In silico studies on potential binding sites of amyloid inhibitor compounds on amyloid beta peptide

Abstract

The formation of structurally similar insoluble fibrillar protein aggregates, called amyloids, is known to cause several neuronal and non-neuronal degenerative diseases such as Alzheimer‟s disease, Parkinson‟s disease, Huntington‟s disease and Diabetes mellitus type II. In the present scenario, there is still an absence of efficient and medically approved therapeutic agent which could effectively inhibit the formation of amyloid fibrils. The similarity in structure of the amyloid fibrils of different proteins can be exploited to device a common mechanism to inhibit its formation. However, in aqueous solution their tendency to aggregate hinders the effective conformational studies. Thus in the present study we employ in silico approach to explore the inhibition mechanism of amyloidogenesis based on the interaction of an amyloidogenic protein with certain small molecules which have been demonstrated to effectively inhibit fibrillar assemblies. We have chosen an amyloidogenic protein called Beta-amyloid (1-42) which is found to play a crucial role in the onset of Alzheimer‟s disease. The small molecules chosen here are mostly polyphenol molecules which have been found to, specifically and efficiently, inhibit amyloid fibrillogenesis in vitro and attenuate their associated cytotoxicity. Based on the results obtained we attempt to propose a mechanism by which these small molecules inhibit the fibril formation which might be relevant in future for de novo synthesis of small molecule inhibitors for the treatment of amyloidosis.