Acetylcholinesterase (AChE) is an enzyme present in the neuromuscular junction and responsible for the hydrolysis of the neurotransmitter acetylcholine. Regular transmission of nerve input is directly related to the action of AChE. AChE inhibitors are responsible to against neurodegenerative disorder like Parkinson’s disease, Alzheimer’s disease, myastimiahenia gravis or Huntington’s disease . Neurodegenerative disorder is characterized by the progressive loss of structure or function and, eventually, death of neurons. Inhibition of AChE is the fundamental therapeutic step to against these diseases. Several studies shown that there are some side effects and oral activities restrict the application of AChE inhibitors, such as physostigmine and tacrine to act as effective drugs. However, some findings found that piperidine derivative are promising AChE inhibitor that able to overcome the unfavourable side effects and poor pharmacokinetics. Thus, molecular docking techniques are applied to study some piperidine derivative inhibitor of AChE and propose new AChE inhibitors as potential new drugs against neurodegenerative disorders. Molecular dynamics stimulations are the following step to adjust ligands at the target sites and to estimate interaction energy. The interaction between the potential inhibitors and AChE can be investigated by docking and molecular modelling techniques.
First, a series of piperidine derivative are selected for analysis of the potent inhibitors of AChE. The 3D structures of each compound in the neutral forms were constructed using the Spartan software. AMI semiempirical method is used to assign the partial atomic charges of the compound. The 3D structure of AChE was obtained from the Protein Data Bank. Compound 1 to 14 of piperidine derivatives were docked into the AChE binding site using the Molegro Virtual Docker (MVD). MVD used MolDock scoring function as a simplified potential whose parameter are fit to protein-ligand structures and binding data scoring function and further extended in generic evolutionary method for molecular dock with new hydrogen bonding term and new charge schemes. Piecewise linear potential (PLP) is used for approximating the steric (Van der Waals) term between atoms and another stronger potential for hydrogen bonds. PLP also used to describes the electrostatic interactions between the charged atoms.
The internal energy of ligand is divided into three terms. The first term is double summation which is between all atoms pairs in the ligand, excluding atom pairs which are linked by two bonds. The second term is torsional energy term, where is the torsional angle of the bond. The last term assign a penalty of 1000 if the distance between two heavy atoms is less than 2.0A. These functions are used to automatically superimpose a flexible molecule onto a rigid template molecule. The combination of the guided differential evolution algorithm and differential evolution optimization technique allows for a fast and accurate identification of potential binding modes. The interaction modes of the ligand with the enzyme active site were determined as the highest energy scored protein-ligand complex used during docking and the conformers of each compound were mostly associated with bioactive conformations of donepezil.
As a result, a link between the MolDock scoring function, structural properties of piperidine analogs, and their biological activity against the AChE was established by docked binding mode. Molegro cavity prediction algorithm is used to calculate out the potential binding sites of AChE. A cavity of 230.40 A3 (surface = 574.72 A2) was observed in the AChE and the side chains of amino acid residues from 6 Å of the cavity surface were considered flexible. Multiple linear regression (MLR) was used to model the relationship between the independent energy term values and values by fitting a linear equation to the observed data.The more negative energy values (most negative) , the higher stability of complexes between ligand and protein. The negative coefficients correspond to interactions between the ligand and the amino acid residues in the protein active site. These interactions improve the potency of the inhibitors. For example, donepezil is the most potent and stable compound. By correlating the docking results obtained with experimental data, seventeen structure of derivatives was proposed as potential AChE inhibitors. Docking simulation is used for further evaluation of these compound at the AChE active site.
QM calculations of piperidine derivatives in the AChE active site are needed in order to investigate the influence of electronic effects on the relative binding energy. The results were performed by calculating the relative binding energy at the QM/MM level from docking structures. QM method is used to calculate a specified region around the active center, while the rest of the protein was treated at an MM level. The QM region includes the ligand and its surrounding amino acid residues. The relative binding energies at the QM/MM level showed a very good agreement with the docking energy calculation. The orientations and hydrogen bonds of piperidine derivatives into the AChE active site can be evaluated by docking calculations using molecular mechanics methods.
The docking studies found out that the best pose of compound 2 inside AChE, was submitted to additional Molecular Dynamic (MD) simulation steps carried out using the GROMACS 4.5.4 package with the force field OPLS/AA. OPLS/AA force field parameters for the ligands were used, and the semiempirical quantum chemistry SQM can calculate atomic partial charges. The dynamic behaviour of the complex AChE-compound 2 was simulated and submitted to four energy minimization steps. The minimized complex was then submitted to MD simulations in two steps which 500ps of MD was performed at 300K with PR for the entire system and 20ns of MD was performed without restriction. The electrostatic interactions were calculated using the particle mesh Ewald method (PME). Around 1000 conformations were obtained during each simulation.
As a conclusion, molecular docking technique accelerate the discovery of AChE inhibitor as potential new drugs against neurodegenerative disorders. The principle and method that discussed in this review highlight the strategies by which molecular docking and molecular dynamic stimulation have been applied in the identification of novel bioactive compounds. The binding modes between ligand and receptor binding sites can be predicted through molecular docking program. However, some findings found out that the current algorithms do not estimate the absolute energy associated with the intermolecular interaction with satisfactory accuracy. Further refinements on the structure of compound should be performed in more experimental studies so that more new and effective AChE inhibitors can be proposed in the future
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