Skip to main content

Advertisement

SpringerLink
Log in

Binding selectivity studies of PKBα using molecular dynamics simulation and free energy calculations

  • Original Paper
  • Published:
Journal of Molecular Modeling Aims and scope Submit manuscript

Abstract

Designing selective protein kinase B (PKB/Akt) inhibitor is an area of intense research to develop potential anticancer drugs. In the present study, the molecular basis governing PKB-selective inhibition has been investigated using molecular dynamics simulation. The binding free energies calculated by MM/PBSA gave a good correlation with the experimental biological activity and a good explanation of the activity difference of the studied inhibitors. The decomposition of free energies by MM/GBSA indicates that the ethyl group on pyrrolo[2,3-d]pyrimidine ring of inhibitor Lig1 (N-{[(3S)-3-amino-1-(5-ethyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)pyrrolidin-3-yl]-methyl}-2,4-difluoro-benzamide) is an important contributor to its PKBα selectivity due to its hydrophobic interaction with the side chain of Thr291 in PKBα. The substituted groups on the pyrrolidine ring of Lig1 also show a strong tendency to mediate protein-ligand interactions through the hydrogen bonds formed between the amino or amide groups of Lig1 and the carboxyl O atoms of Glu234, Glu278, and Asp292 of PKBα. It was reported that there are only three key amino acid differences between PKBα (Thr211, Ala230, Met281) and PKA (Val104, Val123, Leu173) within the clefts of ATP-binding sites. These differences propel a drastic conformational change in PKA, weakening its binding interactions with inhibitor. The impact was also confirmed by MD simulated interaction modes of inhibitor binding to PKBα mutants with the in silico mutations of the three key amino acids, respectively. We expect that the results obtained here could be useful for future rational design of specific ATP-competitive inhibitors of PKBα.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9
Fig. 10

Similar content being viewed by others

Abbreviations

PKB/Akt:

Protein kinase B

MD:

Molecular dynamics

PKA:

Protein kinase A

References

  1. Barnett SF, Bilodeau MT, Lindsley CW (2005) The Akt/PKB family of protein kinases: a review of small molecule inhibitors and progress towards target validation. Curr Top Med 5:109–125

    Article  CAS  Google Scholar 

  2. Lindsley CW, Barnett SF, Yaroschak M, Bilodeau MT, Layton ME (2007) Recent progress in the development of ATP-competitive and allosteric Akt kinase inhibitors. Curr Top Med 7:1349–1363

    Article  CAS  Google Scholar 

  3. Fayard E, Tintignac LA, Baudry A, Hemmings BA (2005) Protein kinase B/Akt at a glance. J Cell Sci 118(24):5675–5678

    Article  CAS  Google Scholar 

  4. Li Q, Zhu G-D (2002) Targeting serine/threonine protein kinase B/Akt and cell-cycle checkpoint kinases for treating cancer. Curr Top Med 2(9):939–971

    Article  CAS  Google Scholar 

  5. Cheng GZ, Park S, Shu S, He L, Kong W, Zhang W, Yuan Z, Wang L-H, Cheng JQ (2008) Advances of AKT pathway in human oncogenesis and as a target for anti-cancer drug discovery. Curr Cancer Drug Tar 8:2–6

    Article  CAS  Google Scholar 

  6. Thakur DS, Kumar P, Kumar P, Lal C (2010) Akt: a new approach for cancer treatment. Int J Pharm Sci Res 1(suppl8):29–36

    Google Scholar 

  7. Freeman-Cook KD, Autry C, Borzillo G, Gordon D, Barbacci-Tobin E, Bernardo V, Briere D, Clark T, Corbett M, Jakubczak J, Kakar S, Knauth E, Lippa B, Luzzio MJ, Mansour M, Martinelli G, Marx M, Nelson K, Pandit J, Rajamohan F, Robinson S, Subramanyam C, Wei L, Wythes M, Morris J (2010) Design of selective, ATP-competitive inhibitors of Akt. J Med Chem 53:4615–4622

    Article  CAS  Google Scholar 

  8. Rhodes N, Heerding DA, Duckett DR, Eberwein DJ, Knick VB, Lansing TJ, McConnell RT, Gilmer TM, Zhang S-Y, Robell K, Kahana JA, Geske RS, Kleymenova EV, Choudhry AE, Lai Z, Leber JD, Minthorn EA, Strum SL, Wood ER, Huang PS, Copeland RA, Kumar R (2008) Characterization of an Akt kinase inhibitor with potent pharmacodynamic and antitumor activity. Cancer Res 68(7):2366–2374

    Article  CAS  Google Scholar 

  9. Blake JF, Xu R, Bencsik JR, Xiao D, Kallan NC, Schlachter S, Mitchell IS, Spencer KL, Banka AL, Wallace EM, Gloor SL, Martinson M, Woessner RD, Vigers GPA, Brandhuber BJ, Liang J, Safina BS, Li J, Zhang B, Chabot C, Do S, Lee L, Oeh J, Sampath D, Lee BB, Lin K, Liederer BM, Skelton NJ (2012) Discovery and preclinical pharmacology of a selective ATP competitive Akt inhibitor (GDC-0068) for the treatment of human tumors. J Med Chem 55(18):8110–8127

    Article  CAS  Google Scholar 

  10. Xu R, Banka A, Blake JF, Mitchell IS, Wallace EM, Bencsik JR, Kallan NC, Spencer KL, Gloor SL, Martinson M, Risom T, Gross SD, Morales TH, Wu W-I, Vigers GPA, Brandhuber BJ, Skelton NJ (2011) Discovery of spirocyclic sulfonamides as potent Akt inhibitors with exquisite selectivity against PKA. Bioorg Med Chem Lett 21:2335–2340

    Article  CAS  Google Scholar 

  11. Kallan NC, Spencer KL, Blake JF, Xu R, Heizer J, Bencsik JR, Mitchell IS, Gloor SL, Martinson M, Risom T, Gross SD, Morales TH, Wu W-I, Vigers GPA, Brandhuber BJ, Skelton NJ (2011) Discovery and SAR of spirochromane Akt inhibitors. Bioorg Med Chem Lett 21:2410–2414

    Article  CAS  Google Scholar 

  12. Bencsik JR, Xiao D, Blake JF, Kallan NC, Mitchell IS, Spencer KL, Xu R, Gloor SL, Martinson M, Risom T, Woessner RD, Dizon F, Wu W-I, Vigers GPA, Brandhuber BJ, Skelton NJ, Prior WW, Murray LJ (2010) Discovery of dihydrothieno- and dihydrofuropyrimidines as potent pan Akt inhibitors. Bioorg Med Chem Lett 20:7037–7041

    Article  CAS  Google Scholar 

  13. Mascarenhas NM, Bhattacharyya D, Ghoshal N (2010) Why pyridine containing pyrido[2,3-d]pyrimidin-7-ones selectively inhibit CDK4 than CDK2: Insights from molecular dynamics simulation. J Mol Graph Mod 28:695–706

    Article  CAS  Google Scholar 

  14. Yang Y, Qin J, Liu H, Yao X (2011) Molecular dynamics simulation, free energy calculation and structure-based 3D-QSAR studies of B-RAF kinase inhibitors. J Chem Inf Model 51:680–692

    Article  CAS  Google Scholar 

  15. Yang Y, Shen Y, Liu H, Yao X (2011) Molecular dynamics simulation and free energy calculation studies of the binding mechanism of allostericinhibitors with p38α MAP kinase. J Chem Inf Model 51:3235–3246

    Google Scholar 

  16. Chen Q, Cui W, Cheng Y, Zhang F, Ji M (2011) Studying the mechanism that enables paullones to selectively inhibit glycogen synthase kinase 3 rather than cyclin-dependent kinase 5 by molecular dynamics simulations and free-energy calculations. J Mol Model 17:795–803

    Article  CAS  Google Scholar 

  17. Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE (2000) Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res 33:889–897

    Article  CAS  Google Scholar 

  18. 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 330:891–913

    Article  CAS  Google Scholar 

  19. Wong S, Amaro RE, McCammon JA (2009) MM-PBSA captures key role of intercalating water molecules at a protein-protein interface. J Chem Theory Comput 5:422–429

    Article  CAS  Google Scholar 

  20. Jiao D, Zhang J, Duke RE, Li G, Schnieders MJ, Ren P (2009) Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential. J Comput Chem 30(11):1701–1711

    Google Scholar 

  21. Jain AN (2007) Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search. J Comput Aided Mol Des 21:281–306

    Article  CAS  Google Scholar 

  22. Case DA, Darden TA, Cheatham TE, Simmerling CL, Wang J, Duke RE, Luo R, Walker RC, Zhang W, Merz KM, Roberts B, Wang B, Hayik S, Roitberg A, Seabra G, Kolossváry I, Wong KF, Paesani F, Vanicek J, Liu J, Wu X, Brozell SR, Steinbrecher T, Gohlke H, Cai Q, Ye X, Wang J, Hsieh MJ, Cui G, Roe DR, Mathews DH, Seetin MG, Sagui C, Babin V, Luchko T, Gusarov S, Kovalenko A, Kollman P (2010) AMBER 2011 University of California, San Francisco

  23. Jorgensen W, Chandrasekhar J, Madura J, Impey R, Klein M (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926–935

    Article  CAS  Google Scholar 

  24. Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W, Yang R, Cieplak P, Luo R, Lee T, Caldwell J, Wang J, Kollman P (2003) A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem 24:1999–2012

    Article  CAS  Google Scholar 

  25. Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004) Development and testing of a general amber force field. J Comput Chem 25:1157–1174

    Article  CAS  Google Scholar 

  26. Darden T, York D, Pedersen L (1993) Particle mesh Ewald: An N . log(N) method for Ewald sums in large systems. J Chem Phys 98:10089–10092

    Article  CAS  Google Scholar 

  27. Berendsen HJC, Postma JPM, Gunsteren WFV, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684–3690

    Article  CAS  Google Scholar 

  28. Ryckaert J-P, Ciccotti G, Berendsen HJC (1977) Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 23(3):327–341

    Article  CAS  Google Scholar 

  29. Case DA, Darden TA, Cheatham TE, Simmerling CL, Wang J, Duke RE, Luo R, Walker RC, Zhang W, Merz KM, Roberts B, Wang B, Hayik S, Roitberg A, Seabra G, Kolossváry I, Wong KF, Paesani F, Vanicek J, Liu J, Wu X, Brozell SR, Steinbrecher T, Gohlke H, Cai Q, Ye X, Wang J, Hsieh MJ, Cui G, Roe DR, Mathews DH, Seetin MG, Sagui C, Babin V, Luchko T, Gusarov S, Kovalenko A, Kollman P.(2012) AMBER 2012 University of California, San Francisco

  30. Rocchia W, Alexov E, Honig B (2001) Extending the applicability of the nonlinear Poisson-Boltzmann equation: multiple dielectric constants and multivalent ions. J Phys Chem B 105:6507–6514

    Google Scholar 

  31. Onufriev A, Bashford D, Case DA (2004) Exploring protein native states and large-scale conformational changes with a modified generalized Born model. Proteins Struct, Funct, Bioinform 55(2):383–394

    Article  CAS  Google Scholar 

  32. Weiser J, Shenkin PS, Still WC (1999) Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO). J Comput Chem 20:217–230

    Article  CAS  Google Scholar 

  33. Li Y, Zhang J, He D, Liang Q, Wang Y (2012) Characterization of molecular recognition of Phosphoinositide-3-kinase α inhibitor through molecular dynamics simulation. J Mol Model 18:1907–1916

    Article  CAS  Google Scholar 

  34. Lu S-Y, Jiang Y-J, Zou J-W, Wu T-X (2012) Effect of double mutations K214/A–E215/Q of FRATide on GSK3β: insights from molecular dynamics simulation and normal mode analysis. Amino Acids 43:267–277

    Article  CAS  Google Scholar 

  35. Bayly CI, Cieplak P, Cornell WD, Kollman PA (1993) A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model. J Phys Chem 97:10269–10280

    Article  CAS  Google Scholar 

  36. Rizzo RC, Tirado-Rives J, Jorgensen WL (2001) Estimation of binding affinities for HEPT and nevirapine analogues with HIV-1 reverse transcriptase via Monte Carlo simulations. J Med Chem 44:145–154

    Google Scholar 

  37. Alexey O, Donald B, David AC (2004) Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins 55:383–394

    Article  Google Scholar 

  38. Davies TG, Verdonk ML, Graham B, Saalau-Bethell S, Hamlett CCF, McHardy T, Collins I, Garrett MD, Workman P, Woodhead SJ, Jhoti H, Barford D (2007) A structural comparison of inhibitor binding to PKB, PKA and PKA-PKB chimera. J Mol Biol 367:882–894

    Google Scholar 

Download references

Acknowledgments

The authors are thankful to the College of Pharmaceutical Sciences, Zhejiang University for providing necessary facilities.

Author information

Authors and Affiliations

  1. Institute of Materia Medica, College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Rd, Hangzhou, Zhejiang, 310058, China

    Shi-Feng Chen, Yang Cao, Jiong-Jiong Chen & Jian-Zhong Chen

Authors
  1. Shi-Feng Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yang Cao
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jiong-Jiong Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jian-Zhong Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jian-Zhong Chen.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Chen, SF., Cao, Y., Chen, JJ. et al. Binding selectivity studies of PKBα using molecular dynamics simulation and free energy calculations. J Mol Model 19, 5097–5112 (2013). https://doi.org/10.1007/s00894-013-1997-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00894-013-1997-3

Keywords

Search

Navigation