Predicting Relative Binding Free Energies of Tacrine−Huperzine A Hybrids as Inhibitors of Acetylcholinesterase^§

Abstract

The binding of the 9-methyl derivative of tacrine-huperzine A hybrid to Torpedo californica acetylcholinesterase (AChE) has been studied by computational methods. Molecular dynamics simulations have been performed for the AChE-drug complex considering two different ionization states of the protein and two different orientations of the drug in the binding pocket, which were chosen from a previous screening procedure. Analysis of structural fluctuations and of the pattern of interactions between drug and enzyme clearly favor one binding mode for the tacrine-huperzine A hydrid, which mixes effectively some of the binding features of tacrine and huperzine A. The differences in inhibitory activity for a series of related derivatives have been successfully predicted by free energy calculations, which reinforces the confidence in the binding mode and its usefulness for molecular modeling studies. The same techniques have been used to make de novo predictions for a new 3-fluoro-9-ethyl derivative, which can be used to verify a posteriori the goodness of the binding mode. Finally, we have also investigated the effect of replacing Phe300 in the Torpedo californica enzyme by Tyr, which is present in the human AChE. The results indicate that the Phe330-->Tyr mutation is expected to have little effect on the binding affinities. Overall, the whole of results supports the validity of the putative binding model to explain the binding of tacrine-huperzine A hybrids to AChE.

New Tacrine−Huperzine A Hybrids (Huprines): Highly Potent Tight-Binding Acetylcholinesterase Inhibitors of Interest for the Treatment of Alzheimer's Disease

“…Moreover, all of these huprines proved to be much more active than tacrine in reversing the neuromuscular blockade induced by d-tubocurarine. The molecular modeling studies of the complexes of (-)-huprines having a chlorine atom at position 3 and an Et group at position 9 with TcAChE and the Phe330 f Tyr mutated enzyme using the previously proposed model 17,18 are in reasonable agreement with the experimental activity values. Despite the agreement with the experimental data, the definite validation of the binding model has to await a 3D X-ray structure of the complex.…”

“…Though the use of a cap of water molecules is an approximate treatment, we adopted it in order to enable comparison of the TI-MD results for chlorine derivatives with those previously reported for related compounds. 18 The system was partitioned into a mobile and a rigid region. The former included the inhibitor, all the protein residues containing at least one atom within 14 Å from the inhibitor, and all the water molecules, while the rest of atoms defined the rigid part.…”

“…Molecular modeling of the interaction of these compounds with Torpedo californica AChE (TcAChE) suggested that they behave as true tacrine-huperzine A hybrids, since the 4-aminoquinoline and bicyclo[3.3.1]-nonadiene subunits roughly occupy the same positions of the corresponding moieties in tacrine and (-)-huperzine A, respectively, as determined from their crystallographic complexes with AChE. 17,18 Later, replacement of fluorine by chlorine at position 3 (rac-30) was found to improve the inhibitory activity, leading to an inhibition constant (K i ) for human AChE around 30 pM, which means an affinity around 1200-fold higher than that of tacrine. 20 Since these derivatives bind to AChE with very high affinity, it is of interest to explore in more detail the effect of these structural changes on the AChE inhibitory activity.…”

Modulation of Binding Strength in Several Classes of Active Site Inhibitors of Acetylcholinesterase Studied by Comparative Binding Energy Analysis

“…Since all AChE inhibitors included in this study possess the same tricyclic tetrahydroacridine-like structure, it is safe to assume that they share with tacrine a common mode of binding to AChE. 30 In fact, the binding mode for huprine derivatives that was anticipated from molecular modeling studies 7,26,27 and later confirmed by the X-ray crystal structure of the AChE-huprine X complex 31 shows that the tetrahydro-9-aminoacridine rings of both tacrine and huprine X appear virtually superimposed when the CR traces of the enzyme in both complexes are overlaid. Furthermore, chlorination at position 6 in tacrine and 1,4-methylenetacrine, or at the equivalent position 3 in dihydroquinazoline and huprine, gives rise in all cases to a significant increase in the inhibitory potencies (Tables 1-3).…”

“…Importantly, this choice of inhibitors is particularly well suited for our purposes, because the COMBINE results can be directly contrasted with high-quality information provided by both X-ray crystallographic structures 30,31 and previous free energy calculations. 7,26,27,32 Experimental Data Normalization. IC 50 values for tacrine (Table 1) and dihydroquinazoline (Table 3) derivatives, as well as for the test set of tacrine-related compounds (Table 6), were derived from inhibition of human erythrocyte AChE.…”