Theoretical study of classical acetylcholinesterase inhibitors

Bidirectional Regulation of Intracellular Enzyme Activity Using Light-Driven Nano-Inhibitors

Photochemical regulation provides precise control over enzyme activities with high spatiotemporal resolution. A promising approach involves anchoring "photoswitches" at enzyme active sites to modulate substrate recognition. However, current methods often require genetic mutations and irreversible enzyme modifications for the site-specific anchoring of "photoswitches", potentially compromising the enzyme activities. Herein, we present a pioneering reversible nano-inhibitor based on molecular imprinting technique for bidirectional regulation of intracellular enzyme activity. The nano-inhibitor employs a molecularly imprinted polymer nanoparticle as its body and azobenzene-modified inhibitors ("photoswitches") as the arms. By using a target enzyme as the molecular template, the nano-inhibitor acquires oriented binding sites on its surface, resulting in a high affinity for the target enzyme and non-covalently firm anchoring of the azobenzene-modified inhibitor to the enzyme active site. Harnessing the reversible isomerization of azobenzene units upon exposure to ultraviolet and visible light, the nano-inhibitor achieves bidirectional enzyme activity regulation by precisely docking and undocking inhibitor at the active site. Notably, this innovative approach enables the facile in situ regulation of intracellular endogenous enzymes, such as carbonic anhydrase. Our results represent a practical and versatile tool for precise enzyme activity regulation in complex intracellular environments.

Electronic and structural study of T315I mutated form in DFG-out conformation of BCR-ABL inhibitors

In this work, the four main drugs for the treatment of chronic myeloid leukemia were analyzed, being imatinib, dasatinib, nilotinib and ponatinib followed by four derivative molecules of nilotinib and ponatinib. For these derivative molecules, the fluorine atoms were replaced by hydrogen and chlorine atoms in order to shade light to the structural effects on this set of inhibitors. Electronic studies were performed at density functional theory level with the B3LYP functional and 6-311+G(d,p) basis set. The frontier molecular orbitals, gap HOMO-LUMO, and NBO were analyzed and compared to docking studies for mutant T315I tyrosine kinase protein structure code 3IK3, in the DFG-out conformation. Structural similarities were pointed out, such as the presence of groups common to all inhibitors and modifications raised up on new generations of imatinib-based inhibitors. One of them is the trifluoromethyl group present in nilotinib and later included in ponatinib, in addition to the 1-methylpiperazin-1-ium group that is present in imatinib and ponatinib. The frontier molecular orbitals of imatinib and ponatinib are contributing to the same amino acid residues, and the ineffectiveness of imatinib against the T315I mutation was discussed.Communicated by Ramaswamy H. Sarma.

In silico study of tacrine and acetylcholine binding profile with human acetylcholinesterase: docking and electronic structure

Alzheimer disease (AD) is a neurodegenerative process, one of the most common and incident dementia in the population over 60 years. AD manifests the presence of complex biochemical processes involved in neuronal degeneration, such as the formation of senile plaques containing amyloid-β peptides, the development of intracellular neurofibrillary tangles, and the suppression of the acetylcholine neurotransmitter. In this way, we performed a set of theoretical tests of tacrine ligand and acetylcholine neurotransmitter against the human acetylcholinesterase enzyme. Molecular docking was used to understand the most important interactions of these molecules with the enzyme. Computational chemistry calculation was carried out using MP2, DFT, and semi-empirical methods, starting from molecular docking structures. We have also performed studies regarding the non-covalent interactions, electron localization function, molecular electrostatic potential and explicit water molecule influence. For Trp86 residue, we show two main interactions in accordance to the results of the literature for TcAChE. First, intermolecular interactions of the cation-π and sigma-π type were found. Second, close stacking interactions were stablished between THA+ and Trp86 residue on one side and with Tyr337 residue on the other side.

Bioactivity of hamamelitannin, flavokawain A, and triacetyl resveratrol as natural compounds: Molecular docking study, anti‐colon cancer and anti‐Alzheimer potentials

In this study, we worked on anticolon cancer effects and anti-Alzheimer's disease with molecular docking studies. Hamamelitannin, flavokawain A, and triacetyl resveratrol compounds showed good inhibitory activities on acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) enzymes. The inhibition effects of flavokawain A, hamamelitannin, and triacetyl resveratrol on AChE and BuChE enzymes were determined spectrophotometrically conforming to Ellman. IC₅₀ values of these enzymes were ranging between 0.95 ± 0.12 and 93.27 ± 8.14 nM for AChE and 5.71 ± 0.77 and 52.10 ± 8.41 nM for BuChE. The inhibitory activities of some chemical compounds such as flavokawain A, hamamelitannin, and triacetyl resveratrol were assessed by performing the molecular docking study in the presence of AChE and BuChE. Also, the features of the ligand-enzyme complex had value of -7.722 kcal/mol for flavokawain A against AChE and -5.530 kcal/mol against BuChE. The molecular docking calculations indicated the probable interactions and their characteristics at an atomic level. Due to the outcomes gained from docking, the affinity of the chemical compounds to the enzymes was considerable. In vitro cell viabilities of flavokawain A, hamamelitannin, and triacetyl resveratrol with various concentrations on SW620, DLD-1, HT29, HCT8, and HCT116 were investigated by MTT assay with Doxorubicin as the control compound.

Observation of quantum signature in rivastigmine chemical bond break-up and quantum energetics, spectral studies of anti-Alzheimer inhibitors

Semi-empirical calculations on the torsion potential for dihedral angle of rivastigmine linking NAP and Carbamyle moieties consistently show regions of several discontinuities and a cusp indicating molecular instability and eventual break-up of rivastigmine observed in the X-ray structure. The phenomena can be explained both by definition of large classical force or quantum nature of chemical bond break-up. Also, to better understand the molecular properties and quantum energetics of the inhibitor molecules, we have performed several ab initio based calculations on all four inhibitors at equilibrium geometry, in ground state and gas phase using the density functional theory level wB97X/6-31G* and HF/6-31G*. A number of properties like computational vibrational (IR), Raman and nuclear magnetic resonance (NMR) spectra as well as HOMO and LUMO orbital energies at optimized geometries have been computed by SPARTAN16 and Gaussian16 utilities. Also, the thermodynamic and QSAR properties of the inhibitors have been assessed and compared by a number of different semi-quantum, Hartree-Fock and density functional methods. The theoretical NMR and IR spectra have been benchmarked against experimental spectrum to compare and assess suitability of the computational methodologies and basis set levels for the calculations.Communicated by Ramaswamy H. Sarma.

Structure-activity relationship of tacrine and its analogues in relation to inhibitory activity against Alzheimer's disease

Alzheimer's disease is a widespread type of neurodegenerative dementia that mainly affects the elderly. Currently, this disease can only be treated palliatively. Existing drugs can only improve patients' symptoms. The search for new drugs that can effectively treat this disease is an important field of research in medicinal chemistry. Here we report a structure-activity relationship study of tacrine and some of its analogues in relation to their inhibitory activities against Alzheimer's disease. All of the molecular descriptors were calculated at the M062X/6-311++G(d,p) level of theory. Principal component analysis of the molecular descriptors showed that the compounds could be categorized into active and inactive compounds using just two descriptors: the HOMO and LUMO energies. These results should help us to explain the activities of tacrine derivatives and to model new tacrine analogues that are active against Alzheimer's disease. Graphical abstract PCA score plot for tacrine and its analogues.

Similarity search combined with docking and molecular dynamics for novel hAChE inhibitor scaffolds

The main purpose of this study was to address the performance of virtual screening methods based on ligands and the protein structure of acetylcholinesterase (AChE) in order to retrieve novel human AChE (hAChE) inhibitors. In addition, a protocol was developed to identify novel hit compounds and propose new promising AChE inhibitors from the ZINC database with 10 million commercially available compounds. In this sense, 3D similarity searches using rapid overlay of chemical structures and similarity analysis through comparison of electrostatic overlay of docked hits were used to retrieve AChE inhibitors from collected databases. Molecular dynamics simulation of 100 ns was carried out to study the best docked compounds from similarity searches. Some key residues were identified as crucial for the dual binding mode of inhibitor with the interaction site. All results indicated the relevant use of EON and docking strategy for identifying novel hit compounds as promising potential anticholinesterase candidates, and seven new structures were selected as potential hAChE inhibitors. Graphical abstract Compound N01 in the 4M0E hAChE crystallography structure from docking results. Yellow dashed lines Hydrogen bonds, blue dashed lines π-stacking interactions, green dashed lines cation-π interactions.

Potential acetylcholinesterase inhibitors: molecular docking, molecular dynamics, and in silico prediction

This paper deals with molecular modeling of new therapeutic agents for treating the Alzheimer's disease. The therapeutic line adopted for this study is the cholinergic hypothesis. To modulate positively the cholinergic function through the inhibition of the acetylcholinesterase, a set of candidates was designed from a natural compound extracted from the cashew nutshell liquid, anacardic acid. In silico screening of this chemical library revealed a ligand that is more promising once it is correlated with an active drug through specific topological and electronic descriptors. The protein-ligand docking showed stable binding modes and the binding free energy computed for the active site of the receptor suggests that our ligand presents a potential biological response. Graphical Abstract Representation of the three dimensional structure of the AChE, showing the important binding sites of the Gorge and the conformation of the ligand.

Halogen-directed drug design for Alzheimer's disease: a combined density functional and molecular docking study

A series of halogen-directed donepezil drugs has been designed to inhibit acetyl cholinesterase (AChE). Density Functional theory (DFT) has been employed to optimize the chair as well as boat conformers of the parent drug and modified ligands at B3LYP/MidiX and B3LYP/6-311G + (d,p) level of theories. Charge distribution, dipole moment, enthalpy, free energy and molecular orbitals of these ligands are also investigated to understand how the halogen-directed modifications impact the ligand structure and govern the non-bonding interactions with the receptors. Molecular docking calculation has been performed to understand the similarities and differences between the binding modes of unmodified and halogenated chair-formed ligands. Molecular docking indicated donepezil and modified ligands had non-covalent interactions with hydrophobic gorges and anionic subsites of AChE. The -CF3-directed ligand possessed the most negative binding affinity. Non-covalent interactions within the ligand-receptor systems were found to be mostly hydrophobic and π- stacking type. F, Cl and -CF3 containing ligands emerge as effective and selective AChE inhibitors, which can strongly interact with the two active sites of AChE. In addition, we have also investigated selected pharmacokinetic parameters of the parent and modified ligands.

Mapping of the interaction sites of galanthamine: a quantitative analysis through pairwise potentials and quantum chemistry

A quantitative analysis of the interaction sites of the anti-Alzheimer drug galanthamine with molecular probes (water and benzene molecules) representative of its surroundings in the binding site of acetylcholinesterase (AChE) has been realized through pairwise potentials calculations and quantum chemistry. This strategy allows a full and accurate exploration of the galanthamine potential energy surface of interaction. Significantly different results are obtained according to the distances of approaches between the various molecular fragments and the conformation of the galanthamine N-methyl substituent. The geometry of the most relevant complexes has then been fully optimized through MPWB1K/6-31 + G(d,p) calculations, final energies being recomputed at the LMP2/aug-cc-pVTZ(-f) level of theory. Unexpectedly, galanthamine is found to interact mainly from its hydrogen-bond donor groups. Among those, CH groups in the vicinity of the ammonium group are prominent. The trends obtained provide rationales to the predilection of the equatorial orientation of the galanthamine N-methyl substituent for binding to AChE. The analysis of the interaction energies pointed out the independence between the various interaction sites and the rigid character of galanthamine. The comparison between the cluster calculations and the crystallographic observations in galanthamine-AChE co-crystals allows the validation of the theoretical methodology. In particular, the positions of several water molecules appearing as strongly conserved in galanthamine-AChE co-crystals are predicted by the calculations. Moreover, the experimental position and orientation of lateral chains of functionally important aminoacid residues are in close agreement with the ones predicted theoretically. Our study provides relevant information for a rational drug design of galanthamine based AChE inhibitors.

Hologram QSAR models of 4-[(diethylamino)methyl]-phenol inhibitors of acetyl/butyrylcholinesterase enzymes as potential anti-Alzheimer agents

Hologram QSAR models were developed for a series of 36 inhibitors (29 training set and seven test set compounds) of acetyl/butyrylcholinesterase (AChE/BChE) enzymes, an attractive molecular target for Alzheimer’s disease (AD) treatment. The HQSAR models (N = 29) exhibited significant cross-validated (AChE, q² = 0.787; BChE, q² = 0. 904) and non-cross-validated (AChE, r² = 0.965; BChE, r² = 0.952) correlation coefficients. The models were used to predict the inhibitory potencies of the test set compounds, and agreement between the experimental and predicted values was verified, exhibiting a powerful predictive capability. Contribution maps show that structural fragments containing aromatic moieties and long side chains increase potency. Both the HQSAR models and the contribution maps should be useful for the further design of novel, structurally related cholinesterase inhibitors.

Electronic structure and PCA analysis of covalent and non-covalent acetylcholinesterase inhibitors

Hartree-Fock and density functional methods were used to analyze electronic and structural properties of known drugs to evaluate the influence of these data on acetylcholinesterase inhibition. The energies of the frontier orbitals and the distances between the more acidic hydrogen species were investigated to determine their contributions to the activity of a group of acetylcholinesterase inhibitors. Electrostatic potential maps indicated suitable sites for drugs-enzyme interactions. In this study, the structural, electronic and spatial properties of nine drugs with known inhibitory effects on acetylcholinesterase were examined. The data were obtained based on calculations at the B3LYP/6-31 + G(d,p) level. Multivariate principal components analysis was applied to 18 parameters to determine the pharmacophoric profile of acetylcholinesterase inhibitors. Desirable features for acetylcholinesterase inhibitor molecules include aromatic systems or groups that simulate the surface electrostatic potential of aromatic systems and the presence of a sufficient number of hydrogen acceptors and few hydrogen donors. PCA showed that electronic properties, including the HOMO-1 orbital energy, logP and aromatic system quantity, as well as structural data, such as volume, size and H-H distance, are the most significant properties.