Hot spots in prion protein for pathogenic conversion

Abstract

Prion proteins are key molecules in transmissible spongiform encephalopathies (TSEs), but the precise mechanism of the conversion from the cellular form (PrP C ) to the scrapie form (PrP Sc ) is still unknown. Here we discovered a chemical chaperone to stabilize the PrP C 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 PrP Sc . 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 PrP C , will open the way to the development of novel anti-prion drugs.anti-prion compound ͉ binding sites ͉ chemical chaperone ͉ dynamicsbased drug discovery ͉ transmissible spongiform encephalopathy

Molecular Dynamics as an Approach to Study Prion Protein Misfolding and the Effect of Pathogenic Mutations

“…Yamamoto and Kuwata [174] first performed a 100 ns MD simulation of the initially obtained binding mode in water, to refine the PrP-GN8 structure further. The obtained binding mode agreed with NMR chemical shift data [173]. Also, the flexibility of the PrP structure was decreased in comparison with the equivalent simulation without GN8.…”

“…An example is N,N′-(methylenedi-4,1-phenylene)bis[2-(1-pyrrolidinyl)acetamide], or GN8. This compound was found to inhibit PrP Sc production in vitro and prion-infected mice treated with GN8 showed prolonged survival [173]. The molecule was selected based on virtual screening of compounds that would bind in the region of the HA-S2 loop and the HB-HC loop of mouse PrP.…”

A Fluorescent Styrylquinoline with Combined Therapeutic and Diagnostic Activities against Alzheimer’s and Prion Diseases

“…A similar profile was found for GN8, an antiprion drug candidate, for which a specific binding with PrP has been experimentally demonstrated. 26 Taken together, these results show that our candidate molecule 3 is indeed able to recognize, stain and modulate Aβ 42 and PrP Sc fibril aggregation in vitro.…”

FK506 reduces abnormal prion protein through the activation of autolysosomal degradation and prolongs survival in prion-infected mice

“…27 The positive control, GN8, that is known to bind to PRNP C and inhibit the conversion, 28 showed the typical binding signals in a dosedependent manner, while the affinity of FK506 to recPRNP was very low (Fig. S3).…”