The present article reviews published efforts to study acetylcholinesterase and butyrylcholinesterase structure and function using computer-based modeling and simulation techniques. Structures and models of both enzymes from various organisms, including rays, mice, and humans, are discussed to highlight key structural similarities in the active site gorges of the two enzymes, such as flexibility, binding site location, and function, as well as differences, such as gorge volume and binding site residue composition. Catalytic studies are also described, with an emphasis on the mechanism of acetylcholine hydrolysis by each enzyme and novel mutants that increase catalytic efficiency. The inhibitory activities of myriad compounds have been computationally assessed, primarily through Monte Carlo-based docking calculations and molecular dynamics simulations. Pharmaceutical compounds examined herein include FDA-approved therapeutics and their derivatives, as well as several other prescription drug derivatives. Cholinesterase interactions with both narcotics and organophosphate compounds are discussed, with the latter focusing primarily on molecular recognition studies of potential therapeutic value and on improving our understanding of the reactivation of cholinesterases that are bound to toxins. This review also explores the inhibitory properties of several other organic and biological moieties, as well as advancements in virtual screening methodologies with respect to these enzymes.

All-atom molecular dynamics simulations of butyrylcholinesterase (BChE) sans inhibitor and in complex with each of fifteen dialkyl phenyl phosphate derivatives were conducted to characterize inhibitor binding modes and strengths. Each system was sampled on the 250 ns timescale in explicit ionic solvent, for a total of over 4 μs of simulation time. A K-means algorithm was used to cluster the resulting structures into distinct binding modes, which were further characterized based on atomic-level contacts between inhibitor chemical groups and active site residues. Comparison of experimentally observed inhibition constants (K_I) with the resulting contact tables provides structural explanations for relative binding coefficients and highlights several notable interaction motifs. These include ubiquitous contact between glycines in the oxyanion hole and the inhibitor phosphate group; a sterically-driven binding preference for positional isomers that extend aromaticity; a stereochemical binding preference for choline-containing inhibitors, which mimic natural BChE substrates; and the mechanically-induced opening of the omega loop region to fully expose the active site gorge in the presence of choline-containing inhibitors. Taken together, these observations can greatly inform future design of BChE inhibitors, and the approach reported herein is generalizable to other enzyme-inhibitor systems and similar complexes that depend on non-covalent molecular recognition.

Molecular docking plays an increasingly necessary role in interdisciplinary research, particularly in modern drug design. Pharmaceutical companies compose a trillion dollar per year industry and the public is generally unaware of how beneficial pharmaceutics come to be. Despite this increasing relevance in contemporary research, docking and, by extension, computational science, have been under-represented in undergraduate education in the chemical, biochemical, and biophysical sciences. We describe herein how a multidisciplinary approach is used to design novel inhibitors of the butyrylcholinesterase enzyme (BChE), an upregulated protein in patients suffering from Alzheimer’s disease. Students will then be able to compare their designed inhibitors to known BChE inhibitors via molecular docking using this easily adapted hands-on computational laboratory exercise or at-home activity that provides users with a module in which to learn the fundamentals of computer-aided drug design. While being well suited for upper-division courses in biology/biochemistry and physics/physical chemistry, the accessibility of this module allows for its incorporation into college curricula as early as second-term organic chemistry. Highly portable freeware makes this an ideal learning tool by which to infuse single- or multidisciplinary drug design reasoning into college level curricula at no cost to the student or instructor.