Acetylcholinesterase complexed with bivalent ligands related to huperzine a: experimental evidence for species-dependent protein-ligand complementarity

Customizing scoring functions for docking

Empirical scoring functions used in protein-ligand docking calculations are typically trained on a dataset of complexes with known affinities with the aim of generalizing across different docking applications. We report a novel method of scoring-function optimization that supports the use of additional information to constrain scoring function parameters, which can be used to focus a scoring function's training towards a particular application, such as screening enrichment. The approach combines multiple instance learning, positive data in the form of ligands of protein binding sites of known and unknown affinity and binding geometry, and negative (decoy) data of ligands thought not to bind particular protein binding sites or known not to bind in particular geometries. Performance of the method for the Surflex-Dock scoring function is shown in cross-validation studies and in eight blind test cases. Tuned functions optimized with a sufficient amount of data exhibited either improved or undiminished screening performance relative to the original function across all eight complexes. Analysis of the changes to the scoring function suggest that modifications can be learned that are related to protein-specific features such as active-site mobility.

Structural biology in plant natural product biosynthesis--architecture of enzymes from monoterpenoid indole and tropane alkaloid biosynthesis

Several cDNAs of enzymes catalyzing biosynthetic pathways of plant-derived alkaloids have recently been heterologously expressed, and the production of appropriate enzymes from ajmaline and tropane alkaloid biosynthesis in bacteria allows their crystallization. This review describes the architecture of these enzymes with and without their ligands.

Targeting acetylcholinesterase to treat neurodegeneration

Neurodegenerative disorders, such as Alzheimer's disease, are often characterised by the degeneration of the cholinergic system. Thus, the aim of many treatment regimens is to support this system either by means of muscarinic agonists or by inhibitors of acetylcholinesterase (AChE), the latter being able to increase the concentration of acetylcholine. However, both pharmacological groups of drugs can only help in the beginning of the progressive disease. The finding that the occupation of the peripheral anionic site of AChE is able to stop the formation of the amyloid plaque led to the development of bivalent ligands that occupy both the active and the peripheral site. This dual action might be more beneficial for treatment of Alzheimer s disease than simple inhibition of the acetylcholine hydrolysis. Thus, the new bivalent ligands are the focus of this review.

A model study of interactions between TcAChE peripheral site segment Tyr70Val71 and loop 1 of Fasciculin 2

The continuous chain of residues (Thr7 to Ala12) of Loop1 of Fas2 (F1) and its interaction with the peripheral binding sites (Tyr70-Val71) of AChE (P1) has been studied. Our results suggest that the flexibility of Loop1 might be caused by either the partially protonated guanidine group of Arg11 under experimental conditions or by the interaction with the negatively charged center of substrates. The binding energy of F1-P1 is predicted to be -16.6 kcal/mol at the B3LYP/6-311G(d,p) level, which is assumed to originate from one isolated O7...HN10 H-bond, one possible O10...HC71 unconventional O...HC type H-bonding, and the improved pi-bonding cooperativity around the peptide group of the AChE segment Tyr70-Val71. The classical Kitaura-Morokuma energy decomposition analysis, the NPA charge analysis, and the AIM analysis consistently reveal that the peptide group in segment P1 is more polarizable, which might play the key role in the interactions between F1 and P1. The PCM solvent effect corrected results reveal decrease of the interaction energy of the considered model. The importance of Thr8 of Fas2 in the P-site binding of AChE is also concluded. Site-directed mutations on either the Fas2 residue of Thr8 or the AChE residue of Tyr70 are expected to alter the binding behavior of the Loop1 of Fas2 with AChE.

Capillary electrophoresis versus differential scanning calorimetry for the analysis of free enzyme versus enzyme-ligand complexes: in the search of the ligand-free status of cholinesterases

Cholinesterases (ChEs) are highly efficient biocatalysts whose active site is buried in a deep, narrow gorge. The talent of CE to discover inhibitors in the gorge of highly purified preparations has fairly altered the meaning of a ChE ligand-free status. To attempt at a description of this one, we investigated the stability of Bungarus fasciatus acetylcholinesterase (AChE), alone or complexed with different inhibitors. Determination of mid-transition temperature for thermal denaturation, using differential scanning calorimetry (DSC) and CE, provided conflicting results. Discrepancies strongly question the reality of a ligand-free AChE state. DSC allowed estimation of the stability of AChE-ligands complexes, and to rank the stabilizing effect of different inhibitors. CE acted as a detector of hidden ligands, provided that they were charged, reversibly bound, and thus dissociable upon action of electric fields. Then, CE allowed quantification of the stability of ligand-free AChE. CE and DSC providing each fractional and nonredundant information, cautious attention must be paid for actual estimation of the conformational stability of ChEs. Because inhibitors used in purification of ChEs by affinity chromatography are charged, CE remains a leading method to estimate enzyme stability and detect the presence of bound hidden ligands.

Investigation of the binding mode of (−)-meptazinol and bis-meptazinol derivatives on acetylcholinesterase using a molecular docking method

Molecular docking has been performed to investigate the binding mode of (-)-meptazinol (MEP) with acetylcholinesterase (AChE) and to screen bis-meptazinol (bis-MEP) derivatives for preferable synthetic candidates virtually. A reliable and practical docking method for investigation of AChE ligands was established by the comparison of two widely used docking programs, FlexX and GOLD. In our hands, we had more luck using GOLD than FlexX in reproducing the experimental poses of known ligands (RMSD<1.5 A). GOLD fitness values of known ligands were also in good agreement with their activities. In the present GOLD docking protocol, (-)-MEP seemed to bind with the enzyme catalytic site in an open-gate conformation through strong hydrophobic interactions and a hydrogen bond. Virtual screening of a potential candidate compound library suggested that the most promising 15 bis-MEP derivatives on the list were mainly derived from (-)-MEP with conformations of (S,S) and (SR,RS) and with a 2- to 7-carbon linkage. Although there are still no biological results to confirm the predictive power of this method, the current study could provide an alternate tool for structural optimization of (-)-MEP as new AChE inhibitors. [Figure: see text].

Design and activity of cationic fullerene derivatives as inhibitors of acetylcholinesterase

Four different regioisomers of cationic bis-N,N-dimethylfulleropyrrolidinium salts have been prepared and evaluated as inhibitors of the enzymatic activity of acetylcholinesterase. These fullerene-based derivatives were found to be noncompetitive inhibitors of acetylthiocholine hydrolysis. Molecular modelling was used to describe the possible interactions between the fullerene cage and the amino acids surrounding the cavity of the enzyme. The cationic C(60) derivatives used in this study represent a new class of molecules potentially able to modulate the enzymatic activity of acetylcholinesterase.

Can herbs provide a new generation of drugs for treating Alzheimer's disease?

The overall aim of this review is to discuss cellular mechanisms at work in the progression of AD and current therapeutic strategies for treating AD, with a focus on the potential efficacy of herbal treatments. Recent advances in molecular, cellular, and animal model studies have revealed that formation of the 4-kDa amyloid beta peptide is a key factor in the development and progression of AD. Several cellular changes have been identified that are related to amyloid beta plaques and neurofibrillary tangles found in the autopsied brains of AD patients and in AD animal models. Several therapeutic strategies have been developed to treat AD, including anti-inflammatory, anti-oxidant, and anti-amyloid approaches. Recently, herbal treatments have been tested in animal and cellular models of AD and in clinical trials with AD subjects. In AD animal models and cell models, herbal extracts appear to have fewer adverse effects than beneficial effects on A beta and cognitive functions. These extracts have multi-functional properties (pro-cholinergic, anti-oxidant, anti-amyloid, and anti-inflammatory), and their use in the treatment of AD patients looks promising. The chemical compositions of herbs and their potential for alleviating or reducing symptoms of AD or for affecting the disease mechanism need to be further studied.

Synthesis and acetylcholinesterase inhibition of derivatives of huperzine B

By targeting dual active sites of AChE, a number of new derivatives of HupB have been synthesized and tested as acetylcholinesterase inhibitors. The most potent compound, bis-HupB 5b is 72-fold more potent in AChE inhibition and 79-fold more selective for AChE versus BChE than HupB.

CH/π hydrogen bonds as evidenced in the substrate specificity of acetylcholine esterase

The crystal structure of acetylcholine esterase (AchE) in complex with various inhibitors, investigated as drugs for improvement of the cognitive ability of early stage Alzheimer's disease, has been analyzed with the use of our program CHPI. A number of CH/pi hydrogen bonds have been disclosed in the binding of the inhibitors with Torpedo californica AchE. It has been demonstrated that, in order to be effective in the binding with AchE, C-H bonds in the inhibitor need not be polarized.

Nonspanning Bivalent Ligands as Improved Surface Receptor Binding Inhibitors of the Cholera Toxin B Pentamer

A series of bivalent ligands of varying length were synthesized to inhibit the receptor-binding process of cholera toxin. Competitive surface receptor binding assays showed that significant potency gains relative to the constituent monovalent ligands were achieved independently from the ability of the extended bivalent ligands to span binding sites within the toxin pentamer. Several models that could account for the unexpected improvement in IC(50) values are examined, taking into account crystallographic analysis of each ligand in complex with the toxin pentamer. Evidence is presented that steric blocking at the receptor binding surface may play a role. The results of our study suggest that the use of relatively short, "nonspanning" bivalent ligands, or monovalent ligands of similar topology and bulk may be an effective way of blocking the interaction of multimeric proteins with their cell surface receptors.

Ten new Lycopodium alkaloids having the lycopodane skeleton isolated from Lycopodium serratum Thunb

Ten new alkaloids, lycoposerramines-F (1), -G (2), -H (3), -I (4), -J (5), -K (6), -L (7), -M (8), -N (9), and -O (10), having lycopodine-related structures, were isolated from the club moss Lycopodium serratum THUNB. and their structures were elucidated on the basis of spectroscopic analysis and/or chemical transformation.

Rational design of alkylene-linked bis-pyridiniumaldoximes as improved acetylcholinesterase reactivators

To improve the potency of 2-pralidoxime (2-PAM) for treating organophosphate poisoning, we dimerized 2-PAM and its analogs according to Wilson's pioneering work and the 3D structure of human acetylcholinesterase (hAChE) inactivated by isoflurophate. 1,7-Heptylene-bis-N,N'-syn-2-pyridiniumaldoxime, the most potent of the alkylene-linked dimeric reactivators, was readily synthesized using bistriflate and is 100 times more potent than 2-PAM in reactivating hAChE poisoned by isoflurophate. Experimental and computational studies confirm that 2-PAM in its biologically active form adopts the syn-I configuration. Further, they suggest that the improved performance of dimeric oximes is conferred by two-site binding with one oxime pointing toward the diisopropyl ester at the catalytic site of hAChE and the other anchored at the peripheral site. This type of binding may induce a conformational change in the acyl pocket loop which modulates the catalytic site via a domino effect.