Computational evaluation of bioactive compounds from Viscum album (mistletoe) as inhibitors of p63 for pancreatic cancer treatment

References

• Aguirre, A. J., Bardeesy, N., Sinha, M., Lopez, L., Tuveson, D. A., Horner, J., … DePinho, R. A. (2003). Activated Kras and Ink4a/Arf deficiency cooperate to produce metastatic pancreatic ductal adenocarcinoma. Genes & Development, 17(24), 3112–3126.
   PubMed Web of Science ®Google Scholar
• Al-Makhzumi, Q., M. A. H., Abdullah, H. I., & Al-Ani, R. R. (2018). Theoretical study of N-methyl-3-phenyl-3-(4-(trifluoromethyl) phenoxy) propan as a drug and its five derivatives. Journal of Biosciences and Medicines, 6(8), 80–98.
   Google Scholar
• Andricovich, J., Perkail, S., Kai, Y., Casasanta, N., Peng, W., & Tzatsos, A. (2018). Loss of KDM6A activates super-enhancers to induce gender-specific squamous-like pancreatic cancer and confers sensitivity to BET inhibitors. Cancer Cell, 33(3), 512–526.
   PubMed Web of Science ®Google Scholar
• Bailey, P., Chang, D. K., Nones, K., Johns, A. L., Patch, A.-M., Gingras, M.-C., Miller, D. K., Christ, A. N., Bruxner, T. J. C., Quinn, M. C., Nourse, C., Murtaugh, L. C., Harliwong, I., Idrisoglu, S., Manning, S., Nourbakhsh, E., Wani, S., Fink, L., Holmes, O., … Grimmond, S. M. (2016). Genomic analyses identify molecular subtypes of pancreatic cancer. Nature, 531(7592), 47–52. https://doi.org/10.1038/nature16965
   PubMed Web of Science ®Google Scholar
• Basturk, O., Khanani, F., Sarkar, F., Levi, E., Cheng, J. D., & Adsay, N. V. (2005). DeltaNp63 expression in pancreas and pancreatic neoplasia. Modern Pathology, 18(9), 1193–1198.
   PubMed Web of Science ®Google Scholar
• Becke, A. D. (1992). Density‐functional thermochemistry. I. The effect of the exchange‐only gradient correction. The Journal of Chemical Physics, 96(3), 2155–2160.
   Web of Science ®Google Scholar
• Benet, L. Z., Hosey, C. M., Ursu, O., & Oprea, T. I. (2016). BDDCS, the Rule of 5 and drugability. Advanced Drug Delivery Reviews, 101, 89–98. https://doi.org/10.1016/j.addr.2016.05.007
   PubMed Web of Science ®Google Scholar
• Borovic Sunjic, S., Cipak Gasparovic, A., Vukovic, T., Weiss, T., Sussman Weiss, E., Soldo, I., … Zarkovic, N. (2015). Adjuvant cancer biotherapy by Viscum album extract Isorel: Overview of evidence-based medicine findings. Collegium Antropologicum, 39(3), 701–708.
   PubMedGoogle Scholar
• Bussing, A. (2000). Mistletoe. The genus Viscum. Hardwood Academic Publishers.
   Google Scholar
• Câmara, V. S., Chaves, O. A., de Araújo, B. B., Gonçalves, P. F. B., Iglesias, B. A., Ceschi, M. A., & Rodembusch, F. S. (2022). Photoactive homomolecular bis (n)-Lophine dyads: Multicomponent synthesis, photophysical properties, theoretical investigation, docking and interaction studies with biomacromolecules. Journal of Molecular Liquids, 349, 118084.
   Web of Science ®Google Scholar
• Cazacu, M., Oniu, T., Lungoci, C., Mihailov, A., Cipak, A., Klinger, R., … Zarkovic, N. (2003). The influence of Isorel on the advanced colorectal cancer. Cancer Biotherapy and Radiopharmaceuticals, 18(1), 27–34.
   PubMed Web of Science ®Google Scholar
• Chai, J. D., &Head-Gordon, M. (2008). Physical Chemistry Chemical Physics. Long-Range Corrected Hybrid Density Functionals with Damped Atom–atom Dispersion Corrections, 10(44), 6615–6620.
   Google Scholar
• Chen, B., Gao, Z. Q., Liu, Y., Zheng, Y. M., Han, Y., Zhang, J. P., & Hu, C. Q. (2017). Embryo and developmental toxicity of cefazolin sodium impurities in zebrafish. Frontiers in Pharmacology, 8, 403.
   PubMed Web of Science ®Google Scholar
• Cheng, F.,Li, W.,Zhou, Y.,Jie, S.,Wu, Z.,Liu, G.,Lee, P. W., &Tang, Y. (2012). admetSAR: A comprehensive source and free tool for assess ment of chemical ADMET properties. Journal of Chemical Information and Modeling, 52(11), 3099–3105.
   PubMed Web of Science ®Google Scholar
• de Souza, G. L., & Peterson, K. A. (2021). Benchmarking antioxidant-related properties for gallic acid through the use of DFT, MP2, CCSD, and CCSD (T) approaches. The Journal of Physical Chemistry A, 125(1), 198–208.
   PubMed Web of Science ®Google Scholar
• Deeni, Y. Y., & Sadiq, N. M. (2002). Antimicrobial properties and phytochemical constituents of the leaves of African mistletoe (Tapinanthus dodoneifolius (DC) Danser)(Loranthaceae): an ethnomedicinal plant of Hausaland, Northern Nigeria. Journal of Ethnopharmacology, 83(3), 235–240.
   PubMed Web of Science ®Google Scholar
• Ditchfield, R., Hehre, W. J., & Pople, J. A. (1971). Self-Consistent molecular-orbital methods. IX. An extended Gaussian-type basis for molecular-orbital studies of organic molecules. Journal of Chemical Physics, 54, 724–728.
   Web of Science ®Google Scholar
• Dunning Jr, T. H. (1989). Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen. The Journal of Chemical Physics, 90(2), 1007–1023.
   Web of Science ®Google Scholar
• Frisch, M. E., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., … Fox, D. J. (2016). Gaussian, 16
   Google Scholar
• Geerlings, P., & De Proft, F. (2002). Chemical reactivity as described by quantum chemical methods. International Journal of Molecular Sciences, 3(4), 276–309.
   Web of Science ®Google Scholar
• Grabocka, E., Pylayeva-Gupta, Y., Jones, M. J., Lubkov, V., Yemanaberhan, E., Taylor, L., … Bar-Sagi, D. (2014). Wild-type H-and N-Ras promote mutant K-Ras-driven tumorigenesis by modulating the DNA damage response. Cancer Cell, 25(2), 243–256.
   PubMed Web of Science ®Google Scholar
• Hajto, T., Hostanska, K., & Gabius, H. J. (1989). Modulatory potency of the β-galactoside-specific lectin from mistletoe extract (Iscador) on the host defense system in vivo in rabbits and patients. Cancer Research, 49(17), 4803–4808.
   PubMed Web of Science ®Google Scholar
• Hehre, W. J., Ditchfield, R., & Pople, J. A. (1972). Self-Consistent molecular orbital methods. XII. Further extensions of Gaussian-type basis sets for use in molecular orbital studies of organic molecule. The Journal of Chemical Physics, 56, 2257–2261.
   Web of Science ®Google Scholar
• Hernández-Aquino, E., & Muriel, P. (2018). Beneficial effects of naringenin in liver diseases: Molecular mechanisms. World Journal of Gastroenterology, 24(16), 1679.
   PubMed Web of Science ®Google Scholar
• Hingorani, S. R., Petricoin, E. F., III, Maitra, A., Rajapakse, V., King, C., Jacobetz, M. A., … Tuveson, D. A. (2003). Preinvasive and invasive ductal pancreatic cancer and its early detection in the mouse. Cancer Cell, 4(6), 437–450.
   PubMed Web of Science ®Google Scholar
• Hingorani, S. R., Wang, L., Multani, A. S., Combs, C., Deramaudt, T. B., Hruban, R. H., … Tuveson, D. A. (2005). Trp53R172H and KrasG12D cooperate to promote chromosomal instability and widely metastatic pancreatic ductal adenocarcinoma in mice. Cancer Cell, 7(5), 469–483.
   PubMed Web of Science ®Google Scholar
• Holtskog, R., Sandvig, K., & Olsnes, S. (1988). Characterization of a toxic lectin in Iscador, a mistletoe preparation with alleged cancerostatic properties. Oncology, 45(3), 172–179.
   PubMed Web of Science ®Google Scholar
• Idu, M., Ovuakporie-Uvo, O., & Nwaokolo, M. J. (2016). Phytochemistry and microscopy of Tapinanthus dodoneifolius (DC)(Danser)(Santalales: Loranthaceae)(African mistletoes) from guava, rubber and orange host trees. Brazilian Journal of Biological Sciences, 3(5), 27–35.
   Google Scholar
• Jacobson, M. P., Pincus, D. L., Rapp, C. S., Day, T. J., Honig, B., Shaw, D. E., & Friesner, R. A. (2004). A hierarchical approach to all‐atom protein loop prediction. Proteins, 55(2), 351–367.
   PubMed Web of Science ®Google Scholar
• Jayaraman, J., Jesudoss, V. A. S., Menon, V. P., & Namasivayam, N. (2012). Anti-inflammatory role of naringenin in rats with ethanol induced liver injury. Toxicology Mechanisms and Methods, 22(7), 568–576.
   PubMed Web of Science ®Google Scholar
• Jensen, F. (2001). Polarization consistent basis sets: Principles. The Journal of Chemical Physics, 115(20), 9113–9125.
   Web of Science ®Google Scholar
• Jorgensen, W. L.,Chandrasekhar, J.,Madura, J. D.,Impey, R. W., &Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79(2), 926–935.
   Web of Science ®Google Scholar
• Kim, C., & Kim, B. (2018). Anti-cancer natural products and their bioactive compounds inducing ER stress-mediated apoptosis: A review. Nutrients, 10(8), 1021.
   PubMed Web of Science ®Google Scholar
• Lev, E., Ephraim, M., & Ben-Arye, E. (2011). European and Oriental mistletoe: From mythology to contemporary integrative cancer care. European Journal of Integrative Medicine, 3(3), e133–e137.
   Web of Science ®Google Scholar
• Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (1997). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 23(1-3), 3–25.
   Web of Science ®Google Scholar
• Lou, C.,Zhang, F.,Yang, M.,Zhao, J.,Zeng, W.,Fang, X., &Liang, W. (2012). Naringenin decreases invasiveness and metastasis by inhibiting TGF-β-induced epithelial to mesenchymal transition in pancreatic cancer cells. PLoS One., 7(12), e50956.
   PubMed Web of Science ®Google Scholar
• Mills, A. A., Zheng, B., Wang, X. J., Vogel, H., Roop, D. R., & Bradley, A. (1999). p63 is a p53 homologue required for limb and epidermal morphogenesis. Nature, 398(6729), 708–713. https://doi.org/10.1038/19531
   PubMed Web of Science ®Google Scholar
• Morohoshi, T., Held, G., & Klöppel, G. (1983). Exocrine pancreatic tumours and their histological classification. A study based on 167 autopsy and 97 surgical cases. Histopathology, 7(5), 645–661.
   PubMed Web of Science ®Google Scholar
• Ndamitso, M. M., Musah, M., Mohammed-Hadi, Z., Idris, S., Tijani, O. J., Shaba, E. Y., & Umar, A. (2013). Analysis of phytochemical content and antibacterial activity of Tapinanthus dodoneifolius extracts. Researcher, 5(5), 54–59.
   Google Scholar
• Nobili, S., Lippi, D., Witort, E., Donnini, M., Bausi, L., Mini, E., & Capaccioli, S. (2009). Natural compounds for cancer treatment and prevention. Pharmacological Research, 59(6), 365–378.
   PubMed Web of Science ®Google Scholar
• Obot, I. B., Kaya, S., Kaya, C., & Tüzün, B. (2016). Theoretical evaluation of triazine derivatives as steel corrosion inhibitors: DFT and Monte Carlo simulation approaches. Research on Chemical Intermediates, 42(5), 4963–4983.
   Web of Science ®Google Scholar
• Owen, H. C., Appiah, S., Hasan, N., Ghali, L., Elayat, G., & Bell, C. (2017). Phytochemical modulation of apoptosis and autophagy: Strategies to overcome chemoresistance in leukemic stem cells in the bone marrow microenvironment. International Review of Neurobiology, 135, 249–278. https://doi.org/10.1016/bs.irn.2017.02.012
   PubMed Web of Science ®Google Scholar
• Pearson, R. G. (1986). Absolute electronegativity and hardness correlated with molecular orbital theory. Proceedings of the National Academy of Sciences, 83(22), 8440–8441.
   PubMed Web of Science ®Google Scholar
• Pietrzak, W., & Nowak, R. (2021). Impact of harvest conditions and host tree species on chemical composition and antioxidant activity of extracts from Viscum album L. Molecules, 26(12), 3741.
   PubMed Web of Science ®Google Scholar
• Pribram-Jones, A.,Gross, D. A., &Burke, K. (2015). DFT: A Theory Full of Holes?. Annual Review of Physical Chemistry, 66, 283–304. https://doi.org/10.1146/annurev-physchem-040214-121420 25830374
   PubMed Web of Science ®Google Scholar
• Rauf, A., Shariati, M. A., Imran, M., Bashir, K., Khan, S. A., Mitra, S., … Zengin, G. (2022). Comprehensive review on naringenin and naringin polyphenols as a potent anticancer agent. Environmental Science and Pollution Research, 29(21), 31025-31041.
   Web of Science ®Google Scholar
• Sastry, G., Adzhigirey, M., Day, T., Annabhimoju, R., & Sherman, W. (2013). Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments. Journal of Computer-Aided Molecular Design, 27(3), 221–234. https://doi.org/10.1007/s10822-013-9644-8
   PubMed Web of Science ®Google Scholar
• Schrödinger. (2018). Schrödinger release 201 8-4: Maestro Schrödinger. LLC.
   Google Scholar
• Siegel, R. L., Miller, K. D., & Jemal, A. (2019). Cancer statistics, 2019. CA: a Cancer Journal for Clinicians, 69(1), 7–34.
   PubMed Web of Science ®Google Scholar
• Soares, E., & Zhou, H. (2018). Master regulatory role of p63 in epidermal development and disease. Cellular and Molecular Life Sciences, 75(7), 1179–1190.
   PubMed Web of Science ®Google Scholar
• Somerville, T. D., Xu, Y., Miyabayashi, K., Tiriac, H., Cleary, C. R., Maia-Silva, D., … Vakoc, C. R. (2018). TP63-mediated enhancer reprogramming drives the squamous subtype of pancreatic ductal adenocarcinoma. Cell Reports, 25(7), 1741–1755.
   PubMed Web of Science ®Google Scholar
• Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., … Mesirov, J. P. (2005). Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences, 102(43), 15545–15550.
   PubMed Web of Science ®Google Scholar
• Szurpnicka, A., Zjawiony, J. K., & Szterk, A. (2019). Therapeutic potential of mistletoe in CNS-related neurological disorders and the chemical composition of Viscum species. Journal of Ethnopharmacology, 231, 241–252. https://doi.org/10.1016/j.jep.2018.11.025
   PubMed Web of Science ®Google Scholar
• Toden, S., Okugawa, Y., Jascur, T., Wodarz, D., Komarova, N. L., Buhrmann, C., … Goel, A. (2015). Curcumin mediates chemosensitization to 5-fluorouracil through miRNA-induced suppression of epithelial-to-mesenchymal transition in chemoresistant colorectal cancer. Carcinogenesis, 36(3), 355–367.
   PubMed Web of Science ®Google Scholar
• Wang, N. X.,Venkatesh, K., &Wilson, A. K. (2006). Behavior of density functionals with respect to basis set. 3. Basis set superposition error. The Journal of Physical Chemistry A, 110(2), 779–784.
   PubMed Web of Science ®Google Scholar
• Wang, N. X., &Wilson, A. K. (2005). Density functional theory and the correlation consistent basis sets: The tight d effect on HSO and HOS. The Journal of Physical Chemistry A, 109(32), 7187–7196.
   PubMed Web of Science ®Google Scholar
• Weis, A.,Katebzadeh, K.,Söderhjelm, P.,Nilsson, I., &Ryde, U. (2006). Ligand affinities predicted with the MM/PBSA method: dependence on the simulation method and the force field. Journal of Medicinal Chemistry, 49(22), 6596–6606.
   PubMed Web of Science ®Google Scholar
• Xu, X. H., Li, T., Fong, C. M. V., Chen, X., Chen, X. J., Wang, Y. T., … Lu, J. J. (2016). Saponins from Chinese medicines as anticancer agents. Molecules, 21(10), 1326.
   PubMed Web of Science ®Google Scholar
• Yang, H., Lou, C., Sun, L., Li, J., Cai, Y., Wang, Z., … Tang, Y. (2019). admetSAR 2.0: web-service for prediction and optimization of chemical ADMET properties. Bioinformatics, 35(6), 1067–1069.
   PubMed Web of Science ®Google Scholar
• Yokoi, Y., Kano, K., Minoshima, Y., & Takayanagi, T. (2014). Application of long-range corrected density-functional theory to excess electron attachment to biomolecules. Computational and Theoretical Chemistry, 1046, 99–106.
   Web of Science ®Google Scholar
• Young, A., Lou, D., & McCormick, F. (2013). Oncogenic and wild-type ras play divergent roles in the regulation of mitogen-activated protein kinase signalingregulation of signaling by wild-type and oncogenic ras. Cancer Discovery, 3(1), 112–123.
   PubMed Web of Science ®Google Scholar
• Zarkovic, N., Vukovic, T., Loncaric, I., Miletic, M., Zarkovic, K., Borovic, S., … Mang, S. (2001). An overview on anticancer activities of the Viscum album extract Isorel®. Cancer Biotherapy and Radiopharmaceuticals, 16(1), 55–62.
   PubMed Web of Science ®Google Scholar
• Zhang, J., Qian, J., Tong, J., Zhang, D., & Hu, C. (2013). Toxic effects of cephalosporins with specific functional groups as indicated by zebrafish embryo toxicity testing. Chemical Research in Toxicology, 26(8), 1168–1181.
   PubMed Web of Science ®Google Scholar