DOI QR코드

DOI QR Code

Molecular Docking Analysis of Protein Phosphatase 1D (PPM1D) Receptor with SL-175, SL-176 and CDC5L

  • 투고 : 2018.01.22
  • 심사 : 2018.03.25
  • 발행 : 2018.03.30

초록

Protein phosphatase manganese dependent 1D (PPM1D), a Ser/Thr protein phosphatise, play major role in the cancer tumorigenesis of various tumors including neuroblastoma, pancreatic adenocarcinoma, medulloblastoma, breast cancer, prostate cancer and ovarian cancer. Hence, analysis on the structural features required for the formation of PPM1D-inhibitor complex becomes essential. In this study, we have performed molecular docking of SL-175 and -176 and protein-protein docking of CDC5L with PPM1D. On analysing the docked complexes, we have identified the important residues involved in the formation of protein-ligand complex. Research concentrating on these residues could be helpful in understanding the pathophysiology of various tumors related to PPM1D.

키워드

참고문헌

  1. X. Lu, T. A. Nguyen, S. H. Moon, Y. Darlington, M. Sommer, and L. A. Donehower, "The type 2C phosphatase Wip1: an oncogenic regulator of tumor suppressor and DNA damage response pathways", Cancer Metastasis Rev., Vol. 27, pp. 123-135, 2008. https://doi.org/10.1007/s10555-008-9127-x
  2. H. Yang, X.-Y. Gao, P. Li, and T.-S. Jiang, "PPM1D overexpression predicts poor prognosis in non-small cell lung cancer", Tumour Biology, Vol. 36, pp. 2176-2184, 2015.
  3. F. Saito-Ohara, I. Imoto, J. Inoue, H. Hosoi, A. Nakagawara, T. Sugimoto, and J. Inazawa, "PPM1D is a potential target for 17q gain in neuroblastoma", Cancer Res., Vol. 63, pp. 1876-1883, 2003.
  4. P. Loukopoulos, T. Shibata, H. Katoh, A. Kokubu, M. Sakamoto, K. Yamazaki, T. Kosuge, Y. Kanai, F. Hosoda, I. Imoto, M. Ohki, J. Inazawa, and S. Hirohashi, "Genome-wide array-based comparative genomic hybridization analysis of pancreatic adenocarcinoma: identification of genetic indicators that predict patient outcome", Cancer Sci., Vol. 98, pp. 392-400, 2007. https://doi.org/10.1111/j.1349-7006.2007.00395.x
  5. R. C. Castellino, M. De Bortoli, X. Lu, S. H. Moon, T. A. Nguyen, M. A. Shepard, P. H. Rao, L. A. Donehower, and J. Y. Kim, "Medulloblastomas overexpress the p53-inactivating oncogene WIP1/PPM1D", J Neurooncol., Vol. 86, pp. 245-256, 2008. https://doi.org/10.1007/s11060-007-9470-8
  6. M. B. Lambros, R. Natrajan, F. C. Geyer, M. A. Lopez-Garcia, K. J. Dedes, K. Savage, M. Lacroix-Triki, R. L. Jones, C. J. Lord, S. Linardopoulos, A. Ashworth, and J. S. Reis-Filho, "PPM1D gene amplification and overexpression in breast cancer: a qRT-PCR and chromogenic in situ hybridization study", Mod. Pathol., Vol. 23, pp. 1334-1345, 2010. https://doi.org/10.1038/modpathol.2010.121
  7. J. Parssinen, E. L. Alarmo, S. Khan, R. Karhu, M. Vihinen, and A. Kallioniemi, "Identification of differentially expressed genes after PPM1D silencing in breast cancer", Cancer Lett., Vol. 259, pp. 61-70, 2008. https://doi.org/10.1016/j.canlet.2007.09.019
  8. S. Shreeram, O. N. Demidov, W. K. Hee, H. Yamaguchi, N. Onishi, C. Kek, O. N. Timofeev, C. Dudgeon, A. J. Fornace, C. W. Anderson, Y. Minami, E. Appella, and D. V. Bulavin, "Wip1 Phosphatase Modulates ATM-Dependent Signaling Pathways", Mol. Cell, Vol. 23, pp. 757-764, 2006. https://doi.org/10.1016/j.molcel.2006.07.010
  9. L. Jiao, D. Shen, G. Liu, J. Jia, J. Geng, H. Wang, and Y. Sun, "PPM1D as a novel biomarker for prostate cancer after radical prostatectomy", Anticancer Res., Vol. 34, pp. 2919-2925, 2014.
  10. S. Nagarajan and T. Madhavan, "Protein phosphatase 1d (ppm1d) structure prediction using homology modeling", J. Chosun Natural Sci., Vol. 9, pp. 35-40, 2016. https://doi.org/10.13160/ricns.2016.9.1.35
  11. S. Ogasawara, Y. Kiyota, Y. Chuman, A. Kowata, F. Yoshimura, K. Tanino, and R. Kamada, K. Sakaguchi, "Novel inhibitors targeting PPM1D phosphatase potently suppress cancer cell proliferation", Bioorg. Med. Chem., Vol. 23, pp. 6246-6249, 2015. https://doi.org/10.1016/j.bmc.2015.08.042
  12. SYBYL Software, Tripos Associates Inc, St. Louis, USA, 2002.
  13. A. N. Jain, "Scoring functions for protein-ligand docking", Curr. Protein Pept. Sci., Vol. 7, pp. 407-420, 2006. https://doi.org/10.2174/138920306778559395
  14. A. N. Jain, "Scoring non-covalent protein-ligand interactions: a continuous differentiable function tuned to compute binding", J. Comput. Aided Mol. Des., Vol. 10, pp. 427-440, 1996. https://doi.org/10.1007/BF00124474
  15. S. R. Comeau, D. W. Gatchell, S. Vajda, and C. J. Camacho, "ClusPro: an automated docking and discrimination method for the prediction of protein complexes", Bioinformatics, Vol. 20, pp. 45-50, 2004. https://doi.org/10.1093/bioinformatics/btg371
  16. S. R. Comeau, D. W. Gatchell, S. Vajda, and C. J. Camacho, "ClusPro: a fully automated algorithm for protein-protein docking", Nucleic Acids Res., Vol. 32, pp. 96-99, 2004.
  17. D. Kozakov, D. Beglov, T. Bohnuud, S. Mottarella, B. Xia, D. Hall, and S. Vajda, "How good is automated protein docking?", Proteins, Vol. 81, pp. 2159-2166, 2013. https://doi.org/10.1002/prot.24403
  18. M. F. Lensink and S. J. Wodak, "Docking, scoring, and affinity prediction in CAPRI", Proteins, Vol. 81, pp. 2082-2095, 2013. https://doi.org/10.1002/prot.24428
  19. D. Kozakov, R. Brenke, S. R. Comeau, and S. Vajda S "PIPER: An FFT-based protein docking program with pairwise potentials", Proteins, Vol. 65, pp. 392-406, 2006. https://doi.org/10.1002/prot.21117

피인용 문헌

  1. 3D Structure Prediction of Human 5-Hydroxytryptamine Receptor 7 (5-HT7R) vol.11, pp.2, 2018, https://doi.org/10.13160/ricns.2018.11.2.87