Multimodal small-molecule screening for human prion protein binders

Abstract

Prion disease is a rapidly progressive neurodegenerative disorder caused by misfolding and aggregation of the prion protein (PrP), and there are currently no therapeutic options. PrP ligands could theoretically antagonize prion formation by protecting the native protein from misfolding or by targeting it for degradation, but no validated small-molecule binders have been discovered to date. We deployed a variety of screening methods in an effort to discover binders of PrP, including 19 F-observed and saturation transfer difference (STD) nuclear magnetic resonance (NMR) spectroscopy, differential scanning fluorimetry (DSF), DNA-encoded library selection, and in silico screening. A single benzimidazole compound was confirmed in concentration-response, but affinity was very weak (Kd > 1 mM), and it could not be advanced further. The exceptionally low hit rate observed here suggests that PrP is a difficult target for small-molecule binders. While orthogonal binder discovery methods could yield high affinity compounds, non-small-molecule modalities may offer independent paths forward against prion disease.

Machine Learning Prediction of Allosteric Drug Activity from Molecular Dynamics

“…The improved knowledge of gene organization coupled with the advances in gene editing and structural analysis methods can potentially start a whole new era in drug discovery. , In particular, improved target identification can shed light on biomolecules whose perturbation via small-molecule binding results in a functional response, transforming a disease phenotype into a normal one. The extraordinary complexity of biochemical networks in healthy and disease conditions , and the costs associated with drug discovery are however hampering the advent of this new era of therapeutics, as shown by the relatively low numbers of new drugs approved in the past few years. , Most drug discovery efforts aim at targeting the active sites of enzymes or the orthosteric sites of regulatory proteins. Because of the evolutionary and structural conservation of such sites across the proteome, issues related to selectivity, off-target effects, and development of drug resistance have started to appear.…”