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Research Articles

Structure-based pharmacophore mapping and virtual screening of natural products to identify polypharmacological inhibitor against c-MET/EGFR/VEGFR-2

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Pages 2956-2970 | Received 10 Nov 2021, Accepted 09 Feb 2022, Published online: 23 Feb 2022

References

  • Acharya, R., Chacko, S., Bose, P., Lapenna, A., & Pattanayak, S. P. (2019). Structure based multitargeted molecular docking analysis of selected furanocoumarins against breast cancer. Scientific Reports, 9(1), 1–13. [Internet]. Dec 1 [cited 2021 Jun 5]. https://doi.org/10.1038/s41598-019-52162-0
  • Agrawal, P. K., Agarwal, S. K., & Rastogi, R. P. (1980). Dihydroflavonols from Cedrus deodara. Phytochemistry, 19(5), 893–896. https://doi.org/10.1016/0031-9422(80)85133-8
  • Aliebrahimi, S., Kouhsari, S. M., Arab, S. S., Shadboorestan, A., & Ostad, S. N. (2018). Phytochemicals, withaferin A and carnosol, overcome pancreatic cancer stem cells as c-Met inhibitors. Biomedicine & Pharmacotherapy = Biomedecine & Pharmacotherapie, 106, 1527–1536. https://doi.org/10.1016/j.biopha.2018.07.055
  • Aliebrahimi, S., Montasser Kouhsari, S., Ostad, S. N., Arab, S. S., & Karami, L. (2018). Identification of phytochemicals targeting c-met kinase domain using consensus docking and molecular dynamics simulation studies. Cell Biochemistry and Biophysics, 76(1–2), 135–145. [Internet]. Jun 1 [cited 2020 Dec 4]. http://zinc.docking.org/ https://doi.org/10.1007/s12013-017-0821-6
  • Allen, B. K., Mehta, S., Ember, S. W. J., Schonbrunn, E., Ayad, N., & Schürer, S. C. (2015). Large-scale computational screening identifies first in class multitarget inhibitor of EGFR kinase and BRD4. Scientific Reports, 5, 16924. 24https://doi.org/10.1038/srep16924
  • Amawi, H., Ashby, C. R., Samuel, T., Peraman, R., & Tiwari, A. K. (2017). Polyphenolic nutrients in cancer chemoprevention and metastasis: Role of the epithelial-to-mesenchymal (EMT) pathway [Internet]. Nutrients, 9(8), 911.; [cited 2020 Dec 6]. https://pubmed.ncbi.nlm.nih.gov/28825675/ https://doi.org/10.3390/nu9080911
  • Anbuselvam, M., Easwaran, M., Meyyazhagan, A., Anbuselvam, J., Bhotla, H. K., & Sivasubramanian, M. (2020). Structure-based virtual screening, pharmacokinetic prediction, molecular dynamics studies for the identification of novel EGFR inhibitors in breast cancer. Journal of Biomolecular Structure and Dynamics, 39(12), 4462-4471. [Internet]. [cited 2020 Dec 4]; . https://www.tandfonline.com/doi/abs/10.1080/07391102.2020.1777899
  • Angelucci, A. cancers Targeting tyrosine kinases in cancer: Lessons for an effective targeted therapy in the clinic. www.mdpi.com/journal/cancers
  • Banerjee, P., Erehman, J., Gohlke, B. O., Wilhelm, T., Preissner, R., & Dunkel, M. (2015). Super Natural II-a database of natural products. Nucleic Acids Research, 43(Database issue), D935–9. [Internet]. Jan 28 [cited 2020 Sep 21]. /pmc/articles/PMC4384003/?report = abstract https://doi.org/10.1093/nar/gku886
  • Baselga, J. (2006). Targeting tyrosine kinases in cancer: The second wave. Science (New York, NY), 312(5777), 1175–1178. [Internet]. [cited 2020 Sep 21]. Available from: https://pubmed.ncbi.nlm.nih.gov/16728632/
  • Bray, F., Ferlay, J., Soerjomataram, I., Siegel, R. L., Torre, L. A., & Jemal, A. (2018). Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA: A Cancer Journal for Clinicians, 68(6), 394–424. Nov [cited 2020 Sep 21]. https://pubmed.ncbi.nlm.nih.gov/30207593/ https://doi.org/10.3322/caac.21492
  • Bresso, E., Furlan, A., Noel, P., Leroux, V., Maina, F., Dono, R., & Maigret, B. (2020). Large-scale virtual screening against the MET kinase domain identifies a new putative inhibitor type. Molecules, 25(4), 938. [Internet]. Feb 19 [cited 2020 Dec 4]. https://www.mdpi.com/1420-3049/25/4/938 https://doi.org/10.3390/molecules25040938
  • Carocho, M. and CFR Ferreira, I. (2013). The role of phenolic compounds in the fight against cancer–a review. Anti-Cancer Agents in Medicinal Chemistry (Formerly Current Medicinal Chemistry-Anti-Cancer Agents), 13(8), 1236–1258.
  • Chaudhary, A. K., Ahmad, S., & Mazumder, A. (2012). Study of antibacterial and antifungal activity of traditional Cedrus deodara and Pinus roxburghii Sarg. Tang [Humanitas Medicine], 2(4), 37.1–37.4. https://doi.org/10.5667/tang.2012.0036
  • Chen, X., Guan, Z., Lu, J., Wang, H., Zuo, Z., Ye, F., Huang, J., & Teng, L. (2018). Synergistic antitumor effects of cMet inhibitor in combination with anti-VEGF in colorectal cancer patient-derived xenograft models. Journal of Cancer, 9(7), 1207–1217. https://doi.org/10.7150/jca.20964
  • Dancey, J., & Discovery Es-N Reviews, D. (2003). undefined. Issues and progress with protein kinase inhibitors for cancer treatment. nature.com [Internet]. [cited 2020 Sep 21]; https://idp.nature.com/authorize/casa?redirect_uri=https://www.nature.com/articles/nrd1066&casa_token=leT1e1ro2JQAAAAA:qUfN9GdDS8QTN20aBiWFVG1wbGDPTiiTJMKNRvZ0A3nZAuIDE997GksyVjTS9UC-jK2K_RfL67i_n8HO
  • Doebele, R. C., Oton, A. B., Peled, N., Camidge, D. R., & Bunn, P. A. (2010). New strategies to overcome limitations of reversible EGFR tyrosine kinase inhibitor therapy in non-small cell lung cancer [Internet]. Lung Cancer (Amsterdam, Netherlands), 69(1), 1–12. [cited 2020 Sep 21]. https://pubmed.ncbi.nlm.nih.gov/20092908/ https://doi.org/10.1016/j.lungcan.2009.12.009
  • Gaurav, A., & Gautam, V. (2014). Structure-based three-dimensional pharmacophores as an alternative to traditional methodologies. [cited 2020 Sep 21]; https://doi.org/10.2147/JRLCR.S46845
  • Gu, J., Gui, Y., Chen, L., Yuan, G., Lu, H. Z., & Xu, X. (2013). Use of natural products as chemical library for drug discovery and network pharmacology. Cox D, editor. PLoS One, 8(4), e62839. [Internet]. Apr 25 [cited 2020 Sep 22]Available from: https://dx.plos.org/10.1371/journal.pone.0062839 https://doi.org/10.1371/journal.pone.0062839
  • Guterres, H., & Im, W. (2020). Improving protein-ligand docking results with high-throughput molecular dynamics simulations. Journal of Chemical Information and Modeling, 60(4), 2189–2198. [Internet]. Apr 27 [cited 2021 Aug 26]. https://pubs.acs.org/doi/abs/10.1021/acs.jcim.0c00057 https://doi.org/10.1021/acs.jcim.0c00057
  • Harvey, A. L. (2008). Natural products in drug discovery. Drug Discovery Today, 13(19–20), 894–901. [Internet]. [cited 2020 Sep 22]. https://pubmed.ncbi.nlm.nih.gov/18691670/ https://doi.org/10.1016/j.drudis.2008.07.004
  • Holmes, K., Roberts, O., & Thomas, A, signalling MC-C. (2007). undefined. Vascular endothelial growth factor receptor-2: structure, function, intracellular signalling and therapeutic inhibition. Elsevier [Internet]. [cited 2020 Sep 21]; https://www.sciencedirect.com/science/article/pii/S0898656807001532?casa_token=m7k3syULrxEAAAAA:Oo4xfoprCFmxZh3gmvjJPDqhjgp9l5j9sgfk7DkGkz5MUpzCeLqZcl-axkYF4odTCcVLlX3NSQ
  • Ibrahim, M. T., Uzairu, A., Uba, S., & Shallangwa, G. A. (2020). Computational virtual screening and structure-based design of some epidermal growth factor receptor inhibitors. Future Journal of Pharmaceutical Sciences, 6(1), 1–16. [Internet]. Dec 18 [cited 2020 Dec 4]. https://link.springer.com/articles/10.1186/s43094-020-00074-6 https://doi.org/10.1186/s43094-020-00074-6
  • Jaccard, P. (1912). The distribution of the flora in the alpine zone. New Phytologist, 11(2), 37–50. https://doi.org/10.1111/j.1469-8137.1912.tb05611.x
  • Jo, M., Beer Stolz, D., Esplen, J. E., Dorko, K., Michalopoulos, G. K., & Strom, S. C. (2000). Cross-talk between epidermal growth factor receptor and c-met signal pathways in transformed cells* [Internet]. [cited 2020 Sep 21]. http://www.jbc.org/
  • Kaushik, P., Khokra, L., Rana, A. C., & Kaushik, D. (2014). Pharmacophore modeling and molecular docking studies on pinus roxburghii as a target for diabetes Mellitus. hindawi.com [Internet]. Advances in Bioinformatics, 2014, 903246. https://doi.org/10.1155/2014/903246
  • Kaushik, P., Khokra, L., Rana, A. C., & Kaushik, D. (2015). Evaluation of anticancer activity of Pinus roxburghii Sarg. Against IMR-32 human neuroblastoma cancer cell line. International Journal of Pharmaceutical and Clinical Research, 7 (1), 105–108. [cited 2020 Dec 6]. www.ijpcr.com
  • Kulshrestha, S., Habib Khan, S., Saima, C., & Khan, H. (2019). Evaluation of anticancer activity of Pinus roxburghii Sarg against A549 human lung cancer cell line. . Journal of Pharmacognosy Phytochemistry, 8(2), 2268.
  • Li, Z., Natarajan, P., Ye, Y., Hrabe, T., & Godzik, A. (2014). POSA: a user-driven, interactive multiple protein structure alignment server. Nucleic Acids Research, 42(Web Server issue), W240–5. [Internet]. Jul 1 [cited 2021 Aug 17]. https://academic.oup.com/nar/article/42/W1/W240/2436962
  • Mahernia, S., Hassanzadeh, M., Sharifi, N., Mehravi, B., Paytam, F., Adib, M., & Amanlou, M. (2018). Structure-based pharmacophore design and virtual screening for novel potential inhibitors of epidermal growth factor receptor as an approach to breast cancer chemotherapy. Molecular Diversity, 22(1), 173–181. [Internet]. Feb 1 [cited 2020 Dec 4]. https://doi.org/10.1007/s11030-017-9799-7
  • Martorana, A., Monica, G., La., & Lauria, A. (2020). Quinoline-based molecules targeting c-Met, EGF, and VEGF receptors and the proteins involved in related carcinogenic pathways. Molecules, 25(18), 4279. [Internet]. [cited 2021 Oct 3]. https://www.mdpi.com/1420-3049/25/18/4279/htm https://doi.org/10.3390/molecules25184279
  • Mattapally, S., Singh, M., Murthy, K. S., Asthana, S., & Banerjee, S. K. (2018). Computational modeling suggests impaired interactions between NKX2.5 and GATA4 in individuals carrying a novel pathogenic D16N NKX2.5 mutation. Oncotarget, 9(17), 13713–13732. [Internet]. [cited 2020 Oct 8]. /pmc/articles/PMC5862610/?report = abstract https://doi.org/10.18632/oncotarget.24459
  • Mittal, L., Srivastava, M., & Asthana, S. (2019). Conformational characterization of linker revealed the mechanism of cavity formation by 227G in BVDV RDRP. The Journal of Physical Chemistry. B, 123(29), 6150–6160. [Internet]. Jun 28 [cited 2020 Oct 12]. https://www.uniprot.org/ https://doi.org/10.1021/acs.jpcb.9b01859
  • Nakachi, I., Naoki, K., Soejima, K., Kawada, I., Watanabe, H., Yasuda, H., Nakayama, S., Yoda, S., Satomi, R., Ikemura, S., Terai, H., Sato, T., & Ishizaka, A. (2010). The combination of multiple receptor tyrosine kinase inhibitor and mammalian target of rapamycin inhibitor overcomes erlotinib resistance in lung cancer cell lines through c-met inhibition. Molecular Cancer Research: MCR, 8(8), 1142–1151. [Internet]. Aug 1 [cited 2021 Oct 3]. https://mcr.aacrjournals.org/content/8/8/1142 https://doi.org/10.1158/1541-7786.MCR-09-0388
  • Nakade, J., Takeuchi, S., Nakagawa, T., Ishikawa, D., Sano, T., Nanjo, S., Yamada, T., Ebi, H., Zhao, L., Yasumoto, K., Matsumoto, K., Yonekura, K., & Yano, S. (2014). Triple inhibition of EGFR, met, and VEGF suppresses regrowth of HGF-triggered, erlotinib-resistant lung cancer harboring an EGFR mutation. Journal of Thoracic Oncology: Official Publication of the International Association for the Study of Lung Cancer, 9(6), 775–783. [Internet]. [cited 2020 Sep 21]. https://pubmed.ncbi.nlm.nih.gov/24828661/ https://doi.org/10.1097/JTO.0000000000000170
  • Oguro, Y., Miyamoto, N., Okada, K, … TT-B& medicinal. (2010)., undefined. pyrimidine derivatives: novel VEGFR2 kinase inhibitors binding to inactive kinase. Elsevier [Internet]. [cited 2020 Sep 22]; https://www.sciencedirect.com/science/article/pii/S0968089610007546?casa_token=Um2Y64NbRIkAAAAA: hqiHDKdNGPrL2ME4R3o71nBUD0vzCP0LsqPkAYgGLhEkUbJ0O3NdK5WAA1xWQ3Yam7EGZqdecA
  • Oprea, T. I. (2002). Virtual screening in lead discovery: A viewpoint. Molecules, 7(1), 51–62. [Internet]. 2002 Jan 31 [cited 2021 Sep 27]. https://www.mdpi.com/1420-3049/7/1/51/htm https://doi.org/10.3390/70100051
  • Pal, S., Kumar, V., Kundu, B., Bhattacharya, D., Preethy, N., Reddy, M. P., & Talukdar, A. (2019). Ligand-based pharmacophore modeling, virtual screening and molecular docking studies for discovery of potential topoisomerase i inhibitors. Computational and Structural Biotechnology Journal, 17, 291–310. https://doi.org/10.1016/j.csbj.2019.02.006
  • Panwar, S., Kumari, A., Kumar, H., Tiwari, A. K., Tripathi, P., & Asthana, S. Structure-based virtual screening, molecular dynamics simulation and in vitro evaluation to identify inhibitors against NAMPT. https://doi.org/10.1080/0739110220211943526 [Internet]. 2021 [cited 2021 Oct 3]; https://www.tandfonline.com/doi/abs/10.1080/07391102.2021.1943526 https://doi.org/10.1080/07391102.2021.1943526
  • Peach, M. L., Tan, N., Choyke, S. J., Giubellino, A., Athauda, G., Burke, T. R., Nicklaus, M. C., & Bottaro, D. P. (2009). Directed discovery of agents targeting the met tyrosine kinase domain by virtual screening. Journal of Medicinal Chemistry, 52(4), 943–951. [Internet]. Feb 26 [cited 2020 Sep 22]. /pmc/articles/PMC2698034/?report = abstract https://doi.org/10.1021/jm800791f
  • Pirhadi, S., Damghani, T., Avestan, M. S., & Sharifi, S. (2020). Dual potent c-Met and ALK inhibitors: from common feature pharmacophore modeling to structure based virtual screening. Journal of Receptor and Signal Transduction Research, 40(4), 357–364. [Internet]. Jul 3 [cited 2020 Dec 4]. https://doi.org/10.1080/10799893.2020.1735418
  • Purushotham, N., Singh, M., Paramesha, B., Kumar, V., Wakode, S., & Banerjee, S. K. (2020). Design and synthesis of amino acid derivatives of substituted benzimidazoles and pyrazoles as selective sirt1 inhibitors. Apr 27 [cited 2020 Oct 8]; /articles/preprint/Design_and_Synthesis_of_Amino_Acid_Derivatives_of_Substituted_Benzimidazoles_and_Pyrazoles_as_Selective_Sirt1_Inhibitors/12196200/1
  • Raghavendra, N. M., Pingili, D., Kadasi, S., Mettu, A., & Prasad, S. V. U. M. (2018). Dual or multi-targeting inhibitors: The next generation anticancer agents [Internet]. European Journal of Medicinal Chemistry, 143, 1277–1300. ]. Elsevier Masson SAS; [cited 2020 Sep 22]. Available from: https://pubmed.ncbi.nlm.nih.gov/29126724/ https://doi.org/10.1016/j.ejmech.2017.10.021
  • Rampogu, S., Baek, A., Zeb, A., & Lee, K. W. (2018). Exploration for novel inhibitors showing back-to-front approach against VEGFR-2 kinase domain (4AG8) employing molecular docking mechanism and molecular dynamics simulations. BMC Cancer, 18(1), 1–21. [Internet]. Mar 7 [cited 2020 Dec 4]. https://doi.org/10.1186/s12885-018-4050-1
  • Rathi, E., Kumar, A., & Kini, S. G. (2019). Molecular dynamics guided insight, binding free energy calculations and pharmacophore-based virtual screening for the identification of potential VEGFR2 inhibitors. Journal of Receptor and Signal Transduction Research, 39(5–6), 415–433. [Internet]. Nov 2 [cited 2020 Dec 4]. https://doi.org/10.1080/10799893.2019.1690509
  • Sharma, A., Sharma, L., & Goyal, R. (2018). A review on himalayan pine species: Ethnopharmacological, phytochemical and pharmacological aspects. Pharmacognosy Journal, 10(4), 611–619. https://doi.org/10.5530/pj.2018.4.100
  • Singh, M., Srivastava, M., Wakode, S. R., & Asthana, S. (2021). Elucidation of structural determinants delineates the residues playing key roles in differential dynamics and selective inhibition of Sirt1-3. Journal of Chemical Information and Modeling, 61(3), 1105–1124. [Internet]. Mar 22 [cited 2021 Oct 3]. https://doi.org/10.1021/acs.jcim.0c01193
  • Singh, S. K., Shanmugavel, M., Kampasi, H., Singh, R., Mondhe, D. M., Rao, J. M., Adwankar, M. K., Saxena, A. K., & Qazi, G. N. (2007). Chemically standardized isolates from Cedrus deodara stem wood having anticancer activity. Planta Medica, 73(6), 519–526. [Internet]. Jun [cited 2020 Dec 6]. https://pubmed.ncbi.nlm.nih.gov/17534788/ https://doi.org/10.1055/s-2007-967185
  • Smellie, A., Teig, S. L., & Towbin, P. (1995). Poling: Promoting conformational variation. Journal of Computational Chemistry, 16(2), 171–187. [Internet]. Feb 1 [cited 2021 Aug 26]. https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.540160205 https://doi.org/10.1002/jcc.540160205
  • Stone, A. (2014). EGFR and c-met inhibitors are effective in reducing tumorigenicity in cancer. Journal of Carcinogenesis Mutagen, 5(3), 1–9. [Internet]. [cited 2020 Sep 22]. https://www.longdom.org/abstract/egfr-and-cmet-inhibitors-are-effective-in-reducing-tumorigenicity-in-cancer-49403.html
  • Tai, W., Lu, T., Yuan, H., Wang, F., Liu, H., Lu, S., Leng, Y., Zhang, W., Jiang, Y., & Chen, Y. (2012). Pharmacophore modeling and virtual screening studies to identify new c-Met inhibitors. Journal of Molecular Modeling, 18(7), 3087–3100. [Internet]. Jul 28 [cited 2020 Sep 22]. https://link.springer.com/article/10.1007/s00894-011-1328-5 https://doi.org/10.1007/s00894-011-1328-5
  • van de Waterbeemd, H., & Gifford, E. (2003). ADMET in silico modelling: Towards prediction paradise? Nature Reviews. Drug Discovery, 2(3), 192–204. [Internet]. [cited 2020 Sep 22]. . https://pubmed.ncbi.nlm.nih.gov/12612645/ https://doi.org/10.1038/nrd1032
  • Widmer, N., Bardin, C., Chatelut, E., Paci, A., Beijnen, J., Levêque, D., Veal, G., & Astier, A. (2014). Review of therapeutic drug monitoring of anticancer drugs part two-targeted therapies. European Journal of Cancer (Oxford, England: 1990), 50(12), 2020–2036. Elsevier Ltd; [cited 2020 Sep 22]. https://pubmed.ncbi.nlm.nih.gov/24928190/ https://doi.org/10.1016/j.ejca.2014.04.015
  • Yang, S. Y. (2010). Pharmacophore modeling and applications in drug discovery: Challenges and recent advances. Drug Discovery Today, 15(11-12), 444–450. https://doi.org/10.1016/j.drudis.2010.03.013
  • Ye, Y., & Godzik, A. (2005). Multiple flexible structure alignment using partial order graphs. Bioinformatics, 21(10), 2362–2369. [Internet]. May 15 [cited 2021 Aug 17]. https://academic.oup.com/bioinformatics/article/21/10/2362/207583 https://doi.org/10.1093/bioinformatics/bti353
  • Yousuf, Z., Iman, K., Iftikhar, N., & Mirza, M. U. (2017). Structure-based virtual screening and molecular docking for the identification of potential multi-targeted inhibitors against breast cancer. Breast Cancer: Targets and Therapy, 9, 447–459. [Internet]. Jun 14 [cited 2020 Dec 4]. /pmc/articles/PMC5476443/?report = abstract https://doi.org/10.2147/BCTT.S132074
  • Zhang, W., Pei, J., & Lai, L. (2017). Computational multitarget drug design. Journal of Chemical Information and Modeling, 57(3), 403–412. [cited 2021 Jun 5]. https://pubs.acs.org/sharingguidelines https://doi.org/10.1021/acs.jcim.6b00491
  • Zhang, X., Gureasko, J., Shen, K., Cole, P. A., & Kuriyan, J. (2006). An allosteric mechanism for activation of the kinase domain of epidermal growth factor receptor. Cell, 125(6), 1137–1149. [Internet]. Jun [cited 2020 Sep 22]. https://pubmed.ncbi.nlm.nih.gov/16777603/ https://doi.org/10.1016/j.cell.2006.05.013
  • Zhou, Y., Di, B., & Niu, M. M. (2019). Structure-based pharmacophore design and virtual screening for novel tubulin inhibitors with potential anticancer activity. Molecules, 24(17), 3181. [Internet]. Sep 1 [cited 2020 Sep 22]Available from:/pmc/articles/PMC6749218/?report = abstract https://doi.org/10.3390/molecules24173181

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