Docking against AChE

and BuChE.

• Prepared by:
Dhruvi R. Pandya

M.Pharm Sem 1

L.M.COLLEGE OF
Department of pharmaceutical
PHARMACY Chemistry .
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 Acetylcholinesterase AChE & BuChE:-
• Acetylcholinesterase  also known as AChE or acetylhydrolase, is the primary
cholinesterase in the body. It is an enzyme that catalyzes the breakdown of
acetylcholine and of some other choline esters that function as neurotransmitters.
• Butyrylcholinesterase  also known as BChE, BuChE, pseudocholinesterase, or
plasma (cholin)esterase, is a nonspecific cholinesterase enzyme that hydrolyses
many different choline-based esters. In humans, it is made in the liver, found mainly
in blood and plasma.

bhttps://www.google.com/searchq=butyrylcholinesterase&oq=buty&aqs=chrome.1.69i
57j0i67l2j0i433j0l6.7357j0j15&sourceid=chrome&ie=UTF-8y the BCHE gene.

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• The enzyme acetylcholinesterase and butyryl cholinesterase is a serine
hydrolases, which includes many proteases, such as a trypsin.
o Both enzymes are closely related in molecular structure but differing in
their distribution, substrate specificity.
o AChE found in cerebrospinal fluids, while BuChE has a wide spread
distribution, being found in tissues such as liver, skin, brain and GI
smooth muscles, as well as in soluble form in the plasma.

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• Both these enzymes catalyzes the hydrolysis of the neurotransmitter
acetylcholine (ACh) to choline and acetic acid. This condition leads to
decrease in the level of acetylcholine.
o Low levels of ACh lead to cognitive impairment and dementia .The
inhibition of AChE increases the ACh levels and also improves the
affected cognitive function .
o AChE inhibitors (AChEIs) are the main drugs currently in use for
treatment of Alzheimer’s disease (AD), the most common form of
dementia.
• Donepezil, galantamine, and rivastigmine are AChEIs. They have
moderate affinity to AChE and provide delay in AD progression.

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 Mechanism of AchE:-
• Acetylcholinesterase is involved in the
https://images.app.goo.gl/DFnoKREsfP7oDyVL9
termination of impulse transmission by
rapid hydrolysis of the neurotransmitter
acetylcholine in numerous cholinergic
pathways in the central and peripheral
nervous systems. The enzyme
inactivation, induced by various
inhibitors, leads to acetylcholine
accumulation, hyperstimulation of
nicotinic and muscarinic receptors.
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 AChE Inhibitors with classification:-
• AChEIs are classified as followed:-

1. Short duration anticholinseterases:-

# E.g.:- Edrophonium - 4◦ ammonium compound, binds to anionic site.
It is reversible and use for diagnostic purpose.
2. Medium duration anticholinesterase:-
# E.g.:- Neostigmine and Pyridostigmine
They are reversibly acting 4◦ ammonium compound and binds to anionic site.
Physostigmine, a tertiary amine .
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 3. Irreversible anticholinesterase:-
# E.g.:- Ecothiopate, parathion, malathion

They are pentavalent phosphorus compounds containing a labile group such as oraganic
group in ecothiopate,etc.

• Most of them were developed as a ‘War Gases’ and pesticides.

• They interact only with esteratic site of the enzyme and have no cationic group.
• Whereas, Ecothiopate is an exception as in having a quarternary nitrogen group
designed to bind also to the anionic site.
• Cholinesterase inhibitors affect peripheral as well as central cholinergic synapse.
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 Molecular Docking:-

o Molecular docking involves a computational process of searching for a

conformation of the ligand that is able to fit both geometrically and
energetically into the binding site of a protein.
o Docking calculations are required to predict the binding mode of new
hypothetical compounds.
• DOCK:-Dock is a simple minimization program that generates many
possible orientations of a ligand within a user selective region of the receptor.

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• The docking procedure consists of three components:-

1. Identification of the binding site

2. A search algorithm to effectively sample the search space (the set of
possible ligand positions and conformations on the protein surface) and
3. A scoring function.

• Scoring grid calculations are necessary to identify ligand orientations.

The best scoring poses may be viewed using a molecular graphics
program and the underlying chemistry may be analyzed.

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There are many other widely used molecular docking software packages,
like

1. Flexidock (based on genetic algorithm)

2. Autodock (based on Monte Carlo simula-tions and annealing)
3. MCDOCK (Monte Carlo simulations)&
4. FlexE (Used in protein structures to account for protein flexibility)

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 Acetylcholinesterase inhibitors: molecular
docking in silico prediction
• The molecular modeling of newtherapeutic agents for treating the Alzheimer’s disease. To
modulate 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.
• First described in 1906 , Alzheimer’s disease (AD) is the most common form of
irreversible dementia among the elderly, although it can also affect young people.
• It is a kind of neurodegenerative disorder related to progressive cognitive impairments
such as memory loss, relative decline in language skill and guidance .
• The disease severely compromises the quality of life of the patients, causing a huge
impact for the social, economic, and political areas . Considered a multi-factorial disease.
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factors including :-
1. β-amyloid plaques
2. τ -protein aggregation
3. oxidative stress
4. decreased levels of acetylcholine (ACh) have been associated with the disease’s
pathophysiology.
• The decreased cholinergic neurotransmission gave rise to the cholinergic hypothesis.
According to this hypothesis, the increase in the ACh levels by a reversible inhibition
of AChE would improve the cognitive profile of the patients .
• Conventional therapeutic agents are used to inhibit the action of the AChE,
preventing the hydrolysis of ACh and thus enabling the maintenance of the
neurotransmitter in acceptable levels.
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Fig. Important binding sites for ligand–
receptor mechanism represented
by colors: Red catalytic site, Blue peripheral
anionic site,
Yellow the acyl pocket, Green anionic site,
Magenta oxyanionic hole,
Orange aromatic patch.
peripheral anionic site (PAS) [TYR103,
ASP105, TYR155, GLU316, TRP317,
TYR372], acyl pocket [TRP117], anionic site
[TRP267, PHE326, PHE328], oxyanionic
hole [GLY152, GLY153, ALA235] and
aromatic patch [TYR164, TYR368].

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• The crystal structure used as receptor was the human AChE (PDB entry: 4EY7,
chain A) complexed with donepezil, a drug with a non-competitive and
reversible cholinergic action . AChE cavity looks like a deep narrow fill , with
about 20°A length, and its active site, where AChE hydrolyzes ACh into acetate
and choline, is located at the catalytic site[SER234. GLU365. HSD478].
• AChE also presents other important binding sites for the ligand–receptor .
• In silicoscreening 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.

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 In silico screening and molecular docking:

• Although activity studies have not been made for ligands yet, principal
component analysis (PCA) is a powerful tool for discriminating molecules
with respect to biological response when they present a correlation to an
active drug for a suitable set of descriptors.
• In fact, previous studies showed that PCA was really able to predict, for
molecules designed from other types of phenolic lipid derivatives .
• The use the PCA method to point out the most promising molecule
(ligand), assuming that this screening protocol leads to reliable results.
• For this purpose, donepezil as a target molecule, since we know its
binding mode inside the cavity; such structure was solved by X-ray and it
can be a parameter for comparison.
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• Fig. Acetylcholinesterase structure (PDB entry: 4EY7), chain A. Backbone
(represented by grey surface) and the blue surface to the cavity where the entrance
is located at the Z plane
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• Fig. HOMO and LUMO orbitals plotted for molecule ID 16. HOMO
orbital is concentrated at the ring bonded to the amino group while the
LUMO orbital is concentrated at the dimethoxy-phenyl ring

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• Fig. Pose 1 (Docking of molecule ID16 in active site of the AChE): a Representation of the three
dimensional structure of the AChE, showing the important binding sites of thefill and the
conformation of the ligand with binding energy of −8.5 kcal/mol. B Three-dimensional analysis of
the interactions: π-stacking interactions with TRP117 (acyl pocket), dipole–dipole interaction with
TYR155 (PAS) and hydrogen bond interaction with (catalytic site)
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 Molecular docking of different inhibitors
butyrylcholinesterase:-
• There are three major active sites of butyrylcholinesterase: catalytic site, peripheral
site, and activator site.
• pseudosubstrate inhibitors, 1,3,5-alkylcarbamyloxybenzenes were designed as the
catalytic site directed inhibitors of the enzyme. Automated docking of it into the X-
ray crystal structure of butyrylcholinesterase suggested that the configuration of
the inhibitor in the enzyme complex is in the (1,3,5)-(cis,trans,trans)-form.
• Automated docking of cpds into the enzyme showed that The best bound rotamer
of the inhibitor in the enzyme complex was the trans form.

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• The physiological function of BChE remains unclear. BChE plays a key role in
detoxification by degratation toxic esters, such as succinylcholine and cocaine .
• The X-ray crystal structure of BChE reveals that the enzyme contains a catalytic

triad, Ser-His-Glu, similar to that present in other serine hydrolases.

• The cholinergic system plays important roles in neurotransmission in both peripheral and
central nervous systems.
• The action of cholinergie neurotransmitter acetycholine is terminated by AChE and
BChE.
• In AD Cortical levels of BChE show a significant increase in this disease with high
levels of BChE associated with neuritic plaques and neurofibrillary tangles, the
neuropathological hallmarks of Alzheimer’s disease. Many tangles and plaques in the
brain of AD patients contain BChE activity
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• Many evidences indicate that it might be important to inhibit BChE as
well as AChE in the treatment of Alzheimer’s disease. These observations
have led to the search for more specific BChE inhibitors that improve
learning
and memory in aged rats. Rivastigime is a potent inhibitor of both AChE
and BChE and shows clinical efficacy but without hepatoxicity in the
treatment AD.
• The BChE inhibitors not only improve cognition and increase in
acetylcholine concentration, but also reduce levels off amyloid precursor
protein (APP), which is the source of β-amyloid peptide, the main
component of plaques in Alzheimer’s disease.

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Figure :Molecular docking of inhibitor 1
with free rotation of the carbamyl CN
double bond into the X-ray crystal
structure of BChE : (A) the view
of inhibitor in the active site of the enzyme
and (B) top view
from the entrance (mouth) of the enzyme.
The configuration of
the inhibitor after docking was the (1,3,5)-
(cis,trans,trans)
form.

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Figure:. Superimposition of molecular
docking of Rivastigmine (orange
color) and inhibitor (blue color) into
the X-ray crystal
structures of BChE (A) and human
AChE (A),(b) both inhibitors were
bound to the enzyme in a similar
manner. For (B), the carbamyl moiety
of Rivastigmine was bound to the
acetyl group binding site
of the enzyme while the cis-N-
butylcarbamyl group of inhibitor.

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 References:-
• bhttps://www.google.com/searchq=butyrylcholinesterase&oq=buty&aqs=
chrome.1.69i57j0i67l2j0i433j0l6.7357j0j15&sourceid=chrome&ie=UTF-
8y the BCHE gene.
• https://images.app.goo.gl/DFnoKREsfP7oDyVL9
• J Mol Model (2017) 23:67 DOI 10.1007/s00894-017-3228-9
• http://dx.doi.org/10.1080/07391102.2014.896749

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• Thank you

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