Presentation for Dissertation

In silico screening of multipotent therapeutic

candidates against Type II Diabetes Mellitus and
Alzheimer’s Diseases

Supervisor: Simran Deep Kaur

Sayan Chatterjee 03716001319
University School of Biotechnology
Guru Gobind Singh Indraprastha University
Dwarka, New Delhi
(2020-2022) 1
 INTRODUCTION
• Physiological changes that take place in the human
body leading to senescence, the decline of biological
functions and of the ability to adapt to metabolic
stress is known as aging.
• Aging is heterogeneous.
• Thus, it leads to geriatric disorders, i.e., Age-Related
Medical Conditions & Illnesses.

TYPE 2 CHRONIC
ALZHEIMER’S
DISEASE DIABETES KIDNEY
PARKINSON’S MELLITUS DISEASE
DISEASE ARTHRITIS

2
 TYPE 2 DIABETES MELLITUS
• Type 2 Diabetes mellitus
(T2DM) is a chronic
condition that is
characterized by raised
blood glucose levels
(Hyperglycemia).
• Causes: disturbance in
insulin reception in the
cells, loss of Beta cell
responsiveness

3
 ALZHEIMER’S DISEASE
• Alzheimer's disease: The deterioration of intellectual capabilities,
memory, judgment, and personality to the extent that daily functioning
and quality of life are seriously impaired.
• Generally occurs in the elderly impairing brain function, which can lead to
dementia.

4
 GLYCOGEN SYNTHASE KINASE 3 BETA
(GSK3β AS TARGET)

• kinase that phosphorylates serine and threonine sites (regulated by

phosphorylation and de-phosphorylation)
• auto-phosphorylation on tyrosine-279/216 mediates GSK3-β
activation
• phosphorylation on serine sites 21/9 by protein kinase A and B (PKA-
PKB) which leads to its inhibition
5
 PKB
P Tyrosine phoshorylation

GSK3β Activates GSK3B

Tyr 216
P
Phospholylation of GS
Microtubules
P (neurons)
BACE1 TAU Hyperphoshorylation
P Protein at Thr 216
GS P
β secretase
Inactivated GS
Microtubules disassembly
Amyloid
Aβ peptides
precursor
Glucose protein TAU Protein oligomers
X Aβ oligimers

Neurofibrillary tangles
Glycogen
Aβ plaques

6
 DIETARY COMPONENTS AS
LIGANDS
1. High potential as a neuroprotective agent
2. Induce cell regeneration
3. Effective in reducing glycemia
4. Antioxidant and anti-inflammatory properties
5. Great medicinal and pharmacological
significance
6. Lower toxicity
7. Affordable

7
 THOUGHT MAP
Target
Docking
How to
Ligands
Multipotent
therapeutic
Main
Target candidate Blind Site Specific
diseases purpose Docking Docking
Results
Target
Type II Molecule
AD Autodock Pharmacokinetics
DM studies
GSK3β
Absorption
• Hydrophobic • Binding
Distribution
interactions energy Lipinski’s
Activated by • Hydrogen • Inhibition Metabolism
phosphorylation Rule of 5
bonds constant Excretion
Toxicity
8
 OBJECTIVE
1. To construct an inhibitor library of GSK3β.

2. To perform in silico screening of potential therapeutic candidates of Type

2 Diabetes Mellitus via GSK3β mediated interactions/ pathways.

3. To perform in silico screening of potential therapeutic candidates of

Alzheimer’s diseases via GSK3β mediated interaction/pathways.

4. To construct protein ligand interaction profile of the potential

therapeutic candidates.

5. To shortlist multipotent therapeutic candidates against diabetes and

neurodegenerative diseases based on their pharmacokinetics and
pharmacodynamics studies.
9
St
METHODOLOGY
e • Retrieval of sequences from NCBI
p
1
St
e • Multiple sequence alignment analysis (MSA)
p
2
St
e • Phylogenetic analysis
p
3
St
e • Domain and motif analysis
p
4
St
e • Physicochemical properties of Nitrrilase enzyme
p
5
St
e • 2D structure prediction
p
6
St
e • Homology modeling
p
7
St
e • Validation of the generated model
p 10
8
RESULTS

11
AUTODOCK RESULTS OF CURCUMIN DERIVED DIETARY COMPONENTS
Prior to docking, a grid box located at (x = 24.926, y = 24.926, z = 27.613) which correlates
with the ATP site of GSK3B was defined for ligand sampling.
Binding energy Inhibition constant (Ki) Internal energy
Ligands (kcal/mol) (uM/micromolar) (kcal/mol) RMSD (Å)
CURCUMIN
(Control) -4.61 415.2 -3.5 0.8
C1 -4.27 735.84 -3.62 1
C2 -4.26 749.22 -3.26 1
C3 -4.57 447.18 -3.88 0.88
C4 -5.14 170.53 -4.04 0.94
C5 -4.31 695.42 -3.56 0.94
C6 -4.21 822.61 -3.72 1
C7 -5.06 196.48 -4.29 0.86
C8 -4.99 221.24 -3.1 0.94
C9 -3.58 2370 -1.82 1
C10 -3.24 4240 -2 1
C11 -3.71 1900 -2.81 0.94
C12 -3.57 2430 -2.39 1
C13 -3.95 1280 -3.04 1
C14 -3.83 1560 -2.66 0.74
C15 -2.53 1401 -1.66 1
C16 -2.1 2886 -1.5 1
C17 -5.14 170.18 -5.14 0.76 12
C18 -4.75 327.89 -3.95 0.74
 CHOICE OF CONTROLS
CONTROL AGAINST TYPE II DM
METFORMIN
• produced under license by Bristol-
Myers Squibb
• preferred first-line oral blood
glucose-lowering agent to manage
type 2 diabetes.
CONTROL AGAINST ALZHEIMER’S
DISEASE
MEMANTINE
• first synthesized and patented
by Eli Lilly and Company in 1968.
• It works by decreasing abnormal
activity in the brain and may
improve the ability to think and
remember 13
CRYSTAL STRUCTURE OF GSK3Β
(TARGET) AND CONTROLS

B C
A: GSK3β
B: Metformin (Control against T2DM)
C: Memantine (Control against AD) 14
AUTODOCK RESULTS OF CURCUMIN DERIVED DIETARY COMPONENTS
Prior to docking, a grid box located at (x = 24.926, y = 24.926, z = 27.613) which correlates with the
ATP site of GSK3B was defined for ligand sampling.
Binding energy Inhibition constant (Ki) Internal energy
Ligands (kcal/mol) (uM/micromolar) (kcal/mol) RMSD (Å)

Metformin (Control) -4.85 276.25 -4.82 0.3

Memantine (Control) -3.78 1700 -3.69 0.22
C4 -5.14 170.53 -4.04 0.94
C7 -5.06 196.48 -4.29 0.86
C8 -4.99 221.24 -3.1 0.94
C17 -5.14 170.18 -5.14 0.76
Cirsimaritin -3.33 3600 -3.33 0
Delphinidin -4.63 401.52 -3.65 0.68
Eriodictyol -3.94 1030 -3.9 0
Galangin -4.08 1020 -3.85 0.56
Heterophyllin -4.46 540.83 -3.95 0.45
Hispidulin -4.43 566.1 -3.89 0.59
Lanceoletin -4.37 630.21 -3.63 0.88
Malvidin -5 217.61 -4.53 0.35
15
 GSK3Β DOCKED WITH METFORMIN
(CONTROL) AND THEIR INTERACTION STUDIES

Hydrophobic Interactions Hydrogen Bonds

Index Resid Distan
Index Residue AA Distance AA
ue ce
1 258A PRO 3.4 1 144B ARG 2.95
2 221A TYR 2.42
2 260A ASP 3.78
3 258A PRO 2.37
4 264A ASP 2.73 16
 GSK3Β DOCKED WITH MEMANTINE
(CONTROL) AND THEIR INTERACTION STUDIES

Hydrogen Bonds
Index Residu AA Distanc
e e
1 148B ARG 2.87
2 268A GLU 2.83
3 271A LYS 3.45
17
GSK3Β DOCKED WITH C4 AND THEIR INTERACTION STUDIES

Hydrophobic Interactions Hydrogen Bonds

Index Residu AA Distanc Index Residu AA
Distanc
e e e e
1 140B TYR 3.6 1 140B TYR 3.21
2 143B ALA 3.17 2 140B TYR 3.21
3 249B GLU 3.4 3 144B ARG 4.03
4 258A PRO 3.78 4 144B ARG 3.21
5 148B ARG 3.07
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6 249B GLU 3.5
GSK3Β DOCKED WITH C7 AND THEIR
INTERACTION STUDIES

Hydrophobic Interactions Hydrogen Bonds

Index Residu AA Distanc Index Resid AA
Distan
e e ue ce
1 143B ALA 3.77 1
2
144B ARG 3.81
148B ARG 3.47 2
3 144B ARG 3.06
249B GLU 3.4
3 147B SER 3.53
4 258A PRO 3.37
4 148B ARG 4.01
5 148B ARG 2.67 19
 GSK3Β DOCKED WITH C8 AND THEIR
INTERACTION STUDIES

Hydrophobic Interactions Hydrogen Bonds

Residu Distanc
Index Residu AA Distanc Index
e
AA
e
e e
1 144B ARG 2.6
1 140B TYR 3.91 2 144B ARG 3.37
2 148B ARG 3.95 3 147B SER 3.95
3 148B ARG 3.47 4 148B ARG 2.76
5 148B ARG 4.09
6 271A LYS 3.06 20
 GSK3Β DOCKED WITH C17 AND THEIR
INTERACTION STUDIES

Hydrophobic Interactions Hydrogen Bonds

Index Residu AA Distanc Index Residu AA Distanc
e e e e
1 143B ALA 3.82 1 144B ARG 3.06
2 249B GLU 3.21 2 144B ARG 3.72
3 254B GLN 3.37 3 147B SER 3.23
4 150B LYS 3.51
21
GSK3Β DOCKED WITH DELPHINIDIN AND
THEIR INTERACTION STUDIES

Hydrogen Bonds
Index Residue AA Distance
1 140B TYR 2.62
2 147B SER 3.84
3 221A TYR 3.91
4 221A TYR 3.91
5 249B GLU 2.56
6 249B GLU 3.83
7 253B GLY 4.02
8 254A GLN 3.99
22
9 254A GLN 2.93
GSK3Β DOCKED WITH MALVIDIN AND
THEIR INTERACTION STUDIES

Hydrophobic Interactions Hydrogen Bonds

Index Residu AA Distanc Index Residu AA Distanc

e e e e
1 143B ALA 3.97 1 253B GLY 3.92
2 249B GLU 3.41 2 254A GLN 3.04

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 PHARMACOKINETICS STUDY
LIPINSKI’S RULE OF FIVE
Molecular H-Bond H-Bond Rotatable Rule Drug
AlogP
Weight Acceptor Donor Bonds Violation Likeness
Ligand
<500 <5 <10 <5 <3 <2 YES
STANDARD
C4 310.35 4.24 4 4 5 1 YES

C7 400.47 4.95 4 2 8 1 YES

C8 490.6 7.98 4 2 11 1 YES

C17 236.27 2.24 4 3 4 1 YES

Delphinidin 303.25 2.61 6 6 1 0 YES

Malvidin 331.3 3.22 6 4 3 0 YES

All the selected ligands have LESS THAN 2 RULE VIOLATIONS which
24
indicates that their bioavailability will be good in human biological system.
 PHARMACODYNAMICS STUDY
1. ABSORPTION
Skin
Intestinal absorption
WATER SOLUBILITY Permeability
Ligands (human) (%
(log mol/L) Numeric (log
Absorbed)
Kp)
STANDARD Lower value= Less than 30% >
log Kp < -2.5
good absorption good absorption
C4 -4.07 86.63 -2.942
C7 -4.912 92.128 -2.765
C8 -5.565 89.288 -2.735
C17 -1.398 89.313 -3.02
Delphinidin -2.905 67.048 -2.735
Malvidin -3.628 76.227 -2.735
C7, C8 and malvidin ligands show best results in the absorption category
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PHARMACODYNAMICS STUDY
2. DISTRIBUTION
BBB permeability (log BB) CNS permeability (log
Ligands
PS)

STANDARD logBB > -1 = Good (logPS)> -2 = Good

distribution penetration
C4 -0.863 -2.783
C7 -0.444 -2.184
C8 -0.504 -1.645
C17 -0.869 -2.569
Delphinidin -1.751 -2.556
Malvidin -1.026 -1.951

C7, C8 and malvidin ligands show best results in the

distribution category
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 PHARMACODYNAMICS STUDY
3. METABOLISM
CYP2D6 CYP3A4 CYP1A2 CYP2C9 CYP2D6 CYP3A4
Ligands substrate substrate inhibitior inhibitior inhibitior inhibitior
(Yes/No) (Yes/No) (Yes/No) (Yes/No) (Yes/No) (Yes/No)

STANDARD
RANGE Yes Yes Yes Yes Yes Yes
C4 No No Yes Yes No Yes
C7 No Yes No Yes No Yes
C8 No Yes No Yes No Yes
C17 No No No No No No
Delphinidin No Yes Yes No No No
Malvidin No Yes Yes Yes No No
C4, C7, C8 and malvidin ligands show best results in the metabolism
category
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PHARMACODYNAMICS STUDY
4. EXCRETION
Total Clearance (log
Ligands
ml/min/kg)
STANDARD RANGE > 0.5
C4 0.148
C7 0.141
C8 0.187
C17 0.201
Delphinidin 0.728
Malvidin 0.826

Delphinidin and Malvidin ligands show best results in the excretion

category
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 PHARMACODYNAMICS STUDY
5. TOXICITY
Skin
AMES toxicity Hepatotoxicity
Ligands (Yes/No) (Yes/No) Sensitisation
(Yes/No)
STANDARD RANGE No No No
C4 No No No
C7 No No No
C8 No No No
C17 No No No
Delphinidin No No No
Malvidin No No No

All the selected ligands (C4, C7, C8, C17, delphinidin and
malvidin) do not show any type of toxicity effect.

29
 RESULTS SUMMARY
• Metformin and Memantine are the standard drugs
approved by FDA which have been used as control. These
standard drugs are popularly reported to act as an
inhibitor to progression of T2DM and AD respectively.
• As per the Auto Dock 4.2 software C4, C7, C8, C17,
Delphinidin and Malvidin are the top six potential drug
candidates which may bind to the same site as both the
standard drugs.
• As per the pharmacokinetics studies, C4, C7, C8, C17,
Delphinidin and Malvidin follow Lipinski’s Rule of Five.
• As per the pharmacodynamics studies, C7, C8 and
Malvidin are the top 3 potential drug candidates which
follow 4 parameters of ADMET studies.
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 RESULTS INTERPRETATION
Ligands/ C4 C7 C8 C17 DELPHINIDIN MALVIDI
Parameter N
AUTO DOCK YES YES YES YES YES YES
RO5 YES YES YES YES YES YES
ABSORPTION NO YES YES NO NO YES
DISTRIBUTION NO YES YES NO NO YES
METABOLISM YES YES YES NO NO YES
EXCRETION NO NO NO NO YES YES
TOXICITY YES YES YES YES YES YES
• Based on the study done, it can be interpreted from the results that
C7, C8 and Malvidin may act as the potential therapeutic drug
candidates.
• Amongst them, Malvidin is the best multi targeted therapeutic drug
candidate to target GSK3B against both Type 2 Diabetes Mellitus and
Alzheimer’s disease. 31
 CONCLUSION
1. Based on Auto Dock 4.2 only C4, C7, C8, C14, Delphinidin
and Malvidin would perform better than the standard
drugs.
2. With respect to our studies it is observed that AutoDock
4.2 is a preliminary study and pharmacokinetics and
pharmacodynamics has more stringent selection
mechanism as compared to other studies.
3. We propose MALVIDIN as the best multipotent candidate
from our library against both T2DM and AD based on its
relative performance in all the software used.
4. It is advised that in vivo and in vitro investigations should
be used to further validate the data reported in this study.
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Thank you !
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