Understanding the disrupting mechanism of the Tau aggregation motif 306VQIVYK311 by phenylthiazolyl-hydrazides inhibitors
Alzheimer's disease is a progressive neurodegenerative disorder characterized by the abnormal processing of the Tau and the amyloid precursor proteins. The unusual aggregation of Tau is based on the formation of intermolecular ?-sheets through two motifs: 275VQIINK280 and 306VQIVYK311. Phenylth...
- Autores:
- Tipo de recurso:
- Fecha de publicación:
- 2020
- Institución:
- Universidad de Medellín
- Repositorio:
- Repositorio UDEM
- Idioma:
- eng
- OAI Identifier:
- oai:repository.udem.edu.co:11407/5749
- Acceso en línea:
- http://hdl.handle.net/11407/5749
- Palabra clave:
- LIE
MM-GBSA
molecular docking
molecular dynamics
phenylthiazolyl-hydrazides
Tau protein
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- http://purl.org/coar/access_right/c_16ec
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Understanding the disrupting mechanism of the Tau aggregation motif 306VQIVYK311 by phenylthiazolyl-hydrazides inhibitors |
| title |
Understanding the disrupting mechanism of the Tau aggregation motif 306VQIVYK311 by phenylthiazolyl-hydrazides inhibitors |
| spellingShingle |
Understanding the disrupting mechanism of the Tau aggregation motif 306VQIVYK311 by phenylthiazolyl-hydrazides inhibitors LIE MM-GBSA molecular docking molecular dynamics phenylthiazolyl-hydrazides Tau protein |
| title_short |
Understanding the disrupting mechanism of the Tau aggregation motif 306VQIVYK311 by phenylthiazolyl-hydrazides inhibitors |
| title_full |
Understanding the disrupting mechanism of the Tau aggregation motif 306VQIVYK311 by phenylthiazolyl-hydrazides inhibitors |
| title_fullStr |
Understanding the disrupting mechanism of the Tau aggregation motif 306VQIVYK311 by phenylthiazolyl-hydrazides inhibitors |
| title_full_unstemmed |
Understanding the disrupting mechanism of the Tau aggregation motif 306VQIVYK311 by phenylthiazolyl-hydrazides inhibitors |
| title_sort |
Understanding the disrupting mechanism of the Tau aggregation motif 306VQIVYK311 by phenylthiazolyl-hydrazides inhibitors |
| dc.subject.none.fl_str_mv |
LIE MM-GBSA molecular docking molecular dynamics phenylthiazolyl-hydrazides Tau protein |
| topic |
LIE MM-GBSA molecular docking molecular dynamics phenylthiazolyl-hydrazides Tau protein |
| description |
Alzheimer's disease is a progressive neurodegenerative disorder characterized by the abnormal processing of the Tau and the amyloid precursor proteins. The unusual aggregation of Tau is based on the formation of intermolecular ?-sheets through two motifs: 275VQIINK280 and 306VQIVYK311. Phenylthiazolyl-hydrazides (PTHs) are capable of inhibiting/disassembling Tau aggregates. However, the disaggregation mechanism of Tau oligomers by PTHs is still unknown. In this work, we studied the disruption of the oligomeric form of the Tau motif 306VQIVYK311 by PTHs through molecular docking, molecular dynamics, and free energy calculations. We predicted hydrophobic interactions as the major driving forces for the stabilization of Tau oligomer, with V306 and I308 being the major contributors. Nonpolar component of the binding free energy is essential to stabilize Tau-PTH complexes. PTHs disrupted mainly the van der Waals interactions between the monomers, leading to oligomer destabilization. Destabilization of full Tau filament by PTHs and emodin was not observed in the sampled 20 ns; however, in all cases, the nonpolar component of the binding free energy is essential for the formation of Tau filament-PTH and Tau filament-emodin. These results provide useful clues for the design of more effective Tau-aggregation inhibitors. © 2020 John Wiley & Sons Ltd |
| publishDate |
2020 |
| dc.date.accessioned.none.fl_str_mv |
2020-04-29T14:53:52Z |
| dc.date.available.none.fl_str_mv |
2020-04-29T14:53:52Z |
| dc.date.none.fl_str_mv |
2020 |
| dc.type.eng.fl_str_mv |
Article |
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http://purl.org/coar/version/c_970fb48d4fbd8a85 |
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http://purl.org/coar/resource_type/c_6501 http://purl.org/coar/resource_type/c_2df8fbb1 |
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info:eu-repo/semantics/article |
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9523499 |
| dc.identifier.uri.none.fl_str_mv |
http://hdl.handle.net/11407/5749 |
| dc.identifier.doi.none.fl_str_mv |
10.1002/jmr.2848 |
| identifier_str_mv |
9523499 10.1002/jmr.2848 |
| url |
http://hdl.handle.net/11407/5749 |
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eng |
| language |
eng |
| dc.relation.isversionof.none.fl_str_mv |
https://www.scopus.com/inward/record.uri?eid=2-s2.0-85082511416&doi=10.1002%2fjmr.2848&partnerID=40&md5=6582e54d594aa5958919a5de0c2dd520 |
| dc.relation.references.none.fl_str_mv |
Spillantini, M.G., Goedert, M., Tau protein pathology in neurodegenerative diseases (1998) Trends Neurosci, 21, pp. 428-433 Braak, H., Braak, E., Demonstration of amyloid deposits and neurofibrillary changes in whole brain sections (1991) Brain Pathol, 1, pp. 213-216 Ryan, P., Patel, B., Makwana, V., Peptides, Peptidomimetics and carbohydrate-peptide conjugates as Amyloidogenic aggregation inhibitors for Alzheimer's disease (2018) ACS Chem Neurosci, 9, pp. 1530-1551 Wischik, C.M., Wischik, D.J., Storey, J.M.D., Harrington, C.R., (2010) Rationale for Tau-Aggregation Inhibitor Therapy in Alzheimer's Disease and Other Tauopathies. Vol. 1: Beta-Amyloid, Tau Protein and Glucose Metabolism, , Scotland, UK, Royal Society of Chemistry Wilcock, G.K., Esiri, M.M., Plaques, tangles and dementia. A quantitative study (1982) J Neurol Sci, 56, pp. 343-356 Weingarten, M.D., Lockwood, A.H., Hwo, S.Y., Kirschner, M.W., A protein factor essential for microtubule assembly (1975) Proc Natl Acad Sci U S A, 72, pp. 1858-1862 von Bergen, M., Friedhoff, P., Biernat, J., Heberle, J., Mandelkow, E.M., Mandelkow, E., Assembly of tau protein into Alzheimer paired helical filaments depends on a local sequence motif (306VQIVYK311) forming beta structure (2000) PNAS, 97 (10), pp. 5129-5134 von Bergen, M., Barghorn, S., Li, L., Mutations of tau protein in frontotemporal dementia promote aggregation of paired helical filaments by enhancing local beta structure (2001) J Biol Chem, 276, pp. 48165-48174 Wille, H., Drewes, G., Biernat, J., Mandelkow, E.M., Mandelkow, E., Alzheimer-like paired helical filaments and antiparallel dimers formed from microtubule-associated protein tau in vitro (1992) J Cell Biol, 118, pp. 573-584 Taniguchi, S., Suzuki, N., Masuda, M., Inhibition of heparin-induced tau filament formation by Phenothiazines, polyphenols, and Porphyrins (2005) J Biol Chem, 280, pp. 7614-7623 Bulic, B., Pickhardt, M., Mandelkow, E.M., Mandelkow, E., Tau protein and tau aggregation inhibitors (2010) Neuropharmacology, 59, pp. 276-289 Himmelstein, D.S., Ward, S.M., Lancia, J.K., Patterson, K.R., Binder, L.I., Tau as a therapeutic target in neurodegenerative disease (2012) Pharmacol Ther, 136 (1), pp. 8-22 Pickhardt, M., Larbig, G., Khlistunova, I., Phenylthiazolyl-Hydrazide and its derivatives are potent inhibitors of tau aggregation and toxicity in vitro and in cells (2007) Biochemistry, 46, pp. 10016-10023 Song, M., Sun, Y., Luo, Y., Zhu, Y., Liu, Y., Li, H., Exploring the mechanism of inhibition of au nanoparticles on the aggregation of amyloid-?(16 22) peptides at the atom level by all-atom molecular dynamics (2018) Int J Mol Sci, 19 (6) Sukumaran, S.D., Faraj, F.L., Lee, V.S., Othman, R., Bucklem, M.J.C., 2-Aryl-3-(arylideneamino)-1,2-dihydroquinazoline-4(3H)-ones as inhibitors of cholinesterases and self-induced b-amyloid (Ab)aggregation: biological evaluations and mechanistic insights from molecular dynamics simulations (2018) RSC Adv, 8, pp. 7818-7831 Tran, L., Ha-Duong, T., Exploring the Alzheimer amyloid-? peptide conformational ensemble: a review of molecular dynamics approaches (2015) Peptides, 69, pp. 86-91 Zhao, J.H., Liu, H.L., Chuang, C.K., Liu, K.T., Tsai, W.B., Ho, Y., Molecular dynamics simulations to investigate the stability and aggregation behaviour of the amyloid-forming peptide VQIVYK from Tau protein (2010) Mol Simul, 36 (13), pp. 1013-1024 Berhanu, W.M., Masunov, A.E., Atomistic mechanism of polyphenol amyloid aggregation inhibitors: molecular dynamics study of Curcumin, Exifone, and Myricetin interaction with the segment of tau peptide oligomer (2014) J Biomol Struct Dyn, 33, pp. 1399-1411 Fitzpatrick, A.W.P., Falcon, B., He, S., Cryo-EM structures of tau filaments from Alzheimer's disease (2017) Nature, 547, pp. 185-190 Seo, J.-H., Cha, E., Kim, H.-T., Multiply charged oligomer complexes composed of the amyloid-forming peptides NNQQNY, VQIVYK, and LYQLEN analyzed by collision-induced dissociation with electrospray ionization mass spectroscopy (2017) Int J Mass Spectrom, 415, pp. 55-62 Goux, W.J., Kopplin, L., Nguyen, A.D., The formation of straight and twisted filaments from short tau peptides (2004) J Biol Chem, 279, pp. 26868-26875 Sawaya, M.R., Sambashivan, S., Nelson, R., Atomic structures of amyloid cross-beta spines reveal varied steric zippers (2007) Nature, 447, pp. 453-457 Khlistunova, I., Biernat, J., Wang, Y., Inducible expression of tau repeat domain in cell models of Taupathy. Aggregation is toxic to cells but can be reversed by inhibitors drugs (2006) J Biol Chem, 281 (2), pp. 1205-1214 Wang, R., Lai, L., Wang, S., Further development and validation of empirical scoring functions for structure-based binding affinity prediction (2002) J Comput Aided Mol Des, 16, pp. 11-26 Hernandez Gonzalez, J.E., Hernandez Alvarez, L., Pascutti, P.G., Valiente, P.A., Predicting binding modes of reversible peptide-based inhibitors of falcipain-2 consistent with structure-activity relationships (2017) Proteins, 85, pp. 1666-1683 Stjernschantz, E., Oostenbrink, C., Improved ligand-protein binding affinity predictions using multiple binding modes (2010) Biophys J, 98, pp. 2682-2691 Thompson, D.C., Humblet, C., Joseph-McCarthy, D., Investigation of MM-PBSA rescoring of docking poses (2008) J Chem Inf Model, 48, pp. 1081-1091 Lindstrom, A., Edvinsson, L., Johansson, A., Postprocessing of docked protein-ligand complexes using implicit solvation models (2011) J Chem Inf Model, 51, pp. 267-282 Guimaraes, C.R., Cardozo, M., MM-GB/SA rescoring of docking poses in structure-based lead optimization (2008) J Chem Inf Model, 48, pp. 958-970 Hou, T., Wang, J., Li, Y., Wang, W., Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized born surface area methods. II the accuracy of ranking poses generated from docking (2011) J Comp Chem, 32, pp. 866-877 Rastelli, G., Del Rio, A., Degliesposti, G., Sgobba, M., Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA (2010) J Comput Chem, 31, pp. 797-810 Sun, H., Li, Y., Tian, S., Xu, L., Hou, T., Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set (2014) Phys Chem Chem Phys, 16, pp. 16719-16729 Necula, M., Chirita, C.N., Kuret, J., Cyanine dye N744 inhibits tau fibrillization by blocking filament extension: implications for the treatment of Tauopathic neurodegenerative diseases (2005) Biochemistry, 44 (30), pp. 10227-10237 Chang, E., Congdon, E.E., Honson, N.S., Duff, K.E., Kuret, J., Structure-activity relationship of cyanine tau aggregation inhibitors (2009) J Med Chem, 52 (11), pp. 3539-3547 Pickhardt, M., Biernat, J., Khlistunova, I., N-Phenylamine derivatives as aggregation inhibitors in cell models of Tauopathy (2007) Curr Alzheimer Res, 4, pp. 397-402 Bulic, B., Pickhardt, M., Khlistunova, I., Rhodanine-based tau aggregation inhibitors in cell models of Tauopathy (2007) Angew Chem Int Ed, 46, pp. 9215-9219 Pickhardt, M., Gazova, Z., von Bergen, M., Anthraquinones inhibit tau aggregation and dissolve Alzheimer's paired helical filaments in vitro and in cells (2005) J Biol Chem, 280 (5), pp. 3628-3635 Crowe, A., Huang, W., Ballatore, C., Identification of Aminothienopyridazine inhibitors of tau assembly by quantitative high-throughput screening (2009) Biochemistry, 48 (32), pp. 7732-7745 Mark, A.E., van Gunsteren, W.F., Decomposition of the free energy of a system in terms of specific interactions. Implications for theoretical and experimental studies (1994) J Mol Biol, 240 (2), pp. 167-176 Bissantz, C., Kuhn, B., Stahl, M., A medicinal chemist's guide to molecular interactions (2010) J Med Chem, 53 (14), pp. 5061-5084 Miranda, W.E., Noskov, S.Y., Valiente, P.A., Improving the LIE method for binding free energy calculations of protein?ligand complexes (2015) J Chem Inf Model, 55, pp. 1867-1877 Åqvist, J., Marelius, J., The linear interaction energy method for predicting ligand binding free energies (2001) Comb Chem High Throughput Screen, 4, pp. 613-626 Bjelic, S., Nervall, M., Gutiérrez-de-Terán, H., Ersmark, K., Hallberg, A., Åqvist, J., Computational inhibitor design against malaria plasmepsins (2007) CMLS, 64, pp. 2285-2305 Wang, C.K., Northfield, S.E., Huang, Y.-H., Ramos, M.C., Craik, D.J., Inhibition of tau aggregation using a naturally-occurring cyclic peptide scaffold (2016) Eur J Med Chem, 109, pp. 342-349 Sanner, M.F., Python: a programming language for software integration and development (1999) J Mol Graphics Mod, 17, pp. 57-61 Trott, O., Olson, A.J., Software news and update AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading (2010) J Comput Chem, 31 (2), pp. 455-461 Pronk, S., Páll, S., Schulz, R., GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit (2013) Bioinformatics, 29, pp. 845-854 Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., Simmerling, C., Comparison of multiple Amber force-fields and development of improved protein backbone parameters (2006) Proteins, 65 (3), pp. 712-725 Wang, J.M., Wolf, R.M., Caldwell, J.W., Kollman, P.A., Development and testing of a General Amber force-field (2004) J Comput Chem, 25, pp. 1157-1174 Lindahl, E.R., Molecular dynamics simulations (2008) Molecular Modeling of Proteins, 443, pp. 1-24. , Kukol A, ed., Hertfordshire, UK, Humana Press Case, D.A., Babin, V., Berryman, J.T., (2014) AMBER 14, , San Francisco, CA, University of California |
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John Wiley and Sons Ltd |
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Facultad de Ciencias Básicas |
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Facultad de Ciencias Básicas |
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John Wiley and Sons Ltd |
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Journal of Molecular Recognition |
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Universidad de Medellín |
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Repositorio Institucional Universidad de Medellin |
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repositorio@udem.edu.co |
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1814159157313404928 |
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20202020-04-29T14:53:52Z2020-04-29T14:53:52Z9523499http://hdl.handle.net/11407/574910.1002/jmr.2848Alzheimer's disease is a progressive neurodegenerative disorder characterized by the abnormal processing of the Tau and the amyloid precursor proteins. The unusual aggregation of Tau is based on the formation of intermolecular ?-sheets through two motifs: 275VQIINK280 and 306VQIVYK311. Phenylthiazolyl-hydrazides (PTHs) are capable of inhibiting/disassembling Tau aggregates. However, the disaggregation mechanism of Tau oligomers by PTHs is still unknown. In this work, we studied the disruption of the oligomeric form of the Tau motif 306VQIVYK311 by PTHs through molecular docking, molecular dynamics, and free energy calculations. We predicted hydrophobic interactions as the major driving forces for the stabilization of Tau oligomer, with V306 and I308 being the major contributors. Nonpolar component of the binding free energy is essential to stabilize Tau-PTH complexes. PTHs disrupted mainly the van der Waals interactions between the monomers, leading to oligomer destabilization. Destabilization of full Tau filament by PTHs and emodin was not observed in the sampled 20 ns; however, in all cases, the nonpolar component of the binding free energy is essential for the formation of Tau filament-PTH and Tau filament-emodin. These results provide useful clues for the design of more effective Tau-aggregation inhibitors. © 2020 John Wiley & Sons LtdengJohn Wiley and Sons LtdFacultad de Ciencias BásicasFacultad de Ciencias Básicashttps://www.scopus.com/inward/record.uri?eid=2-s2.0-85082511416&doi=10.1002%2fjmr.2848&partnerID=40&md5=6582e54d594aa5958919a5de0c2dd520Spillantini, M.G., Goedert, M., Tau protein pathology in neurodegenerative diseases (1998) Trends Neurosci, 21, pp. 428-433Braak, H., Braak, E., Demonstration of amyloid deposits and neurofibrillary changes in whole brain sections (1991) Brain Pathol, 1, pp. 213-216Ryan, P., Patel, B., Makwana, V., Peptides, Peptidomimetics and carbohydrate-peptide conjugates as Amyloidogenic aggregation inhibitors for Alzheimer's disease (2018) ACS Chem Neurosci, 9, pp. 1530-1551Wischik, C.M., Wischik, D.J., Storey, J.M.D., Harrington, C.R., (2010) Rationale for Tau-Aggregation Inhibitor Therapy in Alzheimer's Disease and Other Tauopathies. Vol. 1: Beta-Amyloid, Tau Protein and Glucose Metabolism, , Scotland, UK, Royal Society of ChemistryWilcock, G.K., Esiri, M.M., Plaques, tangles and dementia. A quantitative study (1982) J Neurol Sci, 56, pp. 343-356Weingarten, M.D., Lockwood, A.H., Hwo, S.Y., Kirschner, M.W., A protein factor essential for microtubule assembly (1975) Proc Natl Acad Sci U S A, 72, pp. 1858-1862von Bergen, M., Friedhoff, P., Biernat, J., Heberle, J., Mandelkow, E.M., Mandelkow, E., Assembly of tau protein into Alzheimer paired helical filaments depends on a local sequence motif (306VQIVYK311) forming beta structure (2000) PNAS, 97 (10), pp. 5129-5134von Bergen, M., Barghorn, S., Li, L., Mutations of tau protein in frontotemporal dementia promote aggregation of paired helical filaments by enhancing local beta structure (2001) J Biol Chem, 276, pp. 48165-48174Wille, H., Drewes, G., Biernat, J., Mandelkow, E.M., Mandelkow, E., Alzheimer-like paired helical filaments and antiparallel dimers formed from microtubule-associated protein tau in vitro (1992) J Cell Biol, 118, pp. 573-584Taniguchi, S., Suzuki, N., Masuda, M., Inhibition of heparin-induced tau filament formation by Phenothiazines, polyphenols, and Porphyrins (2005) J Biol Chem, 280, pp. 7614-7623Bulic, B., Pickhardt, M., Mandelkow, E.M., Mandelkow, E., Tau protein and tau aggregation inhibitors (2010) Neuropharmacology, 59, pp. 276-289Himmelstein, D.S., Ward, S.M., Lancia, J.K., Patterson, K.R., Binder, L.I., Tau as a therapeutic target in neurodegenerative disease (2012) Pharmacol Ther, 136 (1), pp. 8-22Pickhardt, M., Larbig, G., Khlistunova, I., Phenylthiazolyl-Hydrazide and its derivatives are potent inhibitors of tau aggregation and toxicity in vitro and in cells (2007) Biochemistry, 46, pp. 10016-10023Song, M., Sun, Y., Luo, Y., Zhu, Y., Liu, Y., Li, H., Exploring the mechanism of inhibition of au nanoparticles on the aggregation of amyloid-?(16 22) peptides at the atom level by all-atom molecular dynamics (2018) Int J Mol Sci, 19 (6)Sukumaran, S.D., Faraj, F.L., Lee, V.S., Othman, R., Bucklem, M.J.C., 2-Aryl-3-(arylideneamino)-1,2-dihydroquinazoline-4(3H)-ones as inhibitors of cholinesterases and self-induced b-amyloid (Ab)aggregation: biological evaluations and mechanistic insights from molecular dynamics simulations (2018) RSC Adv, 8, pp. 7818-7831Tran, L., Ha-Duong, T., Exploring the Alzheimer amyloid-? peptide conformational ensemble: a review of molecular dynamics approaches (2015) Peptides, 69, pp. 86-91Zhao, J.H., Liu, H.L., Chuang, C.K., Liu, K.T., Tsai, W.B., Ho, Y., Molecular dynamics simulations to investigate the stability and aggregation behaviour of the amyloid-forming peptide VQIVYK from Tau protein (2010) Mol Simul, 36 (13), pp. 1013-1024Berhanu, W.M., Masunov, A.E., Atomistic mechanism of polyphenol amyloid aggregation inhibitors: molecular dynamics study of Curcumin, Exifone, and Myricetin interaction with the segment of tau peptide oligomer (2014) J Biomol Struct Dyn, 33, pp. 1399-1411Fitzpatrick, A.W.P., Falcon, B., He, S., Cryo-EM structures of tau filaments from Alzheimer's disease (2017) Nature, 547, pp. 185-190Seo, J.-H., Cha, E., Kim, H.-T., Multiply charged oligomer complexes composed of the amyloid-forming peptides NNQQNY, VQIVYK, and LYQLEN analyzed by collision-induced dissociation with electrospray ionization mass spectroscopy (2017) Int J Mass Spectrom, 415, pp. 55-62Goux, W.J., Kopplin, L., Nguyen, A.D., The formation of straight and twisted filaments from short tau peptides (2004) J Biol Chem, 279, pp. 26868-26875Sawaya, M.R., Sambashivan, S., Nelson, R., Atomic structures of amyloid cross-beta spines reveal varied steric zippers (2007) Nature, 447, pp. 453-457Khlistunova, I., Biernat, J., Wang, Y., Inducible expression of tau repeat domain in cell models of Taupathy. Aggregation is toxic to cells but can be reversed by inhibitors drugs (2006) J Biol Chem, 281 (2), pp. 1205-1214Wang, R., Lai, L., Wang, S., Further development and validation of empirical scoring functions for structure-based binding affinity prediction (2002) J Comput Aided Mol Des, 16, pp. 11-26Hernandez Gonzalez, J.E., Hernandez Alvarez, L., Pascutti, P.G., Valiente, P.A., Predicting binding modes of reversible peptide-based inhibitors of falcipain-2 consistent with structure-activity relationships (2017) Proteins, 85, pp. 1666-1683Stjernschantz, E., Oostenbrink, C., Improved ligand-protein binding affinity predictions using multiple binding modes (2010) Biophys J, 98, pp. 2682-2691Thompson, D.C., Humblet, C., Joseph-McCarthy, D., Investigation of MM-PBSA rescoring of docking poses (2008) J Chem Inf Model, 48, pp. 1081-1091Lindstrom, A., Edvinsson, L., Johansson, A., Postprocessing of docked protein-ligand complexes using implicit solvation models (2011) J Chem Inf Model, 51, pp. 267-282Guimaraes, C.R., Cardozo, M., MM-GB/SA rescoring of docking poses in structure-based lead optimization (2008) J Chem Inf Model, 48, pp. 958-970Hou, T., Wang, J., Li, Y., Wang, W., Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized born surface area methods. II the accuracy of ranking poses generated from docking (2011) J Comp Chem, 32, pp. 866-877Rastelli, G., Del Rio, A., Degliesposti, G., Sgobba, M., Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA (2010) J Comput Chem, 31, pp. 797-810Sun, H., Li, Y., Tian, S., Xu, L., Hou, T., Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set (2014) Phys Chem Chem Phys, 16, pp. 16719-16729Necula, M., Chirita, C.N., Kuret, J., Cyanine dye N744 inhibits tau fibrillization by blocking filament extension: implications for the treatment of Tauopathic neurodegenerative diseases (2005) Biochemistry, 44 (30), pp. 10227-10237Chang, E., Congdon, E.E., Honson, N.S., Duff, K.E., Kuret, J., Structure-activity relationship of cyanine tau aggregation inhibitors (2009) J Med Chem, 52 (11), pp. 3539-3547Pickhardt, M., Biernat, J., Khlistunova, I., N-Phenylamine derivatives as aggregation inhibitors in cell models of Tauopathy (2007) Curr Alzheimer Res, 4, pp. 397-402Bulic, B., Pickhardt, M., Khlistunova, I., Rhodanine-based tau aggregation inhibitors in cell models of Tauopathy (2007) Angew Chem Int Ed, 46, pp. 9215-9219Pickhardt, M., Gazova, Z., von Bergen, M., Anthraquinones inhibit tau aggregation and dissolve Alzheimer's paired helical filaments in vitro and in cells (2005) J Biol Chem, 280 (5), pp. 3628-3635Crowe, A., Huang, W., Ballatore, C., Identification of Aminothienopyridazine inhibitors of tau assembly by quantitative high-throughput screening (2009) Biochemistry, 48 (32), pp. 7732-7745Mark, A.E., van Gunsteren, W.F., Decomposition of the free energy of a system in terms of specific interactions. 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