sun, H., Wang, J., Wang, Z., Liu, H., Zhang, J. Z. H., & Hou, T. (2019). End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design. Chemical Reviews, 119(16), 9478–9508. doi:10.1021/acs.chemrev.9b00055
  • Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., & Case, D. A. (2004). Development and testing of a general amber force field. Journal of Computational Chemistry, 25(9), 1157–1174. doi:10.1002/jcc.20035
  • Wortmann, M. (2012). Dementia: A global health priority - highlights from an ADI and World Health Organization report. Alzheimer's Research & Therapy, 4(5), 40doi:10.1186/alzrt143
  • Zhang, Z., Xu, Y., Wu, J., Shen, Y., Cheng, H., & Xiang, Y. (2019). Exploration of the selective binding mechanism of protein kinase Aurora A selectivity via a comprehensive molecular modeling study. PeerJ, 7, e7832. doi:10.7717/peerj.7832

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