ACOPLAMIENTO INVERSO Y MAPEO DE FARMACÓFORO COMO HERRAMIENTAS PARA ENCONTRAR NUEVOS BLANCOS FARMACOLÓGICOS DE COMPUESTOS NATURALES
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Maldonado rojas, W., Noguera Oviedo, K., & Olivero Verbel, J. (2023). ACOPLAMIENTO INVERSO Y MAPEO DE FARMACÓFORO COMO HERRAMIENTAS PARA ENCONTRAR NUEVOS BLANCOS FARMACOLÓGICOS DE COMPUESTOS NATURALES. Revista De La Academia Colombiana De Ciencias Exactas, Físicas Y Naturales, 36(140), 411–420. https://doi.org/10.18257/raccefyn.36(140).2012.2481

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El resurgimiento de los productos naturales en el ámbito de descubrimiento de fármacos tiene su base en la introducción de nuevos enfoques, tecnologías y metodologías, incluyendo el diseño de moléculas bioactivas asistido por ordenador. Los servidores TarFisDock y PharmMapper son herramientas computacionales empleadas para la búsqueda de potenciales blancos farmacológicos para ligandos orgánicos. Este trabajo muestra un ejemplo de aplicación de estos servidores. Los resultados obtenidos sugirieron que moléculas de origen natural, tales como la ascididemina (Didemnum sp. Tunicado), el peyssonol B (Peyssonnelia sp), el ácido asiático (Centella asiatica) y el ácido docosahexaenoico (aceite de pescado), tienen como blancos la dihidroorotato deshidrogenasa, la mieloperoxidasa, el receptor beta del ácido retinoico, y la aldosa reductasa, respectivamente.
Estas proteínas han sido relacionadas con diversas enfermedades y ofrecen una explicación teórica de algunos
de los efectos benéficos reportados para las moléculas evaluadas

https://doi.org/10.18257/raccefyn.36(140).2012.2481

Palabras clave

AutoDock Vina | productos naturales | PharmMapper | farmacóforo | TarFisDock | acoplamiento molecular
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Appleton, d. r.; norrie pearce, A.; Copp, b. r. 2010. Anti-tuberculosis natural products: synthesis and biological evaluation of pyridoacridine lkaloids related to ascididemin. Tetrahedron, 66(27/28):4977-4986.

butler, M. s.; buss, A. d. 2006. Natural products -The future scaffolds for novel antibiotics?. Biochem. Pharmacol. 71(7):919-929.

Cai, J.; han, C.; hu, t.; Zhang, J.; Wu, d.; Wang, f., liu, y.; ding, J.; Chen, K.; yue, J.; shen, X.; Jiang, h. 2006. Peptide deformylase is a potential target for anti-Helicobacter pylori drugs: reverse docking,

Enzymatic assay, and x-ray crystallography validation. Protein Sci. 15(9):2071-2081.

Chen, y. Z.; Ung, C. y. 2002. Computational method for drug target search and application in drug discovery. J. Theor. Comput. Chem. 1(1):1-12.

Chomańska, U.; Kraśnicki, P.; Proniewska-Skretek, E.; Mariak, Z. 2010. Acute phacomorphic glaucoma in patient with diabetes mellitus type 1-case report. Klin. Oczna. 112(7-9):240-242.

Cordell, g. 2000. Biodiversity and drug discovery a symbiotic relationship. Phytochemistry 55(6):463-480.

Delano, W. l. The PyMOL molecular graphics system. DeLano Scientific LLC. 1998-2003. San Carlos, CA, USA. http://www.pymol.org.

Frisch, M. J.; trucks, g. W.; schlegel, h. r.; scuseria, g. e.; robb, M. A.; Cheeseman, J. r.; Montgomery, Jr. J. A.; vreven, t.; Kudin, K. n.; burant, J. C.; Millam, J. M.; Iyengar, s. s.; tomasi, J.; barone, v.; Mennucci, b.; Cossi, M.; scalmani, g.; rega, n.; petersson, g. A.; nakatsuji, h.; hada, M.; ehara, M.; toyota, K.; fukuda, r.; hasegawa, J.; Ishida, M.; nakajima, t.; honda, y.; Kitao, o.; nakai, h.; Klene, M.; li, X.; Knox, J. e.; hratchian, h. p.; Cross, J. b.; bakken, v.; Adamo, C.; Jaramillo, J.; gomperts, r.; stratmann, r. e.; yazyev, o.; Austin, A. J.; Cammi, r.; pomelli, C.; ochterski, J. W.; Ayala, p. y.; Morokuma, K.; voth, g. A.; salvador, p.; dannenberg, J. J.; Zakrzewski, v. g.; dapprich, s.; daniels, A. d.; strain, M. C.; farkas, o.; Malick, d. K.; rabuck, A. d.; raghavachari, K.; foresman, J. b.; ortiz, J. v.; Cui, Q.; baboul, A. g.; Clifford, s.; Cioslowski, J.; stefanov, b. b.; liu, g.; liashenko, A.; piskorz, p.; Komaromi, I.; Martin, r. l.; fox, d. J.; Keith, t.; Al-laham, M. A.; peng, C. y.; nanayakkara, A.; Challacombe, M.; gill, p. M. W.; Johnson, b.; Chen, W.; Wong, M. W.; gonzalez, C.; pople, J. A. Gaussian03.

Gaussian, Inc.: Pittsburgh, PA, USA, 2003. gad, s. C. 2007. Preclinical development handbook: ADME and biophar maceutical properties.; Wiley-Interscience: Cary, North Carolina. DOI 10.1002/9780470249031.

Ganesan, A. 2008. The impact of natural products upon modern drug discovery. Curr. Opin. Chem. Biol. 12(3):306-317.

Gao, Z.; li, h.; Zhang, h.; liu, X.; Kang, l.; luo, X.; Zhu, W.; Chen, K.; Wang, X.; Jiang, h. 2008. PDTD: a web-accessible protein database for drug target identification. BMC Bioinformatics, 9:104.

Guha, r.; howard, M. t.; hutchison, g. r.; Murray-rust, p.; rzepa, h.; steinbeck, C.; Wegner J. K.; Willighagen, e. 2006. The blue obelisk -- Interoperability in chemical informatics. J. Chem. Inf. Model. 46(3):991-998.

Harriman, J.; deleavey, g.; lambropoulos, A.; deslongchamps, g. 2007. Reverse-docking study of the organocatalyzed asymmetric Strecker hydrocyanation of aldimines and ketimines. Tetrahedron, 63(52):13032-13038.

Harvey, A. l. 2007. Natural products as a screening resource. Curr. Opin. Chem. Biol. 11(5):480-484.

Harvey, A. l. 2008. Natural products in drug discovery. Drug Discov. Today. 13(19/20):894-901.

Jain, s.; Chincholikar, A. 2004. Pharmacophore Mapping And Drug Design. Indian J. Pharm. Sci. 66(1):11-17.

Jeong, C.; bode, A. M.; pugliese, A.; Cho,y. y.; Kim, h. g.; shim, J. h.; Jeon, y. J.; li, h.; Jiang, h.; dong, Z. 2009. [6]-Gingerol suppresses colon cancer growth by targeting Leukotriene A4 Hydrolase. Cancer Res. 69(13):5584-5591.

Ji, h.; li, X.; Zhang, h. 2009. Natural products and drug discovery. EMBO reports. 10(3):194-200.

Kada, n.; suzuki, t.; Aizawa, K.; Matsumura, t.; Ishibashi, n.; suzuki, n.; takeda, n.; Munemasa, y.; sawaki, d.; Ishikawa, t.; nagai, r. 2007. Acyclic retinoid inhibits neointima formation through retinoic acid receptor beta-induced apoptosis. Arterioscler. Thromb. Vasc. Biol. 27(7):1535-1541.

Kämper, A; Apostolakis, J.; rarey, M.; Marian , C.; lengauer, t. 2006. Fully automated flexible docking of ligands into flexible synthetic receptors using forward and inverse docking strategies. J. Chem. Inf. Model.46(2):903-911.

Kaneski, C. r.; Moore, d. f.; ries, M.; Zirzow, g. C.; schiffmann, r. 2006. Myeloperoxidase predicts risk of vasculopathic events in hemizgygous males with Fabry disease. Neurology. 67(11):2045-2047.

Kansal, n.; silakari, o.; ravikumar, M. 2010. Three dimensional pharmacophore modelling for c-Kit receptor tyrosine kinase inhibitors. Eur. J. Med. Chem. 45(1):393-404.

Kapetanovic, I. M. 2008. Computer-aided drug discovery and development (CADDD): In silico-chemico-biological approach. Chem. Biol. Interact. 171(2):165-176.

Kulkarni, o. p.; sayyed, s. g.; Kantner, C.; ryu, M.; schnurr, M.; sárdy, M.; leban, J.; Jankowsky, r.; Ammendola, A.; doblhofer, r.; Anders, h. J. 2010. 4SC-101, a novel small molecule dihydroorotate dehydrogenase inhibitor, suppresses systemic lupus erythematosus in MRL-(Fas)lpr mice. Am. J. Pathol. 176(6):2840- 2847.

Kumar, K.; Waldmann, h. 2009. Synthesis of natural product inspired compound collections. Angew. Chem. Int. Ed. Engl. 48(18):3224-42.

lam, K. 2007. New aspects of

lane, A. l.; Mular, l.; drenkard , e. J.; shearer, t. l.; engel, s.; fredericq, s.; fairchild, C. r.; prudhomme, J.; roch , K.; hay, M. e.; Aalbersberg, W.; Kubanek, J. 2010. Ecological leads for natural product discovery: novel sesquiterpene hydroquinones from the red macroalga Peyssonnelia sp. Tetrahedron, 66(2):455-461.

Li, h.; gao, Z.; Kang, l.; Zhang, h.; yang, K.; yul, K.; Zhul, W.; Chen,VK.; shen, J.; Wang, X.; Jiang, h. 2006. TarFisDock: a web serverVfor identifyingVdrug targets with docking approach. Nucl. Acids Res.V34(2):219-224.

Liu, X.; ouyang, s.; yu, b.; liu, y.; huang, K.; gong, J.; Zheng, s.; li, Z.; Jiang, h. 2010. PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach. Nucl. Acids Res. 38(2):609-614.

Mandal, s.; Moudgil, M.; Mandal, s. K. 2009. Rational drug design. Eur. J. Pharmacol. 625(1/3):90-100.

Matsumoto, s.; biggs, J.; Copp, b. r.; holden, J. A.; barrows, l. r. 2003. Mechanism of ascididemin-Induced cytotoxicity. Chem. Res. Toxicol. 16(2):113-122.

Mattingly, C. 2009. Chemical databases for environmental health and clinical research. Toxicol. Lett. 186(1):62-65.

McChesney, J.; venkataraman, s.; henri, t. 2007. Plant natural products: Back to the future or into extinction?. Phytochemistry, 68(14):2015-2022.

Mukherjee, s.; nagar, s.; Mullick, s.; Mukherjee, A.; saha, A. 2008. Pharmacophore mapping of arylbenzothiophene derivatives for MCF cell inhibition using classical and 3D space modeling approaches. J. Mol. Graph. Model. 26(5):884-892.

Mullen, A.; loscher, C. e.; roche, h. M. 2010. Anti-inflammatory effects of EPA and DHA are dependent upon time and dose-response elements associated with LPS stimulation in THP-1-derived macrophages. J. Nutr. Biochem. 21(5):444-450.

Olivero-verbel, J.; Cabarcas-Montalvo, M.; ortega-Zúñiga, C. 2010. Theoretical targets for TCDD: A bioinformatics approach. Chemosphere, 80(10):1160-1166.

Pandey, J.; sharma, A.; tiwari, v. K.; dube, d., ramachandran, r.; Chaturvedi, v.; sinha, s.K.; Mishra, n.n.; shukla, p.K.; tripathi, r. p. 2009. Solution phase synthesis of a library of carbapeptide analogues based on glycosylamino acid scaffolds, their in silico screening and antimicrobial evaluation. J. Comb. Chem. 11(3):422-427.

Patil, s. p.; Maki, s.; Khedkar, s. A., rigby, A. C.; Chan, C. 2010. Withanolide A and asiatic acid modulate multiple targets associated with amyloid-beta precursor protein processing and amyloid-beta protein clearance. J. Nat. Prod. 73(7):1196-1202.

Ramana, K. v. ; tammali, r. ; srivastava, s. K. 2010. Inhibition of aldose reductase prevents growth factor-induced G1-S phase transition through the AKT/phosphoinositide 3-kinase/E2F-1 pathway in human colon cancer cells. Mol. Cancer The. 9(4):813-824.

RCSB PDB Protein Data Bank . www.pdb.org/pdb/home/home.do.

Rishton, g. M. 2008. Natural products as a robust source of new drugs and drug leads: past successes and present day issues. Am. J. Cardiol. 101(10A):44D-49D.

Rudolph, v.; Andrié, r. p.; rudolph, t. K.; friedrichs, K.; Klinke, A.; hirsch-hoffmann, b.; schwoerer, A. p.; lau, d.; fu, X. M.; Klingel, K.; sydow, K.; didié, M.; seniuk, A.; von leitner, e.; szoecs, K.; schrickel, J. W.; treede, h.; Wenzel, U.; lewalter, t.; nickenig, g.; Zimmermann, W.; Meinertz, t.; böger, r. h.; reichenspurner, h.; freeman, b. A.; eschenhagen, t.; ehmke, h.; hazen, s. l.; Willems, s.; baldus, s. 2010. Myeloperoxidase acts as a profibrotic mediator of atrial fibrillation. Nat. Med. 16(4):470-474.

Schneidman-duhovny, d.; dror, o.; Inbar, y.; nussinov, r.; Wolfson, h. J. 2008. PharmaGist: a webserver for ligand-based pharmacophore detection. Nucl. Acids Res. 36(2):223-228.

SYBYL molecular modeling software, Version 8.1. 2007. Tripos, St. Louis, MO, U.S.A.

Tang, y.; Zhu, W.; Chen, K.; Jiang, h. 2006. New technologies in computer-aided drug design: toward target identification and new chemical entity discovery. Drug Discov. Today Technol. 3(3):307-313.

Trott, o.; olson, A. J. 2010. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading. J. Comput. Chem. 31(2):455-461.

Vita, J. A.; brennan, M. l.; gokce, n.; Mann, s. A.; goormastic, M.; shishehbor, M. h.; penn, M.s.; Keaney, J. f.; hazen, s. l. 2004. Serum Myeloperoxidase levels independently predict endothelial dysfunction in humans. Circulation. 110:1134-1139.

Wermuth, C. g.; ganellin, C. r.; lindberg, p.; Mitscher, l. A. 1998. Glossary of terms used in medicinal chemistry. Pure Appl. Chem. 70(5):1129-1143.

Wild, d.; Wiggins, g. 2006. Challenges for chemoinformatics education in drug discovery. Drug Discov. Today. 11(9/10):436-439.

Wilk, W.; Zimmermann, t. J.; Kaiser, M.; Waldmann, h. 2010. Principles, implementation, and application of biology-oriented synthesis (BIOS). Biol Chem. 391(5):491-49Wolber, g.; langer, t. 2005. LigandScout: 3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters. J Chem. Inf. Model. 45(1):160-169.

Wolfe, M. s.; selkoe, d. J. 2010. Giving Alzheimer’s the old one-two. Cell. 142(2):194-196.

Yadav, U. C. ; srivastava, s. K.; ramana, K. v. 2010. Understanding the role of aldose reductase in ocular inflammation. Curr. Mol. Med. 10(6):540-549.

Zameitat, E.; Freymark, G.; Dietz, C. D.; Löffler, M.; Bölker, M. 2007. Functional expression of human dihydroorotate dehydroge-nase (DHODH) in pyr4 mutants of ustilago maydis allows target validation of DHODH inhibitors in vivo. Appl. Environ. Microbiol. 73(10):3371-3379.

Chen, Z., Wang, X., Zhu, W., Cao, X., tong, l., li, h., Xie, h., Xu, y., tan, s., Kuang, d., ding, J., Qian, X. 2011. Acenaphtho [1,2-b] pyrrole-Based selective fibroblast growth factor receptors 1 (FGFR1) Inhibitors: design, synthesis, and biological Activity. J. Med. Chem. 54(11):3732-3745

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