Phosphorylation-dependent activity-based conformational changes in P21-activated kinase family members and screening of novel ATP competitive inhibitors


Autoři: Mehreen Gul aff001;  Muhammad Fakhar aff001;  Najumuddin aff001;  Sajid Rashid aff001
Působiště autorů: National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan aff001
Vyšlo v časopise: PLoS ONE 14(11)
Kategorie: Research Article
doi: 10.1371/journal.pone.0225132

Souhrn

P21-activated kinases (PAKs) are serine/threonine protein kinases that are subdivided into two groups on the basis of their domain architecture: group-I (PAK1–3) and group-II (PAK4–6). PAKs are considered as attractive drug targets that play vital role in cell proliferation, survival, motility, angiogenesis and cytoskeletal dynamics. In current study, molecular dynamics simulation-based comparative residual contributions and differential transitions were monitored in both active and inactive states of human PAK homologs for therapeutic intervention. Due to their involvement in cancer, infectious diseases, and neurological disorders, it is inevitable to develop novel therapeutic strategies that specifically target PAKs on the basis of their activity pattern. In order to isolate novel inhibitors that are able to bind at the active sites of PAK1 and PAK4, high throughput structure-based virtual screening was performed. Multiple lead compounds were proposed on the basis of their binding potential and targeting region either phosphorylated (active) or unphosphorylated PAK isoform (inactive). Thus, ATP-competitive inhibitors may prove ideal therapeutic choice against PAK family members. The detailed conformational readjustements occurring in the PAKs upon phosphorylation-dephosphorylation events may serve as starting point for devising novel drug molecules that are able to target on activity basis. Overall, the observations of current study may add valuable contribution in the inventory of novel inhibitors that may serve as attractive lead compounds for targeting PAK family members on the basis of activity-based conformational changes.

Klíčová slova:

Binding analysis – Kinase inhibitors – Molecular dynamics – Phosphorylation – Protein structure databases – Salt bridges – Sequence analysis – Sequence motif analysis


Zdroje

1. Robinson R. Confirming the importance of the R-spine: new insights into protein kinase regulation. PLoS Biol. 2013;11: e1001681. doi: 10.1371/journal.pbio.1001681 24143134

2. Ubersax JA, Ferrell JE Jr. Mechanisms of specificity in protein phosphorylation. Nat Rev Mol cell Biol. 2007;8: 530. doi: 10.1038/nrm2203 17585314

3. Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S. The protein kinase complement of the human genome. Science (80-). 2002;298: 1912–1934.

4. Caenepeel S, Charydczak G, Sudarsanam S, Hunter T, Manning G. The mouse kinome: discovery and comparative genomics of all mouse protein kinases. Proc Natl Acad Sci. 2004;101: 11707–11712. doi: 10.1073/pnas.0306880101 15289607

5. Kornev AP, Haste NM, Taylor SS, Ten Eyck LF. Surface comparison of active and inactive protein kinases identifies a conserved activation mechanism. Proc Natl Acad Sci. 2006;103: 17783–17788. doi: 10.1073/pnas.0607656103 17095602

6. Kumar R, Sanawar R, Li X, Li F. Structure, biochemistry, and biology of PAK kinases. Gene. 2017;605: 20–31. doi: 10.1016/j.gene.2016.12.014 28007610

7. Bokoch GM. Biology of the p21-activated kinases. Annu Rev Biochem. 2003;72: 743–781. doi: 10.1146/annurev.biochem.72.121801.161742 12676796

8. Shao Y-G, Ning K, Li F. Group II p21-activated kinases as therapeutic targets in gastrointestinal cancer. World J Gastroenterol. 2016;22: 1224. doi: 10.3748/wjg.v22.i3.1224 26811660

9. Karpov AS, Amiri P, Bellamacina C, Bellance MH, Breitenstein W, Daniel D, et al. Optimization of a Dibenzodiazepine Hit to a Potent and Selective Allosteric PAK1 Inhibitor. ACS Med Chem Lett. 2015;6: 776–781. doi: 10.1021/acsmedchemlett.5b00102 26191365

10. Ryu BJ, Kim S, Min B, Kim KY, Lee JS, Park WJ, et al. Discovery and the structural basis of a novel p21-activated kinase 4 inhibitor. Cancer Lett. 2014;349: 45–50. doi: 10.1016/j.canlet.2014.03.024 24704155

11. Lei M, Lu W, Meng W, Parrini M-C, Eck MJ, Mayer BJ, et al. Structure of PAK1 in an autoinhibited conformation reveals a multistage activation switch. Cell. 2000;102: 387–397. doi: 10.1016/s0092-8674(00)00043-x 10975528

12. Wang J, Wu JW, Wang ZX. Structural insights into the autoactivation mechanism of p21-activated protein kinase. Structure. 2011;19: 1752–1761. doi: 10.1016/j.str.2011.10.013 22153498

13. Kumar R, Gururaj AE, Barnes CJ. p21-activated kinases in cancer. Nat Rev Cancer. 2006;6: 459. doi: 10.1038/nrc1892 16723992

14. Jaffer ZM, Chernoff J. p21-activated kinases: three more join the Pak. Int J Biochem Cell Biol. 2002;34: 713–717. doi: 10.1016/s1357-2725(01)00158-3 11950587

15. Vadlamudi RK, Kumar R. P21-activated kinases in human cancer. Cancer Metastasis Rev. 2003;22: 385–393. doi: 10.1023/a:1023729130497 12884913

16. Wen Y-Y, Wang X-X, Pei D-S, Zheng J-N. p21-Activated kinase 5: a pleiotropic kinase. Bioorg Med Chem Lett. 2013;23: 6636–6639. doi: 10.1016/j.bmcl.2013.10.051 24215894

17. Pandey A, Dan I, Kristiansen TZ, Watanabe NM, Voldby J, Kajikawa E, et al. Cloning and characterization of PAK5, a novel member of mammalian p21-activated kinase-II subfamily that is predominantly expressed in brain. Oncogene. 2002;21: 3939–3948. doi: 10.1038/sj.onc.1205478 12032833

18. Cotteret S, Chernoff J. Nucleocytoplasmic shuttling of Pak5 regulates its antiapoptotic properties. Mol Cell Biol. 2006;26: 3215–3230. doi: 10.1128/MCB.26.8.3215-3230.2006 16581795

19. Ching Y-P, Leong VYL, Wong C-M, Kung H-F. Identification of an autoinhibitory domain of p21-activated protein kinase 5. J Biol Chem. 2003;278: 33621–33624. doi: 10.1074/jbc.C300234200 12860998

20. Wang J, Wu J-W, Wang Z-X. Structural insights into the autoactivation mechanism of p21-activated protein kinase. Structure. 2011;19: 1752–1761. doi: 10.1016/j.str.2011.10.013 22153498

21. Wells CM, Jones GE. The emerging importance of group II PAKs. Biochem J. 2010;425: 465–473. doi: 10.1042/BJ20091173 20070256

22. Kaur R, Liu X, Gjoerup O, Zhang A, Yuan X, Balk SP, et al. Activation of p21-activated kinase 6 by MAP kinase kinase 6 and p38 MAP kinase. J Biol Chem. 2005;280: 3323–3330. doi: 10.1074/jbc.M406701200 15550393

23. Itakura A, Aslan JE, Kusanto BT, Phillips KG, Porter JE, Newton PK, et al. p21-Activated kinase (PAK) regulates cytoskeletal reorganization and directional migration in human neutrophils. PLoS One. 2013;8: e73063. doi: 10.1371/journal.pone.0073063 24019894

24. Gao J, Ha BH, Lou HJ, Morse EM, Zhang R, Calderwood DA, et al. Substrate and inhibitor specificity of the type II p21-activated kinase, PAK6. PLoS One. 2013;8: e77818. doi: 10.1371/journal.pone.0077818 24204982

25. Kornev AP, Taylor SS. Defining the conserved internal architecture of a protein kinase. Biochim Biophys Acta (BBA)-Proteins Proteomics. 2010;1804: 440–444.

26. Grant BD, Tsigelny I, Taylor SS, Adams JA. Examination of an active-site electrostatic node in the cAMP-dependent protein kinase catalytic subunit. Protein Sci. 1996;5: 1316–1324. doi: 10.1002/pro.5560050710 8819164

27. Eswaran J, Lee WH, Debreczeni JÉ, Filippakopoulos P, Turnbull A, Fedorov O, et al. Crystal Structures of the p21-activated kinases PAK4, PAK5, and PAK6 reveal catalytic domain plasticity of active group II PAKs. Structure. 2007;15: 201–213. doi: 10.1016/j.str.2007.01.001 17292838

28. Roskoski R. Classification of small molecule protein kinase inhibitors based upon the structures of their drug-enzyme complexes. Pharmacol Res. 2016;103: 26–48. doi: 10.1016/j.phrs.2015.10.021 26529477

29. Aimes RT, Hemmer W, Taylor SS. Serine-53 at the tip of the glycine-rich loop of cAMP-dependent protein kinase: role in catalysis, P-site specificity, and interaction with inhibitors. Biochemistry. 2000;39: 8325–8332. doi: 10.1021/bi992800w 10889042

30. Lei M, Robinson MA, Harrison SC. The active conformation of the PAK1 kinase domain. Structure. 2005;13: 769–778. doi: 10.1016/j.str.2005.03.007 15893667

31. Rudolph J, Crawford JJ, Hoeflich KP, Wang W. Inhibitors of p21-Activated Kinases (PAKs) Miniperspective. J Med Chem. 2014;58: 111–129. doi: 10.1021/jm501613q 25415869

32. Furnari MA, Jobes ML, Nekrasova T, Minden A, Wagner GC. Functional deficits in PAK5, PAK6 and PAK5/PAK6 knockout mice. PLoS One. 2013;8: e61321. doi: 10.1371/journal.pone.0061321 23593460

33. Ndubaku CO, Crawford JJ, Drobnick J, Aliagas I, Campbell D, Dong P, et al. Design of selective PAK1 inhibitor G-5555: improving properties by employing an unorthodox low-p K a polar moiety. ACS Med Chem Lett. 2015;6: 1241–1246. doi: 10.1021/acsmedchemlett.5b00398 26713112

34. Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, et al. UniProt: the universal protein knowledgebase. Nucleic Acids Res. 2004;32: D115—D119. doi: 10.1093/nar/gkh131 14681372

35. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011;7: 539. doi: 10.1038/msb.2011.75 21988835

36. Chen VB, Arendall WB, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr Sect D Biol Crystallogr. 2010;66: 12–21.

37. Bhattacharya A, Tejero R, Montelione GT. Evaluating protein structures determined by structural genomics consortia. Proteins Struct Funct Bioinforma. 2007;66: 778–795.

38. Emsley P, Lohkamp B, Scott WG, Cowtan K. Features and development of Coot. Acta Crystallogr Sect D Biol Crystallogr. 2010;66: 486–501.

39. Meng EC, Pettersen EF, Couch GS, Huang CC, Ferrin TE. Tools for integrated sequence-structure analysis with UCSF Chimera. BMC Bioinformatics. 2006;7: 339. doi: 10.1186/1471-2105-7-339 16836757

40. Abraham MJ, Murtola T, Schulz R, Páll S, Smith JC, Hess B, et al. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX. 2015;1: 19–25.

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

42. Baxter J. Local optima avoidance in depot location. J Oper Res Soc. 1981;32: 815–819.

43. Blum C, Roli A, Sampels M. Hybrid metaheuristics: an emerging approach to optimization. Springer; 2008.

44. Crawford JJ, Lee W, Aliagas I, Mathieu S, Hoeflich KP, Zhou W, et al. Structure-guided design of group I selective p21-activated kinase inhibitors. J Med Chem. 2015;58: 5121–5136. doi: 10.1021/acs.jmedchem.5b00572 26030457

45. Vilar S, Cozza G, Moro S. Medicinal chemistry and the molecular operating environment (MOE): application of QSAR and molecular docking to drug discovery. Curr Top Med Chem. 2008;8: 1555–1572. doi: 10.2174/156802608786786624 19075767

46. Loo T-H, Ng Y-W, Lim L, Manser ED. GIT1 activates p21-activated kinase through a mechanism independent of p21 binding. Mol Cell Biol. 2004;24: 3849–3859. doi: 10.1128/MCB.24.9.3849-3859.2004 15082779

47. Cai X-Z, Wang J, Xiao-Dong L, Wang G-L, Liu F-N, Cheng M-S, et al. Curcumin suppresses proliferation and invasion in human gastric cancer cells by down-regulation of PAK1 activity and cyclin D1 expression. Cancer Biol Ther. 2009;8: 1360–1368. doi: 10.4161/cbt.8.14.8720 19448398

48. Lee J-H, Wittki S, Bräu T, Dreyer FS, Krätzel K, Dindorf J, et al. HIV Nef, paxillin, and Pak1/2 regulate activation and secretion of TACE/ADAM10 proteases. Mol Cell. 2013;49: 668–679. doi: 10.1016/j.molcel.2012.12.004 23317503

49. Ke Y, Wang X, Jin XY, Solaro RJ, Lei M. PAK1 is a novel cardiac protective signaling molecule. Front Med. 2014;8: 399–403. doi: 10.1007/s11684-014-0380-9 25416031

50. Ma Q-L, Yang F, Frautschy SA, Cole GM. PAK in Alzheimer disease, Huntington disease and X-linked mental retardation. Cell Logist. 2012;2: 117–125. doi: 10.4161/cl.21602 23162743

51. Arias-Romero LE, Chernoff J. A tale of two Paks. Biol Cell. 2008;100: 97–108. doi: 10.1042/BC20070109 18199048

52. Zenke FT, King CC, Bohl BP, Bokoch GM. Identification of a central phosphorylation site in p21-activated kinase regulating autoinhibition and kinase activity. J Biol Chem. 1999;274: 32565–32573. doi: 10.1074/jbc.274.46.32565 10551809

53. Ranjitkar P, Brock AM, Maly DJ. Affinity reagents that target a specific inactive form of protein kinases. Chem Biol. 2010;17: 195–206. doi: 10.1016/j.chembiol.2010.01.008 20189109

54. McCoull W, Hennessy EJ, Blades K, Chuaqui C, Dowling JE, Ferguson AD, et al. Optimization of highly kinase selective bis-anilino pyrimidine PAK1 inhibitors. ACS Med Chem Lett. 2016;7: 1118–1123. doi: 10.1021/acsmedchemlett.6b00322 27994749

55. Corvino A, Rosa R, Incisivo GM, Fiorino F, Frecentese F, Magli E, et al. Development of 1, 2, 3-Triazole-Based Sphingosine Kinase Inhibitors and Their Evaluation as Antiproliferative Agents. Int J Mol Sci. 2017;18: 2332.

56. Tariq S, Alam O, Amir M. Synthesis, p38α MAP kinase inhibition, anti-inflammatory activity, and molecular docking studies of 1, 2, 4-triazole-based benzothiazole-2-amines. Arch Pharm (Weinheim). 2018;351: 1700304.

57. Tang Y, Marwaha S, Rutkowski JL, Tennekoon GI, Phillips PC, Field J. A role for Pak protein kinases in Schwann cell transformation. Proc Natl Acad Sci. 1998;95: 5139–5144. doi: 10.1073/pnas.95.9.5139 9560242

58. Buchwald G, Hostinova E, Rudolph MG, Kraemer A, Sickmann A, Meyer HE, et al. Conformational switch and role of phosphorylation in PAK activation. Mol Cell Biol. 2001;21: 5179–5189. doi: 10.1128/MCB.21.15.5179-5189.2001 11438672


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