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Research Articles

Molecular modelling studies and identification of novel phytochemical inhibitor of DLL3

ORCID Icon, ORCID Icon, ORCID Icon, , ORCID Icon & ORCID Icon
Pages 3089-3109 | Received 17 Dec 2021, Accepted 17 Feb 2022, Published online: 27 Feb 2022

Reference

  • Aalinkeel, R., Hu, Z., Nair, B. B., Sykes, D. E., Reynolds, J. L., Mahajan, S. D., & Schwartz, S. A. (2010). Genomic analysis highlights the role of the JAK-STAT signaling in the anti-proliferative effects of dietary flavonoid-'Ashwagandha' in prostate cancer cells. Evidence-Based Complementary and Alternative Medicine: eCAM, 7(2), 177–187. https://doi.org/10.1093/ecam/nem184
  • Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1–2, 19–25. https://doi.org/10.1016/j.softx.2015.06.001
  • Ahmad, T., & Eisen, T. (2004). Kinase inhibition with BAY 43-9006 in renal cell carcinoma. Clinical Cancer Research: An Official Journal of the American Association for Cancer Research, 10(18 Pt 2), 6388S–6392S. https://doi.org/10.1158/1078-0432.CCR-040028
  • Alves, D., Duarte, S., Arsénio, P., Gonçalves, J., Rodrigues, C. M. P., Lourenço, A., & Máximo, P. (2021). Exploring the phytochemicals of Acacia melanoxylon R. Br. Plants (Plants, 10(12), 2698.), https://doi.org/10.3390/plants10122698
  • Appella, E., Weber, I. T., & Blasi, F. (1988). Structure and function of epidermal growth factor-like regions in proteins. FEBS Letters, 231(1), 1–4. https://doi.org/10.1016/0014-5793(88)80690-2
  • Atun, S. (2010). Pemanfaatan bahan alam bumi Indonesia menuju riset yang berkualitas internasional. In Seminar Nasional Kimia. FMIPA Universitas Negeri Yogyakarta.
  • Baldwin, J. J., Ponticello, G. S., Anderson, P. S., Christy, M. E., Murcko, M. A., Randall, W. C., Schwam, H., Sugrue, M. F., Springer, J. P., & Gautheron, P. (1989). Thienothiopyran-2-sulfonamides: Novel topically active carbonic anhydrase inhibitors for the treatment of glaucoma. Journal of Medicinal Chemistry, 32(12), 2510–2513. https://doi.org/10.1021/jm00132a003
  • Beltran, H., & Demichelis, F. (2021). Therapy considerations in neuroendocrine prostate cancer: What next? Endocrine-Related Cancer, 28(8), T67–T78. https://doi.org/10.1530/ERC-21-0140
  • Berendsen, H. J., 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
  • Bhandare, V., & Ramaswamy, A. (2016). Structural dynamics of human argonaute2 and its interaction with siRNAs designed to target mutant tdp43. Advances in Bioinformatics, 2016, 8792814. https://doi.org/10.1155/2016/8792814
  • Bowie, J. U., Luthy, R., & Eisenberg, D. (1991). A method to identify protein sequences that fold into a known three-dimensional structure. Science (New York, N.Y.), 253(5016), 164–170. https://doi.org/10.1126/science.1853201
  • 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. https://doi.org/10.3322/caac.21492
  • Brimblecombe, R. W. (1975). Proceedings: The pharmacology of cimetidine, a new histamine H2-receptor antagonist. British Journal of Pharmacology, 53(3), 435.
  • Buchdunger, E., Zimmermann, J., Mett, H., Meyer, T., Müller, M., Druker, B. J., & Lydon, N. B. (1996). Inhibition of the Abl protein-tyrosine kinase in vitro and in vivo by a 2-phenylaminopyrimidine derivative. Cancer Research, 56(1), 100–104.
  • Bulman, M. P., Kusumi, K., Frayling, T. M., McKeown, C., Garrett, C., Lander, E. S., Krumlauf, R., Hattersley, A. T., Ellard, S., & Turnpenny, P. D. (2000). Mutations in the human delta homologue, DLL3, cause axial skeletal defects in Spondylocostal dysostosis. Nature Genetics, 24(4), 438–441. https://doi.org/10.1038/74307
  • Chao, J. F. (2006). [Chemical constituents from branch of Broussonetia papyrifera]. Zhongguo Zhong Yao Za Zhi, 31(13), 1078–1080.
  • Chapman, G., Sparrow, D. B., Kremmer, E., & Dunwoodie, S. L. (2011). Notch inhibition by the ligand DELTA-LIKE 3 defines the mechanism of abnormal vertebral segmentation in Spondylocostal dysostosis. Human Molecular Genetics, 20(5), 905–916. https://doi.org/10.1093/hmg/ddq529
  • Chen, S., Yong, T., Zhang, Y., Su, J., Jiao, C., & Xie, Y. (2017). Anti-tumor and anti-angiogenic ergosterols from Ganoderma lucidum. Frontiers in Chemistry, 5, 85.
  • Chen, X., Amar, N., Zhu, Y., Wang, C., Xia, C., Yang, X., Wu, D., & Feng, M. (2020). Combined DLL3-targeted bispecific antibody with PD-1 inhibition is efficient to suppress small cell lung cancer growth. Journal for ImmunoTherapy of Cancer, 8(1), e000785. https://doi.org/10.1136/jitc-2020-000785
  • Chen, Y.-K., Kuo, Y.-H., Chiang, B.-H., Lo, J.-M., & Sheen, L.-Y. (2009). Cytotoxic activities of 9,11-dehydroergosterol peroxide and ergosterol peroxide from the fermentation mycelia of Ganoderma lucidum cultivated in the medium containing leguminous plants on Hep 3B cells. Journal of Agricultural and Food Chemistry, 57(13), 5713–5719. https://doi.org/10.1021/jf900581h
  • Christensen, N. J., & Kepp, K. P. (2013). Stability mechanisms of laccase isoforms using a modified FoldX protocol applicable to widely different proteins. Journal of Chemical Theory and Computation, 9(7), 3210–3223. https://doi.org/10.1021/ct4002152
  • Christina, A. J. M., Joseph, D. G., Packialakshmi, M., Kothai, R., Robert, S. J. H., Chidambaranathan, N., & Ramasamy, M. (2004). Anticarcinogenic activity of Withania somnifera Dunal against Dalton's ascitic lymphoma. Journal of Ethnopharmacology, 93(2–3), 359–361. https://doi.org/10.1016/j.jep.2004.04.004
  • Chumkaew, P., Kato, S., & Chantrapromma, K. (2005). A new triterpenoid ester from the fruits of Bruguiera parviflora. Chemical & Pharmaceutical Bulletin, 53(1), 95–96. https://doi.org/10.1248/cpb.53.95
  • Colovos, C., & Yeates, T. O. (1993). Verification of protein structures: Patterns of nonbonded atomic interactions. Protein Science: A Publication of the Protein Society, 2(9), 1511–1519. https://doi.org/10.1002/pro.5560020916
  • Combet, C., Blanchet, C., Geourjon, C., & Deléage, G. (2000). NPS@: Network protein sequence analysis. Trends in Biochemical Sciences, 25(3), 147–150. https://doi.org/10.1016/S0968-0004(99)01540-6
  • Consortium, T. U. (2018). UniProt: A worldwide hub of protein knowledge. Nucleic Acids Research, 47(D1), D506–D515.
  • Council of Scientific Industrial Research. (2000). The wealth of India: Dictionary of Indian raw materials & industrial products. Publications & Information Directorate, Council of Scientific & Industrial Research (India), pp. 1–5.
  • Cragg, G. M. (1999). Natural product drug discovery and development. In J. T. Romeo (Ed.), Phytochemicals in human health protection, nutrition, and plant defense (pp. 1–29). Springer.
  • Cushman, D. W., & Ondetti, M. A. (1999). Design of angiotensin converting enzyme inhibitors. Nature Medicine, 5(10), 1110–1112. https://doi.org/10.1038/13423
  • 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, 42717.
  • Dallakyan, S., & Olson, A. J. (2015). Small-molecule library screening by docking with PyRx. Methods in Molecular Biology (Clifton, N.J.), 1263, 243–250.
  • Davis, C. G. (1990). The many faces of epidermal growth factor repeats. The New Biologist, 2(5), 410–419.
  • Dhanavade, M. J., Jalkute, C. B., Barage, S. H., & Sonawane, K. D. (2013). Homology modeling, molecular docking and MD simulation studies to investigate role of cysteine protease from Xanthomonas campestris in degradation of Aβ peptide. Computers in Biology and Medicine, 43(12), 2063–2070. https://doi.org/10.1016/j.compbiomed.2013.09.021
  • Ebrahimi, K. S., Ansari, M., Hosseyni Moghaddam, M. S., Ebrahimi, Z., Salehi, Z., Shahlaei, M., & Moradi, S. (2021). In silico investigation on the inhibitory effect of fungal secondary metabolites on RNA dependent RNA polymerase of SARS-CoV-II: A docking and molecular dynamic simulation study. Computers in Biology and Medicine, 135, 104613.
  • Edmunds, K., Tuffaha, H., Galvão, D. A., Scuffham, P., & Newton, R. U. (2020). Incidence of the adverse effects of androgen deprivation therapy for prostate cancer: a systematic literature review. Supportive Care in Cancer: Official Journal of the Multinational Association of Supportive Care in Cancer, 28(5), 2079–2093. https://doi.org/10.1007/s00520-019-05255-5
  • Eo, H. J., Park, J. H., Park, G. H., Lee, M. H., Lee, J. R., Koo, J. S., & Jeong, J. B. (2014). Anti-inflammatory and anti-cancer activity of mulberry (Morus alba L.) root bark. BMC Complementary and Alternative Medicine, 14(1), 200. https://doi.org/10.1186/1472-6882-14-200
  • Falcoz, C., Jenkins, J. M., Bye, C., Hardman, T. C., Kenney, K. B., Studenberg, S., Fuder, H., & Prince, W. T. (2002). Pharmacokinetics of GW433908, a prodrug of amprenavir, in healthy male volunteers. Journal of Clinical Pharmacology, 42(8), 887–898. https://doi.org/10.1177/009127002401102803
  • Fang, L., Geng, M., Liu, C., Wang, J., Min, W., & Liu, J. (2019). Structural and molecular basis of angiotensin-converting enzyme by computational modeling: Insights into the mechanisms of different inhibitors. PloS One, 14(4), e0215609. https://doi.org/10.1371/journal.pone.0215609
  • Faris, M. A.-I E., Takruri, H. R., Shomaf, M. S., & Bustanji, Y. K. (2009). Chemopreventive effect of raw and cooked lentils (Lens culinaris L) and soybeans (Glycine max) against azoxymethane-induced aberrant crypt foci. Nutrition Research, 29(5), 355–362. https://doi.org/10.1016/j.nutres.2009.05.005
  • Ferlay, J., Soerjomataram, I., Dikshit, R., Eser, S., Mathers, C., Rebelo, M., Parkin, D. M., Forman, D., & Bray, F. (2015). Cancer incidence and mortality worldwide: Sources, methods and major patterns in GLOBOCAN 2012. International Journal of Cancer, 136(5), E359–86. https://doi.org/10.1002/ijc.29210
  • Ferrari, F., & Monache, F. D. (2004). A new phenolic glycoside from Sorocea ilicifolia stem bark. Fitoterapia, 75(3–4), 417–419. https://doi.org/10.1016/j.fitote.2003.12.011
  • Fischer, A., Smieško, M., Sellner, M., & Lill, M. A. (2021). Decision making in structure-based drug discovery: Visual inspection of docking results. Journal of Medicinal Chemistry, 64(5), 2489–2500. https://doi.org/10.1021/acs.jmedchem.0c02227
  • Fridlender, M., Kapulnik, Y., & Koltai, H. (2015). Plant derived substances with anti-cancer activity: From folklore to practice. Frontiers in Plant Science, 6, 799.
  • Gasteiger, E. (2005). Protein identification and analysis tools on the ExPASy server. In J. M. Walker (Ed.), The proteomics protocols handbook (pp. 571–607). Humana Press.
  • Gaulton, A., Hersey, A., Nowotka, M., Bento, A. P., Chambers, J., Mendez, D., Mutowo, P., Atkinson, F., Bellis, L. J., Cibrián-Uhalte, E., Davies, M., Dedman, N., Karlsson, A., Magariños, M. P., Overington, J. P., Papadatos, G., Smit, I., & Leach, A. R. (2017). The ChEMBL database in 2017. Nucleic Acids Research, 45(D1), D945–D954. https://doi.org/10.1093/nar/gkw1074
  • GeneCards. (2022). Aliases for DLL3 gene. https://www.genecards.org/cgi-bin/carddisp.pl?gene=DLL3
  • Giffin, M. J., Cooke, K., Lobenhofer, E. K., Estrada, J., Zhan, J., Deegen, P., Thomas, M., Murawsky, C. M., Werner, J., Liu, S., Lee, F., Homann, O., Friedrich, M., Pearson, J. T., Raum, T., Yang, Y., Caenepeel, S., Stevens, J., Beltran, P. J., … Hughes, P. E. (2021). AMG 757, a half-life extended, DLL3-targeted bispecific T-cell engager, shows high potency and sensitivity in preclinical models of small-cell lung cancer. Clinical Cancer Research, 27(5), 1526–1537. https://doi.org/10.1158/1078-0432.CCR-20-2845
  • Gill, S. C., & von Hippel, P. H. (1989). Calculation of protein extinction coefficients from amino acid sequence data. Analytical Biochemistry, 182(2), 319–326. https://doi.org/10.1016/0003-2697(89)90602-7
  • Grienke, U., Mihály-Bison, J., Schuster, D., Afonyushkin, T., Binder, M., Guan, S.-H., Cheng, C.-R., Wolber, G., Stuppner, H., Guo, D.-A., Bochkov, V. N., & Rollinger, J. M. (2011). Pharmacophore-based discovery of FXR-agonists. Part II: Identification of bioactive triterpenes from Ganoderma lucidum. Bioorganic & Medicinal Chemistry, 19(22), 6779–6791. https://doi.org/10.1016/j.bmc.2011.09.039
  • Guruprasad, K., Reddy, B. V., & Pandit, M. W. (1990). Correlation between stability of a protein and its dipeptide composition: A novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Engineering, 4(2), 155–161. https://doi.org/10.1093/protein/4.2.155
  • Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. https://doi.org/10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
  • Higano, C. S. (2020). Cardiovascular disease and androgen axis-targeted drugs for prostate cancer. The New England Journal of Medicine, 382(23), 2257–2259. https://doi.org/10.1056/NEJMe2016433
  • Hollingsworth, S. A., & Dror, R. O. (2018). Molecular dynamics simulation for all. Neuron, 99(6), 1129–1143. https://doi.org/10.1016/j.neuron.2018.08.011
  • Hsu, H. Y., Lian, S. L., & Lin, C. C. (1990). Radioprotective effect of Ganoderma lucidum (Leyss. ex. Fr.) Karst after X-ray irradiation in mice. The American Journal of Chinese Medicine, 18(1–2), 61–69. https://doi.org/10.1142/S0192415X90000095
  • Ikai, A. (1980). Thermostability and aliphatic index of globular proteins. Journal of Biochemistry, 88(6), 1895–1898.
  • Iliya, I., Tanaka, T., Iinuma, M., Ali, Z., Furasawa, M., Nakaya, K-i., Shirataki, Y., Murata, J., & Darnaedi, D. (2002). Stilbene derivatives from two species of Gnetaceae. Chemical & Pharmaceutical Bulletin, 50(6), 796–801. https://doi.org/10.1248/cpb.50.796
  • Isobe, Y., Sato, K., Nishinaga, Y., Takahashi, K., Taki, S., Yasui, H., Shimizu, M., Endo, R., Koike, C., Kuramoto, N., Yukawa, H., Nakamura, S., Fukui, T., Kawaguchi, K., Chen-Yoshikawa, T. F., Baba, Y., & Hasegawa, Y. (2020). Near infrared photoimmunotherapy targeting DLL3 for small cell lung cancer. EBioMedicine, 52, 102632.
  • Jagusch, C., Negri, M., Hille, U. E., Hu, Q., Bartels, M., Jahn-Hoffmann, K., Pinto-Bazurco Mendieta, M. A. E., Rodenwaldt, B., Müller-Vieira, U., Schmidt, D., Lauterbach, T., Recanatini, M., Cavalli, A., & Hartmann, R. W. (2008). Synthesis, biological evaluation and molecular modelling studies of methyleneimidazole substituted biaryls as inhibitors of human 17alpha-hydroxylase-17,20-lyase (CYP17). Part I: Heterocyclic modifications of the core structure. Bioorganic & Medicinal Chemistry, 16(4), 1992–2010. https://doi.org/10.1016/j.bmc.2007.10.094
  • Jensen, A. A., Zlotos, D. P., & Liljefors, T. (2007). Pharmacological characteristics and binding modes of Caracurine V analogues and related compounds at the neuronal alpha7 nicotinic acetylcholine receptor. Journal of Medicinal Chemistry, 50(19), 4616–4629. https://doi.org/10.1021/jm070574f
  • Jiang, Y. J., Aerne, B. L., Smithers, L., Haddon, C., Ish-Horowicz, D., & Lewis, J. (2000). Notch signalling and the synchronization of the somite segmentation clock. Nature, 408(6811), 475–479. https://doi.org/10.1038/35044091
  • Jiménez, J., Škalič, M., Martínez-Rosell, G., & De Fabritiis, G. (2018). KDEEP: Protein-ligand absolute binding affinity prediction via 3D-convolutional neural networks. Journal of Chemical Information and Modeling, 58(2), 287–296. https://doi.org/10.1021/acs.jcim.7b00650
  • Kaennakam, S., Aree, T., Rassamee, K., Siripong, P., & Tip-Pyang, S. (2018). A new tocopherol derivative and cytotoxicity from the leaves of Dalbergia velutina. Natural Product Communications, 13(12), 1934578X1801301–1934578X1801622. https://doi.org/10.1177/1934578X1801301212
  • Kantardjieff, K. A., & Rupp, B. (2004). Protein isoelectric point as a predictor for increased crystallization screening efficiency. Bioinformatics (Oxford, England), 20(14), 2162–2168. https://doi.org/10.1093/bioinformatics/bth066
  • Kathiresan, K., Boopathy, N. S., & Kavitha, S. (2006). Coastal vegetation—An underexplored source of anticancer drugs. http://hdl.handle.net/123456789/7954
  • Korsen, J. (2020). Delta-like Ligand 3 (DLL3) is a novel target for molecular imaging of neuroendocrine prostate cancer. Journal of Nuclear Medicine, 61(supplement 1), 133–133.
  • Krieger, E., & Vriend, G. (2014). YASARA view - Molecular graphics for all devices - From smartphones to workstations. Bioinformatics (Oxford, England), 30(20), 2981–2982. https://doi.org/10.1093/bioinformatics/btu426
  • Krogh, A., Larsson, B., von Heijne, G., & Sonnhammer, E. L. (2001). Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. Journal of Molecular Biology, 305(3), 567–580. https://doi.org/10.1006/jmbi.2000.4315
  • Kunnimalaiyaan, M., & Chen, H. (2007). Tumor suppressor role of Notch-1 signaling in neuroendocrine tumors. The Oncologist, 12(5), 535–542. https://doi.org/10.1634/theoncologist.12-5-535
  • Kuo, Y. H., Chang, C. I., Li, S. Y., Chou, C. J., Chen, C. F., Kuo, Y. H., & Lee, K. H. (1997). Cytotoxic constituents from the stems of Diospyros maritima. Planta Medica, 63(4), 363–365. https://doi.org/10.1055/s-2006-957703
  • Kyte, J., & Doolittle, R. F. (1982). A simple method for displaying the hydropathic character of a protein. Journal of Molecular Biology, 157(1), 105–132. https://doi.org/10.1016/0022-2836(82)90515-0
  • Ladi, E., Nichols, J. T., Ge, W., Miyamoto, A., Yao, C., Yang, L.-T., Boulter, J., Sun, Y. E., Kintner, C., & Weinmaster, G. (2005). The divergent DSL ligand Dll3 does not activate Notch signaling but cell autonomously attenuates signaling induced by other DSL ligands. The Journal of Cell Biology, 170(6), 983–992. https://doi.org/10.1083/jcb.200503113
  • Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993). PROCHECK: a program to check the stereochemical quality of protein structures. Journal of Applied Crystallography, 26(2), 283–291. https://doi.org/10.1107/S0021889892009944
  • Lee, H. Y., Yum, J. H., Rho, Y. K., Oh, S. J., Choi, H. S., Chang, H. B., Choi, D. H., Leem, M.-J., Choi, E. J., Ryu, J. M., & Hwang, S. B. (2007). Inhibition of HCV replicon cell growth by 2-arylbenzofuran derivatives isolated from Mori Cortex Radicis. Planta Medica, 73(14), 1481–1485. https://doi.org/10.1055/s-2007-990249
  • Levitt, M., & Lifson, S. (1969). Refinement of protein conformations using a macromolecular energy minimization procedure. Journal of Molecular Biology, 46(2), 269–279. https://doi.org/10.1016/0022-2836(69)90421-5
  • Li, Y., Li, H., Zhang, Y., Li, L., & Qin, C. (2013). In vitro antioxidant and anticancer activities of the extract from paper mulberry (Broussonetia papyrifera L.) fruit. Asian Journal of Chemistry, 25(10), 5453–5456. https://doi.org/10.14233/ajchem.2013.14594
  • Liang, D. (2018). Effects of nicotine on the metabolism and gene expression profile of SpragueDawley rat primary osteoblasts. Molecular Medicine Reports, 17(6), 8269–8281.
  • Liede, A., Hallett, D. C., Hope, K., Graham, A., Arellano, J., & Shahinian, V. B. (2016). International survey of androgen deprivation therapy (ADT) for non-metastatic prostate cancer in 19 countries. ESMO Open, 1(2), e000040. https://doi.org/10.1136/esmoopen-2016-000040
  • Lin, M., & Yao, C.-S. (2006). Natural oligostilbenes. In R. Atta ur (Ed.), Studies in natural products chemistry (pp. 601–644). Elsevier.
  • Liu, R., Tawa, G., & Wallqvist, A. (2012). Locally weighted learning methods for predicting dose-dependent toxicity with application to the human maximum recommended daily dose. Chemical Research in Toxicology, 25(10), 2216–2226. https://doi.org/10.1021/tx300279f
  • Liu, Z., Su, M., Han, L., Liu, J., Yang, Q., Li, Y., & Wang, R. (2017). Forging the basis for developing protein-ligand interaction scoring functions. Accounts of Chemical Research, 50(2), 302–309. https://doi.org/10.1021/acs.accounts.6b00491
  • Loukola, A., Buchwald, J., Gupta, R., Palviainen, T., Hällfors, J., Tikkanen, E., Korhonen, T., Ollikainen, M., Sarin, A.-P., Ripatti, S., Lehtimäki, T., Raitakari, O., Salomaa, V., Rose, R. J., Tyndale, R. F., & Kaprio, J. (2015). A genome-wide association study of a biomarker of nicotine metabolism. PLoS Genetics, 11(9), e1005498. https://doi.org/10.1371/journal.pgen.1005498
  • Lu, S., Wang, J., Chitsaz, F., Derbyshire, M. K., Geer, R. C., Gonzales, N. R., Gwadz, M., Hurwitz, D. I., Marchler, G. H., Song, J. S., Thanki, N., Yamashita, R. A., Yang, M., Zhang, D., Zheng, C., Lanczycki, C. J., & Marchler-Bauer, A. (2020). CDD/SPARCLE: The conserved domain database in 2020. Nucleic Acids Research, 48(D1), D265–D268. https://doi.org/10.1093/nar/gkz991
  • Luthy, R., Bowie, J. U., & Eisenberg, D. (1992). Assessment of protein models with three-dimensional profiles. Nature, 356(6364), 83–85. https://doi.org/10.1038/356083a0
  • Macias, F. A. (2006). Bioactive steroids from Oryza sativa L. Steroids, 71(7), 603–608.
  • Mali, R., & Mahale, N. (2008). Evaluation of Rhynchosia minima (Linn.) DC leaves for anthelmintic activity. International Journal of Pharmaceutical Sciences and Nanotechnology, 1(2), 191–194.
  • Mishra, R., Bhadauria, S., Murthy, P. K., & Murthy, P. S. R. (2011). Glycine soya diet synergistically enhances the suppressive effect of tamoxifen and inhibits tamoxifen-promoted hepatocarcinogenesis in 7,12-dimethylbenz[α]anthracene-induced rat mammary tumor model. Food and Chemical Toxicology: An International Journal Published for the British Industrial Biological Research Association, 49(2), 434–440. https://doi.org/10.1016/j.fct.2010.11.020
  • Misra, L., Mishra, P., Pandey, A., Sangwan, R. S., & Sangwan, N. S. (2012). 1,4-Dioxane and ergosterol derivatives from Withania somnifera roots. Journal of Asian Natural Products Research, 14(1), 39–45. https://doi.org/10.1080/10286020.2011.622719
  • Mohanraj, K., Karthikeyan, B. S., Vivek-Ananth, R. P., Chand, R. P. B., Aparna, S. R., Mangalapandi, P., & Samal, A. (2018). IMPPAT: A curated database of Indian medicinal plants, phytochemistry and therapeutics. Scientific Reports, 8(1), 4329. https://doi.org/10.1038/s41598-018-22631-z
  • 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
  • Mukherjee, A. K., Basu, S., Sarkar, N., & Ghosh, A. C. (2001). Advances in cancer therapy with plant based natural products. Current Medicinal Chemistry, 8(12), 1467–1486. https://doi.org/10.2174/0929867013372094
  • Munagala, R., Kausar, H., Munjal, C., & Gupta, R. C. (2011). Withaferin A induces p53-dependent apoptosis by repression of HPV oncogenes and upregulation of tumor suppressor proteins in human cervical cancer cells. Carcinogenesis, 32(11), 1697–1705. https://doi.org/10.1093/carcin/bgr192
  • Ng, H. L., Quail, E., Cruickshank, M. N., & Ulgiati, D. (2021). To be, or notch to be: mediating cell fate from embryogenesis to lymphopoiesis. Biomolecules, 11(6), 849. https://doi.org/10.3390/biom11060849
  • Nguyen, N. T., Nguyen, T. H., Pham, T. N. H., Huy, N. T., Bay, M. V., Pham, M. Q., Nam, P. C., Vu, V. V., & Ngo, S. T. (2020). Autodock vina adopts more accurate binding poses but autodock4 forms better binding affinity. Journal of Chemical Information and Modeling, 60(1), 204–211. https://doi.org/10.1021/acs.jcim.9b00778
  • O’Boyle, N. (2011). Open babel: an open chemical toolbox. Journal of Cheminformatics, 3(1), 33.
  • Ogbonna, J. (2012). Different approaches to formulation of herbal extracts/phytopharmaceuticals/bioactive phytochstituents-A review. International Journal of Pharmaceutical Sciences Review and Research, 16(1), 1–8.
  • Páll, S. (2014). Tackling exascale software challenges in molecular dynamics simulations with GROMACS. In International Conference on Exascale Applications and Software. Springer.
  • Parrinello, M., & Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics, 52(12), 7182–7190. https://doi.org/10.1063/1.328693
  • 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
  • Pires, D. E., Ascher, D. B., & Blundell, T. L. (2014). DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach. Nucleic Acids Research, 42(Web Server issue), W314–W319. https://doi.org/10.1093/nar/gku411
  • Pires, D. E., Ascher, D. B., & Blundell, T. L. (2014). mCSM: predicting the effects of mutations in proteins using graph-based signatures. Bioinformatics (Oxford, England), 30(3), 335–342. https://doi.org/10.1093/bioinformatics/btt691
  • Prada-Gracia, D., Huerta-Yepez, S., & Moreno-Vargas, L. M. (2016). Application of computational methods for anticancer drug discovery, design, and optimization. Boletin Medico Del Hospital Infantil de Mexico, 73(6), 411–423. https://doi.org/10.1016/j.bmhimx.2016.10.006
  • Puca, L., Gavyert, K., Sailer, V., Conteduca, V., Dardenne, E., Sigouros, M., Isse, K., Kearney, M., Vosoughi, A., Fernandez, L., Pan, H., Motanagh, S., Hess, J., Donoghue, A. J., Sboner, A., Wang, Y., Dittamore, R., Rickman, D., Nanus, D. M., … Beltran, H. (2019). Delta-like protein 3 expression and therapeutic targeting in neuroendocrine prostate cancer. Science Translational Medicine, 11(484), eaav0891. https://doi.org/10.1126/scitranslmed.aav0891
  • Puca, L., Vlachostergios, P. J., & Beltran, H. (2019). Neuroendocrine differentiation in prostate cancer: Emerging biology, models, and therapies. Cold Spring Harbor Perspectives in Medicine, 9(2), a030593. https://doi.org/10.1101/cshperspect.a030593
  • Quintanal-Villalonga, Á., Chan, J. M., Yu, H. A., Pe'er, D., Sawyers, C. L., Sen, T., & Rudin, C. M. (2020). Lineage plasticity in cancer: A shared pathway of therapeutic resistance. Nature Reviews. Clinical Oncology, 17(6), 360–371. https://doi.org/10.1038/s41571-020-0340-z
  • Ramachandran, G. N., Ramakrishnan, C., & Sasisekharan, V. (1963). Stereochemistry of polypeptide chain configurations. Journal of Molecular Biology, 7, 95–99.
  • Rao, A. S., Reddy, S. G., Babu, P. P., & Reddy, A. R. (2010). The antioxidant and antiproliferative activities of methanolic extracts from Njavara rice bran. BMC Complementary and Alternative Medicine, 10, 4.
  • Rastogi, R. P., & Mehrotra, B. (1990). Compendium of Indian medicinal plants. Central Drug Research Institute, pp. 1–5.
  • Rentzsch, R., & Renard, B. Y. (2015). Docking small peptides remains a great challenge: An assessment using AutoDock Vina. Briefings in Bioinformatics, 16(6), 1045–1056. https://doi.org/10.1093/bib/bbv008
  • Rudin, C. M., Pietanza, M. C., Bauer, T. M., Ready, N., Morgensztern, D., Glisson, B. S., Byers, L. A., Johnson, M. L., Burris, H. A., Robert, F., Han, T. H., Bheddah, S., Theiss, N., Watson, S., Mathur, D., Vennapusa, B., Zayed, H., Lally, S., Strickland, D. K., … Spigel, D. R. (2017). Rovalpituzumab tesirine, a DLL3-targeted antibody-drug conjugate, in recurrent small-cell lung cancer: a first-in-human, first-in-class, open-label, phase 1 study. The Lancet. Oncology, 18(1), 42–51. https://doi.org/10.1016/S1470-2045(16)30565-4
  • Sahay, A., & Shakya, M. (2010). In silico analysis and homology modelling of antioxidant proteins of spinach. Journal of Proteomics & Bioinformatics, 3(5), 148–154. https://doi.org/10.4172/jpb.1000134
  • Salo-Ahen, O. M. H., Alanko, I., Bhadane, R., Bonvin, A. M. J. J., Honorato, R. V., Hossain, S., Juffer, A. H., Kabedev, A., Lahtela-Kakkonen, M., Larsen, A. S., Lescrinier, E., Marimuthu, P., Mirza, M. U., Mustafa, G., Nunes-Alves, A., Pantsar, T., Saadabadi, A., Singaravelu, K., & Vanmeert, M. (2020). Molecular dynamics simulations in drug discovery and pharmaceutical development. Processes, 9(1), 71. https://doi.org/10.3390/pr9010071
  • Santos, L. H. S., Ferreira, R. S., & Caffarena, E. R. (2019). Integrating molecular docking and molecular dynamics simulations. Methods in Molecular Biology (Clifton, N.J.), 2053, 13–34.
  • Schyman, P., Liu, R., Desai, V., & Wallqvist, A. (2017). vNN web server for ADMET predictions. Frontiers in Pharmacology, 8, 889.
  • Schymkowitz, J., Borg, J., Stricher, F., Nys, R., Rousseau, F., & Serrano, L. (2005). The FoldX web server: An online force field. Nucleic Acids Research, 33(Web Server issue), W382–W388. https://doi.org/10.1093/nar/gki387
  • Serth, K., Schuster-Gossler, K., Kremmer, E., Hansen, B., Marohn-Köhn, B., & Gossler, A. (2015). O-fucosylation of DLL3 is required for its function during somitogenesis. PloS One, 10(4), e0123776. https://doi.org/10.1371/journal.pone.0123776
  • Sharma, S., & Bhatia, V. (2021). Phytochemicals for drug discovery in Alzheimer's disease: In silico advances. Current Pharmaceutical Design, 27(25), 2848–2860. https://doi.org/10.2174/1381612826666200928161721
  • Shim, S. Y., Sung, S. H., & Lee, M. (2018). Anti-inflammatory activity of Mulberrofuran K isolated from the bark of Morus bombycis. International Immunopharmacology, 58, 117–124. https://doi.org/10.1016/j.intimp.2017.11.002
  • Sigerist, H. E. (1987). A history of medicine (Vol. 2). Oxford University Press.
  • Sigrist, C. J. A., Cerutti, L., Hulo, N., Gattiker, A., Falquet, L., Pagni, M., Bairoch, A., & Bucher, P. (2002). PROSITE: A documented database using patterns and profiles as motif descriptors. Briefings in Bioinformatics, 3(3), 265–274. https://doi.org/10.1093/bib/3.3.265
  • Sigrist, C. J. A., de Castro, E., Cerutti, L., Cuche, B. A., Hulo, N., Bridge, A., Bougueleret, L., & Xenarios, I. (2013). New and continuing developments at PROSITE. Nucleic Acids Research, 41(Database issue), D344–D347. Database issue): https://doi.org/10.1093/nar/gks1067
  • Silalahi, M. (2020). Gnetum gnemon L. Gnetaceae. In F. Merlin Franco (Ed.), Ethnobotany of the mountain regions of southeast asia (pp. 1–7). Springer.
  • Sliva, D., Labarrere, C., Slivova, V., Sedlak, M., Lloyd, F. P., & Ho, N. W. Y. (2002). Ganoderma lucidum suppresses motility of highly invasive breast and prostate cancer cells. Biochemical and Biophysical Research Communications, 298(4), 603–612. https://doi.org/10.1016/S0006-291X(02)02496-8
  • Sliwoski, G., Kothiwale, S., Meiler, J., & Lowe, E. W. (2014). Computational methods in drug discovery. Pharmacological Reviews, 66(1), 334–395. https://doi.org/10.1124/pr.112.007336
  • Sung, H., Ferlay, J., Siegel, R. L., Laversanne, M., Soerjomataram, I., Jemal, A., & Bray, F. (2021). Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA: A Cancer Journal for Clinicians, 71(3), 209–249. https://doi.org/10.3322/caac.21660
  • Thyagarajan, A., Jedinak, A., Nguyen, H., Terry, C., Baldridge, L. A., Jiang, J., & Sliva, D. (2010). Triterpenes from Ganoderma lucidum induce autophagy in colon cancer through the inhibition of p38 mitogen-activated kinase (p38 MAPK). Nutrition and Cancer, 62(5), 630–640. https://doi.org/10.1080/01635580903532390
  • 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
  • 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
  • Turnpenny, P. D., Whittock, N., Duncan, J., Dunwoodie, S., Kusumi, K., & Ellard, S. (2003). Novel mutations in DLL3, a somitogenesis gene encoding a ligand for the Notch signalling pathway, cause a consistent pattern of abnormal vertebral segmentation in spondylocostal dysostosis. Journal of Medical Genetics, 40(5), 333–339. https://doi.org/10.1136/jmg.40.5.333
  • UCLA. (2022). SAVES v5.0: https://servicesn.mbi.ucla.edu/SAVES/.
  • Van Durme, J., Delgado, J., Stricher, F., Serrano, L., Schymkowitz, J., & Rousseau, F. (2011). A graphical interface for the FoldX forcefield. Bioinformatics (Oxford, England), 27(12), 1711–1712. https://doi.org/10.1093/bioinformatics/btr254
  • Vaque, M., Arola, A., Aliagas, C., & Pujadas, G. (2006). BDT: an easy-to-use front-end application for automation of massive docking tasks and complex docking strategies with AutoDock. Bioinformatics, 22(14), 1803–1804. https://doi.org/10.1093/bioinformatics/btl197
  • Verpoorte, R., & Svendsen, A. B. (1978). Alkaloids of Strychnos dolichothyrsa gilg ex onochie et hepper. Journal of Pharmaceutical Sciences, 67(2), 171–174. https://doi.org/10.1002/jps.2600670213
  • Vetrivel, U. (2021). Phytochemical moieties from Indian traditional medicine for targeting dual hotspots on SARS-CoV-2 spike protein: An integrative in-silico approach. Frontiers in Medicine, 8, 545.
  • Vivek-Ananth, R. P., Rana, A., Rajan, N., Biswal, H. S., & Samal, A. (2020). In silico identification of potential natural product inhibitors of human proteases key to SARS-CoV-2 infection. Molecules, 25(17), 3822. https://doi.org/10.3390/molecules25173822
  • Vlachostergios, P. J., Puca, L., & Beltran, H. (2017). Emerging variants of castration-resistant prostate cancer. Current Oncology Reports, 19(5), 32. https://doi.org/10.1007/s11912-017-0593-6
  • von Arx, C., Capozzi, M., López-Jiménez, E., Ottaiano, A., Tatangelo, F., Di Mauro, A., Nasti, G., Tornesello, M. L., & Tafuto, S. (2019). Updates on the role of molecular alterations and NOTCH signalling in the development of neuroendocrine neoplasms. Journal of Clinical Medicine, 8(9), 1277. https://doi.org/10.3390/jcm8091277
  • Walker, J. M. (2005). The proteomics protocols handbook. Springer.
  • Walker, L. M., & Santos-Iglesias, P. (2020). On the relationship between erectile function and sexual distress in men with prostate cancer. Archives of Sexual Behavior, 49(5), 1575–1588. https://doi.org/10.1007/s10508-019-01603-y
  • Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F. T., de Beer, T. A. P., Rempfer, C., Bordoli, L., Lepore, R., & Schwede, T. (2018). SWISS-MODEL: Homology modelling of protein structures and complexes. Nucleic Acids Research, 46(W1), W296–W303. https://doi.org/10.1093/nar/gky427
  • Wilding, S., Downing, A., Selby, P., Cross, W., Wright, P., Watson, E. K., Wagland, R., Kind, P., Donnelly, D. W., Hounsome, L., Mottram, R., Allen, M., Kearney, T., Butcher, H., Gavin, A., & Glaser, A. (2020). Decision regret in men living with and beyond nonmetastatic prostate cancer in the United Kingdom: A population-based patient-reported outcome study. Psycho-oncology, 29(5), 886–893. https://doi.org/10.1002/pon.5362
  • Wilkins, M. R., Gasteiger, E., Bairoch, A., Sanchez, J. C., Williams, K. L., Appel, R. D., & Hochstrasser, D. F. (1999). Protein identification and analysis tools in the ExPASy server. Methods in Molecular Biology (Clifton, N.J.), 112, 531–552.
  • Wollersheim, B. M., van Stam, M.-A., Bosch, R. J. L. H., Pos, F. J., Tillier, C. N., van der Poel, H. G., & Aaronson, N. K. (2020). Unmet expectations in prostate cancer patients and their association with decision regret. Journal of Cancer Survivorship: Research and Practice, 14(5), 731–738. https://doi.org/10.1007/s11764-020-00888-6
  • Wood, E. R., Truesdale, A. T., McDonald, O. B., Yuan, D., Hassell, A., Dickerson, S. H., Ellis, B., Pennisi, C., Horne, E., Lackey, K., Alligood, K. J., Rusnak, D. W., Gilmer, T. M., & Shewchuk, L. (2004). A unique structure for epidermal growth factor receptor bound to GW572016 (Lapatinib): Relationships among protein conformation, inhibitor off-rate, and receptor activity in tumor cells. Cancer Research, 64(18), 6652–6659. https://doi.org/10.1158/0008-5472.CAN-04-1168
  • Worth, C. L., Preissner, R., & Blundell, T. L. (2011). SDM-A server for predicting effects of mutations on protein stability and malfunction. Nucleic Acids Research, 39(Web Server issue), W215–W222. https://doi.org/10.1093/nar/gkr363
  • Wu, H.-Y., Yang, F.-L., Li, L.-H., Rao, Y. K., Ju, T.-C., Wong, W.-T., Hsieh, C.-Y., Pivkin, M. V., Hua, K.-F., & Wu, S.-H. (2018). Ergosterol peroxide from marine fungus Phoma sp. induces ROS-dependent apoptosis and autophagy in human lung adenocarcinoma cells. Scientific Reports, 8(1), 17956. https://doi.org/10.1038/s41598-018-36411-2
  • Xiu, M. X., Liu, Y. M., & Kuang, B. H. (2020). The role of DLLs in cancer: A novel therapeutic target. OncoTargets and Therapy, 13, 3881–3901. https://doi.org/10.2147/OTT.S244860
  • Yachdav, G., Kloppmann, E., Kajan, L., Hecht, M., Goldberg, T., Hamp, T., Hönigschmid, P., Schafferhans, A., Roos, M., Bernhofer, M., Richter, L., Ashkenazy, H., Punta, M., Schlessinger, A., Bromberg, Y., Schneider, R., Vriend, G., Sander, C., Ben-Tal, N., & Rost, B. (2014). PredictProtein-an open resource for online prediction of protein structural and functional features. Nucleic Acids Research, 42(Web Server issue), W337–W343. https://doi.org/10.1093/nar/gku366
  • Yan, R., Xu, D., Yang, J., Walker, S., & Zhang, Y. (2013). A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction. Scientific Reports, 3(1), 2619–2619. https://doi.org/10.1038/srep02619
  • Yang, J., Yan, R., Roy, A., Xu, D., Poisson, J., & Zhang, Y. (2015). The I-TASSER suite: Protein structure and function prediction. Nature Methods, 12(1), 7–8. https://doi.org/10.1038/nmeth.3213
  • Yu, W., & MacKerell, A. D. (2017). Computer-aided drug design methods, in Antibiotics. Springer. p. 85–106.
  • Yuan, C., Chang, K., Xu, C., Li, Q., & Du, Z. (2021). High expression of DLL3 is associated with a poor prognosis and immune infiltration in invasive breast cancer patients. Translational Oncology, 14(7), 101080. https://doi.org/10.1016/j.tranon.2021.101080
  • Yuen, J. W., & Gohel, M. D. (2005). Anticancer effects of Ganoderma lucidum: A review of scientific evidence. Nutrition and Cancer, 53(1), 11–17. https://doi.org/10.1207/s15327914nc5301_2
  • Zlotos, D. P. (2000). Stereochemistry of Caracurine V. Journal of Natural Products, 63(6), 864–865. https://doi.org/10.1021/np990500+
  • Zlotos, D. P. (2004). Stereochemistry of Caracurine V, iso‐Caracurine V, Bisnortoxiferine, and Tetrahydrocaracurine V ring systems. European Journal of Organic Chemistry, 2004(11), 2375–2380. https://doi.org/10.1002/ejoc.200300722
  • Zlotos, D. P., Tränkle, C., Holzgrabe, U., Gündisch, D., & Jensen, A. A. (2014). Semisynthetic analogues of Toxiferine I and their pharmacological properties at α7 nAChRs, muscle-type nAChRs, and the allosteric binding site of muscarinic M2 receptors. Journal of Natural Products, 77(9), 2006–2013. https://doi.org/10.1021/np500259j

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