Molecular dynamics simulations of the interaction of Mouse and Torpedo acetylcholinesterase with covalent inhibitors explain their differential reactivity: Implications for drug design

Nellore Bhanu Chandar,Irena Efremenko,Israel Silman,Jan M.L Martin,Joel L Sussman

doi:10.1016/j.cbi.2019.06.028

Nellore Bhanu Chandar, Irena Efremenko + Show 3 more

Open Access

https://doi.org/10.1016/j.cbi.2019.06.028

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Abstract

Although the three-dimensional structures of mouse and Torpedo californica acetylcholinesterase are very similar, their responses to the covalent sulfonylating agents benzenesulfonyl fluoride and phenylmethylsulfonyl fluoride are qualitatively different. Both agents inhibit the mouse enzyme effectively by covalent modification of its active-site serine. In contrast, whereas the Torpedo enzyme is effectively inhibited by benzenesulfonyl fluoride, it is almost completely resistant to phenylmethylsulfonyl fluoride. A bottleneck midway down the active-site gorge in both enzymes restricts access of ligands to the active site at the bottom of the gorge. Molecular dynamics simulations revealed that the mouse enzyme is substantially more flexible than the Torpedo enzyme, suggesting that enhanced ‘breathing motions’ of the mouse enzyme relative to the Torpedo enzyme may explain why phenylmethylsulfonyl fluoride can reach the active site in mouse acetylcholinesterase, but not in the Torpedo enzyme. Accordingly, we performed docking of the two sulfonylating agents to the two enzymes, followed by molecular dynamics simulations. Whereas benzenesulfonyl fluoride closely approaches the active-site serine in both mouse and Torpedo acetylcholinesterase in such simulations, phenylmethylsulfonyl fluoride is able to approach the active-site serine of mouse acetylcholinesterase, but remains trapped above the bottleneck in the Torpedo enzyme. Our studies demonstrate that reliance on docking tools in drug design can produce misleading information. Docking studies should, therefore, also be complemented by molecular dynamics simulations in selection of lead compounds. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:CHEMBIOINT:2.

Highlights

The principal biological role of acetylcholinesterase (AChE) is termination of transmission at cholinergic synapses by rapid hydrolysis of the neurotransmitter, acetylcholine (ACh) [1, 2].The crystal structure of TcAChE revealed that, despite the high catalytic activity of AChE, which approaches diffusion control [3], its active site is near the bottom of a long and narrow gorge, >15 Å long, a large part of the surface of which is lined by aromatic residues [4]
We reported that AChE from the electric organ of another electric fish, Torpedo californica (Tc) AChE, is resistant to Phenylmethylsulfonyl fluoride (PMSF), but is irreversibly inhibited very effectively by its homolog benzenesulfonyl fluoride (BSF) (Scheme 1) [13]
TcAChE being replaced by Y337 in mouse AChE (mAChE), with the sidechains of these two residues being oriented very differently (Fig 3). (ii) In mAChE there are four residues, P258-P259-G260-G261, which are absent in TcAChE (Fig 4)

Summary

Introduction

The crystal structure of TcAChE revealed that, despite the high catalytic activity of AChE, which approaches diffusion control [3], its active site is near the bottom of a long and narrow gorge, >15 Å long, a large part of the surface of which is lined by aromatic residues [4]. In TcAChE, the cross-section at the narrowest point of the bottleneck is ~5 Å [4]. In mAChE, the narrowest point of the bottleneck has a cross-section of 2.4 Å [5]. Space-filling representations of two ACh molecules are seen, one lodged above the gorge, and one below it [6] This representation clearly illustrates that the AChE molecule needs to ‘breathe’ substantially in order for the ACh molecule to pass through the bottleneck to reach the active site

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