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Research Articles

Identification of novel anti-cancer agents, applying in silico method for SENP1 protease inhibition

, , ORCID Icon &
Pages 6228-6242 | Received 30 Sep 2020, Accepted 19 Jan 2021, Published online: 03 Feb 2021

References

  • Ahmadi, H., Nayeri, Z., Minuchehr, Z., Sabouni, F., & Mohammadi, M. (2020). Betanin purification from red beetroots and evaluation of its anti-oxidant and anti-inflammatory activity on LPS-activated microglial cells. PLoS One, 15(5), e0233088. https://doi.org/10.1371/journal.pone.0233088
  • Alemi, M., Sabouni, F., Sanjarian, F., Haghbeen, K., & Ansari, S. (2013). Anti-inflammatory effect of seeds and callus of Nigella sativa L. extracts on mix glial cells with regard to their thymoquinone content. AAPS PharmSciTech, 14(1), 160–167. https://doi.org/10.1208/s12249-012-9899-8
  • Amiraslani, B., Sabouni, F., Abbasi, S., Nazem, H., & Sabet, M. (2012). Recognition of betaine as an inhibitor of lipopolysaccharide-induced nitric oxide production in activated microglial cells. Iranian Biomedical Journal, 16(2), 84–89. https://doi.org/10.6091/ibj.1012.2012
  • Andreoli, F., & Del Rio, A. (2015). Computer-aided molecular design of compounds targeting histone modifying enzymes. Computational and Structural Biotechnology Journal, 13, 358–365. https://doi.org/10.1016/j.csbj.2015.04.007
  • Azad, P., Zhao, H. W., Cabrales, P. J., Ronen, R., Zhou, D., Poulsen, O., Appenzeller, O., Hsiao, Y. H., Bafna, V., & Haddad, G. G. (2016). Senp1 drives hypoxia-induced polycythemia via GATA1 and Bcl-xL in subjects with Monge's disease. The Journal of Experimental Medicine, 213(12), 2729–2744. https://doi.org/10.1084/jem.20151920
  • Bawa-Khalfe, T., Cheng, J., Lin, S.-H., Ittmann, M. M., & Yeh, E. T. H. (2010). SENP1 induces prostatic intraepithelial neoplasia through multiple mechanisms. The Journal of Biological Chemistry, 285(33), 25859–25866. https://doi.org/10.1074/jbc.M110.134874
  • Bawa-Khalfe, T., Cheng, J., Wang, Z., & Yeh, E. T. H. (2007). Induction of the SUMO-specific protease 1 transcription by the androgen receptor in prostate cancer cells. The Journal of Biological Chemistry, 282(52), 37341–37349. https://doi.org/10.1074/jbc.M706978200
  • Biovia, D. S. (2017). Discovery studio visualizer, Release 2017. Dassault Systèmes. Retrieved December 12, 2017, from http://accelrys.com/products/collaborative-science/biovia-discovery-studio/visualization-download.php.
  • Brems-Eskildsen, A. S., Zieger, K., Toldbod, H., Holcomb, C., Higuchi, R., Mansilla, F., Munksgaard, P. P., Borre, M., Ørntoft, T. F., & Dyrskjøt, L. (2010). Prediction and diagnosis of bladder cancer recurrence based on urinary content of hTERT, SENP1, PPP1CA, and MCM5 transcripts. BMC Cancer, 10(1), 646. https://doi.org/10.1186/1471-2407-10-646
  • Chen, Y., Wen, D., Huang, Z., Huang, M., Luo, Y., Liu, B., Lu, H., Wu, Y., Peng, Y., & Zhang, J. (2012). 2-(4-Chlorophenyl)-2-oxoethyl 4-benzamidobenzoate derivatives, a novel class of SENP1 inhibitors: Virtual screening, synthesis and biological evaluation. Bioorganic & Medicinal Chemistry Letters, 22(22), 6867–6870. https://doi.org/10.1016/j.bmcl.2012.09.037
  • Cheng, F. (2012). admetSAR: a comprehensive source and free tool for assessment of chemical ADMET properties. ACS Publications.
  • Cheng, J., Bawa, T., Lee, P., Gong, L., & Yeh, E. T. H. (2006). Role of desumoylation in the development of prostate cancer. Neoplasia (New York, N.Y.), 8(8), 667–676. https://doi.org/10.1593/neo.06445
  • Ciemny, M., Kurcinski, M., Kamel, K., Kolinski, A., Alam, N., Schueler-Furman, O., & Kmiecik, S. (2018). Protein-peptide docking: opportunities and challenges. Drug Discovery Today, 23(8), 1530–1537. https://doi.org/10.1016/j.drudis.2018.05.006
  • Conigliaro, A., Tripodi, M., & Parola, M. (2017). SENP1 activity sustains cancer stem cell in hypoxic HCC. Gut, 66(12), 2051–2052. https://doi.org/10.1136/gutjnl-2017-313946
  • Consortium, U. (2014). UniProt: A hub for protein information. Nucleic Acids Research, 43(D1), D204–D212.
  • Cui, C.-P., Wong, C. C.-L., Kai, A. K.-L., Ho, D. W.-H., Lau, E. Y.-T., Tsui, Y.-M., Chan, L.-K., Cheung, T.-T., Chok, K. S.-H., Chan, A. C. Y., Lo, R. C.-L., Lee, J. M.-F., Lee, T. K.-W., & Ng, I. O. L. (2017). SENP1 promotes hypoxia-induced cancer stemness by HIF-1α deSUMOylation and SENP1/HIF-1α positive feedback loop. Gut, 66(12), 2149–2159. https://doi.org/10.1136/gutjnl-2016-313264
  • Duffy, R., Wade, C., & Chang, R. (2012). Discovery of anticancer drugs from antimalarial natural products: A MEDLINE literature review. Drug Discovery Today, 17(17–18), 942–953. https://doi.org/10.1016/j.drudis.2012.03.013
  • Esmaeilzadeh, E., Gardaneh, M., Gharib, E., & Sabouni, F. (2013). Shikonin protects dopaminergic cell line PC12 against 6-hydroxydopamine-mediated neurotoxicity via both glutathione-dependent and independent pathways and by inhibiting apoptosis. Neurochemical Research, 38(8), 1590–1604. https://doi.org/10.1007/s11064-013-1061-9
  • Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. The Journal of Chemical Physics, 103(19), 8577–8593. https://doi.org/10.1063/1.470117
  • Feligioni, M., & Nisticò, R. (2013). SUMO: A (oxidative) stressed protein. Neuromolecular Medicine, 15(4), 707–719. https://doi.org/10.1007/s12017-013-8266-6
  • Guo, J., Yuan, Y., Lu, D., Du, B., Xiong, L., Shi, J., Yang, L., Liu, W., Yuan, X., Zhang, G., & Wang, F. (2014). Two natural products, trans-phytol and (22E)-ergosta-6, 9, 22-triene-3β, 5α, 8α-triol, inhibit the biosynthesis of estrogen in human ovarian granulosa cells by aromatase (CYP19). Toxicology and Applied Pharmacology, 279(1), 23–32.
  • Harvey, A. L. (2008). Natural products in drug discovery. Drug Discovery Today, 13(19-20), 894–901. https://doi.org/10.1016/j.drudis.2008.07.004
  • Irwin, J. J., Sterling, T., Mysinger, M. M., Bolstad, E. S., & Coleman, R. G. (2012). ZINC: A free tool to discover chemistry for biology. Journal of Chemical Information and Modeling, 52(7), 1757–1768. https://doi.org/10.1021/ci3001277
  • Jacques, C., Baris, O., Prunier-Mirebeau, D., Savagner, F., Rodien, P., Rohmer, V., Franc, B., Guyetant, S., Malthiery, Y., & Reynier, P. (2005). Two-step differential expression analysis reveals a new set of genes involved in thyroid oncocytic tumors. The Journal of Clinical Endocrinology and Metabolism, 90(4), 2314–2320. https://doi.org/10.1210/jc.2004-1337
  • Kim, J. H., & Baek, S. H. (2009). Emerging roles of desumoylating enzymes. Biochimica et Biophysica Acta, 1792(3), 155–162. https://doi.org/10.1016/j.bbadis.2008.12.008
  • 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
  • Kumar, A., Ito, A., Takemoto, M., Yoshida, M., & Zhang, K. Y. J. (2014). Identification of 1,2,5-oxadiazoles as a new class of SENP2 inhibitors using structure based virtual screening. Journal of Chemical Information and Modeling, 54(3), 870–880. https://doi.org/10.1021/ci4007134
  • Laskowski, R. A., & Swindells, M. B. (2011). LigPlot+: multiple ligand–protein interaction diagrams for drug discovery. ACS Publications.
  • Lee, J. S., Choi, H. J., & Baek, S. H. (2017). Sumoylation and Its contribution to cancer. In SUMO regulation of cellular processes (pp. 283–298.). Springer.
  • Li, A. P. (2005). Preclinical in vitro screening assays for drug-like properties. Drug Discovery Today. Technologies, 2(2), 179–185. https://doi.org/10.1016/j.ddtec.2005.05.024
  • Lipinski, C. A. (2000). Drug-like properties and the causes of poor solubility and poor permeability. Journal of Pharmacological and Toxicological Methods, 44(1), 235–249. https://doi.org/10.1016/S1056-8719(00)00107-6
  • Ma, C., Wu, B., Huang, X., Yuan, Z., Nong, K., Dong, B., Bai, Y., Zhu, H., Wang, W., & Ai, K. (2014). SUMO-specific protease 1 regulates pancreatic cancer cell proliferation and invasion by targeting MMP-9. Tumour Biology: The Journal of the International Society for Oncodevelopmental Biology and Medicine, 35(12), 12729–12735. https://doi.org/10.1007/s13277-014-2598-1
  • Massova, I., & Kollman, P. A. (2000). Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding. Perspectives in Drug Discovery and Design, 18(1), 113–135. https://doi.org/10.1023/A:1008763014207
  • 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
  • Mukhopadhyay, D., & Dasso, M. (2007). Modification in reverse: The SUMO proteases. Trends in Biochemical Sciences, 32(6), 286–295. https://doi.org/10.1016/j.tibs.2007.05.002
  • Nayak, A., & Müller, S. (2014). SUMO-specific proteases/isopeptidases: SENPs and beyond. Genome Biology, 15(7), 422. https://doi.org/10.1186/s13059-014-0422-2
  • Nithya, G., & Sakthisekaran, D. (2015). In silico docking studies on the anti-cancer effect of thymoquinone on interaction with phosphatase and tensin homolog located on chromosome 10q23: A regulator of PI3K/AKT pathway. Asian Journal of Pharmaceutical and Clinical Research, 8, 192–195.
  • Qiao, Z., Wang, W., Wang, L., Wen, D., Zhao, Y., Wang, Q., Meng, Q., Chen, G., Wu, Y., & Zhou, H. (2011). Design, synthesis, and biological evaluation of benzodiazepine-based SUMO-specific protease 1 inhibitors. Bioorganic & Medicinal Chemistry Letters, 21(21), 6389–6392. https://doi.org/10.1016/j.bmcl.2011.08.101
  • Rashid, M., Sanjarin, F., & Sabouni, F. (2019). Thymoquinone effects on cell viability, apoptosis and VEGF-A gene expression level in AGS (CRL-1739) cell line. Anti-Cancer Agents in Medicinal Chemistry (Formerly Current Medicinal Chemistry-Anti-Cancer Agents), 19(6), 820–826.
  • Rather, M. A., Dutta, S., Guttula, P. K., Dhandare, B. C., Yusufzai, S. I., & Zafar, M. I. (2020). Structural analysis, molecular docking and molecular dynamics simulations of G-protein-coupled receptor (kisspeptin) in fish. Journal of Biomolecular Structure & Dynamics, 38(8), 2422–2439. https://doi.org/10.1080/07391102.2019.1633407
  • Rose, P. W. (2016). The RCSB protein data bank: Integrative view of protein, gene and 3D structural information. Nucleic Acids Research, 45(D1), D271–D281.
  • Saffari-Chaleshtori, J. (2019). The study of drug resistance properties of ABCG2 (ATP-binding cassette G2) in contact with thymoquinone, gallic acid, and hesperetin antioxidants. Journal of Herbmed Pharmacology, 8(2), 108–113.
  • Saffari-Chaleshtori, J., Heidari-Sureshjani, E., Moradi, F., Jazi, H. M., & Heidarian, E. (2017). The study of apoptosis-inducing effects of three pre-apoptotic factors by gallic acid, using simulation analysis and the comet assay technique on the prostatic cancer cell line PC3. The Malaysian Journal of Medical Sciences: MJMS, 24(4), 18–29. https://doi.org/10.21315/mjms2017.24.4.3
  • Safi, M., & Lilien, R. H. (2012). Efficient a priori identification of drug resistant mutations using Dead-End Elimination and MM-PBSA. Journal of Chemical Information and Modeling, 52(6), 1529–1541. https://doi.org/10.1021/ci200626m
  • Sanha, A. M. F., Kumar, S., & Sharma, P. K. (2019). Phenolic compounds from plants–An important class of phytomedicine in wrestle against cancer-A review. Global Journal of Medical Research.
  • Schüttelkopf, A. W., & Van Aalten, D. M. (2004). PRODRG: A tool for high-throughput crystallography of protein–ligand complexes. Acta Crystallographica Section D Biological Crystallography, 60(8), 1355–1363. https://doi.org/10.1107/S0907444904011679
  • Sheppard, G. S., & Bouska, J. J. (2005). Why optimize cancer drugs for ADMET? Drug Discovery Today: Therapeutic Strategies, 2(4), 343–349.
  • Singh, S. (2018). Natural products as anticancerous therapeutic molecules with special reference to enzymatic targets topoisomerase, COX, LOX and aromatase. Current Protein and Peptide Science, 19(3), 238–274.
  • Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. C. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718. https://doi.org/10.1002/jcc.20291
  • Verma, S., Singh, A., & Mishra, A. (2013). Gallic acid: Molecular rival of cancer. Environmental Toxicology and Pharmacology, 35(3), 473–485. https://doi.org/10.1016/j.etap.2013.02.011
  • Vineis, P., & Wild, C. P. (2014). Global cancer patterns: Causes and prevention. The Lancet, 383(9916), 549–557. https://doi.org/10.1016/S0140-6736(13)62224-2
  • Vora, J., Patel, S., Athar, M., Sinha, S., Chhabria, M. T., Jha, P. C., & Shrivastava, N. (2019). Pharmacophore modeling, molecular docking and molecular dynamics simulation for screening and identifying anti-dengue phytocompounds. Journal of Biomolecular Structure and Dynamics, 38(6), 1726–1740. https://doi.org/10.1080/07391102.2019.1615002
  • Wang, F., Yang, W., Shi, Y., & Le, G. (2015). 3D-QSAR, molecular docking and molecular dynamics studies of a series of RORγt inhibitors. Journal of Biomolecular Structure & Dynamics, 33(9), 1929–1940. https://doi.org/10.1080/07391102.2014.980321
  • Wang, Q., Xia, N., Li, T., Xu, Y., Zou, Y., Zuo, Y., Fan, Q., Bawa-Khalfe, T., Yeh, E. T. H., & Cheng, J. (2013). SUMO-specific protease 1 promotes prostate cancer progression and metastasis. Oncogene, 32(19), 2493–2498. https://doi.org/10.1038/onc.2012.250
  • Wang, R.-T., Zhi, X.-Y., Zhang, Y., & Zhang, J. (2013). Inhibition of SENP1 induces radiosensitization in lung cancer cells. Experimental and Therapeutic Medicine, 6(4), 1054–1058. https://doi.org/10.3892/etm.2013.1259
  • Wang, Z., Jin, J., Zhang, J., Wang, L., & Cao, J. (2016). Depletion of SENP1 suppresses the proliferation and invasion of triple-negative breast cancer cells. Oncology Reports, 36(4), 2071–2078. https://doi.org/10.3892/or.2016.5036
  • Wu, J., Lei, H., Zhang, J., Chen, X., Tang, C., Wang, W., Xu, H., Xiao, W., Gu, W., & Wu, Y. (2016). Momordin Ic, a new natural SENP1 inhibitor, inhibits prostate cancer cell proliferation. Oncotarget, 7(37), 58995–59005. https://doi.org/10.18632/oncotarget.10636
  • Xiang‐Ming, Y. (2016). SENP1 regulates cell migration and invasion in neuroblastoma. Biotechnology and Applied Biochemistry, 63(3), 435–440.
  • Xu, J., Sun, H.-Y., Xiao, F.-J., Wang, H., Yang, Y., Wang, L., Gao, C.-J., Guo, Z.-K., Wu, C.-T., & Wang, L.-S. (2015). SENP1 inhibition induces apoptosis and growth arrest of multiple myeloma cells through modulation of NF-κB signaling. Biochemical and Biophysical Research Communications, 460(2), 409–415. https://doi.org/10.1016/j.bbrc.2015.03.047
  • Xu, Y., Li, J., Zuo, Y., Deng, J., Wang, L.-S., & Chen, G.-Q. (2011). SUMO-specific protease 1 regulates the in vitro and in vivo growth of colon cancer cells with the upregulated expression of CDK inhibitors. Cancer Letters, 309(1), 78–84. https://doi.org/10.1016/j.canlet.2011.05.019
  • Zhang, Q.-S., Zhang, M., Huang, X.-J., Liu, X.-J., & Li, W.-P. (2016). Downregulation of SENP1 inhibits cell proliferation, migration and promotes apoptosis in human glioma cells. Oncology Letters, 12(1), 217–221. https://doi.org/10.3892/ol.2016.4558
  • Zhang, W., Sun, H., Shi, X., Wang, H., Cui, C., Xiao, F., Wu, CTse., Guo, X., & Wang, L. (2016). SENP1 regulates hepatocyte growth factor-induced migration and epithelial-mesenchymal transition of hepatocellular carcinoma. Tumour Biology: The Journal of the International Society for Oncodevelopmental Biology and Medicine, 37(6), 7741–7748. https://doi.org/10.1007/s13277-015-4406-y
  • Zhao, Y., Wang, Z., Zhang, J., & Zhou, H. (2016). Identification of SENP1 inhibitors through in silico screening and rational drug design. European Journal of Medicinal Chemistry, 122, 178–184. https://doi.org/10.1016/j.ejmech.2016.06.018

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