Design, synthesis and SAR studies of pyridine dicarbonitriles as potential prion therapeutics

• Main Author: Reddy, Tummala Ramakrishna
• Published: University of Sheffield 2006
• Subjects: 615
• Online Access: http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.485118

Transmissible spongiform encephalopathies (TSEs) also known as prion diseases are a family of invariably fatal neurodegenerative disorders which affect a range of mammalian species. As yet no effective therapy exists for the prevention of either infection or disease progression. It is clear that effective therapeutics for the prion diseases is urgently needed. The central cause of pathogenesis in TSEs is the conversion of normal protease-sensitive prion protein (Prpc) into its abnormal protease-resistant isoform (PrPSC ). This project aims to identify compounds that bind to human Prpc (huPrpc) and stabilize it against this conversion. Using GOLD docking studies followed by biological screening pyridine-3,5dicarbonitriles were identified as lead compounds. Two types of compound libraries were generated using different approaches. Initially, a library of 384 compounds based on the lead compound was generated through derivatisation at 2, 4 and 6 positions of the central pyridine ring. Docking and evaluation using GOLD scores revealed that most of these analogues were predicted to interact better with huPrpc than the parent lead. But there are limitations for many of the targets in this library in terms of synthetic accessibility and hence a reaction based library was generated taking into account the availability of the reactants. A virtual reaction based library of 1,050 compounds of pyridine -3,5-dicarbonitriles was constructed. Docking and evaluation using GOLD scores assisted the initial selection of compounds for synthesis. This selection was augmented with further compounds to increase structural diversity. A total of 46 compounds were synthesized via a one-pot three-component coupling reaction. The mechanism of the three-component coupling reaction was investigated, and it was discovered that chemical oxidation is required for the last step, formation of the pyridine ring (aromatization). All the compounds synthesized were evaluated by in vitro screening using SPR (Surface Plasmon Resonance) technique to measure their affinity towards different forms of prion protein. These compounds were also screened against 5MB cell lines for their ability to prevent the formation of abnormal prion protein (PrPSC ). A set of 19 compounds was identified as binders to one or more forms of prion prote~n. Another set of 8 compounds was active on cell lines at JlM concentrations. No discernable correlation could be found between binding of pyridine . dicarbonitrile analogues to huPrpc and activity in the 5MB cell line assay. The most active compounds 46 and 47 inhibit the formation of Prpsc in 5MB cell lines with an ECso of 1 l!M and 1.5 l!M respectively. Structural modification studies were carried out on best three binders (43, 49 and 60) and also on compound 47, which is one of the most active compounds in 5MB cell lines. Various analogues of these lead compounds were synthesised and the screening results revealed that the best two compounds 43d and 47c showed significant binding affinity towards huPrp c and also showed cell line activity displaying ECso values of 14 l!M and 28 l!M respectively. HQSAR was also carried out to investigate the potential relationship between activity/affinity and structure relating to the holograms, fragment size and fragment distinction parameters. Within the range of compounds tested, no discernible correlation between structure and binding affinity/activity was observed.