Identifying promising anticancer Sulforaphane derivatives using QSAR, Docking, and ADME studies

Martin Y. C. (2005). A bioavailability score. Journal of medicinal chemistry, 48(9), 3164–3170. https://doi.org/10.1021/jm0492002

Sulforaphane Molecule-- Anti-Aging and role in Cancer. Sulforaphane Molecule -- Anti-Aging and Senolytic Properties. (n.d.). https://www.worldofmolecules.com/anti-aging-and-senolytics/sulforaphane-molecule.html.

Fofaria, N. M., Ranjan, A., Kim, S. H., & Srivastava, S. K. (2015). Mechanisms of the Anticancer Effects of Isothiocyanates. The Enzymes, 37, 111–137. https://doi.org/10.1016/bs.enz.2015.06.001

Kim, J. K., & Park, S. U. (2016). Current potential health benefits of sulforaphane. EXCLI journal, 15, 571–577. https://doi.org/10.17179/excli2016-485

Matusheski, N. V., Juvik, J. A., & Jeffery, E. H. (2004). Heating decreases epithiospecifier protein activity and increases sulforaphane formation in broccoli. Phytochemistry, 65(9), 1273–1281. https://doi.org/10.1016/j.phytochem.2004.04.013

Matusheski, N. V., Juvik, J. A., & Jeffery, E. H. (2004). Heating decreases epithiospecifier protein activity and increases sulforaphane formation in broccoli. Phytochemistry, 65(9), 1273–1281. https://doi.org/10.1016/j.phytochem.2004.04.013

Kensler, T. W., Egner, P. A., Agyeman, A. S., Visvanathan, K., Groopman, J. D., Chen, J. G., Chen, T. Y., Fahey, J. W., & Talalay, P. (2013). Keap1-nrf2 signaling: a target for cancer prevention by sulforaphane. Topics in current chemistry, 329, 163–177. https://doi.org/10.1007/128_2012_339

Kubo, E., Chhunchha, B., Singh, P., Sasaki, H., & Singh, D. P. (2017). Sulforaphane reactivates cellular antioxidant defense by inducing Nrf2/ARE/Prdx6 activity during aging and oxidative stress. Scientific reports, 7(1), 14130. https://doi.org/10.1038/s41598-017-14520-8

Jabbarzadeh Kaboli, Parham & Afzalipoor, Masoomeh & Mohammadi, Mahsa & Abiri, Ardavan & Mokhtarian, Roya & Vazifehmand, Reza & Amanollahi, Shima & Sani, Shaghayegh & Li, Mingxing & Zhao, Yueshui & Wu, Xu & Shen, Jing & Cho, Chi & Xiao, Zhangang. (2020). Targets and mechanisms of sulforaphane derivatives obtained from cruciferous plants with special focus on breast cancer – contradictory effects and future perspectives. Biomedicine & Pharmacotherapy. 121. 109635. 10.1016/j.biopha.2019.109635.

Keum, Y. S., Yu, S., Chang, P. P., Yuan, X., Kim, J. H., Xu, C., Han, J., Agarwal, A., & Kong, A. N. (2006). Mechanism of action of sulforaphane: inhibition of p38 mitogen-activated protein kinase isoforms contributing to the induction of antioxidant response element-mediated heme oxygenase-1 in human hepatoma HepG2 cells. Cancer research, 66(17), 8804–8813. https://doi.org/10.1158/0008-5472.CAN-05-3513

Kaufman-Szymczyk, A., Majewski, G., Lubecka-Pietruszewska, K., & Fabianowska-Majewska, K. (2015). The Role of Sulforaphane in Epigenetic Mechanisms, Including Interdependence between Histone Modification and DNA Methylation. International journal of molecular sciences, 16(12), 29732–29743. https://doi.org/10.3390/ijms161226195

Wang, H., Khor, T. O., Yang, Q., Huang, Y., Wu, T. Y., Saw, C. L., Lin, W., Androulakis, I. P., & Kong, A. N. (2012). Pharmacokinetics and pharmacodynamics of phase II drug metabolizing/antioxidant enzymes gene response by anticancer agent sulforaphane in rat lymphocytes. Molecular pharmaceutics, 9(10), 2819–2827. https://doi.org/10.1021/mp300130k

H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne. (2000) The Protein Data Bank Nucleic Acids Research, 28: 235-242.

Santos-Martins, D., Eberhardt, J., Tillack, A.F., Forli, S. (2020). AutoDock Vina 1.2.0. Improved software with new docking methods, expanded force field, and Python bindings.

Daina, Antoine & Michielin, Olivier & Zoete, Vincent. (2017). SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports. 7. 42717. 10.1038/srep42717.

Kwon, S., Bae, H., Jo, J., & Yoon, S, (2019). Comprehensive ensemble in QSAR prediction for drug discovery. BMC bioinformatics, 20(1), 521. https://doi.org/10.1186/s12859-019-3135-4

AlvaDesc molecular descriptors (n.d.). https://www.alvascience.com/alvadesc-descriptors

Hanwell, M.D., Curtis, D.E., Lonie, D.C. et al. (2012, August 13) Avogadro: an advanced semantic chemical editor, visualization, and analysis platform. J Cheminform 4, 17 (2012). https://doi.org/10.1186/1758-2946-4-17.

Neese, Frank, (2017, July 17) Software update: the ORCA program system, version 4.0. Wiley Interdiscip. Rev.: Comput. Mol. Sci., 8, e1327, https://doi.org/10.1002/wcms.1327

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. https://doi.org/10.1002/jcc.21256

Trott, O., & 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(2), 455–461. https://doi.org/10.1002/jcc.21334

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. https://doi.org/10.1002/jcc.20084

Dassault Systèmes BIOVIA, (2017) Discovery Studio Modeling Environment, San Diego: Dassault Systèmes, 2016. https://www.3ds.com/products-services/biovia/products/molecular-modeling-simulation/biovia-discovery-studio/visualization/

Mauri, A. (2020). alvaDesc: A tool to calculate and analyze molecular descriptors and fingerprints. In K. Roy (Ed.), Ecotoxicological QSARs (pp. 801–820). Humana Press Inc. https://lnkd.in/dHmPQS5

Create a molfile. (n.d.). Cheminfo. http://www.cheminfo.org/Chemistry/Generate_molfiles/index.html.

U.S. Department of Health and Human Services. (n.d.). Online SMILES Translator. National Institutes of Health. https://cactus.nci.nih.gov/translate/.

Monge, A., Arrault, A., Marot, C., & Morin-Allory, L. (2006). Managing, profiling and analyzing a library of 2.6 million compounds gathered from 32 chemical providers. Molecular diversity, 10(3), 389–403. https://doi.org/10.1007/s11030-006-9033-5

Spencer, E. S., Dale, E. J., Gommans, A. L., Rutledge, M. T., Vo, C. T., Nakatani, Y., Gamble, A. B., Smith, R. A., Wilbanks, S. M., Hampton, M. B., & Tyndall, J. D. (2015). Multiple binding modes of isothiocyanates that inhibit macrophage migration inhibitory factor. European journal of medicinal chemistry, 93, 501–510. https://doi.org/10.1016/j.ejmech.2015.02.012

Blair, J. A., Rauh, D., Kung, C., Yun, C. H., Fan, Q. W., Rode, H., Zhang, C., Eck, M. J., Weiss, W. A., & Shokat, K. M. (2007). Structure-guided development of affinity probes for tyrosine kinases using chemical genetics. Nature chemical biology, 3(4), 229–238. https://doi.org/10.1038/nchembio866

Lauffer, B. E., Mintzer, R., Fong, R., Mukund, S., Tam, C., Zilberleyb, I., Flicke, B., Ritscher, A., Fedorowicz, G., Vallero, R., Ortwine, D. F., Gunzner, J., Modrusan, Z., Neumann, L., Koth, C. M., Lupardus, P. J., Kaminker, J. S., Heise, C. E., & Steiner, P. (2013). Histone deacetylase (HDAC) inhibitor kinetic rate constants correlate with cellular histone acetylation but not transcription and cell viability. The Journal of biological chemistry, 288(37), 26926–26943. https://doi.org/10.1074/jbc.M113.490706

Ross, L. S., Gamo, F. J., Lafuente-Monasterio, M. J., Singh, O. M., Rowland, P., Wiegand, R. C., & Wirth, D. F. (2014). In vitro resistance selections for Plasmodium falciparum dihydroorotate dehydrogenase inhibitors give mutants with multiple point mutations in the drug-binding site and altered growth. The Journal of biological chemistry, 289(26), 17980–17995. https://doi.org/10.1074/jbc.M114.558353

Bart, A. G., & Scott, E. E. (2018). Structures of human cytochrome P450 1A1 with bergamottin and erlotinib reveal active-site modifications for binding of diverse ligands. The Journal of biological chemistry, 293(50), 19201–19210. https://doi.org/10.1074/jbc.RA118.005588

Bartolini, D., Bührmann, M., Barreca, M. L., Manfroni, G., Cecchetti, V., Rauh, D., & Galli, F. (2019). Co-crystal structure determination and cellular evaluation of 1,4-dihydropyrazolo[4,3-c] [1,2] benzothiazine 5,5-dioxide p38α MAPK inhibitors. Biochemical and biophysical research communications, 511(3), 579–586. https://doi.org/10.1016/j.bbrc.2019.02.063

Kidger, A. M., Munck, J. M., Saini, H. K., Balmanno, K., Minihane, E., Courtin, A., Graham, B., O'Reilly, M., Odle, R., & Cook, S. J. (2020). Dual-Mechanism ERK1/2 Inhibitors Exploit a Distinct Binding Mode to Block Phosphorylation and Nuclear Accumulation of ERK1/2. Molecular cancer therapeutics, 19(2), 525–539. https://doi.org/10.1158/1535-7163.MCT-19-0505

Reßing, N., Sönnichsen, M., Osko, J. D., Schöler, A., Schliehe-Diecks, J., Skerhut, A., Borkhardt, A., Hauer, J., Kassack, M. U., Christianson, D. W., Bhatia, S., & Hansen, F. K. (2020). Multicomponent Synthesis, Binding Mode, and Structure-Activity Relationship of Selective Histone Deacetylase 6 (HDAC6) Inhibitors with Bifurcated Capping Groups. Journal of medicinal chemistry, 63(18), 10339–10351. https://doi.org/10.1021/acs.jmedchem.9b01888

Zhang, Z. M., Liu, S., Lin, K., Luo, Y., Perry, J. J., Wang, Y., & Song, J. (2015). Crystal Structure of Human DNA Methyltransferase 1. Journal of molecular biology, 427(15), 2520–2531. https://doi.org/10.1016/j.jmb.2015.06.001

He, H., Chen, Q., & Georgiadis, M. M. (2014). High-resolution crystal structures reveal plasticity in the metal binding site of apurinic/apyrimidinic endonuclease I. Biochemistry, 53(41), 6520–6529. https://doi.org/10.1021/bi500676p

Ekstrom, J. L., Tolbert, W. D., Xiong, H., Pegg, A. E., & Ealick, S. E. (2001). Structure of a human S-adenosylmethionine decarboxylase self-processing ester intermediate and mechanism of putrescine stimulation of processing as revealed by the H243A mutant. Biochemistry, 40(32), 9495–9504. https://doi.org/10.1021/bi010736o

Davies, T. G., Wixted, W. E., Coyle, J. E., Griffiths-Jones, C., Hearn, K., McMenamin, R., Norton, D., Rich, S. J., Richardson, C., Saxty, G., Willems, H. M., Woolford, A. J., Cottom, J. E., Kou, J. P., Yonchuk, J. G., Feldser, H. G., Sanchez, Y., Foley, J. P., Bolognese, B. J., Logan, G., … Kerns, J. K. (2016). Monoacidic Inhibitors of the Kelch-like ECH-Associated Protein 1: Nuclear Factor Erythroid 2-Related Factor 2 (KEAP1:NRF2) Protein-Protein Interaction with High Cell Potency Identified by Fragment-Based Discovery. Journal of medicinal chemistry, 59(8), 3991–4006. https://doi.org/10.1021/acs.jmedchem.6b00228

Sugishima, M., Migita, C. T., Zhang, X., Yoshida, T., & Fukuyama, K. (2004). Crystal structure of heme oxygenase-1 from cyanobacterium Synechocystis sp. PCC 6803 in complex with heme. European journal of biochemistry, 271(22), 4517–4525. https://doi.org/10.1111/j.1432-1033.2004.04411.x

Finch, A., & Pillans, P. (2014). P-glycoprotein and its role in drug-drug interactions. Australian Prescriber, 37(4), 137–139. https://doi.org/10.18773/austprescr.2014.050

Martin Y. C. (2005). A bioavailability score. Journal of medicinal chemistry, 48(9), 3164–3170. https://doi.org/10.1021/jm0492002

P, Surat. (2021, February 01). Importance of Solubility and Lipophilicity in Drug Development. AZoLifeSciences. Retrieved on July 02, 2021 from https://www.azolifesciences.com/article/Importance-of-Solubility-and-Lipophilicity-in-Drug-Development.aspx.

Dougherty D. A. (1996). Cation-pi interactions in chemistry and biology: a new view of benzene, Phe, Tyr, and Trp. Science (New York, N.Y.), 271(5246), 163–168. https://doi.org/10.1126/science.271.5246.163

Meyer, E. A., Castellano, R. K., & Diederich, F. (2003). Interactions with aromatic rings in chemical and biological recognition. Angewandte Chemie (International ed. in English), 42(11), 1210–1250. https://doi.org/10.1002/anie.200390319

Grossi, V., Peserico, A., Tezil, T., & Simone, C. (2014). p38α MAPK pathway: a key factor in colorectal cancer therapy and chemoresistance. World journal of gastroenterology, 20(29), 9744–9758. https://doi.org/10.3748/wjg.v20.i29.9744

Zhuang, W. R., Wang, Y., Cui, P. F., Xing, L., Lee, J., Kim, D., Jiang, H. L., & Oh, Y. K. (2019). Applications of π-π stacking interactions in the design of drug-delivery systems. Journal of controlled release : official journal of the Controlled Release Society, 294, 311–326. https://doi.org/10.1016/j.jconrel.2018.12.014

Jozkowicz, A., Was, H., & Dulak, J. (2007). Heme oxygenase-1 in tumors: is it a false friend?. Antioxidants & redox signaling, 9(12), 2099–2117. https://doi.org/10.1089/ars.2007.1659

Walsh, A. A., Szklarz, G. D., & Scott, E. E. (2013). Human cytochrome P450 1A1 structure and utility in understanding drug and xenobiotic metabolism. The Journal of biological chemistry, 288(18), 12932–12943. https://doi.org/10.1074/jbc.M113.452953

Lněničková, K., Dymáková, A., Szotáková, B., & Boušová, I. (2017). Sulforaphane Alters β-Naphthoflavone-Induced Changes in Activity and Expression of Drug-Metabolizing Enzymes in Rat Hepatocytes. Molecules (Basel, Switzerland), 22(11), 1983. https://doi.org/10.3390/molecules22111983

Koomoa, D. L., Borsics, T., Feith, D. J., Coleman, C. C., Wallick, C. J., Gamper, I., Pegg, A. E., & Bachmann, A. S. (2009). Inhibition of S-adenosylmethionine decarboxylase by inhibitor SAM486A connects polyamine metabolism with p53-Mdm2-Akt/protein kinase B regulation and apoptosis in neuroblastoma. Molecular cancer therapeutics, 8(7), 2067–2075. https://doi.org/10.1158/1535-7163.MCT-08-1217