Chemical Papers

, Volume 69, Issue 9, pp 1253–1261 | Cite as

Computational insights into allosteric interaction between benzoazepin-2-ones and lung cancer-associated PDK1: Implications for activator design

  • Gang Guo
  • Cui Yang
  • Gao-Feng LiEmail author
  • Heng Li
  • Qian-Li Ma
  • Qi Guo
  • Xiu-Mei Yang
Original Paper


3-Phosphoinositide-dependent kinase-1 (PDK1) plays a key role in the regulation of physiological processes and its catalytic activity is tightly regulated by allosteric modulators which bind to the PDK1 Interacting Fragment (PIF) pocket. However, details on the allosteric modulators regulation of the PDK1 catalytic activity remain elusive. Here, molecular docking and molecular dynamics (MD) simulations were performed to investigate the allosteric regulation of PDK1 induced by one of the benzoazepin-2-ones, the most potent compound 17 (BAZ2O). Molecular docking and MD simulation revealed that BAZ2O was located in the PIF pocket formed by residues from β4 and β5 sheets and helices αB and αC. BAZ2O formed a hydrogen bond with Arg131 and participated in hydrophobic interactions with Ile119, Thr148, Gln150, Leu155 and Phe157. Further comparative analyses of PDK1 in its apo and BAZ2O-bound states unveiled that BAZ2O promoted the structural coupling between the important catalytic domains of PDK1, including the activation loop and the helices αB and αC, thereby stabilizing the PDK1 conformation for catalysis. Understanding the allosteric interaction of PDK1 with small molecules provides a potentially valuable possibility of designing more potent allosteric modulators with therapeutic implications for lung cancer.


PDK1 molecular docking MD simulations allosteric regulation PIF pocket 


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  1. Amadei, A., Linssen, A. B. M., & Berendsen, H. J. C. (1993). Essential dynamics of proteins. Proteins. Proteins: Structure, Function, and Bioinformatic, 17, 412–425. DOI:  10.1002/prot.340170408.CrossRefGoogle Scholar
  2. Arencibia, J. M., Pastor-Flores, D., Bauer, A. F., Schulze, J. O., & Biondi, R. M. (2013). AGC protein kinases: From structural mechanism of regulation to allosteric drug development for the treatment of human diseases. Biochimca et Biophysica Acta (BBA) — Proteins and Proteomics, 1834, 1302–1321. DOI:  10.1016/j.bbapap.2013.03.010.CrossRefGoogle Scholar
  3. Balendran, A., Biondi, R. M., Cheung, P. C. F., Casamayor, A., Deak, M., & Alessi, D. R. (2000). A 3-phosphoinositide-dependent protein kinase-1 (PDK1) docking site is required for the phosphorylation of protein kinase Cζ (PKCζ)and PKC-related kinase 2 by PDK1. Journal of Biological Chemistry, 275, 20806–20813. DOI:  10.1074/jbc.m000421200.CrossRefGoogle Scholar
  4. Bellon, S., Fitzgibbon, M. J., Fox, T., Hsiao, H. M., & Wilson, K. P. (1999). The structure of phosphorylated p38γ is monomeric and reveals a conserved activation-loop conformation. Structure, 7, 1057–1065. DOI:  10.1016/s0969-2126(99)80173-7.CrossRefGoogle Scholar
  5. Biondi, R. M., Cheung, P. C. F., Casamayor, A., Deak, M., Currie, R. A., & Alessi, D. R. (2000). Identification of a pocket in the PDK1 kinase domain that interacts with PIF and the C-terminal residues of PKA. The EMBO Journal, 19, 979–988. DOI:  10.1093/emboj/19.5.979.CrossRefGoogle Scholar
  6. Biondi, R. M., Kieloch, A., Currie, R. A., Deak, M., & Alessi, D. R. (2001). The PIF-binding pocket in PDK1 is essential for activation of S6K and SGK, but not PKB. The EMBO Journal, 20, 4380–4390. DOI:  10.1093/emboj/20.16.4380.CrossRefGoogle Scholar
  7. Brown, N. R., Noble, M. E. M., Endicott, J. A., & Johnson, L. N. (1999). The structural basis for specificity of substrate and recruitment peptides for cyclin-dependent kinases. Nature Cell Biology, 1, 438–443. DOI:  10.1038/15674.CrossRefGoogle Scholar
  8. Casamayor, A., Morrice, N. A., & Alessi, D. R. (1999). Phosphorylation of Ser-241 is essential for the activity of 3-phosphoinositide-dependent protein kinase-1: Identification of five sites of phosphorylation in vivo. Biochemical Journal, 342, 287–292.CrossRefGoogle Scholar
  9. Case, D. A., Cheatham, T. E., III, Darden, T., Gohlke, H., Luo, R., Merz, K. M., Jr., Onufriev, A., Simmerling, C., Wang, B., & Woods, R. J. (2005). The Amber biomolecular simulation programs. Journal of Computational Chemistry, 26, 1668–1688. DOI:  10.1002/jcc.20290.CrossRefGoogle Scholar
  10. Cheng, Y. H., Zhang, Y. K., & McCammon, J. A. (2005). How does the cAMP-dependent protein kinase catalyze the phosphorylation reaction: An ab initio QM/MM study. Journal of the American Chemical Society, 127, 1553–1562. DOI:  10.1021/ja0464084.CrossRefGoogle Scholar
  11. Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N log(N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98, 10089–10092. DOI:  10.1063/1.464397.CrossRefGoogle Scholar
  12. Downward, J. (2008). Targeting RAS and PI3K in lung cancer. Nature Medicine, 14, 1315–1316. DOI:  10.1038/nm1208-1315.CrossRefGoogle Scholar
  13. Duan, Y., Wu, C., Chowdhury, S. S., Lee, M. C., Xiong, G. M., Zhang, W., Yang, R., Cieplak, P., Luo, R., Lee, T. S., Caldwell, J., Wang, J. M., & Kollman, P. (2003). A point-charge force field for molecular mechanics simulations of proteins. Journal of Computational Chemistry, 24, 1999–2012. DOI:  10.1002/jcc.10349.CrossRefGoogle Scholar
  14. Frödin, M., Jensen, C. J., Merienne, K., & Gammeltoft, S. (2000). A phosphoserine-regulated docking site in the protein kinase RSK2 that recruits and activates PDK1. The EMBO Journal, 19, 2924–2934. DOI:  10.1093/emboj/19.12.2924.CrossRefGoogle Scholar
  15. Garcia, A. V., Al-Yousif, M., & Hirt, H. (2012). Role of AGC kinases in plant growth and stress responses. Cellular and Molecular Life Sciences, 69, 3259–3267. DOI:  10.1007/s00018-012-1093-3.CrossRefGoogle Scholar
  16. Goodey, N. M., & Benkovic, S. J. (2008). Allosteric regulation and catalysis emerge via a common route. Nature Chemical Biology, 4, 474–482. DOI:  10.1038/nchembio.98.CrossRefGoogle Scholar
  17. Hindie, V., Stroba, A., Zhang, H., Lopez-Garcia, L. A., Idrissova, L., Zeuzem, S., Hirschberg, D., Schaeffer, F., Jørgensen, T. J. D., Engel, M., Alzari, P. M., & Biondi, R. M. (2009). Structure and allosteric effects of low-molecular-weight activators on the protein kinase PDK1. Nature Chemical Biology, 5, 758–764. DOI:  10.1038/nchembio.208.CrossRefGoogle Scholar
  18. Huang, W. K., Lu, S. Y., Huang, Z. M., Liu, X. Y., Mou, L. K., Luo, Y., Zhao, Y. L., Liu, Y. Q., Chen, Z. J., Hou, T. J., & Zhang, J. (2013). Allosite: A method for predicting allosteric sites. Bioinformatics, 29, 2357–2359. DOI:  10.1093/bioinformatics/btt399.CrossRefGoogle Scholar
  19. Huang, Z. M., Mou, L. K., Shen, Q. C., Lu, S. Y., Li, C. G., Liu, X. Y., Wang, G. Q., Li, S., Geng, L., Liu, Y. Q., Wu, J. W., Chen, G. Q., & Zhang, J. (2014). ASD v2.0: Updated content and novel features focusing on allosteric regulation. Nucleic Acids Research, 41, D510–D516. DOI:  10.1093/nar/gkt1247.CrossRefGoogle Scholar
  20. Jiang, Y., Li, L. L., Zhang, H. Y., Feng, W., & Tan, T. W. (2014). Lid closure mechanism of Yarrowia lipolytica lipase in methanol investigated by molecular dynamics simulation. Journal of Chemical Information and Modeling, 54, 2033–2041. DOI:  10.1021/ci500163y.CrossRefGoogle Scholar
  21. Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential function for simulating liquid water. The Journal of Chemical Physics, 79, 926–935. DOI:  10.1063/1.445869.CrossRefGoogle Scholar
  22. Komander, D., Kular, G., Deak, M., Alessi, D. R., & van Aalten, D. M. F. (2005). Role of T-loop phosphorylation in PDK1 activation, stability and substrate binding. Journal of Biological Chemistry, 280, 18797–18802. DOI:  10.1074/jbc.m500977200.CrossRefGoogle Scholar
  23. Li, X. B., Chen, Y. Y., Lu, S. Y., Huang, Z. M., Liu, X. Y., Wang, Q., Shi, T., & Zhang, J. (2013). Toward an understanding of the sequence and structural basis of allosteric proteins. Journal of Molecular and Graphics Modelling, 40, 30–39. DOI:  10.1016/j.jmgm.2012.12.011.CrossRefGoogle Scholar
  24. Lin, K., Lin, J., Wu, W. I., Ballard, J., Lee, B. B., Gloor, S. L., Vigers, G. P. A., Morales, T. H., Friedman, L. S., Skelton, N., & Brandhuber, B. J. (2012). An ATP-site on-off switch that restricts phosphatase accessibility of Akt. Science Signaling, 5, ra37. DOI:  10.1126/scisignal.2002618.Google Scholar
  25. Lu, S. Y., Huang, W. K., Li, X. B., Huang, Z. M., Liu, X. Y., Chen, Y. Y., Shi, T., & Zhang, J. (2012). Insights into the role of magnesium traid in myo-inositol monophosphatase: Metal mechanism, substrate binding and lithium therapy. Journal of Chemical Information and Modeling, 52, 2398–2409. DOI:  10.1021/ci300172r.CrossRefGoogle Scholar
  26. Lu, S. Y., Huang, W. K., Wang, Q., Shen, Q. C., Li, S., Nussinov, R., & Zhang, J. (2014a). The structural basis of ATP as an allosteric modulator. PLoS Computational Biology, 10, e1003831. DOI:  10.1371/journal.pcbi.1003831.CrossRefGoogle Scholar
  27. Lu, S. Y., Li, S., & Zhang, J. (2014b). Harnessing allostery: A novel approach to drug discovery. Medicinal Research Reviews, 34, 1242–1285. DOI:  10.1002/med.21317.CrossRefGoogle Scholar
  28. Lu, S. Y., Huang, W. K., & Zhang, J. (2014c). Recent computational advances in the identification of allosteric sites in proteins. Drug Discovery Today, 19, 1595–1600. DOI:  10.1016/j.drudis.2014.07.012.CrossRefGoogle Scholar
  29. Manning, B. D., & Cantley, L. C. (2007). AKT/PKB signaling: Navigating downstream. Cell, 129, 1261–1274. DOI:  10.1016/j.cell.2007.06.009.CrossRefGoogle Scholar
  30. Melo, E., de Silva, S. M., & Paula, F. R. (2014). Molecular modeling and quantitatively structure-activity relationship studies of anatoxin-a and epibatidine derivatives with affinity to rodent nAChR receptors. Chemical Papers, 68, 1121–1131. DOI:  10.2478/s11696-014-0545-7.CrossRefGoogle Scholar
  31. 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, 2785–2791. DOI:  10.1002/jcc.21256.CrossRefGoogle Scholar
  32. Papadimitrakopoulou, V. (2012). Development of PI3K/AKT/mTOR pathway inhibitors and their application in personalized therapy for non-small-cell lung cancer. Journal of Thoracic Oncology, 7, 1315–1326. DOI:  10.1097/jto.0b013e31825493eb.CrossRefGoogle Scholar
  33. Pearce, L. R., Komander, D., & Alessi, D. R. (2010). The nuts and blots of AGC protein kinases. Nature Reviews Molecular Cell Biology, 11, 9–22. DOI:  10.1038/nrm2822.CrossRefGoogle Scholar
  34. Ryckaert, J. P., Ciccotti, G., & Berendsen, H. J. C. (1977). Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. Journal of Computational Physics, 23, 327–341. DOI:  10.1016/0021-9991(77)90098-5.CrossRefGoogle Scholar
  35. Sahihi, M., & Ghayeb, Y. (2014). Binding of biguanides to β-lactoglobulin: Molecular-docking and molecular dynamics simulation studies. Chemical Papers, 68, 1601–1607. DOI:  10.2478/s11696-014-0598-7.CrossRefGoogle Scholar
  36. Senćanski, M., Ivanović, M., & Došen-Mićović, L. (2014). Modelinling of ORL1 receptor-ligand interactions. Chemical Papers, 68, 1305–1316. DOI:  10.2478/s11696-014-0577-z.Google Scholar
  37. Tsai, C. J., & Nussinov, R. (2014). A unified view of “How allostery works”. PLoS Computational Biology, 10, e1003394. DOI:  10.1371/journal.pcbi.1003394.CrossRefGoogle Scholar
  38. van Westem, G. J. P., Gaulton, A., & Overington, J. P. (2014). Chemical, target and bioactive properties of allosteric modulation. PLoS Computational Biology, 10, e1003559. DOI:  10.1371/journal.pcbi.1003559.CrossRefGoogle Scholar
  39. Wang, J. M., 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, 1157–1174. DOI:  10.1002/jcc.20035.CrossRefGoogle Scholar
  40. Wei, L. Y., Gao, X. Q., Warne, R., Hao, X. S., Bussiere, D., Gu, X. J., Uno, T. S., & Liu, Y. (2010). Design and synthesis of benzoazepin-2-one analogs as allosteric binders targeting the PIF pocket of PDK1. Bioorganic & Medicinal Chemistry Letters, 20, 3897–3902. DOI:  10.1016/j.bmcl.2010.05.019.CrossRefGoogle Scholar
  41. Wu, X. W., & Brooks, B. R. (2003). Self-guided Langevin dynamics simulation method. Chemical Physics Letters, 381, 512–518. DOI:  10.1016/j.cplett.2003.10.013.CrossRefGoogle Scholar
  42. Zheng, J., Trafny, E. A., Knighton, D. R., Xuong, N. H., Taylor, S. S., Ten Eyck, L. F., & Sowadski, J. M. (1993). 2.2 Å refined crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with MnATP and a peptide inhibitor. Acta Crystallographica Section D, 49, 362–365. DOI:  10.1107/s0907444993000423.CrossRefGoogle Scholar

Copyright information

© Institute of Chemistry, Slovak Academy of Sciences 2015

Authors and Affiliations

  • Gang Guo
    • 1
  • Cui Yang
    • 2
  • Gao-Feng Li
    • 1
    Email author
  • Heng Li
    • 1
  • Qian-Li Ma
    • 1
  • Qi Guo
    • 1
  • Xiu-Mei Yang
    • 1
  1. 1.Department of Thoracic SurgeryThird Affiliated Hospital of Kunming Medical UniversityKunmingChina
  2. 2.Ethnic Drug Screening & Pharmacology Center, Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission & Ministry of EducationYunnan University of NationalitiesKunmingChina

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