Screening and Prediction of Potential Compounds from Virgin Olive Oil Acting on Proteins Associated with Cancer Disease

https://doi.org/10.22146/mot.52737

Achmad Rodiansyah(1*)

(1) 1) Department of Biology, Universitas Negeri Malang, Indonesia 2) Department of Biotechnology, School of Life Sciences and Technology, Institut Teknologi Bandung, Indonesia
(*) Corresponding Author

Abstract


Virgin olive oil contains phenolic compounds that were potential for anti-inflammatory and cancer treatment. Computational biology is a beneficial method to understand how this compound can affect the biological process in humans. This research is conducted by the potential screening of VOO compounds, constructing the pharmacological network and enrichment, and docking simulation. The enrichment result showed that the EGFR, BRAF, MAPK1, CCND1, and MDM2 protein have multiple cancer contributions and related pathways. The docking simulation result showed that the interaction of EGFR-luteolin, BRAF-luteolin, MAPK1-luteolin, CCND1-apigenin, and MDM2-1-hydroxypinoresinol has the highest binding affinity. Further research with the in-vitro method is required to check the reliable mechanisms of each compound to their protein target.


Keywords


Olive oils; Phenolics; Cancer; Bioinformatics; Network pharmacology, Molecular docking

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References

AACR Project GENIE: Powering Precision Medicine through an International Consortium, 2017.  Cancer Discov. 7, 818–831.

Alavi, N., Golmakani, M.-T., 2017. Improving oxidative stability of virgin olive oil by addition of microalga Chlorella vulgaris biomass. J. Food Sci. Technol. 54, 2464–2473.

Arthur, D.E., Uzairu, A., 2019. Molecular docking studies on the interaction of NCI anticancer analogues with human Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit. J. King Saud Univ. - Sci.

Assadieskandar, A., Yu, C., Maisonneuve, P., Kurinov, I., Sicheri, F., Zhang, C., 2019. Rigidification Dramatically Improves Inhibitor Selectivity for RAF Kinases. ACS Med. Chem. Lett. 10, 1074–1080.

Basiricò, L., Morera, P., Dipasquale, D., Bernini, R., Santi, L., Romani, A., Lacetera, N., Bernabucci, U., 2019. (-)-Epigallocatechin-3-gallate and hydroxytyrosol improved antioxidative and anti-inflammatory responses in bovine mammary epithelial cells. animal 1–10.

Bindea, G., Mlecnik, B., Hackl, H., Charoentong, P., Tosolini, M., Kirilovsky, A., Fridman, W.-H., Pagès, F., Trajanoski, Z., Galon, J., 2009. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics 25, 1091–1093.

Caffarel, M.M., Coleman, N., 2014. Oncostatin M receptor is a novel therapeutic target in cervical squamous cell carcinoma: OSMR in cervical SCC. J. Pathol. 232, 386–390.

Coccia, A., Mosca, L., Puca, R., Mangino, G., Rossi, A., Lendaro, E., 2016. Extra-virgin olive oil phenols block cell cycle progression and modulate chemotherapeutic toxicity in bladder cancer cells. Oncol. Rep. 36, 3095–3104.

Corominas-Faja, B., Cuyàs, E., Lozano-Sánchez, J., Cufí, S., Verdura, S., Fernández-Arroyo, S., Borrás-Linares, I., Martin-Castillo, B., Martin, Á.G., Lupu, R., Nonell-Canals, A., Sanchez-Martinez, M., Micol, V., Joven, J., Segura-Carretero, A., Menendez, J.A., 2018. Extra-virgin olive oil contains a metabolo-epigenetic inhibitor of cancer stem cells. Carcinogenesis 39, 601–613.

Cruz, F., Julca, I., Gómez-Garrido, J., Loska, D., Marcet-Houben, M., Cano, E., Galán, B., Frias, L., Ribeca, P., Derdak, S., Gut, M., Sánchez-Fernández, M., García, J.L., Gut, I.G., Vargas, P., Alioto, T.S., Gabaldón, T., 2016. Genome sequence of the olive tree, Olea europaea. GigaScience 5, 29.

Daina, A., Michielin, O., Zoete, V., 2019. SwissTargetPrediction: updated data and new features for efficient prediction of protein targets of small molecules. Nucleic Acids Res. 47, W357–W364.

Dallakyan, S., Olson, A.J., 2015. Small-Molecule Library Screening by Docking with PyRx, in: Hempel, J.E., Williams, C.H., Hong, C.C. (Eds.), Chemical Biology. Springer New York, New York, NY, pp. 243–250.

Dembla, V., Somaiah, N., Barata, P., Hess, K., Fu, S., Janku, F., Karp, D.D., Naing, A., Piha-Paul, S.A., Subbiah, V., Tsimberidou, A.M., Shaw, K., Meric-Bernstam, F., Hong, D.S., 2018. Prevalence of MDM2 amplification and coalterations in 523 advanced cancer patients in the MD Anderson phase 1 clinic. Oncotarget 9.

Dey, G., Radhakrishnan, A., Syed, N., Thomas, J.K., Nadig, A., Srikumar, K., Mathur, P.P., Pandey, A., Lin, S.-K., Raju, R., Prasad, T.S.K., 2013. Signaling network of Oncostatin M pathway. J. Cell Commun. Signal. 7, 103–108.

Ernest, N.J., Sontheimer, H., 2009. Glioma, in: Encyclopedia of Neuroscience. Elsevier, pp. 877–884. https://doi.org/10.1016/B978-008045046-9.01008-1

Fu, M., Wang, C., Li, Z., Sakamaki, T., Pestell, R.G., 2004. Minireview: Cyclin D1: Normal and Abnormal Functions. Endocrinology 145, 5439–5447.

Gfeller, D., Grosdidier, A., Wirth, M., Daina, A., Michielin, O., Zoete, V., 2014. SwissTargetPrediction: a web server for target prediction of bioactive small molecules. Nucleic Acids Res. 42, W32–W38.

Godoy-Tundidor, S., Cavarretta, I.T.R., Fuchs, D., Fiechtl, M., Steiner, H., Friedbichler, K., Bartsch, G., Hobisch, A., Culig, Z., 2005. Interleukin-6 and oncostatin M stimulation of proliferation of prostate cancer 22Rv1 cells through the signaling pathways of p38 mitogen-activated protein kinase and phosphatidylinositol 3-kinase. The Prostate 64, 209–216.

Guiley, K.Z., Stevenson, J.W., Lou, K., Barkovich, K.J., Kumarasamy, V., Wijeratne, T.U., Bunch, K.L., Tripathi, S., Knudsen, E.S., Witkiewicz, A.K., Shokat, K.M., Rubin, S.M., 2019. p27 Allosterically Activates Cyclin-Dependent Kinase 4 and Antagonizes Palbociclib Inhibition. Science 366.

Hardin, J., Bertoni, G., Kleinsmith, L.J., Becker, W.M., 2012. Becker’s world of the cell. Benjamin Cummings, Boston.

Hassanpour, S.H., Dehghani, M., 2017. Review of cancer from perspective of molecular. J. Cancer Res. Pract. 4, 127–129.

Ideker, T., Nussinov, R., 2017. Network approaches and applications in biology. PLOS Comput. Biol. 13, e1005771.

Ikeda, Y., Oda, K., Hiraike-Wada, O., Koso, T., Miyasaka, A., Kashiyama, T., Tanikawa, M., Sone, K., Nagasaka, K., Maeda, D., Kawana, K., Nakagawa, S., Fukayama, M., Tetsu, O., Fujii, T., Yano, T., Kozuma, S., 2013. Cyclin D1 harboring the T286I mutation promotes oncogenic activation in endometrial cancer. Oncol. Rep. 30, 584–588.

Iwakuma, T., Lozano, G., 2003. MDM2, An Introduction. Mol. Cancer Res. 1, 993–1000.

JOVČEVSKA, I., KOČEVAR, N., KOMEL, R., 2013. Glioma and glioblastoma - how much do we (not) know? Mol. Clin. Oncol. 1, 935–941.

Junk, D.J., Bryson, B.L., Smigiel, J.M., Parameswaran, N., Bartel, C.A., Jackson, M.W., 2017. Oncostatin M promotes cancer cell plasticity through cooperative STAT3-SMAD3 signaling. Oncogene 36, 4001–4013.

Kairys, V., Baranauskiene, L., Kazlauskiene, M., Matulis, D., Kazlauskas, E., 2019. Binding affinity in drug design: experimental and computational techniques. Expert Opin. Drug Discov. 14, 755–768.

Kashima, K., Kawauchi, H., Tanimura, H., Tachibana, Y., Chiba, T., Torizawa, T., Sakamoto, H., 2020. CH7233163 Overcomes Osimertinib-Resistant EGFR-Del19/T790M/C797S Mutation. Mol. Cancer Ther. 19, 2288–2297.

Kato, S., Ross, J.S., Gay, L., Dayyani, F., Roszik, J., Subbiah, V., Kurzrock, R., 2018. Analysis of MDM2 Amplification: Next-Generation Sequencing of Patients With Diverse Malignancies. JCO Precis. Oncol. 1–14.

Khanal, P., Oh, W.-K., Yun, H.J., Namgoong, G.M., Ahn, S.-G., Kwon, S.-M., Choi, H.-K., Choi, H.S., 2011. p-HPEA-EDA, a phenolic compound of virgin olive oil, activates AMP-activated protein kinase to inhibit carcinogenesis. Carcinogenesis 32, 545–553.

Kharkar, P.S., Warrier, S., Gaud, R.S., 2014. Reverse docking: a powerful tool for drug repositioning and drug rescue. Future Med. Chem. 6, 333–342.

Kim, J.K., Diehl, J.A., 2009. Nuclear cyclin D1: An oncogenic driver in human cancer. J. Cell. Physiol. 220, 292–296.

Kinoshita, Y., Singh, A., Rovito, P.M., Wang, C.Y., Haas, G.P., 2004. Double Primary Cancers of the Prostate and Bladder: A Literature Review. Clin. Prostate Cancer 3, 83–86.

Laronha, H., Caldeira, J., 2020. Structure and Function of Human Matrix Metalloproteinases. Cells 9.

Li, S., Han, Z., Ma, Y., Song, R., Pei, T., Zheng, T., Wang, J., Xu, D., Fang, X., Jiang, H., Liu, L., 2014. Hydroxytyrosol inhibits cholangiocarcinoma tumor growth: An in vivo and in vitro study. Oncol. Rep. 31, 145–152.

Li, X.-W., Tuergan, M., Abulizi, G., 2015. Expression of MAPK1 in cervical cancer and effect of MAPK1 gene silencing on epithelial-mesenchymal transition, invasion and metastasis. Asian Pac. J. Trop. Med. 8, 937–943.

Liang, J., Wang, M., Olounfeh, K.M., Zhao, N., Wang, S., Meng, F., 2019. Network pharmacology-based identifcation of potential targets of the flower of Trollius chinensis Bunge acting on anti-inflammatory effectss. Sci. Rep. 9.

Liu, F., Yang, X., Geng, M., Huang, M., 2018. Targeting ERK, an Achilles’ Heel of the MAPK pathway, in cancer therapy. Acta Pharm. Sin. B 8, 552–562.

Liu, M., Pazgier, M., Li, Changqing, Yuan, W., Li, Chong, Lu, W., 2010. A left handed solution to peptide inhibition of the p53-MDM2 interaction. Angew. Chem. Int. Ed Engl. 49, 3649–3652.

Liu, X., Ouyang, S., Yu, B., Liu, Y., Huang, K., Gong, J., Zheng, S., Li, Z., Li, H., Jiang, H., 2010. PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach. Nucleic Acids Res. 38, W609–W614.

López de las Hazas, M.-C., Piñol, C., Macià, A., Motilva, M.-J., 2017. Hydroxytyrosol and the Colonic Metabolites Derived from Virgin Olive Oil Intake Induce Cell Cycle Arrest and Apoptosis in Colon Cancer Cells. J. Agric. Food Chem. 65, 6467–6476.

López-Biedma, A., Sánchez-Quesada, C., Beltrán, G., Delgado-Rodríguez, M., Gaforio, J.J., 2016. Phytoestrogen (+)-pinoresinol exerts antitumor activity in breast cancer cells with different oestrogen receptor statuses. BMC Complement. Altern. Med. 16.

Lundberg, A., Lindström, L.S., Li, J., Harrell, J.C., Darai-Ramqvist, E., Sifakis, E.G., Foukakis, T., Perou, C.M., Czene, K., Bergh, J., Tobin, N.P., 2019. The long-term prognostic and predictive capacity of cyclin D1 gene amplification in 2305 breast tumours. Breast Cancer Res. 21, 34.

Ma’ayan, A., 2011. Introduction to Network Analysis in Systems Biology. Sci. Signal. 4, tr5–tr5.

Manousaridis, I., Mavridou, S., Goerdt, S., Leverkus, M., Utikal, J., 2013. Cutaneous side effects of inhibitors of the RAS/RAF/MEK/ERK signalling pathway and their management [WWW Document]. J. Eur. Acad. Dermatol. Venereol.

Mansfield, A.S., Dy, G.K., Ahn, M.-J., Adjei, A.A., 2018. 48 - New Targets for Therapy in Lung Cancer, in: Pass, H.I., Ball, D., Scagliotti, G.V. (Eds.), IASLC Thoracic Oncology (Second Edition). Content Repository Only!, Philadelphia, pp. 479-489.e6.

Massagué, J., 2004. G1 cell-cycle control and cancer. Nature 432, 298–306.

Mebratu, Y., Tesfaigzi, Y., 2009. How ERK1/2 Activation Controls Cell Proliferation and Cell Death Is Subcellular Localization the Answer? Cell Cycle Georget. Tex 8, 1168–1175.

Moll, U.M., Petrenko, O., 2003. The MDM2-p53 Interaction. Mol. Cancer Res. 1, 1001–1008.

Moreno-Bueno, G., Rodríguez-Perales, S., Sánchez-Estévez, C., Hardisson, D., Sarrió, D., Prat, J., Cigudosa, J.C., Matias-Guiu, X., Palacios, J., 2003. Cyclin D1 gene (CCND1) mutations in endometrial cancer. Oncogene 22, 6115–6118.

Ni, Y., Müller, P., Wei, L., Ji, Y., 2018. Bayesian graphical models for computational network biology. BMC Bioinformatics 19, 63.

Panagiotakos, D.B., 2008. The Value of p-Value in Biomedical Research. Open Cardiovasc. Med. J. 2, 97–99.

Pantsar, T., Poso, A., 2018. Binding Affinity via Docking: Fact and Fiction. Mol. J. Synth. Chem. Nat. Prod. Chem. 23.

Parenti, M.D., Rastelli, G., 2012. Advances and applications of binding affinity prediction methods in drug discovery. Biotechnol. Adv. 30, 244–250.

Pestell, R.G., 2013. New Roles of Cyclin D1. Am. J. Pathol. 183, 3–9.

Pintilie, L., Stefaniu, A., 2019. In Silico Drug Design and Molecular Docking Studies of Some Quinolone Compound, in: Molecular Docking and Molecular Dynamics [Working Title]. IntechOpen.

Preedy, V.R., Watson, R.R., 2010. Olives and olive oil in health and disease prevention. Elsevier, Amsterdam.

Rupani, B., 2014. Enrichment of Olive Oil with Alpha Linolenic Acid Catalyzed by Lipase Mediated Trans-Esterification. Iran. J. Energy Environ. 5.

Senturk, E., Manfredi, J.J., 2012. Mdm2 and Tumorigenesis. Genes Cancer 3, 192–198.

Serreli, G., Deiana, M., 2018. Biological Relevance of Extra Virgin Olive Oil Polyphenols Metabolites. Antioxidants 7, 170.

Shangary, S., Wang, S., 2008. Targeting the MDM2-p53 Interaction for Cancer Therapy. Clin. Cancer Res. Off. J. Am. Assoc. Cancer Res. 14, 5318–5324.

Shao, G.-L., Wang, M.-C., Fan, X.-L., Zhong, L., Ji, S.-F., Sang, G., Wang, S., 2018. Correlation Between Raf/MEK/ERK Signaling Pathway and Clinicopathological Features and Prognosis for Patients With Breast Cancer Having Axillary Lymph Node Metastasis. Technol. Cancer Res. Treat. 17, 153303461775402.

Sorsa, T., Tjäderhane, L., Salo, T., 2004. Matrix metalloproteinases (MMPs) in oral diseases. Oral Dis. 10, 311–318.

Stroeder, R., Walch-Rückheim, B., Fischbach, J., Juhasz-Böss, I., Rübe, C., Solomayer, E.-F., Smola, S., 2018. Oncostatin M treatment increases the responsiveness toward cisplatin-based chemoradiotherapy in cervical cancer cells in a STAT3-dependent manner. Oncol. Lett. 16, 3351–3358.

Suojun, Z., Feng, W., Dongsheng, G., Ting, L., 2012. Targeting Raf/MEK/ERK pathway in pituitary adenomas. Eur. J. Cancer 48, 389–395.

Suortti, T., 1997. Coupled size-exclusion chromatography-anion-exchange chromatography in the analysis of poly- and oligosaccharides. J. Chromatogr. A 763, 331–335.

Thatcher, J.D., 2010. The Ras-MAPK Signal Transduction Pathway. Sci. Signal. 3, tr1–tr1.

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, 455–461.

Underhill-Day, N., Heath, J.K., 2006. Oncostatin M (OSM) Cytostasis of Breast Tumor Cells: Characterization of an OSM Receptor β–Specific Kernel. Cancer Res. 66, 10891–10901.

Ursem, C., Atreya, C.E., Van Loon, K., 2018. Emerging treatment options for BRAF-mutant colorectal cancer. Gastrointest. Cancer Targets Ther. 8, 13–23.

Vangone, A., Schaarschmidt, J., Koukos, P., Geng, C., Citro, N., Trellet, M.E., Xue, L.C., Bonvin, A.M.J.J., 2018. Large-scale prediction of binding affinity in protein–small ligand complexes: the PRODIGY-LIG web server. Bioinformatics 35, 1585–1587.

Visioli, F., Bernardini, E., 2011. Extra Virgin Olive Oil’s Polyphenols: Biological Activities. Curr. Pharm. Des. 17, 786–804.

Wang, S., Zhao, Y., Aguilar, A., Bernard, D., Yang, C.-Y., 2017. Targeting the MDM2–p53 Protein–Protein Interaction for New Cancer Therapy: Progress and Challenges. Cold Spring Harb. Perspect. Med. 7, a026245.

Wang, X., Shen, Y., Wang, S., Li, S., Zhang, W., Liu, X., Lai, L., Pei, J., Li, H., 2017. PharmMapper 2017 update: a web server for potential drug target identification with a comprehensive target pharmacophore database. Nucleic Acids Res. 45, W356–W360.

Ward, R.A., Bethel, P., Cook, C., Davies, E., Debreczeni, J.E., Fairley, G., Feron, L., Flemington, V., Graham, M.A., Greenwood, R., Griffin, N., Hanson, L., Hopcroft, P., Howard, T.D., Hudson, J., James, M., Jones, C.D., Jones, C.R., Lamont, S., Lewis, R., Lindsay, N., Roberts, K., Simpson, I., St-Gallay, S., Swallow, S., Tang, J., Tonge, M., Wang, Z., Zhai, B., 2017. Structure-Guided Discovery of Potent and Selective Inhibitors of ERK1/2 from a Modestly Active and Promiscuous Chemical Start Point. J. Med. Chem. 60, 3438–3450.

Waterman, E., 2007. Active Components and Clinical Applications of Olive Oil. Olive Oil 12, 12.

Wu, D., Rice, C.M., Wang, X., 2012. Cancer bioinformatics: A new approach to systems clinical medicine. BMC Bioinformatics 13, 71.

Xu, J., Lin, D.I., 2018. Oncogenic c-terminal cyclin D1 (CCND1) mutations are enriched in endometrioid endometrial adenocarcinomas. PLoS ONE 13.

Zalejska-Fiolka, J., Wielkoszyński, T., Rokicki, W., Dąbrowska, N., Strzelczyk, J.K., Kasperczyk, A., Owczarek, A., Błaszczyk, U., Kasperczyk, S., Stawiarska-Pięta, B., Birkner, E., Gamian, A., 2015. The Influence of α -Lipoic Acid and Garlic Administration on Biomarkers of Oxidative Stress and Inflammation in Rabbits Exposed to Oxidized Nutrition Oils. BioMed Res. Int. 2015, 1–11.

 

 

 


 



DOI: https://doi.org/10.22146/mot.52737

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