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Journal of Innovation in Pharmaceutical Sciences (2018);2(1): 1-7

© Guru Nanak Publications, Ibrahimpatnam, Hyderabad, India. 1

Target Based Design of few Tau Protein Inhibitors as Antialzheimers

Subhasis Banerjee*, Shalini Das

*Department of Pharmaceutical Chemistry, Gupta College of Technological Sciences, Asansol West Bengal, India. -713301.

A r t i c l e i n f o Article history: Received 25 February 2018

Received in revised form 21 March 2018 Accepted 25 April 2018

A B S T R A C T

Alzheimer’s Disease (AD) is a progressive,

neurodegenerative disorder affecting elderly patients.

Cognitive impairment is the primary symptoms

associated with this disorder. Recent researches are

highly focused on few markers which are thought to

be characteristics of AD (abnormal aggregate forming

protein e.g. Tau and abnormal plaque forming protein

e.g. Amyloid-Beta). The present study aims at

targeting one of the key protein, i.e.; glycogen synthase kinase 3 beta; (GSK3 beta) serine/threonine

protein kinase that participates in Alzheimer's

disease. Considering the molecular architechture of

GSK3 beta and the 2D pose view of the primary

ligand ANP, (phosphoaminophosphonic acid-

adenylate ester) lies within the target, few of its

analogs were prepared (ss1-ss6). The docking output

clearly demonstrated that the test compound ‘ss1’ with its 20th conformer lying closest to the

complementary residue (GLN185), i.e.; 5.71 Å,

whereas the distance observed between the co-crystal

and GLN 185 was 9.25 Å. Most of the compounds

with a minimum of 5-10 poses are in the proximal

vicinity of the receptive area. The preliminary study

on this novel target was encouraging, hence it needs

to be extended further to make it more meaningful.

KEYWORDS:

Alzheimer’s Disease, Autodock, GSK3 beta

1.INTRODUCTION

Alzheimer’s Disease (AD) is a progressive, neurodegenerative disorder. It gradually destroys a

person’s memory. AD also causes language and

communication problem, difficulty in performing

familiar things. The real cause for AD is unknown, so

the proper diagnostic procedure to cure it properly

still unavailable. Market available medications show

a very small symptometic benefit. Due to dramatic

reduction in cholinergic neuronal activity,

acetylcholine esterase inhibitors, viz; Donepezil is

recommended. Recent researches are highly focused

on few markers which are thought to be characteristics of AD (abnormal aggregate forming

protein e.g. Tau and abnormal plaque forming protein

e.g. Amyloid-Beta). Tau protein,

*Correspondence to:

________________________

Dr. Subhasis Banerjee

Assistant Professor

Department of Pharmaceutical Chemistry

Gupta College of Technological Sciences, Asansol-713301

Email: [email protected]

Ph:9836253021

A microtubule associated protein (MAP) form

intracellular fibrillar structure of aggregation due to

hyperphosphorylation. Tau protein predominantly

found in axons as a highly soluble phosphoprotein. It

is also having various binding region.

Hyperphosphorylated or the toxic tau form variety of

tau aggregation such as oligomers, monomers,

prefilaments, fibrils.

They also form the neuro fibrillary tangles (NFT) a

dense whorl of fibres occupying the entire perinuclear

cytoplasm of cortical pyramidal cells & other large

neuron in the brainstem1. Recent cell based screening

assay have established the ability of various chemical

family as tau aggregation inhibitor such as N-

phenylamines, rhodamines, phenylthiazolhydrazides,

anthraquinones, aminothienopyridazines2. Tau is

marked in its aggregated and phosphorylated form

giving the possible sign of AD.

Current Research Trend Scientific studies of last 25 years have also detected

two biomarkers as characteristics of AD.

Abnormal plaque forming protein Amyloid-Beta and

Abnormal aggregate forming protein Tau.

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Objective

As stated above, abnormal aggregate formation is one

of the major clinical findings in Alzheimer’s disease.

Therefore, possible ways have to be identified to

cease the aggregation. The present work aims at

targeting one of the key protein, i.e.; glycogen

synthase kinase 3 beta; (GSK3 beta) serine/threonine

protein kinase that participates in Alzheimer's

disease. Considering the molecular architechture of

GSK3 beta and the 2D pose view of the primary ligand ANP, (phosphoaminophosphonic acid-

adenylate ester) lies within the target, we have

designed few of its analogs. The principal focus of

this study is to develop an idea of binding pattern of a

suitable inhibitor within the active site of GSK beta

through docking study. Nowadays, molecular docking

study is one of the essential tool which has already

superceded the conventional approach opted in drug

design.

2.MATERIAL AND METHODS

Operating System : LINUX Fedora -8.

Softwares : Autodock 1.5.4, Chemsketch,

pymol, open Babel v2.31

Target (GSK3 beta) Preparation

The experimental target i.e. glycogen synthase kinase

3 beta (Figure 1 and Figure 2) with the PDB entry

code 1J1B3 (co-crystallized with ANP i.e.

phosphoaminophosphonic acid-adenylate ester was

procured from rcsb.org.

Figure 1: 3DStructure of the enzyme (pdb id: 1J1B)

Figure 2: 2D pose view of the co-crystal ANP

within the active site of 1J1B

To make the active site free, we have removed the

ligand i.e.; ANP from the active site.

All hydrogens were added to the remaining part of the enzyme.

The newly prepared enzyme was further saved into

pdb format.

Ligand Preparation

A series of (6) compounds were developed in

chemsketch. Each molecule was further processed in

Open Babel window. After fulfilling the requirement

given by Open Babel the AUTODOCK compatible ligand was generated. The prototypical ligand

template is shown below.

purine/modified purine----acyclic ribose linked to

hydroxamic acid

The data obtained from Open Babel were copied and

pasted into notepad, saved as lig.pdb.

The ligand thus obtained was further saved as

lig.pdbqt format.

Preparation of glg (grid log file) file

i. Atoms were made AD4 type and charges were assigned.

ii. receptor_rigid.pdbqt and lig.pdbqt were opened

respectively in the grid then size of the box

changed (usually it has been assigned

126×126×126) for proper exploration of the

receptor.

iii. Then it was saved as gpf format.

iv. Autogrid4 program was run and the

corresponding glg file was prepared.



Preparation of dlg file

i. Through the Docking options, all the required

files were opened such as rigid file, flexible file

and the ligand.

ii. From the search parameters genetic algorithm

window was opened, depending upon the need

all the alteration have been made like number of

GA runs, etc and subsequently it was closed.

iii. Then, docking parameter option was toggled on

and saved as dpf format.

iv. Autodock4 program was run and the

corresponding dlg file was prepared.

Docking output analysis

dlg file was explored to get an understanding of

various docking pose

3.RESULTS AND DISCUSSION

In our present work, an approach is made to

develop few novel tau aggregation inhibitors

(ss1-ss6).

purine/modified purine

----

acyclic ribose linked to hydroxamic acid

All the compounds considered for the study are given

in Table 1.

Table 1: 2D structure of the cocrystal, ANP and the

compounds (ss1-ss6) considered for docking study

The docking study of each molecule was carried out

with 100 number of Genetic Algorithm runs.

For each compound 100 different conformers were

generated. The binding energy of the conformer

closest to one of the complementary residue as

GLN185, inhibition constant, and the distance were

given in Table 2.

Table 2: Binding energy details of the compounds

ss1-ss6 and the cocrystal ANP

Compound

code

Confo

rmer

No

Distan

ce (Å)

from

GLN

185

Observe

d

binding

energy

(Kcal/mo

le)

Inhibition

constant

(KI)

ss1 20 5.71 -4.7 356.31 µM

ss2 63 18.24 -3.37 3.41 mM

ss3 75 21.64 -2.79 9.09 mM

ss4 12 18.40 -4.41 584.73 µM

ss5 7 18.75 -5.02 217.85 µM

ss6 27 20.67 -3.56 2.46 mM

The docking calibration was performed with the

reference co-crystal ANP. The docking study reveals

the experimental binding conformations of the

reference co-crystal with acceptable root-mean-

square deviation (RMSD) of 0.98 Å.

The docking output clearly demonstrated that the test

compound ‘ss1’ with its 20th conformer lying closest

to the complementary residue (GLN185), i.e.; 5.71 Å, whereas the distance observed between the co-crystal

and GLN 185 was 9.25 Å.

The other compounds in the test series also met the

criteria to become an effective lead in the discovery

of inhibitor of the corresponding target. The

following figures (Figure 3 - Figure 9) represent the

docking energy and docking of the conformer closest

to one of complementary residue within the receptive

site. Most of the compounds with a minimum of 5-10

poses are in the proximal vicinity of the receptive

area.

ANP (co-crystal)

N N

N

N

SH

O

O

O NH

OH

OH

N

N

O

OH

O

O NH

OH

ONH2

N+O-

O

N

N

O

OH

O

ONH

OH

N

N

NH2

ss1 ss2 ss3

N

N

O

OH

O

ONH

OH

NH

N

O

NH2

S

N

O

OH

O

ONH

OH

N

N

NH2

N

N

O

OH

O

ONH

OH

N

N

OH

ss4 ss5 ss6



Figure 3: Docking pose of ANP within the active

site of the enzyme 1J1B and its distance from GLN 185, complementary residue of the receptive area

Figure 4: Docking pose of ss1 within the active site

of the receptor 1J1B and its distance from GLN 185

Figure 5: Docking pose of ss2 within the active site of the receptor 1J1B and its distance from GLN 185





4.CONCLUSION

The rationale behind virtual screening is to develop

an idea about the binding pattern of various

molecular skeleton within the active site of the

target. The overloading demand of antialzheimer’s

drugs led to the exploration of two highly sought

after targets which can be modified physiologically

to make the disease least progressive. The outcome

of our present work clearly revealed the possibility

of test compound ss1 if been optimized both

synthetically and biologically may become a suitable

candidate for the patient suffering from this

degenerative disorder. Let’s put our finger crossed

and believe that illustrating the present study may

results in the development of novel compounds

strongly been considered as a promising one.



ACKNOWLEDGEMENT

The author’s are gratefully acknowledging the

support extended by Principal and Management,

Gupta College of Technological Sciences, Asansol

CONFLICTS OF INTEREST

The authors do not have any conflict of interest.

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