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Electrostatic mechanism of V600E mutation-induced B-Raf constitutive activation in colorectal cancer: molecular implications for the selectivity difference between type-I and type-II inhibitors

  • Tie Liu
  • Zhaoshun Wang
  • Peng Guo
  • Na Ding
Original Article
  • 13 Downloads

Abstract

The oncogenic mutation V600E in B-Raf activation loop (A-loop) has been frequently observed to cause drug resistance in colorectal cancer chemotherapy. Here, the molecular mechanism of V600E-induced conformational flipping of B-Raf activation loop (A-loop) is investigated systematically via continuum electrostatic analysis. It is found that substitution of the electroneutral Val600 residue with negatively charged glutamic acid Glu600 electrostatically destabilizes the inactive DFG-out conformation of B-Raf kinase and promotes its shifting to active DFG-in conformation. This is analogous with natural phosphorylation of Thr598 and/or Ser601 residues in A-loop to activate the kinase, that is, both the mutation and phosphorylation can introduce negative charge to B-Raf A-loop and then trigger the loop flipping. Energetic analysis reveals that the V600E mutation can affect inhibitor binding indirectly via regulation of kinase conformation. Type-I and type-II inhibitors respond distinctly to V600E mutation; the former is sensitized by the mutation, while the latter generally shows a low sensitivity to the mutation. Based on this guideline, the sophisticated type-I pan-kinase inhibitor Staurosporine as well as its analogs Midostaurin and Lestaurtinib are identified as potent mutant-selective inhibitors by modeling analysis and kinase assay, which exhibit a moderate or high selectivity for B-RafV600E over B-RafWT (3.7-fold, 6.1-fold and > 3.1-fold, respectively).

Keywords

B-Raf kinase V600E mutation Constitutive activation Phosphorylation Inhibitor selectivity Colorectal cancer 

Notes

Acknowledgements

This work was supported by the Weifang People’s Hospital.

References

  1. Bai Z, Hou S, Zhang S, Li Z, Zhou P (2017) Targeting self-binding peptides as a novel strategy to regulate protein activity and function: a case study on the proto-oncogene tyrosine protein kinase c-Src. J Chem Inf Model 57:835–845CrossRefPubMedCentralGoogle Scholar
  2. 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 97:10269–10280CrossRefGoogle Scholar
  3. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The protein data bank. Nucleic Acids Res 28:235–242CrossRefPubMedCentralGoogle Scholar
  4. Bollag G, Hirth P, Tsai J, Zhang J, Ibrahim PN, Cho H, Spevak W, Zhang C, Zhang Y, Habets G, Burton EA, Wong B, Tsang G, West BL, Powell B, Shellooe R, Marimuthu A, Nguyen H, Zhang KY, Artis DR, Schlessinger J, Su F, Higgins B, Iyer R, D’Andrea K, Koehler A, Stumm M, Lin PS, Lee RJ, Grippo J, Puzanov I, Kim KB, Ribas A, McArthur GA, Sosman JA, Chapman PB, Flaherty KT, Xu X, Nathanson KL, Nolop K (2010) Clinical efficacy of a RAF inhibitor needs broad target blockade in BRAF-mutant melanoma. Nature 467:596–599CrossRefPubMedCentralGoogle Scholar
  5. Case DA, Cheatham TE, Darden T, Gohlke H, Luo R, Merz KM, Onufriev A, Simmerling C, Wang B, Woods RJ (2005) The amber biomolecular simulation programs. J Comput Chem 26:1668–1688CrossRefPubMedCentralGoogle Scholar
  6. Cho KJ, Park JH, Hancock JF (2013) Staurosporine: a new tool for studying phosphatidylserine trafficking. Commun Integr Biol 6:e24746CrossRefPubMedCentralGoogle Scholar
  7. Davies H, Bignell GR, Cox C, Stephens P, Edkins S, Clegg S, Teague J, Woffendin H, Garnett MJ, Bottomley W, Davis N, Dicks E, Ewing R, Floyd Y, Gray K, Hall S, Hawes R, Hughes J, Kosmidou V, Menzies A, Mould C, Parker A, Stevens C, Watt S, Hooper S, Wilson R, Jayatilake H, Gusterson BA, Cooper C, Shipley J, Hargrave D, Pritchard-Jones K, Maitland N, Chenevix-Trench G, Riggins GJ, Bigner DD, Palmieri G, Cossu A, Flanagan A, Nicholson A, Ho JW, Leung SY, Yuen ST, Weber BL, Seigler HF, Darrow TL, Paterson H, Marais R, Marshall CJ, Wooster R, Stratton MR, Futreal PA (2002) Mutations of the BRAF gene in human cancer. Nature 417:949–954CrossRefPubMedCentralGoogle Scholar
  8. Dietrich J, Hulme C, Hurley LH (2010) The design, synthesis, and evaluation of 8 hybrid DFG-out allosteric kinase inhibitors: a structural analysis of the binding interactions of Gleevec, Nexavar, and BIRB-796. Bioorg Med Chem 18:5738–5748CrossRefPubMedCentralGoogle Scholar
  9. Fiser A, Sali A (2003) ModLoop: automated modeling of loops in protein structures. Bioinformatics 19:2500–2501CrossRefPubMedCentralGoogle Scholar
  10. Fiskus W, Mitsiades N (2016) B-Raf inhibition in the clinic: present and future. Annu Rev Med 67:29–43CrossRefPubMedCentralGoogle Scholar
  11. Grasso M, Estrada MA, Ventocilla C, Samanta M, Maksimoska J, Villanueva J, Winkler JD, Marmorstein R (2016) Chemically linked vemurafenib inhibitors promote an inactive BRAFV600E conformation. ACS Chem Biol 11:2876–2888CrossRefPubMedCentralGoogle Scholar
  12. Growney JD, Clark JJ, Adelsperger J, Stone R, Fabbro D, Griffin JD, Gilliland DG (2005) Activation mutations of human c-KIT resistant to imatinib mesylate are sensitive to the tyrosine kinase inhibitor PKC412. Blood 106:721–724CrossRefPubMedCentralGoogle Scholar
  13. Homeyer N, Gohlke H (2012) Free energy calculations by the molecular mechanics Poisson–Boltzmann surface area method. Mol Inf 31:114–122CrossRefGoogle Scholar
  14. Ikenoue T, Hikiba Y, Kanai F, Aragaki J, Tanaka Y, Imamura J, Imamura T, Ohta M, Ijichi H, Tateishi K, Kawakami T, Matsumura M, Kawabe T, Omata M (2004) Different effects of point mutations within the B-Raf glycine-rich loop in colorectal tumors on mitogen-activated protein/extracellular signal-regulated kinase kinase/extracellular signal-regulated kinase and nuclear factor κB pathway and cellular transformation. Cancer Res 64:3428–3435CrossRefPubMedCentralGoogle Scholar
  15. Jiang H, Shao W, Wang Y, Xu R, Zhou L, Mu X (2018) Molecular mechanism of D816X mutation-induced c-Kit activation and -mediated inhibitor resistance in gastrointestinal stromal tumor. J Mol Graph Model 84:189–196CrossRefPubMedCentralGoogle Scholar
  16. Knapper S, Russell N, Gilkes A, Hills RK, Gale RE, Cavenagh JD, Jones G, Kjeldsen L, Grunwald MR, Thomas I, Konig H, Levis MJ, Burnett AK (2017) A randomized assessment of adding the kinase inhibitor lestaurtinib to first-line chemotherapy for FLT3-mutated AML. Blood 129:1143–1154CrossRefPubMedCentralGoogle 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 33:889–897CrossRefPubMedCentralGoogle Scholar
  18. Kufareva I, Abagyan R (2008) Type-II kinase inhibitor docking, screening, and profiling using modified structures of active kinase states. J Med Chem 51:7921–7932CrossRefPubMedCentralGoogle Scholar
  19. Kumar S, Nussinov R (1999) Salt bridge stability in monomeric proteins. J Mol Biol 293:1241–1255CrossRefPubMedCentralGoogle Scholar
  20. Labbé CM, Pencheva T, Jereva D, Desvillechabrol D, Becot J, Villoutreix BO, Pajeva I, Miteva MA (2017) AMMOS2: a web server for protein-ligand-water complexes refinement via molecular mechanics. Nucleic Acids Res 45:W350–W355CrossRefPubMedCentralGoogle Scholar
  21. Luo H, Du T, Zhou P, Yang L, Mei H, Ng H, Zhang W, Shu M, Tong W, Shi L, Mendrick DL, Hong H (2015) Molecular docking to identify associations between drugs and class I human leukocyte antigens for predicting idiosyncratic drug reactions. Comb Chem High Throughput Screen 18:296–304CrossRefPubMedCentralGoogle Scholar
  22. Marino KA, Sutto L, Gervasio FL (2015) The effect of a widespread cancer-causing mutation on the inactive to active dynamics of the B-Raf kinase. J Am Chem Soc 137:5280–5283CrossRefPubMedCentralGoogle Scholar
  23. Meng L, Huang Z (2018) In silico-in vitro discovery of untargeted kinase-inhibitor interactions from kinase-targeted therapies: a case study on the cancer MAPK signaling pathway. Comput Biol Chem 75:196–204CrossRefPubMedCentralGoogle Scholar
  24. Qin J, Xie P, Ventocilla C, Zhou G, Vultur A, Chen Q, Liu Q, Herlyn M, Winkler J, Marmorstein R (2012) Identification of a novel family of BRAFV600E inhibitors. J Med Chem 55:5220–5230CrossRefPubMedCentralGoogle Scholar
  25. 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 105:6507–6514CrossRefGoogle Scholar
  26. Roskoski R (2016) Classification of small molecule protein kinase inhibitors based upon the structures of their drug-enzyme complexes. Pharmacol Res 103:26–48CrossRefPubMedCentralGoogle Scholar
  27. Sclafani F, Gullo G, Sheahan K, Crown J (2013) B-Raf mutations in melanoma and colorectal cancer: a single oncogenic mutation with different tumour phenotypes and clinical implications. Crit Rev Oncol Hematol 87:55–68CrossRefPubMedCentralGoogle Scholar
  28. Sitkoff D, Sharp KA, Honig B (1994) Accurate calculation of hydration free energies using macroscopic solvent models. J Phys Chem 98:1978–1988CrossRefGoogle Scholar
  29. Steinbrecher T, Latzer J, Case DA (2012) Revised AMBER parameters for bioorganic phosphates. J Chem Theory Comput 8:4405–4412CrossRefPubMedCentralGoogle Scholar
  30. Tian F, Lv Y, Zhou P, Yang L (2011) Characterization of PDZ-peptide interactions using an integrated protocol of QM/MM, PB/SA, and CFEA analyses. J Comput Aided Mol Des 25:947–958CrossRefPubMedCentralGoogle Scholar
  31. Tian F, Yang C, Wang C, Guo T, Zhou P (2014) Mutatomics analysis of the systematic thermostability profile of Bacillus subtilis lipase A. J Mol Model 20:2257CrossRefPubMedCentralGoogle Scholar
  32. Tie J, Desai J (2015) Targeting BRAF mutant metastatic colorectal cancer: clinical implications and emerging therapeutic strategies. Target Oncol 10:179–188CrossRefPubMedCentralGoogle Scholar
  33. Tsai J, Lee JT, Wang W, Zhang J, Cho H, Mamo S, Bremer R, Gillette S, Kong J, Haass NK, Sproesser K, Li L, Smalley KS, Fong D, Zhu YL, Marimuthu A, Nguyen H, Lam B, Liu J, Cheung I, Rice J, Suzuki Y, Luu C, Settachatgul C, Shellooe R, Cantwell J, Kim SH, Schlessinger J, Zhang KY, West BL, Powell B, Habets G, Zhang C, Ibrahim PN, Hirth P, Artis DR, Herlyn M, Bollag G (2008) Discovery of a selective inhibitor of oncogenic B-Raf kinase with potent antimelanoma activity. Proc Natl Acad Sci USA 105:3041–3046CrossRefPubMedCentralGoogle Scholar
  34. Vandrovcova J, Lagerstedt-Robinsson K, Påhlman L, Lindblom A (2006) Somatic BRAF-V600E mutations in familial colorectal cancer. Cancer Epidemiol Biomarkers Prev 15:2270–2273CrossRefPubMedCentralGoogle Scholar
  35. Waizenegger IC, Baum A, Steurer S, Stadtmüller H, Bader G, Schaaf O, Garin-Chesa P, Schlattl A, Schweifer N, Haslinger C, Colbatzky F, Mousa S, Kalkuhl A, Kraut N, Adolf GR (2016) A novel RAF kinase inhibitor with DFG-out-binding mode: high efficacy in BRAF-mutant tumor xenograft models in the absence of normal tissue hyperproliferation. Mol Cancer Ther 15:354–365CrossRefPubMedCentralGoogle Scholar
  36. Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004) Development and testing of a general amber force field. J Comput Chem 25:1157–1174CrossRefGoogle Scholar
  37. Warnecke A, Sandalova T, Achour A, Harris RA (2014) PyTMs: a useful PyMOL plugin for modeling common post-translational modifications. BMC Bioinformatics 15:370CrossRefPubMedCentralGoogle Scholar
  38. Yang C, Wang C, Zhang S, Huang J, Zhou P (2015a) Structural and energetic insights into the intermolecular interaction among human leukocyte antigens, clinical hypersensitive drugs and antigenic peptides. Mol Simul 41:741–751CrossRefGoogle Scholar
  39. Yang C, Zhang S, He P, Wang C, Huang J, Zhou P (2015b) Self-binding peptides: folding or binding. J Chem Inf Model 55:329–342CrossRefPubMedCentralGoogle Scholar
  40. Yang C, Zhang S, Bai Z, Hou S, Wu D, Huang J, Zhou P (2016) A two-step binding mechanism for the self-binding peptide recognition of target domains. Mol BioSyst 12:1201–1213CrossRefPubMedCentralGoogle Scholar
  41. Yao H, Sun Q, Zhu J (2016) Identification and characterization of small-molecule inhibitors to selectively target the DFG-in over DFG-out conformation of the B-Raf kinase V600E mutant in colorectal cancer. Arch Pharm 349:808–815CrossRefGoogle Scholar
  42. Yu H, Zhou P, Deng M, Shang Z (2014) Indirect readout in protein-peptide recognition: a different story from classical biomolecular recognition. J Chem Inf Model 54:2022–2032CrossRefPubMedCentralGoogle Scholar
  43. Zhang BH, Guan KL (2000) Activation of B-Raf kinase requires phosphorylation of the conserved residues Thr599 and Ser602. EMBO J 19:5429–5439CrossRefPubMedCentralGoogle Scholar
  44. Zhang C, Spevak W, Zhang Y, Burton EA, Ma Y, Habets G, Zhang J, Lin J, Ewing T, Matusow B, Tsang G, Marimuthu A, Cho H, Wu G, Wang W, Fong D, Nguyen H, Shi S, Womack P, Nespi M, Shellooe R, Carias H, Powell B, Light E, Sanftner L, Walters J, Tsai J, West BL, Visor G, Rezaei H, Lin PS, Nolop K, Ibrahim PN, Hirth P, Bollag G (2015) RAF inhibitors that evade paradoxical MAPK pathway activation. Nature 526:583–586CrossRefGoogle Scholar
  45. Zhou P, Yang C, Ren Y, Wang C, Tian F (2013a) What are the ideal properties for functional food peptides with antihypertensive effect: a computational peptidology approach. Food Chem 141:2967–2973CrossRefPubMedCentralGoogle Scholar
  46. Zhou P, Wang C, Tian F, Ren Y, Yang C, Huang J (2013b) Biomacromolecular quantitative structure-activity relationship: a proof-of-concept study on the modeling, prediction and interpretation of protein-protein binding affinity. J Comput Aided Mol Des 27:67–78CrossRefPubMedCentralGoogle Scholar
  47. Zhou P, Zhang S, Wang Y, Yang C, Huang J (2016) Structural modeling of HLA-B1502 peptide carbamazepine T-cell receptor complex architecture: implication for the molecular mechanism of carbamazepine induced Stevens–Johnson syndrome/toxic epidermal necrolysis. J Biomol Struct Dyn 34:1806–1817CrossRefPubMedCentralGoogle Scholar

Copyright information

© European Biophysical Societies' Association 2018

Authors and Affiliations

  1. 1.Department of Anorectal SurgeryWeifang People’s Hospital Affiliated to Weifang Medical UniversityWeifangChina

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