Identification of a small peptide that inhibits PCSK9 protein binding to the low density lipoprotein receptor

Journal of Biological Chemistry

Volumn 289, Issue 2, 2014, Pages 942-955

  Zhang, Yingnan ^a   Eigenbrot, Charles ^b   Zhou, Lijuan ^a   Shia, Steven ^b   Li, Wei ^a   Quan, Clifford ^a   Tom, Jeffrey ^a   Moran, Paul ^a   Lello, Paola Di ^b   Skelton, Nicholas J ^c   Kong Beltran, Monica ^a   Peterson, Andrew ^a   Kirchhofer, Daniel ^a  

^a GENENTECH INC   (United States)

^b Departments of Structural Biology   (United States)

^c Departments of Discovery Chemistry   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING PEPTIDE; INHIBITORY MECHANISM; LDL RECEPTORS; LOW DENSITY LIPOPROTEIN RECEPTORS; PROTEIN BINDING;

BIOCHEMISTRY;

PEPTIDES;

MEMBRANE PROTEIN; OXIDIZED LOW DENSITY LIPOPROTEIN RECEPTOR; PEP2-8 PEPTIDE; PROPROTEIN CONVERTASE SUBTILISIN KEXIN TYPE 9; PROTEIN INHIBITOR; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ANIMAL CELL; ARTICLE; BINDING AFFINITY; BINDING SITE; BIOTINYLATION; CARBOXY TERMINAL SEQUENCE; CATALYSIS; CONTROLLED STUDY; CRYSTAL STRUCTURE; CRYSTALLIZATION; ENZYME SPECIFICITY; HUMAN; HUMAN CELL; HYDROGEN BOND; HYDROPHOBICITY; NONHUMAN; PEPTIDE ANALYSIS; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN PROTEIN INTERACTION; PROTEIN PURIFICATION; PROTEIN STRUCTURE;

CRYSTAL STRUCTURE; LDL RECEPTOR; PCSK9; PEPTIDES; PHAGE DISPLAY; PROTEASE; PROTEIN-PROTEIN INTERACTIONS;

AMINO ACID SEQUENCE; ANIMALS; BINDING SITES; BINDING, COMPETITIVE; CHO CELLS; CRICETINAE; CRICETULUS; CRYSTALLOGRAPHY, X-RAY; DOSE-RESPONSE RELATIONSHIP, DRUG; ENZYME INHIBITORS; HEP G2 CELLS; HUMANS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; OLIGOPEPTIDES; PEPTIDE LIBRARY; PROPROTEIN CONVERTASES; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; RECEPTORS, LDL; SERINE ENDOPEPTIDASES;

EID: 84891904473     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M113.514067     Document Type: Article

References (54)

1. Seidah, N. G., Benjannet, S., Wickham, L., Marcinkiewicz, J., Jasmin, S. B., Stifani, S., Basak, A., Prat, A., and Chretien, M. (2003) The secretory proprotein convertase neural apoptosis-regulated convertase 1 (NARC-1). Liver regeneration and neuronal differentiation. Proc. Natl. Acad. Sci. U.S.A. 100, 928-933
2. Costet, P., Krempf, M., and Cariou, B. (2008) PCSK9 and LDL cholesterol. Unravelling the target to design the bullet. Trends Biochem. Sci. 33, 426-434
3. Horton, J. D., Cohen, J. C., and Hobbs, H. H. (2009) PCSK9. A convertase that coordinates LDL catabolism. J. Lipid Res. 50, S172-S177
4. Seidah, N. G. (2009) PCSK9 as a therapeutic target of dyslipidemia. Expert Opin. Ther. Targets 13, 19-28
5. Zhang, D. W., Lagace, T. A., Garuti, R., Zhao, Z., McDonald, M., Horton, J. D., Cohen, J. C., and Hobbs, H. H. (2007) Binding of proprotein convertase subtilisin/kexin type 9 to epidermal growth factor-like repeatAof low density lipoprotein receptor decreases receptor recycling and increases degradation. J. Biol. Chem. 282, 18602-18612
6. Holla, Ø. L., Cameron, J., Tveten, K., Strøm, T. B., Berge, K. E., Laerdahl, J. K., and Leren, T. P. (2011) Role of the C-terminal domain of PCSK9 in degradation of the LDL receptors. J. Lipid Res. 52, 1787-1794
7. Yamamoto, T., Lu, C., and Ryan, R. O. (2011) A two-step binding model of PCSK9 interaction with the low density lipoprotein receptor. J. Biol. Chem. 286, 5464-5470
8. Tveten, K., Holla, Ø. L., Cameron, J., Strøm, T. B., Berge, K. E., Laerdahl, J. K., and Leren, T. P. (2012) Interaction between the ligand-binding domain of the LDL receptor and the C-terminal domain of PCSK9 is required for PCSK9 to remain bound to the LDL receptor during endosomal acidification. Hum. Mol. Genet. 21, 1402-1409
9. DeVay, R. M., Shelton, D. L., and Liang, H. (2013) Characterization of PCSK9 trafficking reveals a novel lysosomal targeting mechanism via APLP2. J. Biol. Chem. 288, 10805-10818
10. Abifadel, M., Varret, M., Rabès, J. P., Allard, D., Ouguerram, K., Devillers, M., Cruaud, C., Benjannet, S., Wickham, L., Erlich, D., Derré, A., Villéger, L., Farnier, M., Beucler, I., Bruckert, E., Chambaz, J., Chanu, B., Lecerf, J. M., Luc, G., Moulin, P., Weissenbach, J., Prat, A., Krempf, M., Junien, C., Seidah, N. G., and Boileau, C. (2003) Mutations in PCSK9 cause autosomal dominant hypercholesterolemia. Nat. Genet. 34, 154-156
11. Cohen, J. C., Boerwinkle, E., Mosley, T. H., Jr., and Hobbs, H. H. (2006) Sequence variations in PCSK9, low LDL, and protection against coronary heart disease. N. Engl. J. Med. 354, 1264-1272
12. Zhao, Z., Tuakli-Wosornu, Y., Lagace, T. A., Kinch, L., Grishin, N. V., Horton, J. D., Cohen, J. C., and Hobbs, H. H. (2006) Molecular characterization of loss-of-function mutations in PCSK9 and identification of a compound heterozygote. Am. J. Hum. Genet. 79, 514-523
13. Stein, E. A., and Swergold, G. D. (2013) Potential of proprotein convertase subtilisin/kexin type 9 based therapeutics. Curr. Atheroscler. Rep. 15, 310
14. Cunningham, D., Danley, D. E., Geoghegan, K. F., Griffor, M. C., Hawkins, J. L., Subashi, T. A., Varghese, A. H., Ammirati, M. J., Culp, J. S., Hoth, L. R., Mansour, M. N., McGrath, K. M., Seddon, A. P., Shenolikar, S., Stutzman-Engwall, K. J., Warren, L. C., Xia, D., and Qiu, X. (2007) Structural and biophysical studies of PCSK9 and its mutants linked to familial hypercholesterolemia. Nat. Struct. Mol. Biol. 14, 413-419
15. Hampton, E. N., Knuth, M. W., Li, J., Harris, J. L., Lesley, S. A., and Spraggon, G. (2007) The self-inhibited structure of full-length PCSK9 at 1.9 Å reveals structural homology with resistin within the C-terminal domain. Proc. Natl. Acad. Sci. U.S.A. 104, 14604-14609
16. Piper, D. E., Jackson, S., Liu, Q., Romanow, W. G., Shetterly, S., Thibault, S. T., Shan, B., and Walker, N. P. (2007) The crystal structure of PCSK9. A regulator of plasma LDL-cholesterol. Structure 15, 545-552
17. Li, J., Tumanut, C., Gavigan, J. A., Huang, W. J., Hampton, E. N., Tumanut, R., Suen, K. F., Trauger, J. W., Spraggon, G., Lesley, S. A., Liau, G., Yowe, D., and Harris, J. L. (2007) Secreted PCSK9 promotes LDL receptor degradation independently of proteolytic activity. Biochem. J. 406, 203-207
18. McNutt, M. C., Lagace, T. A., and Horton, J. D. (2007) Catalytic activity is not required for secreted PCSK9 to reduce low density lipoprotein receptors in HepG2 cells. J. Biol. Chem. 282, 20799-20803
19. Lo Surdo, P., Bottomley, M. J., Calzetta, A., Settembre, E. C., Cirillo, A., Pandit, S., Ni, Y. G., Hubbard, B., Sitlani, A., and Carf?́, A. (2011) Mechanistic implications for LDL receptor degradation from the PCSK9/LDLR structure at neutral pH. EMBO Rep. 12, 1300-1305
20. Kwon, H. J., Lagace, T. A., McNutt, M. C., Horton, J. D., and Deisenhofer, J. (2008) Molecular basis for LDL receptor recognition by PCSK9. Proc. Natl. Acad. Sci. U.S.A. 105, 1820-1825
21. Mayer, G., Poirier, S., and Seidah, N. G. (2008) Annexin A2 is C-terminal PCSK9-binding protein that regulates endogenous low density lipoprotein receptor levels. J. Biol. Chem. 283, 31791-31801
22. Ni, Y. G., Condra, J. H., Orsatti, L., Shen, X., Di Marco, S., Pandit, S., Bottomley, M. J., Ruggeri, L., Cummings, R. T., Cubbon, R. M., Santoro, J. C., Ehrhardt, A., Lewis, D., Fisher, T. S., Ha, S., Njimoluh, L., Wood, D. D., Hammond, H. A., Wisniewski, D., Volpari, C., Noto, A., Lo Surdo, P., Hubbard, B., Carf?́, A., and Sitlani, A. (2010) A proprotein convertase subtilisin-like/kexin type 9 (PCSK9) C-terminal domain antibody antigenbinding fragment inhibits PCSK9 internalization and restores low density lipoprotein uptake. J. Biol. Chem. 285, 12882-12891
23. Seidah, N. G., Poirier, S., Denis, M., Parker, R., Miao, B., Mapelli, C., Prat, A., Wassef, H., Davignon, J., Hajjar, K. A., and Mayer, G. (2012) Annexin A2 is a natural extrahepatic inhibitor of the PCSK9-induced LDL receptor degradation. PLoS One 7, e41865
24. Ross, N. T., Katt, W. P., and Hamilton, A. D. (2010) Synthetic mimetics of protein secondary structure domains. Phil. Trans. R. Soc. A. 368, 989-1008
25. Stanger, K., Steffek, M., Zhou, L., Pozniak, C. D., Quan, C., Franke, Y., Tom, J., Tam, C., Krylova, I., Elliott, J. M., Lewcock, J. W., Zhang, Y., Murray, J., and Hannoush, R. N. (2012) Allosteric peptides bind a caspase zymogen and mediate caspase tetramerization. Nat. Chem. Biol. 8, 655-660
26. Zhang, Y., Zhou, L., Kong-Beltran, M., Li, W., Moran, P., Wang, J., Quan, C., Tom, J., Kolumam, G., Elliott, J. M., Skelton, N. J., Peterson, A. S., and Kirchhofer, D. (2012) Calcium-independent inhibition of PCSK9 by affinity-improved variants of the LDL receptor EGF(A) domain. J. Mol. Biol. 422, 685-696
27. Tonikian, R., Zhang, Y., Boone, C., and Sidhu, S. S. (2007) Identifying specificity profiles for peptide recognition modules from phage-displayed peptide libraries. Nat. Protoc. 2, 1368-1386
28. Kunkel, T. A., Roberts, J. D., and Zakour, R. A. (1987) Rapid and efficient site-specific mutagenesis without phenotypic selection. Methods Enzymol. 154, 367-382
29. Otwinowski, Z., and Minor, W. (1996) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326
30. Winn, M. D., Ballard, C. C., Cowtan, K. D., Dodson, E. J., Emsley, P., Evans, P. R., Keegan, R. M., Krissinel, E. B., Leslie, A. G., McCoy, A., McNicholas, S. J., Murshudov, G. N., Pannu, N. S., Potterton, E. A., Powell, H. R., Read, R. J., Vagin, A., and Wilson, K. S. (2011) Overview of the CCP4 suite and current developments. Acta Crystallogr. D Biol. Crystallogr. 67, 235-242
31. McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C., and Read, R. J. (2007) Phaser crystallographic software. J. Appl. Crystallogr. 40, 658-674
32. Emsley, P., Lohkamp, B., Scott, W. G., and Cowtan, K. (2010) Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486-501
33. Adams, P. D., Afonine, P. V., Bunkóczi, G., Chen, V. B., Davis, I. W., Echols, N., Headd, J. J., Hung, L. W., Kapral, G. J., Grosse-Kunstleve, R. W., Mc-Coy, A. J., Moriarty, N. W., Oeffner, R., Read, R. J., Richardson, D. C., Richardson, J. S., Terwilliger, T. C., and Zwart, P. H. (2010) PHENIX. A comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213-221
34. Delaglio, F., Grzesiek, S., Vuister, G. W., Zhu, G., Pfeifer, J., and Bax, A. (1995) NMRPipe. A multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6, 277-293
35. Johnson, B. A., and Blevins, R. A. (1994)NMRView. A computer program for the visualization and analysis ofNMRdata. J. Biomol.NMR4, 603-614
36. Laskowski, R. A., Rullmannn, J. A., MacArthur, M. W., Kaptein, R., and Thornton, J. M. (1996) AQUA and PROCHECK-NMR. Programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR 8, 477-486
37. Bottomley, M. J., Cirillo, A., Orsatti, L., Ruggeri, L., Fisher, T. S., Santoro, J. C., Cummings, R. T., Cubbon, R. M., Lo Surdo, P., Calzetta, A., Noto, A., Baysarowich, J., Mattu, M., Talamo, F., De Francesco, R., Sparrow, C. P., Sitlani, A., and Carf?́, A. (2009) Structural and biochemical characterization of the wild type PCSK9-EGF(AB) complex and natural familial hypercholesterolemia mutants. J. Biol. Chem. 284, 1313-1323
38. Dennis, M. S., Eigenbrot, C., Skelton, N. J., Ultsch, M. H., Santell, L., Dwyer, M. A., O'Connell, M. P., and Lazarus, R. A. (2000) Peptide exosite inhibitors of factor VIIa as anticoagulants. Nature 404, 465-470
39. Lowman, H. B., Chen, Y. M., Skelton, N. J., Mortensen, D. L., Tomlinson, E. E., Sadick, M. D., Robinson, I. C., and Clark, R. G. (1998) Molecular mimics of insulin-like growth factor 1 (IGF-1) for inhibiting IGF-1. IGFbinding protein interactions. Biochemistry 37, 8870-8878
40. Schaffer, M. L., Deshayes, K., Nakamura, G., Sidhu, S., and Skelton, N. J. (2003) Complex with a phage display-derived peptide provides insight into the function of insulin-like growth factor I. Biochemistry 42, 9324-9334
41. Seidah, N. G., and Prat, A. (2012) The biology and therapeutic targeting of the proprotein convertases. Nat. Rev. Drug Discov. 11, 367-383
42. Pan, B., Li, B., Russell, S. J., Tom, J. Y., Cochran, A. G., and Fairbrother, W. J. (2002) Solution structure of a phage-derived peptide antagonist in complex with vascular endothelial growth factor. J. Mol. Biol. 316, 769-787
43. Zhang, Y., Appleton, B. A., Wiesmann, C., Lau, T., Costa, M., Hannoush, R. N., and Sidhu, S. S. (2009) Inhibition of Wnt signaling by Dishevelled PDZ peptides. Nat. Chem. Biol. 5, 217-219
44. Franklin, M. C., Kadkhodayan, S., Ackerly, H., Alexandru, D., Distefano, M. D., Elliott, L. O., Flygare, J. A., Mausisa, G., Okawa, D. C., Ong, D., Vucic, D., Deshayes, K., and Fairbrother, W. J. (2003) Structure and function analysis of peptide antagonists of melanoma inhibitor of apoptosis (ML-IAP). Biochemistry 42, 8223-8231
45. Zobel, K., Wang, L., Varfolomeev, E., Franklin, M. C., Elliott, L. O., Wallweber, H. J., Okawa, D. C., Flygare, J. A., Vucic, D., Fairbrother, W. J., and Deshayes, K. (2006) Design, synthesis, and biological activity of a potent Smac mimetic that sensitizes cancer cells to apoptosis by antagonizing IAPs. ACS Chem. Biol. 1, 525-533
46. Chan, J. C., Piper, D. E., Cao, Q., Liu, D., King, C., Wang, W., Tang, J., Liu, Q., Higbee, J., Xia, Z., Di, Y., Shetterly, S., Arimura, Z., Salomonis, H., Romanow, W. G., Thibault, S. T., Zhang, R., Cao, P., Yang, X. P., Yu, T., Lu, M., Retter, M. W., Kwon, G., Henne, K., Pan, O., Tsai, M. M., Fuchslocher, B., Yang, E., Zhou, L., Lee, K. J., Daris, M., Sheng, J., Wang, Y., Shen, W. D., Yeh, W. C., Emery, M., Walker, N. P., Shan, B., Schwarz, M., and Jackson, S. M. (2009) A proprotein convertase subtilisin/kexin type 9 neutralizing antibody reduces serum cholesterol in mice and nonhuman primates. Proc. Natl. Acad. Sci. U.S.A. 106, 9820-9825
47. Liang, H., Chaparro-Riggers, J., Strop, P., Geng, T., Sutton, J. E., Tsai, D., Bai, L., Abdiche, Y., Dilley, J., Yu, J., Wu, S., Chin, S. M., Lee, N. A., Rossi, A., Lin, J. C., Rajpal, A., Pons, J., and Shelton, D. L. (2012) Proprotein convertase substilisin/kexin type 9 antagonism reduces low-density lipoprotein cholesterol in statin-treated hypercholesterolemic nonhuman primates. J. Pharmacol. Exp. Ther. 340, 228-236
48. Ni, Y. G., Di Marco, S., Condra, J. H., Peterson, L. B., Wang, W., Wang, F., Pandit, S., Hammond, H. A., Rosa, R., Cummings, R. T., Wood, D. D., Liu, X., Bottomley, M. J., Shen, X., Cubbon, R. M., Wang, S. P., Johns, D. G., Volpari, C., Hamuro, L., Chin, J., Huang, L., Zhao, J. Z., Vitelli, S., Haytko, P., Wisniewski, D., Mitnaul, L. J., Sparrow, C. P., Hubbard, B., Carf?́, A., and Sitlani, A. (2011) A PCSK9-binding antibody that structurally mimics the EGF(A) domain of LDL-receptor reduces LDL cholesterol in vivo. J. Lipid Res. 52, 78-86
49. Stein, E. A., Mellis, S., Yancopoulos, G. D., Stahl, N., Logan, D., Smith, W. B., Lisbon, E., Gutierrez, M., Webb, C., Wu, R., Du, Y., Kranz, T., Gasparino, E., and Swergold, G. D. (2012) Effect of a monoclonal antibody to PCSK9 on LDL cholesterol. N. Engl. J. Med. 366, 1108-1118
50. Shan, L., Pang, L., Zhang, R., Murgolo, N. J., Lan, H., and Hedrick, J. A. (2008) PCSK9 binds to multiple receptors and can be functionally inhibited by an EGF-A peptide. Biochem. Biophys. Res. Commun. 375, 69-73
51. McNutt, M. C., Kwon, H. J., Chen, C., Chen, J. R., Horton, J. D., and Lagace, T. A. (2009) Antagonism of secreted PCSK9 increases low density lipoprotein receptor expression in HepG2 cells. J. Biol. Chem. 284, 10561-10570
52. Du, F., Hui, Y., Zhang, M., Linton, M. F., Fazio, S., and Fan, D. (2011) Novel domain interaction regulates secretion of proprotein convertase subtilisin/kexin type 9 (PCSK9) protein. J. Biol. Chem. 286, 43054-43061
53. Palmer-Smith, H., and Basak, A. (2010) Regulatory effects of peptides from the pro and catalytic domains of proprotein convertase subtilisin/kexin 9 (PCSK9) on low-density lipoprotein receptor (LDL-R). Curr. Med. Chem. 17, 2168-2182
54. Andronati, S. A., Karaseva, T. L., and Krysko, A. A. (2004) Peptidomimetics-antagonists of the fibrinogen receptors. Molecular design, structures, properties and therapeutic applications. Curr. Med. Chem. 11, 1183-1211