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Molecular docking of brazilin and its analogs to barrier-to-autointegration factor 1 (BAF1).

التفاصيل البيبلوغرافية
العنوان: Molecular docking of brazilin and its analogs to barrier-to-autointegration factor 1 (BAF1).
المؤلفون: Correia Soeiro MN; Fundação Oswaldo Cruz, Laboratório de Biologia Celular do Instituto Oswaldo Cruz, Rio de Janeiro, RJ 21040-360, Brazil., Vergoten G; University of Lille, Inserm, INFINITE - U1286, Institut de Chimie Pharmaceutique Albert Lespagnol (ICPAL), Faculté de Pharmacie, Lille, France., Bailly C; OncoWitan, Scientific Consulting Office, Lille (Wasquehal), 59290, France.
المصدر: Annals of the New York Academy of Sciences [Ann N Y Acad Sci] 2022 May; Vol. 1511 (1), pp. 154-163. Date of Electronic Publication: 2022 Jan 21.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: New York Academy of Sciences Country of Publication: United States NLM ID: 7506858 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1749-6632 (Electronic) Linking ISSN: 00778923 NLM ISO Abbreviation: Ann N Y Acad Sci Subsets: MEDLINE
أسماء مطبوعة: Publication: 2006- : New York, NY : Malden, MA : New York Academy of Sciences ; Blackwell
Original Publication: New York, The Academy.
مواضيع طبية MeSH: Caesalpinia*/chemistry, Benzopyrans ; Hematoxylin ; Humans ; Molecular Docking Simulation ; Wood
مستخلص: The tetracyclic phenolic compound brazilin, derived from the wood of Caesalpinia sappan, has been shown to bind to the chromatin protein BAF1 (barrier-to-autointegration factor 1), a protein essential to maintain integrity of the nuclear envelope in cells. BAF1 plays a role in cancer development. Using molecular docking, we have located the binding site for brazilin on the surface of the BAF1 monomer and compared its binding to that of four analogs. The oxidized product brazilein (ΔE = -57.7 kcal/mol) exhibits a higher affinity for BAF1 compared to the reduced form brazilin (ΔE = -38.2 kcal/mol). Incorporation of a 4-hydroxyl substituent on the indenochromene unit affords hematoxylin and hematein. In silico analysis predicts that the oxidized form hematein (ΔE = -66.2 kcal/mol) displays a higher affinity for BAF1 than the reduced form hematoxylin (ΔE = -42.2 kcal/mol). In contrast, the atypical bis-lactone product brazilide A cannot form good complexes with BAF1. The analysis points to the formation of more stable BAF1 complexes with the oxidized molecules compared to the reduced ones, but the position of the binding site on the protein cavity is different for brazilin/hematoxylin compared to brazilein/hematein. Our study may be useful to guide the design of BAF1 ligands.
(© 2022 New York Academy of Sciences.)
References: Halfmann, C.T. & K.J. Roux. 2021. Barrier-to-autointegration factor: a first responder for repair of nuclear ruptures. Cell Cycle 20: 647-660.
Burgess, J.T., C.M. Cheong, A. Suraweera, et al. 2021. Barrier-to-autointegration-factor (Banf1) modulates DNA double-strand break repair pathway choice via regulation of DNA-dependent kinase (DNA-PK) activity. Nucleic Acids Res. 49: 3294-3307.
Wiebe, M.S., A. Jamin. 2016. The barrier to autointegration factor: interlocking antiviral defense with genome maintenance. J. Virol. 90: 3806-3809.
Nichols, R.J., M.S. Wiebe & P. Traktman. 2006. The vaccinia-related kinases phosphorylate the N' terminus of BAF, regulating its interaction with DNA and its retention in the nucleus. Mol. Biol. Cell 17: 2451-2464.
Gorjánácz, M., E.P. Klerkx, V. Galy, et al. 2007. Caenorhabditis elegans BAF-1 and its kinase VRK-1 participate directly in post-mitotic nuclear envelope assembly. EMBO J. 26: 132-143.
Jamin, A., A. Wicklund, M.S. Wiebe. 2014. Cell- and virus-mediated regulation of the barrier-to-autointegration factor's phosphorylation state controls its DNA binding, dimerization, subcellular localization, and antipoxviral activity. J. Virol. 88: 5342-5355.
Zhang, G. 2020. Expression and prognostic significance of BANF1 in triple-negative breast cancer. Cancer Manag. Res. 12: 145-150.
Li, J., B. Hu, L. Fang, et al. 2018. Barrier-to-autointegration factor 1: a novel biomarker for gastric cancer. Oncol. Lett. 16: 6488-6494.
Shen, Q., J.W. Eun, K. Lee, et al. 2018. Barrier to autointegration factor 1, procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3, and splicing factor 3b subunit 4 as early-stage cancer decision markers and drivers of hepatocellular carcinoma. Hepatology 67: 1360-1377.
Li, J., T. Wang, L. Pei, et al. 2017. Expression of VRK1 and the downstream gene BANF1 in esophageal cancer. Biomed. Pharmacother. 89: 1086-1091.
Ren, Z., J. Geng, C. Xiong, et al. 2020. Downregulation of VRK1 reduces the expression of BANF1 and suppresses the proliferative and migratory activity of esophageal cancer cells. Oncol. Lett. 20: 1163-1170.
Jamin, A. & M.S. Wiebe. 2015. Barrier to autointegration factor (BANF1): interwoven roles in nuclear structure, genome integrity, innate immunity, stress responses and progeria. Curr. Opin. Cell. Biol. 34: 61-68.
Marcelot, A., H.J. Worman & S. Zinn-Justin. 2021. Protein structural and mechanistic basis of progeroid laminopathies. FEBS J. 288: 2757-2772.
Burger, M., C. Schmitt-Koopmann & J.C. Leroux. 2020. DNA unchained: two assays to discover and study inhibitors of the DNA clustering function of barrier-to-autointegration factor. Sci. Rep. 10: 12301.
Kim, W., H.N. Lyu, H.S. Kwon, et al. 2013. Obtusilactone B from Machilus thunbergii targets barrier-to-autointegration factor to treat cancer. Mol. Pharmacol. 83: 367-376.
Kim, S.H., H.N. Lyu, Y.S. Kim, et al. 2015. Brazilin isolated from Caesalpinia sappan suppresses nuclear envelope reassembly by inhibiting barrier-to-autointegration factor phosphorylation. J. Pharmacol. Exp. Ther. 352: 175-184.
Qi, B., X. Zhang, H. Yu, et al. 2021. Brazilin prevents against myocardial ischemia-reperfusion injury through the modulation of Nrf2 via the PKC signaling pathway. Ann. Transl. Med. 9: 312.
Liu, F., Y. Wang, J. Sang, et al. 2019. Brazilin inhibits alpha-synuclein fibrillogenesis, disrupts mature fibrils, and protects against amyloid-induced cytotoxicity. J. Agric. Food Chem. 67: 11769-11777.
Nahass, G.R., Y. Sun, Y. Xu, et al. 2021. Brazilin removes toxic alpha-synuclein and seeding competent assemblies from Parkinson brain by altering conformational equilibrium. J. Mol. Biol. 433: 166878.
Henríquez, G., L. Mendez, A. Varela-Ramirez, et al. 2020. Neuroprotective effect of brazilin on amyloid beta (25-35)-induced pathology in a human neuroblastoma model. ACS Omega 5: 13785-13792.
Wang, X., Z. Xiu, Y. Du, et al. 2019. Brazilin treatment produces antidepressant- and anxiolytic-like effects in mice. Biol. Pharm. Bull. 42: 1268-1274.
Nirmal, N.P., M.S. Rajput, R.G. Prasad & M. Ahmad. 2015. Brazilin from Caesalpinia sappan heartwood and its pharmacological activities: a review. Asian Pac. J. Trop. Med. 8: 421-430.
Zhang, Q., J.L. Liu, X.M. Qi, et al. 2014. Inhibitory activities of Lignum Sappan extractives on growth and growth-related signaling of tumor cells. Chin. J. Nat. Med. 12: 607-612.
Zhang, T., X. Fan, L. Song, et al. 2015. c-Fos is involved in inhibition of human bladder carcinoma T24 cells by brazilin. IUBMB Life 67: 175-181.
Jenie, R.I., S. Handayani, R.A. Susidarti, et al. 2018. The cytotoxic and antimigratory activity of brazilin-doxorubicin on MCF-7/HER2 cells. Adv. Pharm. Bull. 8: 507-516.
Jia, Y., X. Tong & J. Fan. 2019. Effect of brazilin on apoptosis and autophagy of tongue cancer Tca8113 cells and its molecular mechanism. Nan Fang Yi Ke Da Xue Xue Bao 39: 351-356.
Jang, H.Y., O.Y. Hong, E.Y. Chung, et al. 2020. Roles of JNK/Nrf2 pathway on hemin-induced heme oxygenase-1 activation in MCF-7 human breast cancer cells. Medicina (Kaunas) 56: 268.
Kang, Y., P. He, H. Wang, et al. 2018. Brazilin induces FOXO3A-dependent autophagic cell death by disturbing calcium homeostasis in osteosarcoma cells. Cancer Chemother. Pharmacol. 82: 479-491.
Hermawan, A. & H. Putri. 2020. Integrative bioinformatics analysis reveals potential target genes and TNFα signaling inhibition by brazilin in metastatic breast cancer cells. Asian Pac. J. Cancer Prev. 21: 2751-2762.
Zhang, T., J. He, S. Zhang, et al. 2018. Brazilin induces T24 cell death through c-Fos and GADD45β independently regulated genes and pathways. IUBMB Life 70: 1101-1110.
Umland, T.C., S.Q. Wei, R. Craigie & D.R. Davies. 2000. Structural basis of DNA bridging by barrier-to-autointegration factor. Biochemistry 39: 9130-9138.
Bradley, C.M., D.R. Ronning, R. Ghirlando, et al. 2005. Structural basis for DNA bridging by barrier-to-autointegration factor. Nat. Struct. Mol. Biol. 12: 935-936.
Cai, M., Y. Huang, J.Y. Suh, et al. 2007. Solution NMR structure of the barrier-to-autointegration factor-Emerin complex. J. Biol. Chem. 282: 14525-14535.
Amador, A.T., A.F.G. Neto, J.N. Cruz, et al. 2019. Molecular electronics including temperature effects based on dyes pigments. J. Nanosci. Nanotechnol. 19: 3631-3636.
Dapson, R.W. & C.L. Bain. 2015. Brazilwood, sappanwood, brazilin and the red dye brazilein: from textile dyeing and folk medicine to biological staining and musical instruments. Biotech. Histochem. 90: 401-423.
Yang, B.O., C.Q. Ke, Z.S. He, et al. 2002. Brazilide A, a novel lactone with an unprecedented skeleton from Caesalpinia sappan. Tetrahedron Lett. 43: 1731-1733.
Wang, X., H. Zhang, X. Yang, et al. 2013. Enantioselective total synthesis of (+)-brazilin, (-)-brazilein and (+)-brazilide A. Chem. Commun. (Camb.) 49: 5405-5407.
Jorgensen, W.L., J.P. Ulmschneider & J. Tirado-Rives. 2004. Free energies of hydration from a generalized Born model and an ALL-atom force field. J. Phys. Chem. B 108: 16264-16270.
Tian, W., C. Chen, X. Lei, et al. 2018. CASTp 3.0: computed atlas of surface topography of proteins. Nucleic Acids Res. 46: W363-W367.
Jorgensen, W.L. & J. Tirado-Rives. 2005. Molecular modeling of organic and biomolecular systems using BOSS and MCPRO. J. Comput. Chem. 26: 1689-1700.
Vergoten, G., I. Mazur, P. Lagant, et al. 2003. The SPASIBA force field as an essential tool for studying the structure and dynamics of saccharides. Biochimie 85: 65-73.
Lagant, P., D. Nolde, R. Stote, et al. 2004. Increasing normal modes analysis accuracy: the SPASIBA spectroscopic force field introduced into the CHARMM program. J. Phys. Chem. A 108: 4019-4029.
Jones, G., P. Willett, R.C. Glen, et al. 1997. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. 267: 727-748.
Zafar, A. & J. Reynisson. 2016. Hydration free energy as a molecular descriptor in drug design: a feasibility study. Mol. Inform. 35: 207-214.
Marcelot, A., A. Petitalot, V. Ropars, et al. 2021. Di-phosphorylated BAF shows altered structural dynamics and binding to DNA, but interacts with its nuclear envelope partners. Nucleic Acids Res. 49: 3841-3855.
Bengtsson, L. & K.L. Wilson. 2006. Barrier-to-autointegration factor phosphorylation on Ser-4 regulates emerin binding to lamin A in vitro and emerin localization in vivo. Mol. Biol. Cell 17: 1154-1163.
Zhuang, X., E. Semenova, D. Maric & R. Craigie. 2014. Dephosphorylation of barrier-to-autointegration factor by protein phosphatase 4 and its role in cell mitosis. J. Biol. Chem. 289: 1119-1127.
Hridya, H., A. Amrita, M. Sankari, et al. 2015. Inhibitory effect of brazilein on tyrosinase and melanin synthesis: kinetics and in silico approach. Int. J. Biol. Macromol. 81: 228-234.
Hsieh, C.Y., P.C. Tsai, C.L. Chu, et al. 2013. Brazilein suppresses migration and invasion of MDA-MB-231 breast cancer cells. Chem. Biol. Interact. 204: 105-115.
Zhong, X., B. Wu, Y.J. Pan & S. Zheng. 2009. Brazilein inhibits survivin protein and mRNA expression and induces apoptosis in hepatocellular carcinoma HepG2 cells. Neoplasma 56: 387-392.
Mou, Z., Y. Wang & Y. Li. 2019. Brazilein induces apoptosis and G1/G0 phase cell cycle arrest by up-regulation of miR-133a in human vestibular schwannoma cells. Exp. Mol. Pathol. 107: 95-101.
Yen, C.T., K. Nakagawa-Goto, T.L. Hwang, et al. 2010. Antitumor agents. 271: total synthesis and evaluation of brazilein and analogs as anti-inflammatory and cytotoxic agents. Bioorg. Med. Chem. Lett. 20: 1039.
Gogoi, D., R. Devi, P. Pahari, et al. 2016. cis-Diastereoselective synthesis of chroman-fused tetralins as B-ring-modified analogues of brazilin. Beilstein J. Org. Chem. 12: 2816-2822.
Handayani, S., R.A. Susidarti, R.I. Jenie & E. Meiyanto. 2017. Two active compounds from Caesalpinia sappan L. in combination with cisplatin synergistically induce apoptosis and cell cycle arrest on WiDr cells. Adv. Pharm. Bull. 7: 375-380.
Hung, M.S., Z. Xu, Y.C. Lin, et al. 2009. Identification of hematein as a novel inhibitor of protein kinase CK2 from a natural product library. BMC Cancer 9: 135.
Tsuyuguchi, M., T. Nakaniwa, A. Hirasawa, et al. 2020. Structural insights for producing CK2α1-specific inhibitors. Bioorg. Med. Chem. Lett. 30: 126837.
Cho, Y.W., H.J. Lim, M.H. Han, et al. 2020. Small molecule inhibitors of IκB kinase β: a chip-based screening and molecular docking simulation. Bioorg. Med. Chem. 28: 115440.
Hung, M.S., Z. Xu, Y. Chen, et al. 2013. Hematein, a casein kinase II inhibitor, inhibits lung cancer tumor growth in a murine xenograft model. Int. J. Oncol. 43: 1517-1522.
Zhang, C., J. Guan, J. Zhang, et al. 2021. Protective effects of three structurally similar polyphenolic compounds against oxidative damage and their binding properties to human serum albumin. Food Chem. 349: 129118.
Bolderson, E., J.T. Burgess, J. Li, et al. 2019. Barrier-to-autointegration factor 1 (Banf1) regulates poly [ADP-ribose] polymerase 1 (PARP1) activity following oxidative DNA damage. Nat. Commun. 10: 5501.
Samson, C., A. Petitalot, F. Celli, et al. 2018. Structural analysis of the ternary complex between lamin A/C, BAF and emerin identifies an interface disrupted in autosomal recessive progeroid diseases. Nucleic Acids Res. 46: 10460-10473.
فهرسة مساهمة: Keywords: anticancer agents; barrier-to-autointegration factor 1; brazilin; cancer; hematein; molecular modeling; natural products
المشرفين على المادة: 0 (Benzopyrans)
FZ39SW1K10 (brazilin)
YKM8PY2Z55 (Hematoxylin)
تواريخ الأحداث: Date Created: 20220121 Date Completed: 20220519 Latest Revision: 20220630
رمز التحديث: 20231215
DOI: 10.1111/nyas.14742
PMID: 35061919
قاعدة البيانات: MEDLINE
الوصف
تدمد:1749-6632
DOI:10.1111/nyas.14742