Exploración "in silico" del proceso inhibitorio de la ß-Secretasa por hidroxietilaminas: Una aproximación geométrica y energética en el tiempo

Tesis (Doctor en Ciencias). -- Universidad de Cartagena. Facultad de Ciencias Exactas y Naturales, 2017

Autores:
Gueto Tettay, Carlos Alberto
Tipo de recurso:
Fecha de publicación:
2017
Institución:
Universidad de Cartagena
Repositorio:
Repositorio Universidad de Cartagena
Idioma:
spa
OAI Identifier:
oai:repositorio.unicartagena.edu.co:11227/9039
Acceso en línea:
https://hdl.handle.net/11227/9039
http://dx.doi.org/10.57799/11227/77
Palabra clave:
Biotecnología
Inhibidores de enzima - Ensayo
Inhibidores de enzima
Inhibidores de enzima - Métodos de simulación
Enzimas - Métodos de simulación
Enzimas - Hidrogenólisis - Métodos de simulación
Rights
License
https://creativecommons.org/licenses/by-nc-nd/4.0
id UCART2_8e643f056ec9c0725039e5dec16fe057
oai_identifier_str oai:repositorio.unicartagena.edu.co:11227/9039
network_acronym_str UCART2
network_name_str Repositorio Universidad de Cartagena
repository_id_str
dc.title.es.fl_str_mv Exploración "in silico" del proceso inhibitorio de la ß-Secretasa por hidroxietilaminas: Una aproximación geométrica y energética en el tiempo
title Exploración "in silico" del proceso inhibitorio de la ß-Secretasa por hidroxietilaminas: Una aproximación geométrica y energética en el tiempo
spellingShingle Exploración "in silico" del proceso inhibitorio de la ß-Secretasa por hidroxietilaminas: Una aproximación geométrica y energética en el tiempo
Biotecnología
Inhibidores de enzima - Ensayo
Inhibidores de enzima
Inhibidores de enzima - Métodos de simulación
Enzimas - Métodos de simulación
Enzimas - Hidrogenólisis - Métodos de simulación
title_short Exploración "in silico" del proceso inhibitorio de la ß-Secretasa por hidroxietilaminas: Una aproximación geométrica y energética en el tiempo
title_full Exploración "in silico" del proceso inhibitorio de la ß-Secretasa por hidroxietilaminas: Una aproximación geométrica y energética en el tiempo
title_fullStr Exploración "in silico" del proceso inhibitorio de la ß-Secretasa por hidroxietilaminas: Una aproximación geométrica y energética en el tiempo
title_full_unstemmed Exploración "in silico" del proceso inhibitorio de la ß-Secretasa por hidroxietilaminas: Una aproximación geométrica y energética en el tiempo
title_sort Exploración "in silico" del proceso inhibitorio de la ß-Secretasa por hidroxietilaminas: Una aproximación geométrica y energética en el tiempo
dc.creator.fl_str_mv Gueto Tettay, Carlos Alberto
dc.contributor.advisor.none.fl_str_mv Drosos Ramírez, Juan Carlos
dc.contributor.author.none.fl_str_mv Gueto Tettay, Carlos Alberto
dc.subject.es.fl_str_mv Biotecnología
Inhibidores de enzima - Ensayo
Inhibidores de enzima
Inhibidores de enzima - Métodos de simulación
Enzimas - Métodos de simulación
Enzimas - Hidrogenólisis - Métodos de simulación
topic Biotecnología
Inhibidores de enzima - Ensayo
Inhibidores de enzima
Inhibidores de enzima - Métodos de simulación
Enzimas - Métodos de simulación
Enzimas - Hidrogenólisis - Métodos de simulación
description Tesis (Doctor en Ciencias). -- Universidad de Cartagena. Facultad de Ciencias Exactas y Naturales, 2017
publishDate 2017
dc.date.issued.none.fl_str_mv 2017
dc.date.accessioned.none.fl_str_mv 2019-08-13T19:33:36Z
dc.date.available.none.fl_str_mv 2019-08-13T19:33:36Z
dc.type.spa.fl_str_mv Trabajo de grado - Doctorado
dc.type.coar.fl_str_mv http://purl.org/coar/resource_type/c_db06
dc.type.driver.none.fl_str_mv info:eu-repo/semantics/doctoralThesis
dc.identifier.citation.es.fl_str_mv TD660.6 / G938
dc.identifier.uri.none.fl_str_mv https://hdl.handle.net/11227/9039
http://dx.doi.org/10.57799/11227/77
identifier_str_mv TD660.6 / G938
url https://hdl.handle.net/11227/9039
http://dx.doi.org/10.57799/11227/77
dc.language.iso.es.fl_str_mv spa
language spa
dc.rights.coar.fl_str_mv http://purl.org/coar/access_right/c_abf2
dc.rights.uri.none.fl_str_mv https://creativecommons.org/licenses/by-nc-nd/4.0
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-nd/4.0
http://purl.org/coar/access_right/c_abf2
dc.format.medium.none.fl_str_mv application/pdf
dc.publisher.es.fl_str_mv Universidad de Cartagena
institution Universidad de Cartagena
bitstream.url.fl_str_mv https://dspace7-unicartagena.metabuscador.org/bitstreams/02d7f31a-fdab-4678-8858-3ce20a3a3f8e/download
https://dspace7-unicartagena.metabuscador.org/bitstreams/0bd65ec1-eda9-49d5-8e7f-77ab4549c444/download
https://dspace7-unicartagena.metabuscador.org/bitstreams/28018b7c-5fe9-4a6f-8324-e9b9f7364e0b/download
https://dspace7-unicartagena.metabuscador.org/bitstreams/8181848f-edf2-445d-b96b-d353132510ff/download
bitstream.checksum.fl_str_mv 16fbc59a27de2341fa46e5db6f9f016b
80f4fab81256c9c749645bab750e44ea
1088dfeda4aee676bbd6dc09d3723e72
5801a8c84b260cc75bfff56b0d4f5daa
bitstream.checksumAlgorithm.fl_str_mv MD5
MD5
MD5
MD5
repository.name.fl_str_mv Biblioteca Digital Universidad de Cartagena
repository.mail.fl_str_mv bdigital@metabiblioteca.com
_version_ 1814214045756030976
spelling Drosos Ramírez, Juan CarlosGueto Tettay, Carlos Alberto2019-08-13T19:33:36Z2019-08-13T19:33:36Z2017TD660.6 / G938https://hdl.handle.net/11227/9039http://dx.doi.org/10.57799/11227/77Tesis (Doctor en Ciencias). -- Universidad de Cartagena. Facultad de Ciencias Exactas y Naturales, 2017Dentro de esta investigación, se busca explorar el mecanismo inhibitorio de la b-secretasa por parte de los hidroxietilaminos empleando técnicas de modelado molecular asistido por computadorasapplication/pdfspaUniversidad de Cartagenahttps://creativecommons.org/licenses/by-nc-nd/4.0http://purl.org/coar/access_right/c_abf2BiotecnologíaInhibidores de enzima - EnsayoInhibidores de enzimaInhibidores de enzima - Métodos de simulaciónEnzimas - Métodos de simulaciónEnzimas - Hidrogenólisis - Métodos de simulaciónExploración "in silico" del proceso inhibitorio de la ß-Secretasa por hidroxietilaminas: Una aproximación geométrica y energética en el tiempoTrabajo de grado - Doctoradoinfo:eu-repo/semantics/doctoralThesishttp://purl.org/coar/resource_type/c_db06Abraham, 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.Adlard, P. A., Tran, B. A., Finkelstein, D. I., Desmond, P. M., Johnston, L. A., Bush, A. I. & Egan, G. F. (2014). A review of beta-amyloid neuroimaging in Alzheimer's disease. Front Neurosci 8: 327.Ambure, P. & Roy, K. (2016). Understanding the structural requirements of cyclic sulfone hydroxyethylamines as hBACE1 inhibitors against Aβ plaques in Alzheimer's disease: a predictive QSAR approach. RSC Adv. 6: 28171-28186.Arodola, O. A. & Soliman, M. E. (2016). Molecular Dynamics Simulations of Ligand-Induced Flap Conformational Changes in Cathepsin-D-A Comparative Study. J Cell Biochem 117: 2643-2657.Barman, A. & Prabhakar, R. (2012). Protonation States of the Catalytic Dyad of β-Secretase (BACE1) in the Presence of Chemically Diverse Inhibitors: A Molecular Docking Study. Journal of Chemical Information and Modeling 52: 1275-1287.Barman, A. & Prabhakar, R. (2012). Protonation States of the Catalytic Dyad of β-Secretase (BACE1) in the Presence of Chemically Diverse Inhibitors: A Molecular Docking Study. Journal of Chemical Information and Modeling 52: 1275-1287.Barman, A. & Prabhakar, R. (2014). Computational Insights into Substrate and Site Specificities, Catalytic Mechanism, and Protonation States of the Catalytic Asp Dyad of β- Secretase. Scientifica 2014: 11Barman, A. & Prabhakar, R. (2014). Computational Insights into Substrate and Site Specificities, Catalytic Mechanism, and Protonation States of the Catalytic Asp Dyad of beta - Secretase. Scientifica (Cairo) 2014: 598728.Barman, A., Schürer, S. & Prabhakar, R. (2011). Computational Modeling of Substrate Specificity and Catalysis of the β-Secretase (BACE1) Enzyme. Biochemistry 50: 4337-4349.Berendsen, H. J. C., van der Spoel, D. & van Drunen, R. (1995). GROMACS: A message-passing parallel molecular dynamics implementation. Computer Physics Communications 91: 43-56.Bernier, F., Sato, Y., Matijevic, M., Desmond, H., McGrath, S., Burns, L., Kaplow, J. M. & Albala, B. (2013). Clinical study of E2609, a novel BACE1 inhibitor, demonstrates target engagement and inhibition of BACE1 activity in CSF. Alzheimer's & Dementia 9: P886.Beswick, P., Charrier, N., Clarke, B., Demont, E., Dingwall, C., Dunsdon, R., Faller, A., Gleave, R., Hawkins, J., Hussain, I., Johnson, C. N., MacPherson, D., Maile, G., Matico, R., Milner, P., Mosley, J., Naylor, A., O'Brien, A., Redshaw, S., Riddell, D., Rowland, P., Skidmore, J., Soleil, V., Smith, K. J., Stanway, S., Stemp, G., Stuart, A., Sweitzer, S., Theobald, P., Vesey, D., Walter, D. S., Ward, J. & Wayne, G. (2008). BACE-1 inhibitors part 3: identification of hydroxy ethylamines (HEAs) with nanomolar potency in cells. Bioorg Med Chem Lett 18: 1022-1026.Brandon, C. J., Martin, B. P., McGee, K. J., Stewart, J. J. P. & Braun-Sand, S. B. (2015). An approach to creating a more realistic working model from a protein data bank entry. Journal of Molecular Modeling 21.Bras, N. F., Fernandes, P. A. & Ramos, M. J. (2014). Molecular dynamics studies on both bound and unbound renin protease. J Biomol Struct Dyn 32: 351-363Cai, Y., Kurt Yilmaz, N., Myint, W., Ishima, R. & Schiffer, C. A. (2012). Differential Flap Dynamics in Wild-Type and a Drug Resistant Variant of HIV-1 Protease Revealed by Molecular Dynamics and NMR Relaxation. Journal of Chemical Theory and Computation 8: 3452- 3462.Clarke, B., Cutler, L., Demont, E., Dingwall, C., Dunsdon, R., Hawkins, J., Howes, C., Hussain, I., Maile, G., Matico, R., Mosley, J., Naylor, A., O'Brien, A., Redshaw, S., Rowland, P., Soleil, V., Smith, K. J., Sweitzer, S., Theobald, P., Vesey, D., Walter, D. S. & Wayne, G. (2010). BACE-1 hydroxyethylamine inhibitors using novel edge-to-face interaction with Arg-296. Bioorg Med Chem Lett 20: 4639-4644.Clarke, B., Demont, E., Dingwall, C., Dunsdon, R., Faller, A., Hawkins, J., Hussain, I., MacPherson, D., Maile, G., Matico, R., Milner, P., Mosley, J., Naylor, A., O'Brien, A., Redshaw, S., Riddell, D., Rowland, P., Soleil, V., Smith, K. J., Stanway, S., Stemp, G., Sweitzer, S., Theobald, P., Vesey, D., Walter, D. S., Ward, J. & Wayne, G. (2008). BACE-1 inhibitors part 1: identification of novel hydroxy ethylamines (HEAs). Bioorg Med Chem Lett 18: 1011-1016.Clarke, B., Demont, E., Dingwall, C., Dunsdon, R., Faller, A., Hawkins, J., Hussain, I., MacPherson, D., Maile, G., Matico, R., Milner, P., Mosley, J., Naylor, A., O'Brien, A., Redshaw, S., Riddell, D., Rowland, P., Soleil, V., Smith, K. J., Stanway, S., Stemp, G., Sweitzer, S., Theobald, P., Vesey, D., Walter, D. S., Ward, J. & Wayne, G. (2008). BACE-1 inhibitors part 2: identification of hydroxy ethylamines (HEAs) with reduced peptidic character. Bioorg Med Chem Lett 18: 1017-1021.Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W. & Kollman, P. A. (1995). A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules. Journal of the American Chemical Society 117: 5179-5197.Coutsias, E. A., Seok, C. & Dill, K. A. (2004). Using quaternions to calculate RMSD. Journal of Computational Chemistry 25: 1849-1857Crunkhorn, S. (2016). Alzheimer disease: BACE1 inhibitor reduces β-amyloid production in humans. Nature Reviews Drug Discovery 16: 18-18.Crunkhorn, S. (2016). Computational chemistry: Novel virtual screening approach. Nature Reviews Drug Discovery 16: 18-18.Czodrowski, P., Sotriffer, C. A. & Klebe, G. (2007). Atypical Protonation States in the Active Site of HIV-1 Protease: A Computational Study. Journal of Chemical Information and Modeling 47: 1590-1598.Chakraborty, S. & Basu, S. (2015). Structural insight into the mechanism of amyloid precursor protein recognition by beta-secretase 1: A molecular dynamics study. Biophys Chem 202: 1-12.Chakraborty, S., Ramachandran, B. & Basu, S. (2014). Encompassing receptor flexibility in virtual screening using ensemble docking-based hybrid QSAR: discovery of novel phytochemicals for BACE1 inhibition. Molecular BioSystems 10: 2684.Chang, W. P., Huang, X., Downs, D., Cirrito, J. R., Koelsch, G., Holtzman, D. M., Ghosh, A. K. & Tang, J. (2010). -Secretase inhibitor GRL-8234 rescues age-related cognitive decline in APP transgenic mice. The FASEB Journal 25: 775-784.Charrier, N., Clarke, B., Cutler, L., Demont, E., Dingwall, C., Dunsdon, R., East, P., Hawkins, J., Howes, C., Hussain, I., Jeffrey, P., Maile, G., Matico, R., Mosley, J., Naylor, A., O’Brien, A., Redshaw, S., Rowland, P., Soleil, V., Smith, K. J., Sweitzer, S., Theobald, P., Vesey, D., Walter, D. S. & Wayne, G. (2008). Second Generation of Hydroxyethylamine BACE-1 Inhibitors: Optimizing Potency and Oral Bioavailability. Journal of Medicinal Chemistry 51: 3313-3317.Charrier, N., Clarke, B., Cutler, L., Demont, E., Dingwall, C., Dunsdon, R., Hawkins, J., Howes, C., Hubbard, J., Hussain, I., Maile, G., Matico, R., Mosley, J., Naylor, A., O'Brien, A., Redshaw, S., Rowland, P., Soleil, V., Smith, K. J., Sweitzer, S., Theobald, P., Vesey, D., Walter, D. S. & Wayne, G. (2009). Second generation of BACE-1 inhibitors part 3: Towards non hydroxyethylamine transition state mimetics. Bioorg Med Chem Lett 19: 3674-3678Charrier, N., Clarke, B., Cutler, L., Demont, E., Dingwall, C., Dunsdon, R., Hawkins, J., Howes, C., Hubbard, J., Hussain, I., Maile, G., Matico, R., Mosley, J., Naylor, A., O'Brien, A., Redshaw, S., Rowland, P., Soleil, V., Smith, K. J., Sweitzer, S., Theobald, P., Vesey, D., Walter, D. S. & Wayne, G. (2009). Second generation of BACE-1 inhibitors. Part 1: The need for improved pharmacokinetics. Bioorg Med Chem Lett 19: 3664-3668.Charrier, N., Clarke, B., Demont, E., Dingwall, C., Dunsdon, R., Hawkins, J., Hubbard, J., Hussain, I., Maile, G., Matico, R., Mosley, J., Naylor, A., O'Brien, A., Redshaw, S., Rowland, P., Soleil, V., Smith, K. J., Sweitzer, S., Theobald, P., Vesey, D., Walter, D. S. & Wayne, G. (2009). Second generation of BACE-1 inhibitors part 2: Optimisation of the non-prime side substituent. Bioorg Med Chem Lett 19: 3669-3673Chéron, N. & Shakhnovich, E. I. (2017). Effect of sampling on BACE-1 ligands binding free energy predictions via MM-PBSA calculations. Journal of Computational ChemistryDarden, 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: 10089.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.Domínguez, J. L., Christopeit, T., Villaverde, M. C., Gossas, T., Otero, J. M., Nyström, S., Baraznenok, V., Lindström, E., Danielson, U. H. & Sussman, F. (2010). Effect of the Protonation State of the Titratable Residues on the Inhibitor Affinity to BACE-1. Biochemistry 49: 7255-7263.Duan, Y., Wu, C., Chowdhury, S., Lee, M. C., Xiong, G., Zhang, W., Yang, R., Cieplak, P., Luo, R., Lee, T., Caldwell, J., Wang, J. & Kollman, P. (2003). A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. Journal of Computational Chemistry 24: 1999-2012.Edwards, G., 3rd, Moreno-Gonzalez, I. & Soto, C. (2016). Amyloid-beta and tau pathology following repetitive mild traumatic brain injury. Biochem Biophys Res Commun.Eketjäll, S., Janson, J., Kaspersson, K., Bogstedt, A., Jeppsson, F., Fälting, J., Haeberlein, S. B., Kugler, A. R., Alexander, R. C., Cebers, G. & Ho, P. (2016). AZD3293: A Novel, Orally Active BACE1 Inhibitor with High Potency and Permeability and Markedly Slow Off-Rate Kinetics. Journal of Alzheimer's Disease 50: 1109-1123.El-Hachem, N., Haibe-Kains, B., Khalil, A., Kobeissy, F. H. & Nemer, G. (2017). AutoDock and AutoDockTools for Protein-Ligand Docking: Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1(BACE1) as a Case Study. 1598: 391-403.Ellis, C. R. & Shen, J. (2015). pH-Dependent Population Shift Regulates BACE1 Activity and Inhibition. Journal of the American Chemical Society 137: 9543-9546.Ellis, C. R., Tsai, C.-C., Lin, F.-Y. & Shen, J. (2017). Conformational dynamics of cathepsin D and binding to a small-molecule BACE1 inhibitor. Journal of Computational Chemistry 38: 1260-1269.Evin, G. (2016). Future Therapeutics in Alzheimer's Disease: Development Status of BACE Inhibitors. BioDrugs 30: 173-194.Fedele, E., Rivera, D., Marengo, B., Pronzato, M. A. & Ricciarelli, R. (2015). Amyloid beta: Walking on the dark side of the moon. Mech Ageing Dev 152: 1-4.Ghosh, A. K. & Osswald, H. L. (2014). BACE1 (β-secretase) inhibitors for the treatment of Alzheimer's disease. Chemical Society Reviews 43: 6765-6813.Gorfe, A. A. & Caflisch, A. (2005). Functional plasticity in the substrate binding site of betasecretase. Structure 13: 1487-1498.Gueto-Tettay, C., Drosos, J. C. & Vivas-Reyes, R. (2011). Quantum mechanics study of the hydroxyethylamines-BACE-1 active site interaction energies. J Comput Aided Mol Des 25: 583-597.H. Al-Nadaf, A. & Taha, M. O. (2015). Identification of Small Molecule Memapsin Inhibitors via Computation-based Virtual Screening. Advances in Pharmacology and Pharmacy 3: 53- 63.Haass, C., Kaether, C., Thinakaran, G. & Sisodia, S. (2012). Trafficking and proteolytic processing of APP. Cold Spring Harb Perspect Med 2: a006270.Harrington, K. D., Lim, Y. Y., Gould, E. & Maruff, P. (2014). Amyloid-beta and depression in healthy older adults: A systematic review. Aust N Z J Psychiatry.Hernandez-Rodriguez, M., Correa-Basurto, J., Gutierrez, A., Vitorica, J. & Rosales-Hernandez, M. C. (2016). Asp32 and Asp228 determine the selective inhibition of BACE1 as shown by docking and molecular dynamics simulations. Eur J Med Chem: IN PRESSHersi, M., Irvine, B., Gupta, P., Gomes, J., Birkett, N. & Krewski, D. (2017). Risk factors associated with the onset and progression of Alzheimer’s disease: A systematic review of the evidence. NeuroToxicology.Hess, B., Bekker, H., Berendsen, H. J. C. & Fraaije, J. G. E. M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry 18: 1463-1472.Hong, L., Koelsch, G., Lin, X., Wu, S., Terzyan, S., Ghosh, A. K., Zhang, X. C. & Tang, J. (2000). Structure of the protease domain of memapsin 2 (beta-secretase) complexed with inhibitor. Science 290: 150-153.Hong, L. & Tang, J. (2004). Flap Position of Free Memapsin 2 (β-Secretase), a Model for Flap Opening in Aspartic Protease Catalysis. Biochemistry 43: 4689-4695.Hornak, V., Okur, A., Rizzo, R. C. & Simmerling, C. (2006). HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations. Proceedings of the National Academy of Sciences 103: 915-920.Huang, D., Liu, Y., Shi, B., Li, Y., Wang, G. & Liang, G. (2013). Comprehensive 3D-QSAR and binding mode of BACE-1 inhibitors using R-group search and molecular docking. J Mol Graph Model 45: 65-83.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: 1145-1152.Humphrey, W., Dalke, A. & Schulten, K. (1996). VMD: visual molecular dynamics. J Mol Graph 14: 33-38, 27-38.Hussain, I., Hawkins, J., Harrison, D., Hille, C., Wayne, G., Cutler, L., Buck, T., Walter, D., Demont, E., Howes, C., Naylor, A., Jeffrey, P., Gonzalez, M. I., Dingwall, C., Michel, A., Redshaw, S. & Davis, J. B. (2007). Oral administration of a potent and selective non-peptidic BACE1 inhibitor decreases ?-cleavage of amyloid precursor protein and amyloid-? production in vivo. Journal of Neurochemistry 100: 802-809.Iqbal, K., Liu, F. & Gong, C. X. (2016). Tau and neurodegenerative disease: the story so far. Nat Rev Neurol 12: 15-27.Ishima, R. & Louis, J. M. (2008). A diverse view of protein dynamics from NMR studies of HIV-1 protease flaps. Proteins 70: 1408-1415John, S., Thangapandian, S., Sakkiah, S. & Lee, K. (2011). Potent bace-1 inhibitor design using pharmacophore modeling, in silico screening and molecular docking studies. BMC Bioinformatics 12: S28.Jonsson, T., Atwal, J. K., Steinberg, S., Snaedal, J., Jonsson, P. V., Bjornsson, S., Stefansson, H., Sulem, P., Gudbjartsson, D., Maloney, J., Hoyte, K., Gustafson, A., Liu, Y., Lu, Y., Bhangale, T., Graham, R. R., Huttenlocher, J., Bjornsdottir, G., Andreassen, O. A., Jonsson, E. G., Palotie, A., Behrens, T. W., Magnusson, O. T., Kong, A., Thorsteinsdottir, U., Watts, R. J. & Stefansson, K. (2012). A mutation in APP protects against Alzheimer's disease and agerelated cognitive decline. Nature 488: 96-99.Kabsch, W. (1976). A solution for the best rotation to relate two sets of vectors. Acta Crystallographica Section A 32: 922-923.Karubiu, W., Bhakat, S., McGillewie, L. & Soliman, M. E. S. (2015). Flap dynamics of plasmepsin proteases: insight into proposed parameters and molecular dynamics. Molecular BioSystems 11: 1061-1066.Klamt, A. & Schüürmann, G. (1993). COSMO: a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient. J. Chem. Soc., Perkin Trans. 2: 799-805.Kocak, A., Erol, I., Yildiz, M. & Can, H. (2016). Computational insights into the protonation states of catalytic dyad in BACE1-acyl guanidine based inhibitor complex. J Mol Graph Model 70: 226-235.Kortum, S. W., Benson, T. E., Bienkowski, M. J., Emmons, T. L., Prince, D. B., Paddock, D. J., Tomasselli, A. G., Moon, J. B., LaBorde, A. & TenBrink, R. E. (2007). Potent and selective isophthalamide S2 hydroxyethylamine inhibitors of BACE1. Bioorg Med Chem Lett 17: 3378-3383.Kumalo, H. M., Bhakat, S. & Soliman, M. E. (2016). Investigation of flap flexibility of betasecretase using molecular dynamic simulations. J Biomol Struct Dyn 34: 1008-1019.Kumalo, H. M. & Soliman, M. E. (2016). A comparative molecular dynamics study on BACE1 and BACE2 flap flexibility. J Recept Signal Transduct Res 36: 505-514.Kumar, A., Roy, S., Tripathi, S. & Sharma, A. (2015). Molecular docking based virtual screening of natural compounds as potential BACE1 inhibitors: 3D QSAR pharmacophore mapping and molecular dynamics analysis. Journal of Biomolecular Structure and Dynamics 34: 239-249.Li, R., Lindholm, K., Yang, L. B., Yue, X., Citron, M., Yan, R., Beach, T., Sue, L., Sabbagh, M., Cai, H., Wong, P., Price, D. & Shen, Y. (2004). Amyloid β peptide load is correlated with increased β-secretase activity in sporadic Alzheimer's disease patients. Proceedings of the National Academy of Sciences of the United States of America 101: 3632-3637Mahanti, M., Bhakat, S., Nilsson, U. J. & Soderhjelm, P. (2016). Flap Dynamics in Aspartic Proteases: A Computational Perspective. Chem Biol Drug Des 88: 159-177.Mahoney, M. W. & Jorgensen, W. L. (2000). A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions. The Journal of Chemical Physics 112: 8910-8922.Maillard, M. C., Hom, R. K., Benson, T. E., Moon, J. B., Mamo, S., Bienkowski, M., Tomasselli, A. G., Woods, D. D., Prince, D. B., Paddock, D. J., Emmons, T. L., Tucker, J. A., Dappen, M. S., Brogley, L., Thorsett, E. D., Jewett, N., Sinha, S. & John, V. (2007). Design, Synthesis, and Crystal Structure of Hydroxyethyl Secondary Amine-Based Peptidomimetic Inhibitors of Human β-Secretase†. Journal of Medicinal Chemistry 50: 776-781.Mandal, M., Zhu, Z., Cumming, J. N., Liu, X., Strickland, C., Mazzola, R. D., Caldwell, J. P., Leach, P., Grzelak, M., Hyde, L., Zhang, Q., Terracina, G., Zhang, L., Chen, X., Kuvelkar, R., Kennedy, M. E., Favreau, L., Cox, K., Orth, P., Buevich, A., Voigt, J., Wang, H., Kazakevich, I., McKittrick, B. A., Greenlee, W., Parker, E. M. & Stamford, A. W. (2012). Design and Validation of Bicyclic Iminopyrimidinones As Beta Amyloid Cleaving Enzyme-1 (BACE1) Inhibitors: Conformational Constraint to Favor a Bioactive Conformation. Journal of Medicinal Chemistry 55: 9331-9345.Manoharan, P., Vijayan, R. S. K. & Ghoshal, N. (2010). Rationalizing fragment based drug discovery for BACE1: insights from FB-QSAR, FB-QSSR, multi objective (MO-QSPR) and MIF studies. Journal of Computer-Aided Molecular Design 24: 843-864.Martin, B. P., Brandon, C. J., Stewart, J. J. P. & Braun-Sand, S. B. (2015). Accuracy issues involved in modelingin vivoprotein structures using PM7. Proteins: Structure, Function, and Bioinformatics 83: 1427-1435.May, P. C., Willis, B. A., Lowe, S. L., Dean, R. A., Monk, S. A., Cocke, P. J., Audia, J. E., Boggs, L. N., Borders, A. R., Brier, R. A., Calligaro, D. O., Day, T. A., Ereshefsky, L., Erickson, J. A., Gevorkyan, H., Gonzales, C. R., James, D. E., Jhee, S. S., Komjathy, S. F., Li, L., Lindstrom, T. D., Mathes, B. M., Martenyi, F., Sheehan, S. M., Stout, S. L., Timm, D. E., Vaught, G. M., Watson, B. M., Winneroski, L. L., Yang, Z. & Mergott, D. J. (2015). The Potent BACE1 Inhibitor LY2886721 Elicits Robust Central A Pharmacodynamic Responses in Mice, Dogs, and Humans. Journal of Neuroscience 35: 1199-1210.Menting, K. W. & Claassen, J. A. (2014). beta-secretase inhibitor; a promising novel therapeutic drug in Alzheimer's disease. Front Aging Neurosci 6: 165.Mishra, S. & Caflisch, A. (2011). Dynamics in the Active Site of β-Secretase: A Network Analysis of Atomistic Simulations. Biochemistry 50: 9328-9339.Miyamoto, S. & Kollman, P. A. (1992). Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models. Journal of Computational Chemistry 13: 952-962.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. J Comput Chem 30: 2785-2791.Morrone, C. D., Liu, M., Black, S. E. & McLaurin, J. (2015). Interaction between therapeutic interventions for Alzheimer’s disease and physiological Aβ clearance mechanisms. Frontiers in Aging Neuroscience 7O'Brien, R. J. & Wong, P. C. (2011). Amyloid precursor protein processing and Alzheimer's disease. Annu Rev Neurosci 34: 185-204.Oehlrich, D., Prokopcova, H. & Gijsen, H. J. M. (2014). The evolution of amidine-based brain penetrant BACE1 inhibitors. Bioorganic & medicinal chemistry letters 24: 2033-2045.Palakurti, R., Sriram, D., Yogeeswari, P. & Vadrevu, R. (2013). Multiple e-Pharmacophore Modeling Combined with High-Throughput Virtual Screening and Docking to Identify Potential Inhibitors of β-Secretase(BACE1). Molecular Informatics 32: 385-398.Park, H. & Lee, S. (2003). Determination of the Active Site Protonation State of β-Secretase from Molecular Dynamics Simulation and Docking Experiment:  Implications for StructureBased Inhibitor Design. Journal of the American Chemical Society 125: 16416-16422.Patel, S., Vuillard, L., Cleasby, A., Murray, C. W. & Yon, J. (2004). Apo and inhibitor complex structures of BACE (beta-secretase). Journal of molecular biology 343: 407-416.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: 1605-1612.Polgar, T. & Keseru, G. M. (2011). Integration of virtual and high throughput screening in lead discovery settings. Comb Chem High Throughput Screen 14: 889-897.Polgar, T., Magyar, C., Simon, I. & Keseru, G. M. (2007). Impact of ligand protonation on virtual screening against beta-secretase (BACE1). J Chem Inf Model 47: 2366-2373.Pradeep, N., Munikumar, M., Swargam, S., Hema, K., Sudheer Kumar, K. & Umamaheswari, A. (2015). 197 Combination of e- harmacophore modeling, multiple docking strategies and molecular dynamic simulations to discover of novel antagonists of BACE1. Journal of Biomolecular Structure and Dynamics 33: 129-130.Prado-Prado, F., Escobar-Cubiella, M. & Garcia-Mera, X. (2011). Review of Bioinformatics and QSAR Studies of β-Secretase Inhibitors. Current Bioinformatics 6: 3-15.Pronk, S., Páll, S., Schulz, R., Larsson, P., Bjelkmar, P., Apostolov, R., Shirts, M. R., Smith, J. C., Kasson, P. M., van der Spoel, D., Hess, B. & Lindahl, E. (2013). GROMACS 4.5: a highthroughput and highly parallel open source molecular simulation toolkit. Bioinformatics.Quartino, A., Huledal, G., Sparve, E., Lüttgen, M., Bueters, T., Karlsson, P., Olsson, T., Paraskos, J., Maltby, J., Claeson-Bohnstedt, K., Lee, C.-M., Alexander, R., Fälting, J. & Paulsson, B. (2014). Population pharmacokinetic and pharmacodynamic analysis of plasma Aβ40and Aβ42following single oral doses of the BACE1 inhibitor AZD3839 to healthy volunteers. Clinical Pharmacology in Drug Development 3: 396-405.Rajamani, R. & Reynolds, C. H. (2004). Modeling the Protonation States of the Catalytic Aspartates in β-Secretase. Journal of Medicinal Chemistry 47: 5159-5166.Reitz, C. & Mayeux, R. (2014). Alzheimer disease: epidemiology, diagnostic criteria, risk factors and biomarkers. Biochem Pharmacol 88: 640-651.Ren, Z., Tam, D., Xu, Y.-Z., Wone, D., Yuan, S., Sham, H. L., Cheung, H., Regnstrom, K., Chen, X., Rudolph, D., Jobling, M. F., Artis, D. R. & Bova, M. P. (2013). Development of a Novel βSecretase Binding Assay Using the AlphaScreen Platform. Journal of Biomolecular Screening 18: 695-704.Rueeger, H., Lueoend, R., Rogel, O., Rondeau, J.-M., Möbitz, H., Machauer, R., Jacobson, L., Staufenbiel, M., Desrayaud, S. & Neumann, U. (2012). Discovery of Cyclic Sulfone Hydroxyethylamines as Potent and Selective β-Site APP-Cleaving Enzyme 1 (BACE1) Inhibitors: Structure-Based Design and in Vivo Reduction of Amyloid β-Peptides. Journal of Medicinal Chemistry 55: 3364-3386.S. Liu, C., Ruthirakuhan, M., A. Chau, S., Herrmann, N., F. Carvalho, A. & L. Lanctôt, K. (2016). Pharmacological Management of Agitation and Aggression in Alzheimer's Disease: A Review of Current and Novel Treatments. Current Alzheimer Research 13: 1134-1144.Sabbah, D. A. & Zhong, H. A. (2016). Modeling the protonation states of β-secretase binding pocket by molecular dynamics simulations and docking studies. Journal of Molecular Graphics and Modelling 68: 206-215.Saito, S. & Ihara, M. (2014). New therapeutic approaches for Alzheimer's disease and cerebral amyloid angiopathy. Front Aging Neurosci 6: 290.Scheltens, P., Blennow, K., Breteler, M. M. B., de Strooper, B., Frisoni, G. B., Salloway, S. & Van der Flier, W. M. (2016). Alzheimer's disease. The Lancet 388: 505-517Serrano-Pozo, A., Frosch, M. P., Masliah, E. & Hyman, B. T. (2011). Neuropathological alterations in Alzheimer disease. Cold Spring Harb. Perspect. Med. 1: a006189Small, S. A. & Duff, K. (2008). Linking Aβ and Tau in Late-Onset Alzheimer's Disease: A Dual Pathway Hypothesis. Neuron 60: 534-542.Soares, R. O., Torres, P. H. M., da Silva, M. L. & Pascutti, P. G. (2016). Dataset showing the impact of the protonation states on molecular dynamics of HIV protease. Data in Brief 8: 1144- 1150.Spronk, S. A. & Carlson, H. A. (2011). The role of tyrosine 71 in modulating the flap conformations of BACE1. Proteins: Structure, Function, and Bioinformatics 79: 2247-2259.Stamford, A. & Strickland, C. (2013). Inhibitors of BACE for treating Alzheimer's disease: a fragment-based drug discovery story. Current Opinion in Chemical Biology 17: 320-328.Stewart, J. J. (2009). Application of the PM6 method to modeling proteins. J Mol Model 15: 765- 805.PublicationORIGINALCarlosGuetoTesisPhD_Final.pdfCarlosGuetoTesisPhD_Final.pdfapplication/pdf53934971https://dspace7-unicartagena.metabuscador.org/bitstreams/02d7f31a-fdab-4678-8858-3ce20a3a3f8e/download16fbc59a27de2341fa46e5db6f9f016bMD51LICENSElicense.txtlicense.txttext/plain; charset=utf-81739https://dspace7-unicartagena.metabuscador.org/bitstreams/0bd65ec1-eda9-49d5-8e7f-77ab4549c444/download80f4fab81256c9c749645bab750e44eaMD52TEXTCarlosGuetoTesisPhD_Final.pdf.txtCarlosGuetoTesisPhD_Final.pdf.txtExtracted texttext/plain519459https://dspace7-unicartagena.metabuscador.org/bitstreams/28018b7c-5fe9-4a6f-8324-e9b9f7364e0b/download1088dfeda4aee676bbd6dc09d3723e72MD53THUMBNAILCarlosGuetoTesisPhD_Final.pdf.jpgCarlosGuetoTesisPhD_Final.pdf.jpgGenerated Thumbnailimage/jpeg6456https://dspace7-unicartagena.metabuscador.org/bitstreams/8181848f-edf2-445d-b96b-d353132510ff/download5801a8c84b260cc75bfff56b0d4f5daaMD5411227/9039oai:dspace7-unicartagena.metabuscador.org:11227/90392024-08-28 17:05:49.002https://creativecommons.org/licenses/by-nc-nd/4.0open.accesshttps://dspace7-unicartagena.metabuscador.orgBiblioteca Digital Universidad de Cartagenabdigital@metabiblioteca.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