Original articles
Dae-Hwan Kim, Chunyan Ren, Chongsuk Ryou, Jiaojie Li. Direct interaction of DNMT inhibitors to PrPC suppresses pathogenic process of prion[J]. Acta Pharmaceutica Sinica B, 2019, 9(5): 952-959

Direct interaction of DNMT inhibitors to PrPC suppresses pathogenic process of prion
Dae-Hwan Kima,b, Chunyan Renc, Chongsuk Ryoua,d, Jiaojie Lie
a Institute of Pharmaceutical Science and Technology, Hanyang University, Ansan 15588, Republic of Korea;
b School of Undergraduate Studies, College of Transdisciplinary Studies, Daegu Gyeongbuk Institute of Science and Technology, Daegu 42988, Republic of Korea;
c Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA;
d Department of Pharmacy, Hanyang University, Ansan 15588, Republic of Korea;
e Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
Abstract:
The conversion of the normal cellular prion protein (PrPC) to the misfolded pathogenic scrapie prion protein (PrPSc) is the biochemical hallmark of prion replication. So far, various chemical compounds that inhibit this conformational conversion have been identified. Here, we report the novel anti-prion activity of SGI-1027 and its meta/meta analogue (M/M), previously known only as potent inhibitors of DNA methyltransferases (DNMTs). These compounds effectively decreased the level of PrPSc in cultured cells with permanent prion infection, without affecting PrPC at the transcriptional or translational levels. Furthermore, SGI-1027 prevented effective prion infection of the cells. In a PrP aggregation assay, both SGI-1027 and M/M blocked the formation of misfolded PrP aggregates, implying that binding of these compounds hinders the PrP conversion process. A series of binding and docking analyses demonstrated that both SGI-1027 and M/M directly interacted with the C-terminal globular domain of PrPC, but only SGI-1027 bound to a specific region of PrPC with high affinity, which correlates with its potent antiprion efficacy. Therefore, we report SGI-1027 and related compounds as a novel class of potential antiprion agents that preferentially function through direct interaction with PrPC.
Key words:    Prion    DNMT    Therapeutic compounds    PrPC    Epigenetic regulation   
Received: 2018-12-27     Revised: 2019-03-17
DOI: 10.1016/j.apsb.2019.04.001
Funds: We thank Keun-Hey Ki, Hye-mi Lee, Jihyun. Lee, Trang H. T. Trinh and Sungeun Lee for their help on RNA extraction, protein expression and purification. This research was supported by the grants from Basic Science Research Program through the National Research Foundation of Korea (NRF-2013R1A1A2011210), and Undergraduate Research Program (URP) through Korea Foundation for the Advancement of Science and Creativity (2017030080). This work was also supported by the Korea Health Technology R&D Project through the Korea Health Industry Development Institute (HI16C1085 and HI16C0965) and the research and development funds of Gwangju Institute of Science and Technology (GK10010, Korea).
Corresponding author: Chongsuk Ryou, Jiaojie Li     Email:cryou2@hanyang.ac.kr;jjli@gist.ac.kr
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Dae-Hwan Kim
Chunyan Ren
Chongsuk Ryou
Jiaojie Li

References:
1. Prusiner SB. Prion diseases and the BSE crisis. Science 1997;278:245-51.
2. Das AS, Zou WQ. Prions:beyond a single protein. Clin Microbiol Rev 2016;29:633-58.
3. Zabel MD, Reid C. A brief history of prions. Pathog Dis 2015;73:ftv087.
4. Race RE, Caughey B, Graham K, Ernst D, Chesebro B. Analyses of frequency of infection, specific infectivity, and prion proteinbiosynthesis in Scrapie-infected neuro-blastoma cell clones. J Virol 1988;62:2845-9.
5. Butler DA, Scott MRD, Bockman JM, Borchelt DR, Taraboulos A, Hsiao KK, et al. Scrapie-infected murine neuro-blastoma cells produce protease-resistant prion proteins. J Virol 1988;62:1558-64.
6. Cobb NJ, Surewicz WK. Prion diseases and their biochemical mechanisms. Biochemist 2009;48:2574-85.
7. Prusiner SB. Novel proteinaceous infectious particles cause scrapie. Science 1982;216:136-44.
8. Aguzzi A, Polymenidou M. Mammalian prion biology:one century of evolving concepts. Cell 2004;116:313-27.
9. Caughey B, Baron GS, Chesebro B, Jeffrey M. Getting a grip on prions:oligomers, amyloids, and pathological membrane interactions. Annu Rev Biochem 2009;78:177-204.
10. Kuwata K, Nishida N, Matsumoto T, Kamatari YO, HosokawaMuto J, Kodama K, et al. Hot spots in prion protein for pathogenic conversion. Proc Natl Acad Sci U S A 2007;104:11921-6.
11. Ferreira NC, Marques IA, Conceicao WA, Macedo B, Machado CS, Mascarello A, et al. Anti-prion activity of a panel of aromatic chemical compounds:in vitro and in silico approaches. PLoS One 2014;9:e84531.
12. Trevitt CR, Collinge J. A systematic review of prion therapeutics in experimental models. Brain 2006;129:2241-65.
13. Cashman NR, Caughey B. Prion diseasesdclose to effective therapy?. Nat Rev Drug Discov 2004;3:874-84.
14. Risse E, Nicoll AJ, Taylor WA, Wright D, Badoni M, Yang XF, et al. Identification of a compound that disrupts binding of amyloid-beta to the prion protein using a novel fluorescence-based assay. J Biol Chem 2015;290:17020-8.
15. Kuwata K, Nishida N, Matsumoto T, Kamatari YO, HosokawaMuto J, Kodama K, et al. Hot spots in prion protein for pathogenic conversion. Proc Natl Acad Sci U S A 2007;104:11921-6.
16. Kimura T, Hosokawa-Muto J, Kamatari YO, Kuwata K. Synthesis of GN8 derivatives and evaluation of their antiprion activity in TSEinfected cells. Bioorg Med Chem Lett 2011;21:1502-7.
17. Hosokawa-Muto J, Kamatari YO, Nakamura HK, Kuwata K. Variety of antiprion compounds discovered through an in silico screen based on cellular-form prion protein structure:correlation between antiprion activity and binding affinity. Antimicrob Agents Chemother 2009;53:765-71.
18. Kimura T, Hosokawa-Muto J, Asami K, Murai T, Kuwata K. Synthesis of 9-substituted 2,3,4,9-tetrahydro-1H-carbazole derivatives and evaluation of their anti-prion activity in TSE-infected cells. Eur J Med Chem 2011;46:5675-9.
19. Ishibashi D, Nakagaki T, Ishikawa T, Atarashi R, Watanabe K, Cruz FA, et al. Structure-based drug discovery for prion disease using a novel binding simulation. Ebiomedicine 2016;9:238-49.
20. Hyeon JW, Choi J, Kim SY, Govindaraj RG, Hwang KJ, Lee YS, et al. Discovery of novel anti-prion compounds using in silico and in vitro approaches. Sci Rep 2015;5:14944.
21. Korth C, May BC, Cohen FE, Prusiner SB. Acridine and phenothiazine derivatives as pharmacotherapeutics for prion disease. Proc Natl Acad Sci U S A 2001;98:9836-41.
22. Doh-Ura K, Iwaki T, Caughey B. Lysosomotropic agents and cysteine protease inhibitors inhibit scrapie-associated prion protein accumulation. J Virol 2000;74:4894-7.
23. Vogtherr M, Grimme S, Elshorst B, Jacobs DM, Fiebig K, Griesinger C, et al. Antimalarial drug quinacrine binds to C-terminal helix of cellular prion protein. J Med Chem 2003;46:3563-4.
24. Bestor TH. The DNA methyltransferases of mammals. Hum Mol Genet 2000;9:2395-402.
25. Datta J, Ghoshal K, Denny WA, Gamage SA, Brooke DG, Phiasivongsa P, et al. A new class of quinoline-based DNA hypomethylating agents reactivates tumor suppressor genes by blocking DNA methyltransferase 1 activity and inducing its degradation. Cancer Res 2009;69:4277-85.
26. Qureshi IA, Mehler MF. Developing epigenetic diagnostics and therapeutics for brain disorders. Trends Mol Med 2013;19:732-41.
27. Urdinguio RG, Sanchez-Mut JV, Esteller M. Epigenetic mechanisms in neurological diseases:genes, syndromes, and therapies. Lancet Neurol 2009;8:1056-72.
28. Saijo E, Kang HE, Bian J, Bowling KG, Browning S, Kim S, et al. Epigenetic dominance of prion conformers. PLoS Pathog 2013;9:e1003692.
29. Valente S, Liu Y, Schnekenburger M, Zwergel C, Cosconati S, Gros C, et al. Selective non-nucleoside inhibitors of human DNA methyltransferases active in cancer including in cancer stem cells. J Med Chem 2014;57:701-13.
30. Ryou C, Legname G, Peretz D, Craig JC, Baldwin MA, Prusiner SB. Differential inhibition of prion propagation by enantiomers of quinacrine. Lab Invest 2003;83:837-43.
31. Kang HE, Weng CC, Saijo E, Saylor V, Bian J, Kim S, et al. Characterization of conformation-dependent prion protein epitopes. J Biol Chem 2012;287:37219-32.
32. Klohn PC, Stoltze L, Flechsig E, Enari M, Weissmann C. A quantitative, highly sensitive cell-based infectivity assay for mouse scrapie prions. Proc Natl Acad Sci U S A 2003;100:11666-71.
33. Kim DH, Lee HM, Ryou C. Evaluation of infective property of recombinant prion protein amyloids in cultured cells overexpressing cellular prion protein. J Korean Med Sci 2014;29:1604-9.
34. Wallace AC, Laskowski RA, Thornton JM. LIGPLOT:a program to generate schematic diagrams of protein-ligand interactions. Protein Eng 1995;8:127-34.
35. Grosdidier A, Zoete V, Michielin O. Fast docking using the CHARMM force field with EADock DSS. J Comput Chem 2011;32:2149-59.
36. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, et al. UCSF chimerada visualization system for exploratory research and analysis. J Comput Chem 2004;25:1605-12.
37. Barreca ML, Iraci N, Biggi S, Cecchetti V, Biasini E. Pharmacological agents targeting the cellular prion protein. Pathogens 2018;7:27.
38. Mallucci G, Collinge J. Rational targeting for prion therapeutics. Nat Rev Neurosci 2005;6:23-34.
39. Murakami-Kubo I, Doh-Ura K, Ishikawa K, Kawatake S, Sasaki K, Kira J, et al. Quinoline derivatives are therapeutic candidates for transmissible spongiform encephalopathies. J Virol 2004;78:1281-8.
40. Kocisko DA, Baron GS, Rubenstein R, Chen J, Kuizon S, Caughey B. New inhibitors of scrapie-associated prion protein formation in a library of 2000 drugs and natural products. J Virol 2003;77:10288-94.
41. Hosokawa-Muto J, Kamatari YO, Nakamura HK, Kuwata K. Variety of antiprion compounds discovered through an in silico screen based on cellular-form prion protein structure:correlation between antiprion activity and binding affinity. Antimicrob Agents Chemother 2009;53:765-71.
42. Kamatari YO, Hayano Y, Yamaguchi K, Hosokawa-Muto J, Kuwata K. Characterizing antiprion compounds based on their binding properties to prion proteins:implications as medical chaperones. Protein Sci 2013;22:22-34.
43. Kawatake S, Nishimura Y, Sakaguchi S, Iwaki T, Doh-ura K. Surface plasmon resonance analysis for the screening of anti-prion compounds. Biol Pharm Bull 2006;29:927-32.
44. Abskharon RN, Giachin G, Wohlkonig A, Soror SH, Pardon E, Legname G, et al. Probing the N-terminal β-sheet conversion in the crystal structure of the human prion protein bound to a nanobody. J Am Chem Soc 2014;136:937-44.
45. Wille H, Bian W, McDonald M, Kendall A, Colby DW, Bloch L, et al. Natural and synthetic prion structure from X-ray fiber diffraction. Proc Natl Acad Sci U S A 2009;106:16990-5.
46. Lee S, Antony L, Hartmann R, Knaus KJ, Surewicz K, Surewicz WK, et al. Conformational diversity in prion protein variants influences intermolecular β-sheet formation. EMBO J 2010;29:251-62.
47. Baskakov IV. Autocatalytic conversion of recombinant prion proteins displays a species barrier. J Biol Chem 2004;279:7671-7.
48. Colby DW, Zhang Q, Wang S, Groth D, Legname G, Riesner D, et al. Prion detection by an amyloid seeding assay. Proc Natl Acad Sci U S A 2007;104:20914-9.
49. Stohr J, Weinmann N, Wille H, Kaimann T, Nagel-Steger L, Birkmann E, et al. Mechanisms of prion protein assembly into amyloid. Proc Natl Acad Sci U S A 2008;105:2409-14.