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Molecular docking results of conjugate MBC into AChE, corresponding to experimental data. Carbon atoms of the target AChE amino acids are colored according to Fig. 4; catalytic residues are colored violet. In the left columns, cyan color shows poses obtained with partial atomic charges derived from the Gasteiger scheme, red-derived from QM calculations according to the Mulliken scheme, and green-derived from QM calculations according to the Löwdin scheme. Results of Schrödinger QM-PLD for each X-ray AChE structure are shown separately in the right column-ligand poses are colored pink
Source publication
Molecular docking is one of the most popular tools of molecular modeling. However, in certain cases, like development of inhibitors of cholinesterases as therapeutic agents for Alzheimer's disease, there are many aspects, which should be taken into account to achieve accurate docking results. For simple molecular docking with popular software and s...
Citations
... On the other hand, the affinity values were determined by an efficient methodology judged by previous assays [39,40], the relationship of some experimental values with those estimated here is in agreement. Thus, the estimated values for boric and phenylboronic acid were the lowest affinity estimated values, in line with the poor action found in this and previous works [41,42]. ...
BACKGROUND
Boron is a trace element with increasing importance in drug design. In this sense, boronic acids are emerging as therapeutic agents for several diseases.
METHODS
Herein, 3- and 4- acetamidophenylboronic acids (A26 and A24) and 4-acetamidophenylboronic acid pinacol ester (A25) were identified as potential inhibitors of acetylcholinesterase through docking assays on eel, rat, and human acetylcholinesterases indicating binding on the gorge region of the target enzymes. Then, these compounds were evaluated in vitro and in vivo.
RESULTS
It was found these compounds showed ability to inhibit acetylcholinesterase as competitive and non-competitive inhibitors. But also, these compounds were non-toxic to PC12 cells at micromolar concentration, and they have the ability to protect those cells against damage by amyloid-beta.
CONCLUSIONS
Noticeably, intraperitoneal administration of these boronic compounds to rats with the cognitive deficit induced by orchiectomy provided ameliorative effects on disrupted behavior and neuronal damage induced by hormonal deprivation. Additional approaches are required to evaluate the possibility of multiple mechanisms of action for the observed effects in the central nervous system.
https://authors.elsevier.com/a/1epz7,LXbk8wFF
... Only for target structure PDB ID 4EY7, position of α-T was not so deep, but also chroman head was located below the bottleneck in the active site ( Fig. 4-B). This is different from earlier findings, that docking results depend on the choice of target protein structure, considering different X-ray structures of hAChE [48][49][50][51]. In case of bulky inhibitors, the deepest position in the hAChE gorge was obtained when X-ray structure PDB ID 4EY7 (co-crystallized with donepezil [21]) was used as the target [50]. ...
... This is different from earlier findings, that docking results depend on the choice of target protein structure, considering different X-ray structures of hAChE [48][49][50][51]. In case of bulky inhibitors, the deepest position in the hAChE gorge was obtained when X-ray structure PDB ID 4EY7 (co-crystallized with donepezil [21]) was used as the target [50]. In the present case, absence ...
Acetylcholinesterase (AChE) is reversibly inhibited by α-tocopherol (α-T). Steady state kinetic analysis shows that α-T is a mixed slow-binding inhibitor of type A of human enzyme (Kci = 0.49 μM; Kui = 1.6 μM) with a residence time of 2 min on target. Molecular dynamics (MD) simulations support this mechanism, and indicate that α-T first forms multiple non-specific interactions with AChE surface near the gorge entrance, then binds to the peripheral side with alkylene chain slowly sliding down the gorge, inducing no significant conformational change.
α-T slightly modulates the progressive inhibition of AChE by the cyclic organophosphorus, cresyl saligenylphosphate, accelerating the fast pseudo-first order process of phosphorylation. A moderate accelerating effect of α-T on phosphorylation by paraoxon was also observed after pre-incubation of AChE in the presence of α-T. This accelerating effect of α-T on ex vivo paraoxon-induced diaphragm muscle weakness was also observed. The effect of α-T on AChE phosphylation was interpreted in light of molecular modeling results. From all results it is clear that α-T does not protect AChE against phosphylation by organophosphorus.
... Partial atomic charges on ligand atoms were assigned from QM data according to the L€ owdin [93] scheme, corresponding to a recent comparison of different atomic charge distribution schemes [94]. ...
An expanded series of alkyl 2-arylhydrazinylidene-3-oxo-3-polyfluoroalkylpropionates (HOPs) 3 was obtained via Cu(OAc)2-catalyzed azo coupling. All were nanomolar inhibitors of carboxylesterase (CES), while moderate or weak inhibitors of acetylcholinesterase and butyrylcholinesterase. Steady-state kinetics studies showed that HOPs 3 are mixed type inhibitors of the three esterases. Molecular docking studies demonstrated that two functional groups in the structure of HOPs, trifluoromethyl ketone (TFK) and ester groups, bind to the CES active site suggesting subsequent reactions: formation of a tetrahedral adduct, and a slow hydrolysis reaction. The results of molecular modeling allowed us to explain some structure-activity relationships of CES inhibition by HOPs 3: their selectivity toward CES in comparison with cholinesterases and the high selectivity of pentafluoroethyl-substituted HOP 3p to hCES1 compared to hCES2. All compounds were predicted to have good intestinal absorption and blood-brain barrier permeability, low cardiac toxicity, good lipophilicity and aqueous solubility, and reasonable overall drug-likeness. HOPs with a TFK group and electron-donor substituents in the arylhydrazone moiety were potent antioxidants. All compounds possessed low cytotoxicity and low acute toxicity. Overall, a new promising type of bifunctional CES inhibitors has been found that are able to interact with the active site of the enzyme with the participation of two functional groups. The results indicate that HOPs have the potential to be good candidates as human CES inhibitors for biomedicinal applications.
... 4EY7 co-crystallized with donepezil has a wider gorge than the other X-ray structures due to rotation of Tyr337. In many cases this allows to better accommodate bulky inhibitors [47]. In this case, rotation of the catalytic serine side chain, forming hydrogen bond with Glu202, not His447 as usual, gives space for TFK to enter in the active site. ...
Kinetic studies and molecular modeling of human acetylcholinesterase (AChE) inhibition by a fluorinated acetophenone derivative, 1-(3-tert-butylphenyl)-2,2,2-trifluoroethanone (TFK), were performed. Fast reversible inhibition of AChE by TFK is of competitive type with Ki = 5.15 nM. However, steady state of inhibition is reached slowly. Kinetic analysis showed that TFK is a slow-binding inhibitor (SBI) of type B with Ki* = 0.53 nM. Reversible binding of TFK provides a long residence time, τ = 20 min, on AChE. After binding, TFK acylates the active serine, forming an hemiketal. Then, disruption of hemiketal (deacylation) is slow. AChE recovers full activity in approximately 40 min. Molecular docking and MD simulations depicted the different steps. It was shown that TFK binds first to the peripheral anionic site. Then, subsequent slow induced-fit step enlarged the gorge, allowing tight adjustment into the catalytic active site. Modeling of interactions between TFK and AChE active site by QM/MM showed that the "isomerization" step of enzyme-inhibitor complex leads to a complex similar to substrate tetrahedral intermediate, a so-called "transition state analog", followed by a labile covalent intermediate. SBIs of AChE show prolonged pharmacological efficacy. Thus, this fluoroalkylketone intended for neuroimaging, could be of interest in palliative therapy of Alzheimer's disease and protection of central AChE against organophosphorus compounds.
... Prior to molecular docking, the geometries of the compounds were quantum-mechanically (QM)-optimized using GAMESS-US [37] software (B3LYP/6-31G*). The optimized structures of the ligands were used with partial atomic charges derived from QM results [38][39][40][41] according to the Mulliken scheme [42] without torsion or any other degree of freedom for the ligands, which were frozen for molecular docking. ...
In this study, novel derivatives based on 6-methyluracil and condensed uracil were synthesized, namely, 2,4-quinazoline-2,4-dione with ω-(ortho-nitrilebenzylethylamino) alkyl chains at the N atoms of the pyrimidine ring. In this series of synthesized compounds, the polymethylene chains were varied from having tetra- to hexamethylene chains, and secondary NH, tertiary ethylamino, and quaternary ammonium groups were introduced into the chains. The molecular modeling of the compounds indicated that they could function as dual binding site acetylcholinesterase inhibitors, binding to both the peripheral anionic site and active site. The data from in vitro experiments show that the most active compounds exhibit affinity toward acetylcholinesterase within a nanomolar range, with selectivity for acetylcholinesterase over butyrylcholinesterase reaching four orders of magnitude. In vivo biological assays demonstrated the potency of these compounds in the treatment of memory impairment using an animal model of Alzheimer disease.
... Only a few docked poses were obtained in the active site (Fig. 7, D) when X-ray structure of AChE-OP conjugate was Fig. 7. Binding of TFK to AChE: (A) Free energy profile process coordinate is distance between the TFK trifluoroketone group and the active site, and (B) main docked poses in the gorge: in the PAS (carbon atoms and dot on PMF colored red), at the gorge rim partly blocking the bottleneck (carbon atoms and dot on PMF colored orange), and in the active site ready to react with the catalytic serine (carbon atoms are colored white). Docking was performed as described in Lushchekina et al. (2018). (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.) ...
Certain ligands slowly bind to acetylcholinesterase. As a result, there is a slow establishment of enzyme-inhibitor equilibrium characterized by a slow onset of inhibition prior reaching steady state. Three mechanisms account for slow-binding inhibition: a) slow binding rate constant kon, b) slow ligand induced-fit following a fast binding step, c) slow conformational selection of an enzyme form. The slow equilibrium may be followed by a chemical step. This later that can be irreversible has been observed with certain alkylating agents and substrate transition state analogs. Slow-binding inhibitors present long residence times on target. This results in prolonged pharmacological or toxicological action.
Through several well-known molecules (e.g. huperzine) and new examples (tocopherol, trifluoroacetophenone and a 6-methyluracil alkylammonium derivative), we show that slow-binding inhibitors of acetylcholinesterase are promising drugs for treatment of neurological diseases such as Alzheimer disease and myasthenia gravis. Moreover, they may be of interest for neuroprotection (prophylaxis) against organophosphorus poisoning.
... Nevertheless, molecular docking often provides useful clues about molecular interactions and it is helpful for comparative studies, as in the present report. Furthermore, there is a body of docking studies about numerous ligands into ChEs, coupled with experimental measurements, serving refinement of this approach [32,33]. Also, substantial efforts have been made to parametrize metal-containing systems [34,35] to provide adequate docking score. ...
... The structure of Probe IV was quantum-mechanically optimized with Gamess-US [51] software (B3LYP/6-31G*). According to previous findings [33], partial atomic were charges assigned according to the Löwdin scheme [52] from quantum mechanics data was used for molecular docking. ...
Enzyme-catalyzed hydrolysis of echothiophate, a P–S bonded organophosphorus (OP) model, was spectrofluorimetrically monitored, using Calbiochem Probe IV as the thiol reagent. OP hydrolases were: the G117H mutant of human butyrylcholinesterase capable of hydrolyzing OPs, and a multiple mutant of Brevundimonas diminuta phosphotriesterase, GG1, designed to hydrolyze a large spectrum of OPs at high rate, including V agents. Molecular modeling of interaction between Probe IV and OP hydrolases (G117H butyrylcholinesterase, GG1, wild types of Brevundimonas diminuta and Sulfolobus solfataricus phosphotriesterases, and human paraoxonase-1) was performed. The high sensitivity of the method allowed steady-state kinetic analysis of echothiophate hydrolysis by highly purified G117H butyrylcholinesterase concentration as low as 0.85 nM. Hydrolysis was michaelian with Km = 0.20 ± 0.03 mM and kcat = 5.4 ± 1.6 min−1. The GG1 phosphotriesterase hydrolyzed echothiophate with a high efficiency (Km = 2.6 ± 0.2 mM; kcat = 53400 min−1). With a kcat/Km = (2.6 ± 1.6) × 107 M−1min−1, GG1 fulfills the required condition of potential catalytic bioscavengers. quantum mechanics/molecular mechanics (QM/MM) and molecular docking indicate that Probe IV does not interact significantly with the selected phosphotriesterases. Moreover, results on G117H mutant show that Probe IV does not inhibit butyrylcholinesterase. Therefore, Probe IV can be recommended for monitoring hydrolysis of P–S bonded OPs by thiol-free OP hydrolases.
... For bulky inhibitors entering deeply into the gorge, molecular docking results were found very sensitive to the protein structure due to varying gorge radius. 29,30 However, in this case, docking results did not depend significantly on the target, because only slim dimethylammonium group and adjacent linker enter the gorge and approach the bottleneck, while the major part of the compound is bound to the gorge rim. ...
Novel ammonium and betaine derivatives of p-tert-butylthiacalix[4]arene in cone and 1,3-alternate conformation were synthesized with high yields for the first time. The obtained compounds form in water spherical nanoparticles. It was shown by molecular docking calculations and in vitro experiments that amino and betaine derivatives can inhibit acetylcholinesterase and butyrylcholinesterase on the level of pyridostigmine while the toxicity of the obtained compounds is much lower than that of pyridostigmine.
... The structure of Probe IV was quantum-mechanically optimized with Gamess-US [24] software (B3LYP/6-31G*). According to previous findings [25], partial atomic were charges assigned according to the Löwdin scheme [26] from quantum mechanics data was used for molecular docking. ...
A new spectrofluorimetric method more sensitive than the Ellman method was developed for determination of both acetylcholinesterase and butyrylcholinesterase activity and for kinetic analysis of these enzymes and their mutants. Two selected mutants of human butyrylcholinesterase (E197Q and E197G) were included in this work. As for the Ellman's method, substrates are thiocholine esters, but the chromogenic reagent, DTNB (dithio-bisnitro benzoic acid) is replaced by a fluorogenic probe, "Calbiochem Probe IV", (3-(7-Hydroxy-2-oxo-2H-chromen-3-ylcarbamoyl)acrylic acid methylester). Compared to the classical Ellman's method, the sensitivity of this new spectrofluorimetric assay is 2 orders of magnitude higher. The method allows measurement of activity in media containing <10-11 M of cholinesterase active sites at low substrate concentrations, either under first order conditions, [S] < Km, or under conditions where kinetics obeys the Michaelis-Menten model, i.e. at [S] < 1 mM for wild-type enzymes. The method adapted to titration plate reader assays is suitable for clinical and toxicological routine analyses, for high throughput screening of novel cholinesterase mutants and screening of inhibitor libraries of pharmacological interest.
... Data for all compounds IV are shown in Table S4. Kinetic studies showed that compounds IV are mixed-type reversible inhibitors [85,86]. ...
... The γ-carboline part of conjugates IV contains a piperidine ring condensed with an aromatic system that implicates conformers and enantiomers. The influence of these configurations on docking of IV molecules into the AChE were previously discussed and explain the structure-activity relationships for AChE inhibition that were obtained [85]. ...
... Molecular docking showed that the positions of the compounds within the AChE and BChE gorges depended markedly on the protonation state of the piperidine fragment (pKa = 7.84 [85]). Conjugates in protonated form mainly occupy the CAS of AChE (Fig. 10A). ...
Alzheimer's disease (AD) is a multifactorial neurodegenerative process whose effective treatment will require drugs that can act simultaneously on multiple pathogenic targets. Here, we present an overview of our previous multi-target studies of five groups of novel hybrid structures that combine, through spacers, five pharmacophores that have been found promising for AD treatment: γ-carbolines, carbazoles, tetrahydrocarbazoles, phenothiazines, and aminoadamantanes. Biological activity of the compounds was assessed by a battery of assays. These included inhibitory potency against acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) as indicators of potential for cognition enhancement and against carboxylesterase (CaE) to exclude unwanted inhibition of this biotransformation pathway. Displacement of propidium from the peripheral anionic site of AChE was determined as a predictor of anti-aggregation activity. Binding to the two sites of the NMDA subtype of the glutamate receptor was conducted as an additional indicator of potential cognition enhancement and neuroprotection. Propensity to protect against mitochondrial triggers of cell death was evaluated by tests of mitochondrial potential and calcium-induced swelling as indicators of mitochondrial permeability transition. Antioxidant potential was measured to evaluate the tendency to prevent oxidative stress. Potential for disease modification was gauged by the ability to stimulate microtubule assembly. Finally, binding modes of conjugates to AChE and BChE were studied using quantum mechanical-assisted molecular docking. We found selective BChE inhibitors (conjugates of γ-carbolines and phenothiazine I, γ-carbolines and carbazoles II, and aminoadamantanes and carbazoles III) as well as inhibitors of both cholinesterases (conjugates of γ-carbolines and Methylene blue IV and bis-γ-carbolines with ditriazole-containing spacers V). These compounds combined potentials for cognition enhancement, neuroprotection, and disease modification. None of the conjugates exhibited high potency against CaE, thereby precluding potential drug-drug interactions from CaE inhibition. Thus, the studied compounds exhibited positive characteristics of multi-target drugs, indicating their potential for the next generation of AD therapeutics.
