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

Journal of Molecular Modeling

Volumn 19, Issue 11, 2013, Pages 5097-5112

  Chen, Shi Feng ^a   Cao, Yang ^a   Chen, Jiong Jiong ^a   Chen, Jian Zhong ^a  

^a ZHEJIANG UNIVERSITY   (China)

Author keywords

Binding free energy; Inhibitor; Molecular dynamics simulation; Protein kinase A PKA; Protein kinase B PKB; Selectivity

Indexed keywords

AMIDE; AMINO ACID; CYCLIC AMP DEPENDENT PROTEIN KINASE; PROTEIN KINASE B; PROTEIN KINASE B INHIBITOR; PYRIMIDINE DERIVATIVE;

ARTICLE; BINDING AFFINITY; BINDING SITE; CALCULATION; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; DECOMPOSITION; ENERGY; HYDROGEN BOND; HYDROPHOBICITY; LIGAND BINDING; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; MOLECULAR MODEL; POINT MUTATION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN INTERACTION; STATIC ELECTRICITY; SURFACE TENSION;

ANTINEOPLASTIC AGENTS; COMPUTER SIMULATION; HYDROGEN BONDING; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; MUTATION; PROTEIN KINASE INHIBITORS; PROTO-ONCOGENE PROTEINS C-AKT; PYRIMIDINES; PYRROLES; STRUCTURE-ACTIVITY RELATIONSHIP; THERMODYNAMICS;

EID: 84888214584     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-013-1997-3     Document Type: Article

References (38)

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
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
3. Fayard E, Tintignac LA, Baudry A, Hemmings BA (2005) Protein kinase B/Akt at a glance. J Cell Sci 118(24):5675-5678
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
26. . log(N) method for Ewald sums in large systems. J Chem Phys 98:10089-10092
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
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
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
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
32. Weiser J, Shenkin PS, Still WC (1999) Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO). J Comput Chem 20:217-230
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
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
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
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
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
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