Inhibition Mechanisms of a Pyridazine-Based Amyloid Inhibitor: As a β-Sheet Destabilizer and a Helix Bridge Maker.

Conformational diseases have been investigated extensively in recent years; as a result, a number of drug candidates have been introduced as amyloid inhibitors; however, no effective therapies have been put forward. RS-0406 with pyridazine as its core chemical structure has so far shown promising results in inhibiting amyloid formation. In the present work, using molecular dynamics, we undertook the investigation of RS-0406 interactions with U-shaped Aβ and Aβ pentamers, Aβ monomers, and double-horseshoe-like Aβ. To set better parameters for the small molecule, experimental and computational log P values were obtained. In addition, an analogue of RS-0406 was also simulated for comparison. The results indicate that RS-0406 may inhibit amyloid formation exploiting two different mechanisms. One mechanism includes stabilizing the α helix, in the monomer peptide, by binding to the flanking sites of the amyloidogenic region. The second mechanism mediates through interaction of the small molecules near the amyloidogenic regions, leading to destabilization of the β-sheets in both the U-shaped and the S-shaped fibril. Notably, a persistent interaction between the imidazole ring of His14 from an S-shaped structure and the pyridazine ring of RS-0406 was observed. The unique structural properties of RS-0406, including aromaticity, H-bonding capability, flexibility, and symmetry, allow the small molecule to noticeably affect amyloid formation.