Hot spots in prion protein for pathogenic conversion

• Published in: Proceedings of the National Academy of Sciences - PNAS 2007-07, Vol.104 (29), p.11921-11926
• Main Authors: Kuwata, Kazuo, Nishida, Noriyuki, Matsumoto, Tomoharu, Kamatari, Yuji O, Hosokawa-Muto, Junji, Kodama, Kota, Nakamura, Hironori K, Kimura, Kiminori, Kawasaki, Makoto, Takakura, Yuka, Shirabe, Susumu, Takata, Jiro, Kataoka, Yasufumi, Katamine, Shigeru
• Format: Article
• Language: English
• Subjects: Acetamides - chemistry; Acetamides - pharmacology; Animals; Binding sites; Biochemistry; Biological Sciences; Cell culture techniques; Cell lines; Chemical equilibrium; Chemicals; Computational Biology; Drug discovery; Hydrogen bonds; Ligands; Mice; Molecules; Neurological disorders; Neurons; Prion diseases; Prions; Protein Structure, Secondary; PrPC Proteins - antagonists & inhibitors; PrPC Proteins - chemistry; PrPC Proteins - pathogenicity; Recombinant Proteins - metabolism; Rodents
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.0702671104

Prion proteins are key molecules in transmissible spongiform encephalopathies (TSEs), but the precise mechanism of the conversion from the cellular form (PrPC) to the scrapie form (PrPSc) is still unknown. Here we discovered a chemical chaperone to stabilize the PrPC conformation and identified the hot spots to stop the pathogenic conversion. We conducted in silico screening to find compounds that fitted into a "pocket" created by residues undergoing the conformational rearrangements between the native and the sparsely populated high-energy states (PrP*) and that directly bind to those residues. Forty-four selected compounds were tested in a TSE-infected cell culture model, among which one, 2-pyrrolidin-1-yl-N-[4-[4-(2-pyrrolidin-1-yl-acetylamino)-benzyl]-phenyl]-acetamide, termed GN8, efficiently reduced PrPSc. Subsequently, administration of GN8 was found to prolong the survival of TSE-infected mice. Heteronuclear NMR and computer simulation showed that the specific binding sites are the A-S2 loop (N159) and the region from helix B (V189, T192, and K194) to B-C loop (E196), indicating that the intercalation of these distant regions (hot spots) hampers the pathogenic conversion process. Dynamics-based drug discovery strategy, demonstrated here focusing on the hot spots of PrPC, will open the way to the development of novel anti-prion drugs.