Network pharmacology-based screening of active constituents of Avicennia marina and their clinical biochemistry related mechanism against breast cancer

References

• Abou Seedo, K., Abido, M. S., Salih, A., & Abahussain, A. (2018). Morphophysiological traits of gray mangrove (Avicennia marina (Forsk.) Vierh.) at different levels of soil salinity. International Journal of Forestry Research, 2018, 1–9. https://doi.org/10.1155/2018/7404907
   Google Scholar
• Afendi, F. M., Okada, T., Yamazaki, M., Hirai-Morita, A., Nakamura, Y., Nakamura, K., Ikeda, S., Takahashi, H., Altaf-Ul-Amin, M., Darusman, L. K., Saito, K., & Kanaya, S. (2012). KNApSAcK family databases: Integrated metabolite–plant species databases for multifaceted plant research. Plant & Cell Physiology, 53(2), e1–e1. https://doi.org/10.1093/pcp/pcr165
   Web of Science ®Google Scholar
• Aslam, S., Ahmad, S., Noor, F., Ashfaq, U. A., Shahid, F., Rehman, A., Tahir Ul Qamar, M., Alatawi, E. A., Alshabrmi, F. M., & Allemailem, K. S. (2021). Designing a multi-epitope vaccine against chlamydia trachomatis by employing integrated core proteomics, immuno-informatics and in silico approaches. Biology (Basel), 10(10), 997. https://doi.org/10.3390/biology10100997
   PubMedGoogle Scholar
• Bailey, A. G., & Lowe, C. P. (2009). MILCH SHAKE: An efficient method for constraint dynamics applied to alkanes. Journal of Computational Chemistry, 30(15), 2485–2493. https://doi.org/10.1002/jcc.21237
   PubMed Web of Science ®Google Scholar
• Batool, S., Javed, M. R., Aslam, S., Noor, F., Javed, H. M. F., Seemab, R., Rehman, A., Aslam, M. F., Paray, B. A., & Gulnaz, A. (2022). Network pharmacology and bioinformatics approach reveals the multi-target pharmacological mechanism of Fumaria Indica in the treatment of liver cancer. Pharmaceuticals, 15(6), 654. https://doi.org/10.3390/ph15060654
   Web of Science ®Google Scholar
• Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, IN., & Bourne, P. E. (2000). The protein data bank. Nucleic Acids Research, 28(1), 235–242. https://doi.org/10.1093/nar/28.1.235
   PubMed Web of Science ®Google Scholar
• Chen, T., Zhang, H., Liu, Y., Liu, Y.-X., & Huang, L. (2021). EVenn: Easy to create repeatable and editable Venn diagrams and Venn networks online. Journal of Genetics and Genomics = Yi Chuan Xue Bao, 48(9), 863–866. https://doi.org/10.1016/j.jgg.2021.07.007
   PubMed Web of Science ®Google Scholar
• Chin, C.-H., Chen, S.-H., Wu, H.-H., Ho, C.-W., Ko, M.-T., & Lin, C.-Y. (2014). CytoHubba: identifying hub objects and sub-networks from complex interactome. BMC Systems Biology. 8, 1–7.
   PubMed Web of Science ®Google Scholar
• Cruceriu, D., Baldasici, O., Balacescu, O., & Berindan-Neagoe, I. (2020). The dual role of tumor necrosis factor-alpha (TNF-α) in breast cancer: Molecular insights and therapeutic approaches. Cellular Oncology (Dordrecht), 43(1), 1–18. https://doi.org/10.1007/s13402-019-00489-1
   PubMed Web of Science ®Google Scholar
• Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7(1), 13. https://doi.org/10.1038/srep42717
   PubMedGoogle Scholar
• Daina, A., Michielin, O., & Zoete, V. (2019). SwissTargetPrediction: Updated data and new features for efficient prediction of protein targets of small molecules. Nucleic Acids Research, 47(W1), W357–W364. https://doi.org/10.1093/nar/gkz382
   PubMed Web of Science ®Google Scholar
• Dallakyan, S., & Olson, A. J. (2015). Small-molecule library screening by docking with PyRx. In Chemical biology. Springer. pp. 243–250.
   Google Scholar
• Dennis, G., Sherman, B. T., Hosack, D. A., Yang, J., Gao, W., Lane, H. C., & Lempicki, R. A. (2003). DAVID: Database for annotation, visualization, and integrated discovery. Genome Biology, 4(5), 1–11. https://doi.org/10.1186/gb-2003-4-5-p3
   Google Scholar
• Derbalah, A., Al‐Sallami, H., Hasegawa, C., Gulati, A., & Duffull, S. B. (2022). A framework for simplification of quantitative systems pharmacology models in clinical pharmacology. British Journal of Clinical Pharmacology, 88(4), 1430–1440. https://doi.org/10.1111/bcp.14451
   PubMed Web of Science ®Google Scholar
• DeSantis, C. E., Fedewa, S. A., Goding Sauer, A., Kramer, J. L., Smith, R. A., & Jemal, A. (2016). Breast cancer statistics, 2015: Convergence of incidence rates between black and white women. CA: A Cancer Journal for Clinicians, 66(1), 31–42. https://doi.org/10.3322/caac.21320
   PubMed Web of Science ®Google Scholar
• ElDohaji, L. M., Hamoda, A. M., Hamdy, R., & Soliman, S. S. M. (2020). Avicennia marina a natural reservoir of phytopharmaceuticals: Curative power and platform of medicines. Journal of Ethnopharmacology, 263, 113179. https://doi.org/10.1016/j.jep.2020.113179
   PubMed Web of Science ®Google Scholar
• Genheden, S., & Ryde, U. (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on Drug Discovery, 10(5), 449–461. https://doi.org/10.1517/17460441.2015.1032936
   PubMed Web of Science ®Google Scholar
• Goddard, T. D., Huang, C. C., Meng, E. C., Pettersen, E. F., Couch, G. S., Morris, J. H., & Ferrin, T. E. (2018). UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Protein Science: A Publication of the Protein Society, 27(1), 14–25. https://doi.org/10.1002/pro.3235
   PubMed Web of Science ®Google Scholar
• Hopkins, A. L. (2007). Network pharmacology. Nature Biotechnology, 25(10), 1110–1111. https://doi.org/10.1038/nbt1007-1110
   PubMed Web of Science ®Google Scholar
• Hopkins, A. L. (2008). Network pharmacology: The next paradigm in drug discovery. Nature Chemical Biology, 4(11), 682–690. https://doi.org/10.1038/nchembio.118
   PubMed Web of Science ®Google Scholar
• Hosen, S. M. Z., Junaid, M., Alam, M. S., Rubayed, M., Dash, R., Akter, R., Sharmin, T., Mouri, N. J., Moni, M. A., Khatun, M., & Mostafa, M. (2022). GreenMolBD: Nature derived bioactive molecules’ database. Medicinal Chemistry (Shariqah (United Arab Emirates)), 18(6), 724–733. https://doi.org/10.2174/1573406418666211129103458
   PubMed Web of Science ®Google Scholar
• Jacsó, P. (2005). Google scholar: The pros and the cons. Online Inf. Rev,
   Web of Science ®Google Scholar
• Jejurikar, B. L., & Rohane, S. H. (2021). Drug designing in discovery studio. Asian Journal of Research in Chemistry, 14, 135–138.
   Google Scholar
• Kim, S., Thiessen, P. A., Bolton, E. E., Chen, J., Fu, G., Gindulyte, A., Han, L., He, J., He, S., Shoemaker, B. A., Wang, J., Yu, B., Zhang, J., & Bryant, S. H. (2016). PubChem substance and compound databases. Nucleic Acids Research, 44(D1), D1202–D1213. https://doi.org/10.1093/nar/gkv951
   PubMed Web of Science ®Google Scholar
• Kuhn, M., von Mering, C., Campillos, M., Jensen, L. J., & Bork, P. (2008). STITCH: Interaction networks of chemicals and proteins. Nucleic Acids Research, 36(Database issue), D684–D688. https://doi.org/10.1093/nar/gkm795
   PubMedGoogle Scholar
• Lalitha, P., & Sivakamasundari, S. (2010). Calculation of molecular lipophilicity and drug likeness for few heterocycles. Oriental Journal of Chemistry. 26, 135.
   Google Scholar
• Li, A. P. (2001). Screening for human ADME/Tox drug properties in drug discovery. Drug Discovery Today, 6(7), 357–366. https://doi.org/10.1016/s1359-6446(01)01712-3
   PubMed Web of Science ®Google Scholar
• Li, S. (2021). Network pharmacology evaluation method guidance-draft. World Journal of Traditional Chinese Medicine, 7, 146.
   Google Scholar
• Li, J., Liu, Z., Chen, R., Hu, D., Li, W., Li, X., Chen, X., Huang, B., & Liao, L. (2014). The quality of reports of randomized clinical trials on traditional Chinese medicine treatments: A systematic review of articles indexed in the china national knowledge infrastructure database from 2005 to 2012. BMC Complementary Alternative Medicine, 14, 1–11.
   PubMed Web of Science ®Google Scholar
• Li, Y., Liu, J., Yu, S., Proksch, P., Gu, J., & Lin, W. (2010). TNF-α inhibitory diterpenoids from the chinese mangrove plant Excoecaria agallocha L. Phytochemistry, 71(17-18), 2124–2131. https://doi.org/10.1016/j.phytochem.2010.08.011
   PubMed Web of Science ®Google Scholar
• Liu, H., Ahmad, S., Chen, J., & Zhao, J. (2020). Molecular dynamics study of the nanoscale boiling heat transfer process on nanostructured surfaces. International Communications in Heat and Mass Transfer, 119, 104963. https://doi.org/10.1016/j.icheatmasstransfer.2020.104963
   Web of Science ®Google Scholar
• Maier, J. A., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser, K. E., & Simmerling, C. (2015). Ff14SB: Improving the accuracy of protein side chain and backbone parameters from Ff99SB. Journal of Chemical Theory and Computation, 11(8), 3696–3713. https://doi.org/10.1021/acs.jctc.5b00255
   PubMed Web of Science ®Google Scholar
• Majeed, W., Aslam, B., Javed, I., Khaliq, T., Muhammad, F., Ali, A., & Raza, A. (2014). Breast cancer: Major risk factors and recent developments in treatment. Asian Pacific Journal of Cancer Prevention: APJCP, 15(8), 3353–3358. https://doi.org/10.7314/apjcp.2014.15.8.3353
   PubMedGoogle Scholar
• Miller, I. I. I., McGee, B. R., Jr, Swails, T. D., Homeyer, J. M., Gohlke, N., Roitberg, H., & Mmpbsa, A. E. (2012). Py: An efficient program for end-state free energy calculations. Journal of Chemical Theory and Computation, 8(9), 3314–3321. https://doi.org/10.1021/ct300418h
   PubMed Web of Science ®Google Scholar
• Mohanraj, K., Karthikeyan, B. S., Vivek-Ananth, R. P., Chand, R. P., Aparna, S. R., Mangalapandi, P., & Samal, A. (2018). IMPPAT: A curated database of Indian medicinal plants, phytochemistry and therapeutics. Scientific Reports, 8(1), 1–17. https://doi.org/10.1038/s41598-018-22631-z
   PubMed Web of Science ®Google Scholar
• Molinspiration, C. (2011). Calculation of molecular properties and bioactivity score. http://www. molinspiration. com/cgi-bin/properties
   Google Scholar
• Nabeelah Bibi, S., Fawzi, M. M., Gokhan, Z., Rajesh, J., Nadeem, N., R. R., R. K., RDDG, A., & Pandian, S. K. (2019). Ethnopharmacology, phytochemistry, and global distribution of mangroves: A comprehensive review. Marine Drugs, 17(4), 231. https://doi.org/10.3390/md17040231
   PubMed Web of Science ®Google Scholar
• Noor, F., Noor, A., Ishaq, A. R., Farzeen, I., Saleem, M. H., Ghaffar, K., Aslam, M. F., Aslam, S., & Chen, J.-T. (2021). Recent advances in diagnostic and therapeutic approaches for breast cancer: a comprehensive review. Current Pharmaceutical Design, 27(20), 2344–2365. https://doi.org/10.2174/1381612827666210303141416
   PubMed Web of Science ®Google Scholar
• Noor, F., Rehman, A., Ashfaq, U. A., Saleem, M. H., Okla, M. K., Al-Hashimi, A., Abdelgawad, H., & Aslam, S. (2022). Integrating network pharmacology and molecular docking approaches to decipher the multi-target pharmacological mechanism of Abrus Precatorius L. acting on diabetes. Pharmaceuticals, 15(4), 414. https://doi.org/10.3390/ph15040414
   Web of Science ®Google Scholar
• Noor, F., Tahir Ul Qamar, M., Ashfaq, U. A., Albutti, A., Alwashmi, A. S. S., & Aljasir, M. A. (2022). Network pharmacology approach for medicinal plants: review and assessment. Pharmaceuticals, 15(5), 572. https://doi.org/10.3390/ph15050572
   Web of Science ®Google Scholar
• O’Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open babel: An open chemical toolbox. Journal of Cheminformatics, 3(S1), 14. https://doi.org/10.1186/1758-2946-3-33
   PubMedGoogle Scholar
• Okla, M. K., Alamri, S. A., Alatar, A. A., Hegazy, A. K., Al-Ghamdi, A. A., Ajarem, J. S., Faisal, M., Abdel-Salam, E. M., Ali, H. M., Salem, M. Z. M., & Abdel-Maksoud, M. A. (2019). Antioxidant, hypoglycemic, and neurobehavioral effects of a leaf extract of avicennia marina on autoimmune diabetic mice. Evidence-Based Complementary and Alternative Medicine, 2019, 1–8. https://doi.org/10.1155/2019/1263260
   Web of Science ®Google Scholar
• Pence, H. E., & Williams, A. (2010). ChemSpider: An Online Chemical Information Resource.
   Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Polyak, K. (2011). Heterogeneity in breast cancer. The Journal of Clinical Investigation, 121(10), 3786–3788. https://doi.org/10.1172/JCI60534
   PubMed Web of Science ®Google Scholar
• Robinson, K. A., & Dickersin, K. (2002). Development of a highly sensitive search strategy for the retrieval of reports of controlled trials using PubMed. International Journal of Epidemiology, 31(1), 150–153. https://doi.org/10.1093/ije/31.1.150
   PubMed Web of Science ®Google Scholar
• Roe, D. R., & Cheatham, T. E. III, (2013). PTRAJ and CPPTRAJ: Software for processing and analysis of molecular dynamics trajectory data. Journal of Chemical Theory and Computation, 9(7), 3084–3095. https://doi.org/10.1021/ct400341p
   PubMed Web of Science ®Google Scholar
• Safran, M., Dalah, I., Alexander, J., Rosen, N., Iny Stein, T., Shmoish, M., Nativ, N., Bahir, I., Doniger, T., Krug, H., Sirota-Madi, A., Olender, T., Golan, Y., Stelzer, G., Harel, A., & Lancet, D. (2010). GeneCards version 3: The human gene integrator. Database, 2010(0), baq020. https://doi.org/10.1093/database/baq020
   PubMedGoogle Scholar
• Saito, R., Smoot, M. E., Ono, K., Ruscheinski, J., Wang, P.-L., Lotia, S., Pico, A. R., Bader, G. D., & Ideker, T. (2012). A travel guide to cytoscape plugins. Nature Methods, 9(11), 1069–1076. https://doi.org/10.1038/nmeth.2212
   PubMed Web of Science ®Google Scholar
• Saladin, A., Rey, J., Thévenet, P., Zacharias, M., Moroy, G., & Tufféry, P. (2014). PEP-SiteFinder: A tool for the blind identification of peptide binding sites on protein surfaces. Nucleic Acids Research, 42(Web Server issue), W221–W226. https://doi.org/10.1093/nar/gku404
   PubMedGoogle Scholar
• Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003). Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research, 13(11), 2498–2504. https://doi.org/10.1101/gr.1239303
   PubMed Web of Science ®Google Scholar
• Siegel, R. L., Miller, K. D., & Jemal, A. (2019). Cancer statistics, 2019. CA: A Cancer Journal for Clinicians, 69(1), 7–34. https://doi.org/10.3322/caac.21551
   PubMed Web of Science ®Google Scholar
• Sietsema, W. K. (1989). The absolute oral bioavailability of selected drugs. International Journal of Clinical Pharmacology, Therapy, and Toxicology, 27(4), 179–211.
   PubMedGoogle Scholar
• Stewart, B. W., & Kleihues, P. (2003). World cancer report. IARC Press Lyon. Vol. 57.
   Google Scholar
• Thatoi, H., Samantaray, D., & Das, S. K. (2016). The genus Avicennia, a pioneer group of dominant mangrove plant species with potential medicinal values: A review. Frontiers in Life Science, 9(4), 267–291. https://doi.org/10.1080/21553769.2016.1235619
   Web of Science ®Google Scholar
• Tian, W., Chen, C., Lei, X., Zhao, J., & Liang, J. (2018). CASTp 3.0: Computed atlas of surface topography of proteins. Nucleic Acids Research, 46(W1), W363–W367. https://doi.org/10.1093/nar/gky473
   PubMed Web of Science ®Google Scholar
• Ursu, O., Rayan, A., Goldblum, A., & Oprea, T. I. (2011). Understanding drug‐likeness. WIREs Computational Molecular Science, 1(5), 760–781. https://doi.org/10.1002/wcms.52
   Google Scholar
• Veber, D. F., Johnson, S. R., Cheng, H.-Y., Smith, B. R., Ward, K. W., & Kopple, K. D. (2002). Molecular properties that influence the oral bioavailability of drug candidates. Journal of Medicinal Chemistry, 45(12), 2615–2623. https://doi.org/10.1021/jm020017n
   PubMed Web of Science ®Google Scholar
• Vilar, S., Cozza, G., & Moro, S. (2008). Medicinal chemistry and the molecular operating environment (MOE): Application of QSAR and molecular docking to drug discovery. Current Topics in Medicinal Chemistry, 8(18), 1555–1572. https://doi.org/10.2174/156802608786786624
   PubMed Web of Science ®Google Scholar
• von Mering, C., Huynen, M., Jaeggi, D., Schmidt, S., Bork, P., & Snel, B. (2003). STRING: A database of predicted functional associations between proteins. Nucleic Acids Research, 31(1), 258–261. https://doi.org/10.1093/nar/gkg034
   PubMed Web of Science ®Google Scholar
• Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., & Case, D. A. (2004). Development and testing of a general amber force field. Journal of Computational Chemistry, 25(9), 1157–1174. https://doi.org/10.1002/jcc.20035
   PubMed Web of Science ®Google Scholar
• Zhang, X., Shen, T., Zhou, X., Tang, X., Gao, R., Xu, L., Wang, L., Zhou, Z., Lin, J., & Hu, Y. (2020). Network pharmacology based virtual screening of active constituents of Prunella Vulgaris L. and the molecular mechanism against breast cancer. Scientific Reports, 10(1), 12. https://doi.org/10.1038/s41598-020-72797-8
   PubMed Web of Science ®Google Scholar
• Zhu, F., Chen, X., Yuan, Y., Huang, M., Sun, H., & Xiang, W. (2009). The chemical investigations of the mangrove plant Avicennia marina and Its Endophytes. Open Nat. Prod. J, 2
   Google Scholar