Phytocompounds screening of Nigella sativa in terms of human cancer by targeting sphingosine kinase-1 and pyruvate kinase-M2: a study based on in silico analysis

References

• Ahmad, M. F., Ahmad, F. A., Ashraf, S. A., Saad, H. H., Wahab, S., Khan, M. I., Ali, M., Mohan, S., Hakeem, K. R., & Athar, M. T. (2021). An updated knowledge of Black seed (Nigella sativa Linn.): Review of phytochemical constituents and pharmacological properties. Journal of Herbal Medicine, 25, 100404. https://doi.org/10.1016/j.hermed.2020.100404
   PubMed Web of Science ®Google Scholar
• Ahmed, S., Rehman, S. U., & Tabish, M. (2022). Cancer nanomedicine: A step towards improving the drug delivery and enhanced efficacy of chemotherapeutic drugs. OpenNano, 7, 100051. https://doi.org/10.1016/j.onano.2022.100051
   Google Scholar
• Alshaker, H., Sauer, L., Monteil, D., Ottaviani, S., Srivats, S., Böhler, T., & Pchejetski, D. (2013). Therapeutic Potential of Targeting SK1 in Human Cancers. In Advances in Cancer Research (Vol. 117, pp. 143–200). Academic Press Inc. https://doi.org/10.1016/B978-0-12-394274-6.00006-6
   Google Scholar
• Berendsen, H. J. C., van der Spoel, D., & van Drunen, R. (1995). GROMACS: A message-passing parallel molecular dynamics implementation. Computer Physics Communications. 91(1-3), 43–56. https://doi.org/10.1016/0010-4655(95)00042-E
   Web of Science ®Google Scholar
• Bielska, E., Lucas, X., Czerwoniec, A., M. Kasprzak, J., H. Kaminska, K., & M. Bujnicki, J. (2011). Virtual screening strategies in drug design—methods and applications. BioTechnologia, 3, 249–264. https://doi.org/10.5114/bta.2011.46542
   Google Scholar
• Bourgou, S., Kchouk, M. E., Bellila, A., & Marzouk, B. (2010). Effect of salinity on phenolic composition and biological activity of nigella sativa. Acta Horticulturae, 853, 57–60. https://doi.org/10.17660/ActaHortic.2010.853.5
   Google Scholar
• Bourgou, S., Ksouri, R., Bellila, A., Skandrani, I., Falleh, H., & Marzouk, B. (2008). Phenolic composition and biological activities of Tunisian Nigella sativa L. shoots and roots. Comptes Rendus Biologies, 331(1), 48–55. https://doi.org/10.1016/j.crvi.2007.11.001
   PubMed Web of Science ®Google Scholar
• Christofk, H. R., Vander Heiden, M. G., Wu, N., Asara, J. M., & Cantley, L. C. (2008). Pyruvate kinase M2 is a phosphotyrosine-binding protein. Nature, 452(7184), 181–186. https://doi.org/10.1038/nature06667
   PubMed Web of Science ®Google Scholar
• Daina, A., Michielin, O., & Zoete, V. (May 2017). SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7(1), 42717. https://doi.org/10.1038/srep42717
   PubMed Web of Science ®Google Scholar
• DeLano, W. L. (2002). Pymol: An open-source molecular graphics tool. CCP4 Newsl. protein Crystallogr, 40(4), 82–92. http://www.ccp4.ac.uk/newsletters/newsletter40/11_pymol.pdf.
   Google Scholar
• Al-Sheddi, E. S., Farshori, N. N., Al-Oqail, J., Musarrat, A., Al-Khedhairy, M., & Siddiqui, A. (2014). Cytotoxicity of nigella sativa seed oil and extract against human lung cancer cell line. Asian Pacific Journal of Cancer Prevention: APJCP, 15(2), 983–987. https://doi.org/10.7314/APJCP.2014.15.2.983
   PubMedGoogle Scholar
• Edris, A. (2009). Anti-cancer properties of Nigella spp. Essential oils and their major constituents, thymoquinone and β-Elemene. Current Clinical Pharmacology, 4(1), 43–46. https://doi.org/10.2174/157488409787236137
   PubMedGoogle Scholar
• Fatima, S., Hussain, I., Ahmed, S., & Tabish, M. (2022). In vitro and in silico binding studies of phytochemical isochroman with calf thymus DNA using multi-spectroscopic and computational modelling techniques. Journal of Biomolecular Structure and Dynamics., 1–15. https://doi.org/10.1080/07391102.2022.2137243
   Web of Science ®Google Scholar
• Filimonov, D. A., Lagunin, A. A., Gloriozova, T. A., Rudik, A. V., Druzhilovskii, D. S., Pogodin, P. V., & Poroikov, V. V. (2014). Prediction of the Biological Activity Spectra of Organic Compounds Using the Pass Online Web Resource. Chemistry of Heterocyclic Compounds, 50(3), 444–457. https://doi.org/10.1007/s10593-014-1496-1
   Web of Science ®Google Scholar
• Fouedjou, R. T., Chtita, S., Bakhouch, M., Belaidi, S., Ouassaf, M., Djoumbissie, L. A., Tapondjou, L. A., & Abul Qais, F. (2022). Cameroonian medicinal plants as potential candidates of SARS-CoV-2 inhibitors. Journal of Biomolecular Structure and Dynamics. 40(19), 8615–8629. https://doi.org/10.1080/07391102.2021.1914170
   PubMed Web of Science ®Google Scholar
• French, K. J., Schrecengost, R. S., Lee, B. D., Zhuang, Y., Smith, S. N., Eberly, J. L., Yun, J. K., & Smith, C. D. (2003). Discovery and evaluation of inhibitors of human sphingosine kinase. Cancer Research, 63(18), 5962–5969. http://www.ncbi.nlm.nih.gov/pubmed/14522923.
   PubMed Web of Science ®Google Scholar
• Fridlender, M., Kapulnik, Y., & Koltai, H. (2015). Plant derived substances with anti-cancer activity: From folklore to practice. Frontiers in Plant Science, 6. https://doi.org/10.3389/fpls.2015.00799
   PubMed Web of Science ®Google Scholar
• Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., & Simmerling, C. (2006). Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins: Structure, Function, and Bioinformatics, 65(3), 712–725. https://doi.org/10.1002/prot.21123
   PubMed Web of Science ®Google Scholar
• Hussain, I., Fatima, S., Ahmed, S., & Tabish, M. (2022). Deciphering the biomolecular interaction of β-resorcylic acid with human lysozyme: A biophysical and bioinformatics outlook. Journal of Molecular Liquids. 346, 117885. https://doi.org/10.1016/j.molliq.2021.117885
   Web of Science ®Google Scholar
• Hussain, I., Fatima, S., Ahmed, S., & Tabish, M. (2023). Biophysical and molecular modelling analysis of the binding of β-resorcylic acid with bovine serum albumin. Food Hydrocoll, 135, 108175. https://doi.org/10.1016/j.foodhyd.2022.108175
   Web of Science ®Google Scholar
• Hussain, I., Fatima, S., Siddiqui, S., Ahmed, S., & Tabish, M. (2021). Exploring the binding mechanism of β-resorcylic acid with calf thymus DNA: Insights from multi-spectroscopic, thermodynamic and bioinformatics approaches. Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy, 260, 119952. https://doi.org/10.1016/j.saa.2021.119952
   PubMed Web of Science ®Google Scholar
• Imamura, K., & Tanaka, T. (1972). Multimolecular forms of pyruvate kinase from rat and other mammalian tissues*. Journal of Biochemistry, 71(6), 1043–1051. https://doi.org/10.1093/oxfordjournals.jbchem.a129852
   PubMed Web of Science ®Google Scholar
• Israelsen, W. J., & Vander Heiden, M. G. (2015). Pyruvate kinase: Function, regulation and role in cancer. Seminars in Cell & Developmental Biology, 43, 43–51. https://doi.org/10.1016/j.semcdb.2015.08.004
   PubMed Web of Science ®Google Scholar
• Jarnuczak, A. F., Najgebauer, H., Barzine, M., Kundu, D. J., Ghavidel, F., Perez-Riverol, Y., Papatheodorou, I., Brazma, A., & Vizcaíno, J. A. (2021). An integrated landscape of protein expression in human cancer. Scientific Data, 8(1), 115. https://doi.org/10.1038/s41597-021-00890-2
   PubMed Web of Science ®Google Scholar
• Kumari, R., Kumar, R., & Lynn, A, Open Source Drug Discovery Consortium. (2014). g_mmpbsa—A GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. https://doi.org/10.1021/ci500020m
   PubMed Web of Science ®Google Scholar
• Lagunin, A. A., Dubovskaja, V. I., Rudik, A. V., Pogodin, P. V., Druzhilovskiy, D. S., Gloriozova, T. A., Filimonov, D. A., Sastry, N. G., & Poroikov, V. V. (2018). CLC-Pred: A freely available web-service for in silico prediction of human cell line cytotoxicity for drug-like compounds. PLoS One. 13(1), e0191838. https://doi.org/10.1371/journal.pone.0191838
   PubMed Web of Science ®Google Scholar
• Lin, J., Sahakian, D., de Morais, S., Xu, J., Polzer, R., & Winter, S. (May 2003). The role of absorption, distribution, metabolism, excretion and toxicity in drug discovery. Current Topics in Medicinal Chemistry, 3(10), 1125–1154. https://doi.org/10.2174/1568026033452096
   PubMed Web of Science ®Google Scholar
• Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (2001). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings 1PII of original article: S0169-409X(96)00423-1. The article was originally published in advanced drug delivery reviews 23 (1997). Advanced Drug Delivery Reviews, 46(1-3), 3–26. https://doi.org/10.1016/S0169-409X(00)00129-0
   PubMed Web of Science ®Google Scholar
• Majdalawieh, A. F., & Fayyad, M. W. (2016). Recent advances on the anti-cancer properties of Nigella sativa, a widely used food additive. Journal of Ayurveda and Integrative Medicine, 7(3), 173–180. https://doi.org/10.1016/j.jaim.2016.07.004
   PubMed Web of Science ®Google Scholar
• Malik, S., Zaman., & K., Atta-Ur-Rahman. (May 1992). Nigellimine: A new isoquinoline alkaloid from the seeds of Nigella sativa. Journal of Natural Products, 55(5), 676–678. https://doi.org/10.1021/np50083a020
   Web of Science ®Google Scholar
• Martin, Y. C. (May 2005). A bioavailability score. Journal of Medicinal Chemistry, 48(9), 3164–3170. https://doi.org/10.1021/jm0492002
   PubMed Web of Science ®Google Scholar
• Matthaus, B., & Özcan, M. M. (2011). Fatty acids, tocopherol, and sterol contents of some Nigella species seed oil. Czech Journal of Food Sciences, 29(2), 145–150. https://doi.org/10.17221/206/2008-CJFS
   Web of Science ®Google Scholar
• Mazurek, S. (2011). Pyruvate kinase type M2: A key regulator of the metabolic budget system in tumor cells. The International Journal of Biochemistry & Cell Biology, 43(7), 969–980. https://doi.org/10.1016/j.biocel.2010.02.005
   PubMed Web of Science ®Google Scholar
• Mbemi, A., Khanna, S., Njiki, S., Yedjou, C. G., & Tchounwou, P. B. (2020). Impact of gene–environment interactions on cancer development. International Journal of Environmental Research and Public Health, 17(21), 8089. https://doi.org/10.3390/ijerph17218089
   PubMed Web of Science ®Google Scholar
• Moretti, A., D'Antuono, L. F., & Elementi, S. (May 2004). Essential oils of Nigella sativa L. and Nigella damascena L. Seed. Journal of Essential Oil Research, 16(3), 182–183. https://doi.org/10.1080/10412905.2004.9698690
   Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Pires, D. E. V., Blundell, T. L., & Ascher, D. B. (2015). pkCSM: Predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures. Journal of Medicinal Chemistry, 58(9), 4066–4072. https://doi.org/10.1021/acs.jmedchem.5b00104
   PubMed Web of Science ®Google Scholar
• Qais, F. A., Alomar, S. Y., Imran, M. A., & Hashmi, M. A. (2022). In-silico analysis of phytocompounds of Olea europaea as potential anti-cancer agents to target PKM2 protein. Molecules, 27(18), 5793. https://doi.org/10.3390/molecules27185793
   PubMed Web of Science ®Google Scholar
• Qais, F. A., Sarwar, T., Ahmad, I., Khan, R. A., Shahzad, S. A., & Husain, F. M. (2021). Glyburide inhibits non-enzymatic glycation of HSA: An approach for the management of AGEs associated diabetic complications. International Journal of Biological Macromolecules, 169, 143–152. https://doi.org/10.1016/j.ijbiomac.2020.12.096
   PubMed Web of Science ®Google Scholar
• Rahman, S. M. M., Atikullah, M., Islam, M. N., Mohaimenul, M., Ahammad, F., Islam, M. S., Saha, B., & Rahman, M. H. (2019). Anti-inflammatory, antinociceptive and antidiarrhoeal activities of methanol and ethyl acetate extract of Hemigraphis alternata leaves in mice. Clinical Phytoscience, 5(1), 16. https://doi.org/10.1186/s40816-019-0110-6
   Google Scholar
• Rath, B., Abul Qais, F., Patro, R., Mohapatra, S., & Sharma, T. (2021). Design, synthesis and molecular modeling studies of novel mesalamine linked coumarin for treatment of inflammatory bowel disease. Bioorganic and Medicinal Chemistry Letters. 41, 128029. 2021.128029. https://doi.org/10.1016/j.bmcl
   PubMed Web of Science ®Google Scholar
• Salehi, B., Quispe, C., Imran, M., Ul-Haq, I., Živković, J., Abu-Reidah, I. M., Sen, S., Taheri, Y., Acharya, K., Azadi, H., del Mar Contreras, M., Segura-Carretero, A., Mnayer, D., Sethi, G., Martorell, M., Abdull Razis, A. F., Sunusi, U., Kamal, R. M., Rasul Suleria, H. A., & Sharifi-Rad, J. (2021). Nigella plants—Traditional uses, bioactive phytoconstituents, preclinical and clinical studies. Frontiers in Pharmacology, 12. https://doi.org/10.3389/fphar.2021.625386
   Web of Science ®Google Scholar
• Shanmugam, M. K., Arfuso, F., Kumar, A. P., Wang, L., Goh, B. C., Ahn, K. S., Bishayee, A., & Sethi, G. (2018). Modulation of diverse oncogenic transcription factors by thymoquinone, an essential oil compound isolated from the seeds of Nigella sativa Linn. Pharmacological Research, 129, 357–364. https://doi.org/10.1016/j.phrs.2017.11.023
   PubMed Web of Science ®Google Scholar
• Shoichet, B. K. (2004). Virtual screening of chemical libraries. Nature, 432(7019), 862–865. https://doi.org/10.1038/nature03197
   Google Scholar
• Siddiqui, S., Ameen, F., Kausar, T., Nayeem, S. M., Ur Rehman, S., & Tabish, M. (2021). Biophysical insight into the binding mechanism of doxofylline to bovine serum albumin: An in vitro and in silico approach. Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy, 249, 119296. https://doi.org/10.1016/j.saa.2020.119296
   PubMed Web of Science ®Google Scholar
• Sousa Da Silva, A. W., & Vranken, W. F. (2012). ACPYPE—AnteChamber PYthon Parser interfacE. BMC Research Notes, 5(1). https://doi.org/10.1186/1756-0500-5-367
   PubMedGoogle Scholar
• Toma, C.-C., Olah, N.-K., Vlase, L., Mogoșan, C., & Mocan, A. (May 2015). Comparative studies on polyphenolic composition, antioxidant and diuretic effects of Nigella sativa L. (Black Cumin) and Nigella damascena L. (Lady-in-a-Mist) seeds. Molecules (Basel, Switzerland), 20(6), 9560–9574. https://doi.org/10.3390/molecules20069560
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Wallace, A. C., Laskowski, R. A., & Thornton, J. M. (1995). LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions The LIGPLOT program automatically generates schematic 2-D representations of protein-ligand complexes from standard Protein Data Bank file input. Protein Engineering, 8(2), 127–134. https://doi.org/10.1093/protein/8.2.127
   PubMedGoogle Scholar
• Wang, Z., Min, X., Xiao, S.-H., Johnstone, S., Romanow, W., Meininger, D., Xu, H., Liu, J., Dai, J., An, S., Thibault, S., & Walker, N. (2013). Molecular basis of sphingosine kinase 1 substrate recognition and catalysis. Structure (London, England: 1993), 21(5), 798–809. https://doi.org/10.1016/j.str.2013.02.025
   PubMed Web of Science ®Google Scholar
• Zhang, Z., Deng, X., Liu, Y., Liu, Y., Sun, L., & Chen, F. (2019). PKM2, function and expression and regulation. Cell & Bioscience, 9(1), 52. https://doi.org/10.1186/s13578-019-0317-8
   PubMedGoogle Scholar