Small molecular inhibitors of Amyloid β and α Synuclein amyloidogenic aggregation, toxicity and in silico design of amyloid-binding ligands

Abstract

Alzheimer’s disease (AD) and Parkinson’s disease (PD) are the most common forms of dementia and a leading cause of death amongst the older population worldwide. Pathologically, both AD and PD are characterized as progressive neurodegenerative disorders, in which there is a progressive loss of neuronal structure and function leading to loss of neurons in parts of the brain associated with cognition, memory and movement. Amyloidogenic protein misfolding and aggregation is at the centre of the neurodegenerative processes associated with AD and PD. In the case of AD, the amyloidogenic protein is amyloid β (Aβ) and in PD, it is the α Synuclein (αS) protein, or its mutant forms such as αSA53T found in familial PD which aggregates and exerts toxicity. In both AD and PD, we lack truly disease-modifying drug treatments, with current medications largely providing only modest and transient symptomatic improvement. Therefore, the aim of this project was to identify a diverse set of new molecules from both natural and synthetic origin, that can alter Aβ and αSA53T aggregation and fibril formation. Mostly small molecule binding has been studied by molecular docking and effects on Aβ and αSA53T aggregation investigated using a ligand-binding fluorescence kinetic assay (Thioflavin T) and transmission electron microscopy (TEM). For neuroprotection studies, a mitochondrial viability (MTT) assay of neuronal cells (PC-12) was used. Finally, using molecular docking and density functional theory (DFT) approaches, a set of novel amyloid-binding ligands was designed in silico through ligand-based drug design. In the first study, four polyphenolic bioactives including a neolignan, ellagitannin and two flavonoid class of compounds have been comparatively studied for their binding interactions with Aβ, effects on fibril and aggregate formation and neuroprotection. In the second study, a structure-based virtual screening method based on molecular docking has been implemented to identify new small molecule inhibitors of Aβ aggregation and neurotoxicity. Five heterocyclic compounds were selected and tested using the anti-aggregation and neuroprotection methods. Of these, the two best ‘hits’ bearing a novel molecular scaffold have been used in further studies. In the third study, the two virtual screening hits, polyphenolic bioactives from first study and two structurally related flavonoids were tested for inhibition of amyloidogenic aggregation and neuroprotection of the pathological αS mutant, αSA53T. Seven molecules have been compared as per the first and second study. Additionally, the impact on native αSA53T protein conformation was investigated by ion mobility mass spectrometry (IM-MS). In the fourth study, a diverse set of natural bioactives including a neolignan, flavonoid, chalcone, diterpene and alkaloid class of compound were tested for anti-aggregative effects on both αSA53T and Aβ proteins. Additionally, their direct interactions with these amyloidogenic protein targets were studied by molecular docking. The final study employed molecular docking and small molecular structure optimization using DFT method for rational design of a set of novel amyloid ligands. The favourable molecular attributes gleaned from both the bioactive neolignan in the first study and a favourable molecular scaffold in the second study were used to optimise binding for potential anti-aggregation. These ligands were predicted to have improved binding to Aβ and αSA53T in silico. Since there is an urgent need of disease-modifying therapies in both AD and PD, identification of anti-amyloidogenic and neuroprotective molecules would facilitate future drug discovery efforts. Design of a novel amyloid binder would be valuable for research and development of a therapeutic candidate or may assist in further design of an amyloid tracer molecule for diagnostic imaging.