Discovery of SBF1 as an allosteric inhibitor targeting the PIF-pocket of 3-phosphoinositide-dependent protein kinase-1

  • Wei Liu
  • Pengfei Li
  • Ye MeiEmail author
Original Paper


3-phosphoinositide-dependent protein kinase-1 (PDK1) plays a crucial role in the signal transduction of massive growth-related protein kinases. In this work, a computational study has been performed to investigate the binding pose of the hydrolyzed product of SBF1 (SBF1) with PDK1. The binding pose was predicted by Vina and was further refined in a molecular dynamics simulation. For comparison, four published low molecular weight compounds (PS48, PS171, PS182, and PS210) binding with PDK1 were also studied. SBF1 was anchored in the PIF-pocket of PDK1 with salt bridge interaction using its carboxylate moiety, which is a common feature among the known ligands. Hydrogen bonds to THR148 and vdW interactions with GLN150 also have contributions to the association affinity. The allosteric regulation on PDK1 via the binding of SBF1 was further addressed. The binding affinity of SBF1 in complex with PDK1 is comparable to those of PS171 and PS182, with an estimated IC50 in a range from 2.0 to 10.0 μ molar. Comparison between the free energy profiles with the presence or absence of SBF1 in the binding pocket indicates that the binding of SBF1 enhances the hinge motion and suppresses the fluctuation of the end-to-end distance in α B of PDK1. These results demonstrate that SBF1 is a promising allosteric regulator of PDK1 targeting the PIF-binding pocket and can serve as a new scaffold template for the design of new drugs targeting PDK1.


3-phosphoinositide-dependent protein kinase-1 SBF1 Allosteric Free energy 



Y.M. is supported by the Ministry of Science and Technology of China (Grant No. 2016YFA0501700), the National Natural Science Foundation of China (Grant No. 21773066) and the Fundamental Research Funds for the Central Universities. CPU time was supported by the Supercomputer Center of East China Normal University (ECNU Public Platform for Innovation No. 001).

Supplementary material

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  1. 1.
    Arencibia JM, Pastor-Flores D, Bauer AF, Schulze JO, Biondi RM (2013) Protein kinases: From structural mechanism of regulation to allosteric drug development for the treatment of human diseases. Biochim Biophys Acta 1834:1302–1321CrossRefGoogle Scholar
  2. 2.
    Hers I, Vincent E, Tavares JM (2011) Akt signalling in health and disease. Cell Signal 23:1515–1527CrossRefGoogle Scholar
  3. 3.
    Pearce LR, Komander D, Alessi DR (2010) The nuts and bolts of AGC protein kinases. Nat Rev Mol Cell Biol 11:9–22CrossRefGoogle Scholar
  4. 4.
    Bayascas JR (2010) PDK1: The major transducer of PI3-kinase actions. Curr Top Microbiol Immunol 346:9–29PubMedGoogle Scholar
  5. 5.
    Huse M, Kuriyan J (2002) The conformational plasticity of protein kinases. Cell 109:275–282CrossRefGoogle Scholar
  6. 6.
    Pawson T, Scott JD (2005) Protein phosphorylation in signaling: 50 years and counting. Trends Biochem Sci 30:286–290CrossRefGoogle Scholar
  7. 7.
    Biondi RM, Cheung PCF, Casamayor A, Deak M, Currie RA, Alessi DR (2000) Identification of a pocket in the PDK1 kinase domain that interacts with PIF and the C-terminal residues of PKA. EMBO J 19:979–988CrossRefGoogle Scholar
  8. 8.
    Hauge C, Antal TL, Hirschberg D, Doehn U, Thorup K, Idrissova L, Hansen K, Jensen ON, Jorgensen TJ, Biondi RM, Frodin M (2007) Mechanism for activation of the growth factor-activated AGC kinases by turn motif phosphorylation. EMBO J 26:2251–2261CrossRefGoogle Scholar
  9. 9.
    Pearl LH, Barford D (2002) Regulation of protein kinases in insulin, growth factor and Wnt signalling. Curr Opin Struct Biol 12:761–767CrossRefGoogle Scholar
  10. 10.
    Biondi PM, Kieloch A, Currie RA, Deak M, Alessi DR (2001) The PIF-binding pocket in PDK1 is essential for activation of S6K and SGK, but not PKB. EMBO J 20:4380–4390CrossRefGoogle Scholar
  11. 11.
    Hindie V, Stroba A, Zhang H, Lopezgarcia LA, Idrissova L, Zeuzem S, Hirschberg D, Schaeffer F, Jorgensen TJD, Engel M, Alzari PM, Biondi RM (2009) Allosteric effects of low-molecular-weight activators on the protein kinase PDK1. Nat Chem Structure Biol 5:758–764CrossRefGoogle Scholar
  12. 12.
    Yang J, Cron P, Thompson V, Good VM, Hess D, Hemmings BA, Barford D (2002) Molecular mechanism for the regulation of protein kinase B/Akt by hydrophobic motif phosphorylation. Mol Cell 9:1227–1240CrossRefGoogle Scholar
  13. 13.
    Lopez-Garcia LA, Schulze JO, Frohner W, Zhang H, Suss E, Weber N, Navratil J, Amon S, Hindie V, Zeuzem S, Jorgensen TJ, Alzari PM, Neimanis S, Engel M, Biondi RM (2011) Allosteric regulation of protein kinase PKCζ by the N-terminal C1 domain and small compounds to the PIF-pocket. Chem Biol 18:1463–1473CrossRefGoogle Scholar
  14. 14.
    Busschots K, Lopez-Garcia LA, Lammi C, Stroba A, Zeuzem S, Piiper A, Alzari PM, Neimanis S, Arencibia JM, Engel M, Schulze JO, Biondi RM (2012) Substrate-selective inhibition of protein kinase PDK1 by small compounds that bind to the PIF-pocket allosteric docking site. Chem Biol 19:1152–1163CrossRefGoogle Scholar
  15. 15.
    Nikaido T, Ohmoto T, Kubo S, Mimaki Y, Sashida Y (1992) Steroidal saponins from the rhizomes of Smilax sieboldii. Phytochemistry 31:2445–2450CrossRefGoogle Scholar
  16. 16.
    Guo C, Fuchs PL (1998) The first synthesis of the aglycone of the potent anti-tumor steroidal saponin OSW-1. Tetrahedron Lett 39:1099–1102CrossRefGoogle Scholar
  17. 17.
    Deng S, Yu B, Lou Y, Hui Y (1999) First total synthesis of an exceptionally potent antitumor saponin, OSW-1. J Org Chem 64:202–208CrossRefGoogle Scholar
  18. 18.
    Ma X, Yu B, Hui Y, Miao Z, Ding J (2001) Synthesis of OSW-1 analogues and a dimer and their antitumor activities. Bioorg Med Chem Lett 11:2153–2156CrossRefGoogle Scholar
  19. 19.
    Yu W, Jin Z (2001) New strategy for the stereoselective introduction of steroid side chain via alpha-alkoxy vinyl cuprates: Total synthesis of a highly potent antitumor natural product OSW-1. J Am Chem Soc 123:3369–3370CrossRefGoogle Scholar
  20. 20.
    Morzycki JW, Wojtkielewicz A, Wolczynski S (2004) Synthesis of analogues of a potent antitumor saponin OSW-1. Bioorg Med Chem Lett 14:3323–3326CrossRefGoogle Scholar
  21. 21.
    Maj J, Morzycki JW, Rarova L, Oklestkova J, Strnad M, Wojtkielewicz A (2011) Biological activity of 22-deoxo-23-oxa analogues of saponin OSW-1. J Med Synthesis Chem 54:3298–3305CrossRefGoogle Scholar
  22. 22.
    Shi B, Wu H, Yu B, Wu J (2004) 23-Oxa-analogues of OSW-1: Efficient synthesis and extremely potent antitumor activity. Angew Chem Int Ed 43:4324–4327CrossRefGoogle Scholar
  23. 23.
    Li W, Song R, Fang X, Wang L, Chen W, Tang P, Yu B, Sun Y, Xu Q (2012) SBF-1, a synthetic steroidal glycoside, inhibits melanoma growth and metastasis through blocking interaction between PDK1 and AKT3. Biochem Pharmacol 84:172–181CrossRefGoogle Scholar
  24. 24.
    Li W, Ouyang Z, Zhang Q, Wang L, Shen Y, Wu X, Gu Y, Shu Y, Yu B, Wu X, Sun Y, Xu Q (2014) SBF-1 exerts strong anticervical cancer effect through inducing endoplasmic reticulum stress-associated cell death via targeting sarco/endoplasmic reticulum C a 2+-ATPase 2. Cell Death Dis 18:e1581CrossRefGoogle Scholar
  25. 25.
    Trott O, Olson AJ (2010) AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 31:455–461PubMedPubMedCentralGoogle Scholar
  26. 26.
    Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ (2009) AutoDock4 and autoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem 30:2785–2791CrossRefGoogle Scholar
  27. 27.
    Maier JA, Martinez C, Kasavajhala K, Wickstrom L, Hauser KE, Simmerling C (2015) FF14SB: Improving the accuracy of protein side chain and backbone parameters from Ff99SB. J Chem Theory Comput 11:3696–3713CrossRefGoogle Scholar
  28. 28.
    Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Montgomery JA Jr, Peralta JE, Ogliaro F, Bearpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov VN, Keith T, Kobayashi R, Normand J, Raghavachari K, Rendell A, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam JM, Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas O, Foresman JB, Ortiz JV, Cioslowski J, Fox D (2010) Gaussian 09, revision B.01, Gaussian, Inc.: Wallingford CTGoogle Scholar
  29. 29.
    Bayly CI, Cieplak P, Cornell WD, Kollman P (1993) Well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model. J Phys Chem 97:10269–10280CrossRefGoogle Scholar
  30. 30.
    Cornell WD, Cieplak P, Bayly CI, Kollmann PA (1993) Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation. J Am Chem Soc 115:9620–9631CrossRefGoogle Scholar
  31. 31.
    Cieplak P, Cornell WD, Bayly C, Kollman P (1995) Application of the multimolecule and multiconformational RESP methodology to biopolymers: Charge derivation for DNA, RNA, and proteins. J Comput Chem 16:1357–1377CrossRefGoogle Scholar
  32. 32.
    Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004) Testing of a general amber force field. J Development Comput Chem 25:1157–1174CrossRefGoogle Scholar
  33. 33.
    Jorgensen WL, Chandresekhar J, Madura JD, Impey RW, Klein ML (1983) Application of the multimolecule and multiconformational resp methodology to biopolymers: Charge derivation for DNA, RNA, and proteins. J Chem Phys 79:926–935CrossRefGoogle Scholar
  34. 34.
    Ryckaert JP, Ciccotti G, Berendsen HJC (1977) Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. J Chem Phys 23:327–341Google Scholar
  35. 35.
    Darden T, York D, Pedersen L (1993) Particle mesh Ewald: An N log(N) method for Ewald sums in large systems. J Chem Phys 98:10089–10092CrossRefGoogle Scholar
  36. 36.
    Essmann U, Perera L, Berkowitz ML (1995) Smooth particle mesh Ewald method. J Chem Phys 103:8577CrossRefGoogle Scholar
  37. 37.
    Case D, Berryman J, Betz R, Cerutti D, Cheatham TI, Darden T, Duke R, Giese T, Gohlke H, Goetz A, Homeyer N, Izadi S, Janowski P, Kaus J, Kovalenko A, Lee T, LeGrand S, Li P, Luchko T, Luo R, Madej B, Merz K, Monard G, Needham P, Nguyen H, Nguyen H, Omelyan I, Onufriev A, Roe D, Roitberg A, Salomon-Ferrer R, Simmerling C, Smith W, Swails J, Walker R, Wang J, Wolf R, Wu X, York D, Kollman P (2015) AMBER 15, University of California San FranciscoGoogle Scholar
  38. 38.
    Miller BR, McGee TD Jr, Swails JM, Homeyer N, Gohlke H, Roitberg AE (2012) An efficient program for end-state free energy calculations. J Chem Theory Comput 8:3314–3321CrossRefGoogle Scholar
  39. 39.
    Luo R, David L, Gilson M (2002) Accelerated Poisson–Boltzmann calculations for static and dynamic systems. J Comput Chem 23:1244–1253CrossRefGoogle Scholar
  40. 40.
    Connolly ML (1983) Analytical molecular surface calculation. J Chem Theory Comput 16:548–558Google Scholar
  41. 41.
    Brooks BR, Janežič D, Karplus M (1995) Harmonic analysis of large systems. I. Methodology. J Comput Chem 16:1522–1542CrossRefGoogle Scholar
  42. 42.
    Gohlke H, Kiel C, Case DA (2003) Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. J Mol Biol 330:891–913CrossRefGoogle Scholar
  43. 43.
    Hou T, Li N, Li Y, Wang W (2012) Characterization of domain-peptide interaction interface: Prediction of SH3 domain-mediated protein–protein interaction network in yeast by generic structure-based models. J Proteome Res 11:2982–2995CrossRefGoogle Scholar
  44. 44.
    Schulze J, Saladino G, Busschots K, Neimanis S, Süß E, Odadzic D, Zeuzem S, Hindie V, Herbrand A, Lisa M-N, Alzari P, Gervasio F, Biondi R (2016) Bidirectional allosteric communication between the ATP-binding site and the regulatory PIF pocket in PDK1 protein kinase. Cell Chem Biol 23:1193–1205CrossRefGoogle Scholar
  45. 45.
    Klimovich PV, Shirts MR, Mobley DL (2015) Guidelines for the analysis of free energy calculations. J Comput Aid Mol Des 29:397–411CrossRefGoogle Scholar
  46. 46.
    Shirt MR, Chodera JD (2008) Statistically optimal analysis of samples from multiple equilibrium states. J Chem Phys 129:124105CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.State Key Laboratory of Precision Spectroscopy, School of Physics and Materials ScienceEast China Normal UniversityShanghaiChina
  2. 2.NYU-ECNU Center for Computational Chemistry at NYU ShanghaiShanghaiChina
  3. 3.Collaborative Innovation Center of Extreme OpticsShanxi UniversityTaiyuanChina

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