Israeli scientists learn important lessons for drug design from acetylcholinesterase

Some pesticides and nerve agents target acetylcholinesterase, an enzyme that has a key role in neuronal signaling. These chemicals are also used in the laboratory to block enzymatic degradation during protein purification.

How these inhibitors block the  target enzyme is often of interest to scientists. Docking studies which model the conformation and orientation of both molecules to determine how the enzyme inhibitor should attach or bind to its target are common in this field. Drug designers commonly make use of such docking studies in developing specific drugs.

But docking studies are not enough to produce reliable results, according to a team of scientists from the Weizmann Institute of Science in Israel. Their experiments with two sulfonylating agents, show that similar three-dimensional geometries of acetylcholinesterase from two different organisms respond differently to acetylcholinesterase inhibitors. As a result, the researchers argue, molecular dynamic simulations are necessary in addition to docking studies.

The mouse and the torpedo fish

The research team used acetylcholinesterase from a mouse and the electric torpedo fish, whose three-dimensional geometries look alike. They tested both with the sulfonylating inhibitors benzenesulfonyl fluoride (BSF) and phenylmethylsulfonylfluoride (PMSF).

What they found was surprising. The torpedo enzyme was inhibited by the benzenesulfonyl fluoride, but was "completely resistant to" PMSF. The mouse enzyme was inhibited by both sulfonylating agents. 

To figure out why this was the case, when they had such similar shapes, the research team carried out docking experiments and then molecular dynamics simulation. The docking experiments could not detect differences between the mouse and torpedo enzymes and predicted both inhibitors would be effective.

However, they determined from the molecular dynamics simulations that the mouse enzyme is more flexible than the torpedo enzyme. The structure of the torpedo enzyme traps the inhibitor in a narrow gorge that creates a bottleneck at its midpoint. The cross-section of the gorge is narrower than that of the inhibitor.

The researchers show how the mouse acetylcholinesterase crystal structure has an intrinsic flexibility, lacking in the torpedo acetylcholinesterase, although the three-dimensional structures "are almost identical." They describe the flexibility of the mouse acetylcholinesterase crystal structure as akin to "breathing motions."

"Our studies demonstrate that reliance on docking tools in drug design can produce misleading information," the researchers conclude. "Docking studies should, therefore, also be complemented by molecular dynamics simulations in selection of lead compounds."

Their research appears in the journal Chemico-Biological Interactions, June 19, 2019.

-----

Nellore Bhanu Chandar et al. Molecular dynamics simulations of the interaction of mouse and torpedo acetylcholinesterase with covalent inhibitors explain their differential reactivity: Implications for drug design. Chemico-Biological Interactions, June 19, 2019. DOI: https://doi.org/10.1016/j.cbi.2019.06.028