تعداد نشریات | 25 |
تعداد شمارهها | 916 |
تعداد مقالات | 7,522 |
تعداد مشاهده مقاله | 12,232,596 |
تعداد دریافت فایل اصل مقاله | 8,651,863 |
مطالعهی قدرت مهاری ترکیبات بیس ایندولی سنتتیک بر فرآیند فیبریلاسیون آمیلوئیدی با استفاده از روشهای شبیهسازی مولکولی | ||
زیست شناسی کاربردی | ||
دوره 33، شماره 1 - شماره پیاپی 63، اردیبهشت 1399، صفحه 24-45 اصل مقاله (1.03 M) | ||
نوع مقاله: مقاله پژوهشی | ||
شناسه دیجیتال (DOI): 10.22051/jab.2020.4844 | ||
نویسندگان | ||
کاوه خدایاری1؛ پرویز عبدالملکی* 2 | ||
1دانشجوی دکترای بیوفیزیک، دانشکده علوم زیستی، گروه بیوفیزیک، دانشگاه تربیت مدرس، تهران، ایران | ||
2استاد.بیوفیزیک، علوم زیستی، تربیت مدرس، تهران، ایران | ||
چکیده | ||
تشکیل ساختارهای آمیلوئیدی به دلیل ایجاد بیماریهایی مانند آلزایمر، پارکینسون، و دیابت نوع 2، مورد توجه محققان است. از جمله مهارکنندههای مهم، حلقههای ایندولی میباشند. مطالعات تجربی بر روی دو نوع ترکیب بیس ایندولی نشان داده است که ترکیب بیس ایندولیل 2-متیل فنیل متان (BI2MPM) مهارکنندهی فیبریلاسیون آمیلوئیدی پروتئین لیزوزیم است. اما ترکیب بیس ایندولیل 3-نیترو فنیل متان (BI3NPM) قدرت مهاری چندانیندارد. در این مطالعه با استفاده از روشهای داکینگ و شبیهسازی دینامیک مولکولی، میانکنش این دو لیگاند با پروتئین مدل شدهی آمیلوئیدی بررسی شد. روش داکینگ مولکولی تمایلی مشابه اما با جایگاه اتصالی متفاوت برای دو لیگاند نشان داد. اما نتایج دینامیک مولکولی نشان داد که لیگاند BI2MPMبا تخریب عمده ساختار بتای هسته های اولیه، موجب کاهش میانکنش بین آنها و با افزایش تغییرات ساختاری در رشتههای بتا باعث ناپایداری و توقف رشد فیبریلاسیون میگردد. اما ترکیب BI3NPM تغییرات اندکی بر ساختار هستههای فیبریلی اعمال میکند. | ||
کلیدواژهها | ||
میانکنشهای پای؛ بیماریهای آمیلوئیدی؛ ساختار بتا؛ حلقه ایندول؛ دینامیک مولکولی | ||
عنوان مقاله [English] | ||
Study of Inhibition Potential of Synthetic Bis-Indole Compounds on Amyloid Fibrillation by Molecular Simulation Methods | ||
نویسندگان [English] | ||
Kaveh Khodayari1؛ Parviz Abdolmaleki.2 | ||
1Biophysics, Biological Sciences, Tarbiat Modares, Tehran, Iran | ||
2Professor. Biophysics, Biological Sciences, Tarbiat Modares, Tehran, Iran | ||
چکیده [English] | ||
Aggregation of proteins lead to form amyloid diseases including Alzheimer, Parkinson and diabetes type II has been increasingly considered recently. Compounds including indole rings are the best amyloid aggregation inhibitors. Experimental studies have shown that bis(indolyl)-2-methyl[H1] [M2] phenylmethane (BI2MPM) has a great [H3] [M4] inhibitory potential on Lysozyme amyloid fibril formation, While bis(indolyl)-3-nitrophenylmethane [M5] (BI3NPM) has shown weaker inhibitory power. In this study, the interaction of these two ligands was investigated on amyloid model protein using molecular docking and molecular dynamics simulation techniques. Molecular Docking method showed similar reluctance to both ligands in amyloid nucleus model but in different binding positions. Molecular dynamics simulation showed that BI2MPM with major degradation on the beta structure of early fibril precursors, leads to lower interaction. It also increases structural changes in the subtypes of beta-strands and induces instability and stops fibrillation growth, but BI3NPM has minimum changes on the fibrils core structures | ||
کلیدواژهها [English] | ||
Amyloid Diseases, Beta structure, Indole Ring, Molecular Dynamics, Pi interactions | ||
مراجع | ||
Abedini, A., Plesner, A., Cao, P., Ridgway, Z., Zhang, J., Tu, L.H., Middleton, C.T., Chao, B., Sartori, D.J., Meng, F., Wang, H., Wong, A.G., Zanni, M.T., Verchere, C.B., Raleigh, D.P. and Schmidt, A.M. (2016). Time-resolved studies define the nature of toxic IAPP intermediates, providing insight for anti-amyloidosis therapeutics. ELife, 5:e12977. Abraham, M.J., Van.der.Spoel, D., Lindahl, E., Hess, B. and the GROMACS development team. GROMACS User Manual. (2019). Armen, R.S. and Daggett, V. (2005). Characterization of two distinct beta2 microglobulin unfolding intermediates that may lead to amyloid fibrils of different morphology. Biochemistry, 44: 16098-16107. Ayton, G.S., Noid, W.G. and Voth, G.A. (2007). Multiscale modeling of biomolecular systems: in serial and in parallel. Current Opinion in Structural Biology, 17: 192-198. Baranczak, A and Kelly, J.W. (2016). A current pharmacologic agent versus the promise of next generation therapeutics to ameliorate protein misfolding and/or aggregation diseases. Current Opinion in Chemical Biology, 32: 10-21. Berendsen, H.J.C., Postma, J.P.M., van.Gunsteren, W.F., Hermans, J. (1981). Interaction Models for Water in Relation to Protein Hydration. Pages 331-342 In: Pullman, B. (eds). Intermolecular Forces. The Jerusalem Symposia on Quantum Chemistry and Biochemistry: Springer. Brancolini, G. and Tozzini, V. (2019). Multiscale modeling of proteins interaction with functionalized nanoparticles. Current Opinion in Colloid & Interface Science, 41: 66-73. Buchete, N.V., Tycko, R. and Hummer, G. (2005). Molecular dynamics simulations of Alzheimer’s beta-amyloid protofilaments. Journal of Molecular Biology, 353: 804-821. Buxbaum, J.N. (2003). Diseases of protein conformation: what do in vitro experiments tell us about in vivo diseases? Trends in Biochemical Science, 28: 585-592. Chauhan, N.B. (2006). Effect of aged garlic extract on APP processing and tau phosphorylation in Alzheimer’s transgenic model Tg2576. Journal of ethnopharmacology, 108: 385-394. Chen, K. and Kurgan, L. (2009). Investigation of atomic level patterns in protein-small ligand interactions. PLoS One, 4: e4473. Cheng, A. and Merz, K.M. (1996). Application of the Nosé-Hoover Chain Algorithm to the Study of Protein Dynamics. Journal of Physical Chemistry, 100: 1927-1937. Chiti, F. and Dobson, C. M. (2006). Protein misfolding, functional amyloid, and human disease. Annual Review of Biochemistry, 75: 333-366. Chiti, F., Stefani, M., Taddei, N., Ramponi, G. and Dobson, C.M. (2003). Rationalization of the effects of mutations on peptide and protein aggregation rates. Nature, 424: 805-808. Darden, T., York, D. and Pedersen, L. (1993). Particle mesh Ewald: An N•log (N) method for Ewald sums in large systems. Journal of Chemical Physics, 98:10089-10092. DeMarco, M.L. and Daggett, V. (2004). From conversion to aggregation: protofibril formation of the prion protein. Proceedings of the National Academy of Sciences of the United States of America, 101: 2293-2298. Deng, N.J., Yan, L., Singh, D. and Cieplak, P. (2006). Molecular basis for the Cu2+ binding-induced destabilization of beta 2-microglobulin revealed by molecular dynamics simulation. Biophysical Journal, 90: 3865-3879. Ding, F., LaRocque, J.J. and Dokholyan, N.V. (2005). Direct observation of protein folding, aggregation, and a prion-like conformational conversion. Journal of Biological Chemistry, 280: 40235-40240. Dische, F.E., Wernstedt, C., Westermark, G.T., Westermark, P., Pepys, M.B., Rennie, J.A., Gilbey, S.G. and Watkins, P.J. (1988). Insulin as an amyloid-fibril protein at sites of repeated insulin injections in a diabetic patient. Pages 158-161. Diabetologia: Springer. Espargaro, A., Castillo, V., de Groot, N.S. and Ventura, S. (2008). The in vivo and in vitro aggregation properties of globular proteins correlate with their conformational stability: the SH3 case. Journal of Molecular Biology, 378: 1116-1131. Fernandez-Escamilla, A.M., Rousseau, F., Schymkowitz, J. and Serrano, L. (2004). Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins. Nature Biotechnology, 22: 1302-1306. Flores, S.C., Bernauer, J., Shin, S., Zhou, R. and Huang X. (2011). Multiscale modeling of macromolecular Biosystems. Pages 395-405 in Briefings in Bioinformatics: Oxford University Press. Gallina, A.M., Bork, P. and Bordo, D. (2014). Structural analysis of protein-ligand interactions: the binding of endogenous compounds and of synthetic drugs. Journal of Molecular Recognition, 27: 65-72. Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S., Wilkins, M.R., Appel, R.D. and Bairoch, A. (2005). Protein Identification and Analysis Tools on the ExPASy Server. Pages 571-607 In John M. Walker (ed): The Proteomics Protocols Handbook, Humana Press. Gupta,V.B. and Rao, K.S. (2007). Anti-amyloidogenic activity of S-allyl-l-cysteine and its activity to destabilize Alzheimer’s beta-amyloid fibrils in vitro. Neuroscience Letters, 429: 75-80. Han, W. and Wu, Y.D. (2005). A strand-loop-strand structure is a possible intermediate in fibril elongation: long time simulations of amyloid-beta peptide (10-35). Journal of American Chemical Society, 127: 15408-15416. Hess, B., Bekker, H., Berendsen, H.J.C. and Fraaije, J.G.E.M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18: 1463-1472. Hunter. C.A. and Sanders. J.K.M. (1990). The nature of pi–pi interactions. Journal of the Chemical Society, 112: 5525-5534. Hunter, C.A., Lawson, K.R., Perkins, J. and Urch, C.J. (2001). Aromatic interactions. Journal of the Chemical Society Perkin Transactions, 2: 651-669. Jaffe, R.L. and Smith, G.D. (1996). A quantum chemistry study of benzene dimer. The Journal of Chemical Physics, 105: 2780-2788. Jahn, T.R., Parker, M.J., Homans, S.W. and Radford, S.E. (2006). Amyloid formation under physiological conditions proceeds via a native-like folding intermediate. Nature Structural & Molecular Biology, 13: 195-201. Janda, K.C., Hemminger, J.C., Winn, J.S., Novick, S.E., Harris, S.J. and Klemperer, W. (1975). Benzene dimer: A polar molecule. The Journal of Chemical Physics, 63: 1419-1421. Janiak, C. (2000). Critical account on pi-pi stacking in metal complexes with aromatic nitrogen containing ligands. Journal of Chemical Society, Dalton Transactions, 21: 3885-3896. Klimov, D.K. and Thirumalai, D. (2003). Dissecting the assembly of Abeta 16-22 amyloid peptides into antiparallel beta sheets. Structure, 11: 295-307. Ko, S.Y., Chang, K.W., Lin, S.C., Hsu, H.C. and Liu, T.Y. (2007). The repressive effect of green tea ingredients on amyloid precursor protein (APP) expression in oral carcinoma cells in vitro and in vivo. Cancer Letters, 245: 81-89. Kueltzo, L.A., Wang, W., Randolph, T.W. and Carpenter, J.F. (2008). Effects of solution conditions, processing parameters, and container materials on aggregation of a monoclonal antibody during freeze-thawing. Journal of Pharmaceutical Sciences, 97: 1801-1812. Kukic, P. and Nielsen. J.E. (2010). Electrostatics in proteins and protein-ligand complexes. Future Medicinal Chemistry, 2: 647-666. Kumar, V., Sharma, V.K. and Kalonia, D.S. )2009(. In situ precipitation and vacuum drying of interferon alpha-2a: development of a single-step process for obtaining dry, stable protein formulation. International Journal of Pharmaceutics, 366: 88-98. Laskowski, R.A. and Swindells, M.B. (2011). LigPlot+: multiple ligand-protein interaction diagrams for drug discovery. Journal of Chemical Information and Modeling, 51: 2778-2786. Lingenheil, M., Denschlag, R., Reichold, R. and Tavan, P. (2008). The Hot Solvent/Cold Solute Problem Revisited. Journal of Chemical Theory and Computation, 4: 1293-1306. Malde, A.K., Zuo, L., Breeze, M., Stroet, M., Poger, D., Nair, P.C., Oostenbrink, C. and Mark, A.E. (2011). An Automated force field Topology Builder (ATB) and repository: Version 1.0. Journal of Chemical Theory and Computation, 7: 4026-4037. Maurer-Stroh, S., Debulpaep, M., Kuemmerer, N., Lopez-de-la-Paz, M., Martins, I.C., Reumers, J., Moris, K.L., Copland, A., Serpel, L., Serrano, L., Schymkovitz, J.W. and Rousseau, F. (2010). Exploring the sequence determinants of amyloid structure using position-specific scoring matrices. National Methods, 7: 237-242. McGaughey, G.B., Gagne, M.R. and Rappe. A.K. (1998). Pi Stacking Interactions Alive and well in proteins. Journal of Biological Chemistry, 273: 15458-15463. Mor, A., Ziv, G. and Levy, Y. (2008). Simulations of Proteins with Inhomogeneous Degrees of Freedom: The Effects of Thermostats. Journal of Computational Chemistry, 29: 1992-1998. Morshedi, D., Rezaei-Ghaleh, N., Ebrahim-Habibi, A., Ahmadian, S. and Nemat-Gorgani, M. (2007). Inhibition of amyloid fibrillation of lysozyme by indole derivatives, possible mechanism of action. The FEBS Journal, 274: 6415-6425. Nelson, R., Sawaya, M.R., Balbirnie, M., Madsen, A., Riekel, C., Grothe, R. and Eisenberg, D. (2005). Structure of the cross-beta spine of amyloid-like fibrils. Nature, 435: 773-778. Neudecker, P., Robustelli, P., Cavalli, A., Walsh, P., Lundstrom, P., Zarrine-Afsar, A., Sharpe, S., Vendruscolo, M. and Kay, L.E. (2012). Structure of an intermediate state in protein folding and aggregation. Science, 336: 362-366. Neves-Petersen, M.T. and Petersen, S.B. (2003). Protein electrostatics: a review of the equations and methods used to model electrostatic equations in biomolecules, applications in biotechnology. Future Medicinal Chemistry, 9: 315-95. Nguyen, H.D. and Hall, C.K. (2006). Spontaneous fibril formation by polyalanines; discontinuous molecular dynamics simulations. Journal of the American Chemical Society, 128: 1890-1901. Obici, L., Perfetti, V., Palladini, G., Moratti, R. and Merlini, G. (2005). Clinical aspects of systemic amyloid diseases. Biochimica et Biophysica acta, 1753: 11-22. Park, S. and Saven, J.G. (2006). Simulation of pH-dependent edge strand rearrangement in human beta-2 microglobulin. Protein Science: a publication of the Protein Society, 15: 200-207. Park, S.Y., Kim, D.S., Cho, E.K., Kwon, B.Y., Phark, S., Hwang, K.W. and Sul, D. (2008). Curcumin protected PC12 cells against beta-amyloid-induced toxicity through the inhibition of oxidative damage and tau hyperphosphorylation. Food and Chemical Toxicology, 46: 2881-2887. Park, S.Y. and Kim, D.S. (2002). Discovery of Natural Products from Curcuma longa that Protect Cells from Beta-Amyloid Insult: A Drug Discovery Effort against Alzheimer’s Disease. Journal of Natural Products, 9: 1227-1231. Parrinello, M. and Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics, 52: 7182-7190. Porat, Y., Abramowitz, A. and Gazit, E. (2006). Inhibition of Amyloid Fibril Formation by Polyphenols: Structural Similarity and Aromatic Interactions as a Common Inhibition Mechanism. Chemical Biology & Drug Desigen, 67: 27-37. Ramazzotti, M., Melani, F., Marchi, L., Mulinacci, N., Gestri, S., Tiribilli, B. and Innocenti, D. (2016). Mechanisms for the inhibition of amyloid aggregation by small ligands. Bioscience Reports, 36: e00385. Ramshini, H., Mannini, B., Khodayari, K., Ebrahim-Habibi, A., Moghaddasi, AZ., Tayebbee, R. and Chiti, F. (2016). Bis (indolyl) phenylmethane derivatives are effective small molecules for inhibition of amyloid fibril formation by hen lysozyme. European Journal of Medicinal Chemistry, 124: 361-371. Schmid, N., Eichenberger, A.P., Choutko, A., Riniker, S., Winger, M., Mark, A.E. and van.Gunsteren, W.F. (2011). Definition and testing of the GROMOS force-field versions 54A7 and 54B7. European Biophysics Journal, 40: 843-856. Sharma, S., Ding, F. and Dokholyan, N.V. (2008). Probing protein aggregation using discrete molecular dynamics. Frontiers in Bioscience: a journal and virtual library, 13: 4795-4808. Shukla, A.A., Gupta, P. and Han, X. (2007). Protein aggregation kinetics during Protein A chromatography: case study for an Fc fusion protein. Journal of Chromatography A, 1171: 22-28. Sinnokrot, M.O. and Sherrill, C.D. (2006). High-Accuracy Quantum Mechanical Studies of π-π Interactions in Benzene Dimers. The Journal of Physical Chemistry A, 110: 10656-10668. Sinnokrot, M.O., Valeev, E.F. and Sherrill, C.D. (2002). Estimates of the ab initio limit for pi-pi interactions: the benzene dimer. Journal of the American Chemical Society, 124: 10887-10893. Tartaglia, G.G., Cavalli, A., Pellarin, R. and Caflisch, A. (2004). The role of aromaticity, exposed surface, and dipole moment in determining protein aggregation rates. Protein Science, 13: 1939-1941. Tartaglia, G.G., Cavalli, A., Pellarin, R. and Caflisch, A. (2005). Prediction of aggregation rate and aggregation-prone segments in polypeptide sequences. Protein Science, 14: 2723-2734. Tayebee, R., Amini, M., Abdollahi, N., Aliakbari, A., Rabiei, S. and Ramshini, H. (2013). Magnetic inorganic-organic hybrid nanomaterial for the catalytic preparation of bis (indolyl) arylmethanes under solvent-free conditions: preparation and characterization of H5PW10V2O40/pyridino-Fe3O4 nanoparticles. Applied Catalysis A: General, 468: 75-87. Tipping, K.W., Karamanos, T.K., Jakhria, T., Iadanza, M.G., Goodchild, S.C., Tuma, R., Ranson, N.A, Hewitt, EW. and Radford, S.E. (2015). PH-induced molecular shedding drives the formation of amyloid fibril-derived oligomers. Proceeding of the National Academy of Sciences of the United States of America, 112: 5691-5696. Tiwari, A., Xu, Z. and Hayward, L.J. (2005). Aberrantly increased hydrophobicity shared by mutants of Cu, Zn-superoxide dismutase in familial amyotrophic lateral sclerosis. The Journal of Biological Chemistry, 280: 29771-29779. Tohda, C., Ichimura, M., Bai, Y., Tanaka, K., Zhu, S. and Komatsu, K. (2008). Inhibitory Effects of Eleutherococcus senticosus Extracts on Amyloid Induced Neuritic Atrophy and Synaptic Loss. Journal of Pharmacological Sciences, 107: 329-339. Tozzini, V. (2010). Multiscale modeling of proteins. Accounts of Chemical Research, 43: 220-230. Trott, O. and Olson, A.J. (2010). AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading. Journal of Computational Chemistry, 31: 455-461. Tsuzuki, S., Honda, K., Uchimaru, T., Mikami, M. and Tanabe, K. (2002). Origin of attraction and directionality of the pi-pi interaction: model chemistry calculations of benzene dimer interaction. Journal of American Chemical Society, 124: 104-112. Van.Gunsteren, W.F. and Berendsen, H.J.C. (1988). A leap-frog algorithm for stochastic dynamics. Molecular Simulation, 1:173-185. Wang, J., Tan, C., Chen, H.F. and Luo, R. (2008). All-atom Computer Simulations of Amyloid Fibrils Disaggregation. Biophysical Journal, 95: 5037-5047. Waters. M.L. (2002). Aromatic interactions in model systems. Current Opinion in Chemical Society, 6 : 736-741. Wu, C. and Shea, J.E. (2011). Coarse-grained models for protein aggregation. Current Opinion in Structural Biology, 21: 209-220. Young, L.M., Cao, P., Raleigh, D.P., Ashcroft, A.E. and Radford, S.E. (2014). Ion mobility spectrometry-mass spectrometry defines the oligomeric intermediates in amylin amyloid formation and the mode of action of inhibitors. Journal of American Chemical Society, 136: 660-670. Zhou, P., Huang, J. and Tian, F. (2012). Specific noncovalent interactions at protein-ligand interface: implications for rational drug design. Current Medicinal Chemistry, 19: 226-238.
| ||
آمار تعداد مشاهده مقاله: 472 تعداد دریافت فایل اصل مقاله: 379 |