Conventional Molecular Dynamics and Metadynamics Simulation Studies of the Binding and Unbinding Mechanism of TTR Stabilizers AG10 and Tafamidis

Abstract

Amyloid transthyretin (ATTR) amyloidosis is a widespread and fatal systemic amyloidosis characterized by the misfolding and amyloid aggregation of transthyretin (TTR). Studies suggest that dissociation of the TTR tetramer is the key step for its misfolding. Because of the importance of tetramer dissociation on ATTR amyloidosis, many TTR stabilizers have been discovered to stabilize the tetramer structure. This paper describes the application conventional molecular dynamics and metadynamics simulations to investigate the binding and unbinding mechanisms of two TTR stabilizers, including AG10 and tafamidis. AG10 has been granted an orphan drug designation by the U.S. Food and Drug Administration (FDA), and tafamidis was the first FDA-approved treatment for ATTR cardiomyopathy. The conventional molecular dynamics simulations reveal that both AG10 and tafamidis can stabilize the TTR tetramer through different mechanisms. AG10 stabilizes TTR tetramer by forming H-bonds with S117 to mimic the protective effect of T119M. Tafamidis stabilizes the tetramer by forming H-bond with S52 in the flexible CD loop to increase its structural stability. Despite the strong binding affinity of tafamidis, the free-energy surface constructed from metadynamics simulation suggests that tafamidis unbinds more readily than AG10 with lower free-energy barriers between the binding state and other intermediates. Finally, by performing pharmacophore analysis, we found two common important moieties of the studied compounds for their binding on the pockets, which can provide valuable guidance for future lead compounds' optimization in designing drugs for ATTR amyloidosis.

Development of a Highly Potent Transthyretin Amyloidogenesis Inhibitor: Design, Synthesis, and Evaluation

“…Molecular dynamics (MD) simulations allow studying the structural dynamics of biological systems at atomic resolution . MD simulations are especially useful in modeling and assessing the binding capacity of small molecules to target proteins since they not only provide atomic information on the interaction but also allow estimation of the binding energetics. , MD simulations have been used to investigate the impact of mutations on TTR conformational flexibility , and to investigate the mechanism of TTR protection by existent kinetic stabilizers. − However, to the best of our knowledge, MD-based methods for estimating binding affinities have not been employed to assist in the design of novel molecules aimed to interact with T 4 -binding sites.…”

“… 49 , 50 MD simulations have been used to investigate the impact of mutations on TTR conformational flexibility 51 , 52 and to investigate the mechanism of TTR protection by existent kinetic stabilizers. 53 − 55 However, to the best of our knowledge, MD-based methods for estimating binding affinities have not been employed to assist in the design of novel molecules aimed to interact with T 4 -binding sites.…”

Clinical and biochemical characterization of hereditary transthyretin amyloidosis caused by E61K mutation

“…Diflunisal acted as a tetramer stabilizer for the treatment of ATTR-CM, as the associated survival benefits were reported to be similar to those of Tafamidis (Maurer et al, 2018 ; Ibrahim et al, 2022 ). AG10 stabilized TTR tetramer by forming H-bonds with S117 (Zhou et al, 2020 ), and AG10 treatment was well-tolerated, achieved target plasma concentrations, and demonstrated near-complete stabilization of TTR (Judge et al, 2019 ; Nelson et al, 2021 ). In this work, it was found that E61K-TTR homozygous proteins and E61K: WT-TTR heterozygous tetramers might respond to current kinetic stabilizers less effectively compared to WT-TTR because full inhibition of fibril formation could be achieved for WT-TTR based on previously reported in vitro results.…”

Effect of Tafamidis on Serum Transthyretin Levels in Non-Trial Patients With Transthyretin Amyloid Cardiomyopathy

“…AG10 has a somewhat different mechanism of stabilization from tafamidis in that it was designed to mimic the structural form of the TTR “super-stabilizer” variant, T119M. AG10 forms hydrogen bonds with serine residues at the same site as the T119M variant and, based on assays of stabilization, it is believed to be a more potent stabilizer of TTR than is tafamidis ( 9 , 10 ). However, a major problem in theorizing improved efficacy of TTR stabilizers based on assays of stabilization is that there are several assays and all are performed under nonphysiologic conditions.…”