Computer aided drug

design

Amit nagal

Birla institute of scientific

research

What is insilico studies

• It is advance computational studies

involving tools and softwares of
bioinformatics and drug designing

• Receptor could be protein /gene /

Enzymes eg.retenoid acid receptor,

• Ligand is active molecule which

has either inhibitory or exhibitory
property it acts on receptor

Why Do We Do Docking?

Drug discovery costs are too high: ~$800 millions,

8~14 years, ~10,000 compounds (DiMasi et al.

2003; Dickson & Gagnon 2004)

Drugs interact with their receptors in a highly

specific and complementary manner.

Core of the target-based structure-based drug

design (SBDD) for lead generation and optimization.

Lead is a compound that



shows biological activity,



is novel, and



has the potential of being structurally modified for improved

bioactivity, selectivity, and drugeability.

Structure based drug

design

HIV protease inhibitor amprenavir

(Agenerase) from Vertex & GSK (Kim
et al. 1995)

HIV: nelfinavir (Viracept) by Pfizer (&

Agouron) (Greer et al. 1994)

Influenza neuraminidase inhibitor

zanamivir (Relenza) by GSK
(Schindler 2000)

Receptor

Ligand

Affinity: G = H -TS

Displaced H

Bound and
associated H

Upon complex formation:

• water molecules are released

• receptor and ligand loose degrees of freedom

• interactions between ligand and receptor

Docking Methodology: Scoring

Dock Score

• Dock Score = – (ligand/receptor interaction

energy + ligand internal energy)

Where
• denotes temperature and entropy and it is

equivalent to -(ligand/receptor interaction

energy)

• H (Enthalpy)is equivalent to ligand

internal energy (denoted by U, or

sometimes E, is the total of the kinetic

energy due to the motion of

molecules(translational, rotational,

vibrational)

Affinity or DOCK SCORE: G = H -TS

TS

Introduction

•

The aim of this project is to identify

suitable anti - inflammatory

compounds based on inhibition of

Human non-secretory

PLA2 receptor

•

This objective may be achieved by the

following steps:

–

Listing of effective drug candidates

–

Docking analysis of the compounds

–

ADME property analysis of the compounds

–

Screening of probable lead

Phospholipase

• Phospholipases A2 (PLA2) enzymatic activity is a

rate-limiting step

rate-limiting step in the formation of arachidonic

acid and subsequently in the synthesis of

leukotrienes and prostaglandins, which in turn

promote

inflammation

inflammation.

• Thus sPLA2 contributes to the pathogenesis of

various inflammatory diseases, including Sepsis

Sepsis

and

Rheumatoid Arthritis

• PLA2s are also involved in the generation of a wide

range of biomediators like

• Lysophospholipids,
• Arachidonic acid and its metabolites .

These lipids can enhance

• Tumor cell growth
• Invasion and
• Metastasis

Phospholipids

Archadonoic acid

Prostaglandins

Inflamma

tion

sPLA2

Cyclo-

oxygenase

Novel

Molecule

NSAIDs

Locus-1p35

Biochemical pathway involving sPLA2

Workflow

Protein

Responsible

Disease /Symptom Identification

Receptor Identified

Ligands Identified based on Qsar Studies in literature

review

Docking and affinity studies for receptor and the

corresponding ligands

Selection of the drugs with best Docking scores Affinity values

Final confirmation of selected drugs with best A.D.M.E.

properties.

Structure of the Target-

Protein (1DCY) Phospholipase

• Structure of protein

with its natural
ligand

Detailed Methodology

Study

biochemical pathway

biochemical pathway of inflammation and

receptors

receptors responsible

Analysis of

active site

active site of inflammatory receptors.

Study available

drugs

drugs and the

mechanisms

mechanisms by which they block the

biochemical pathway of inflammation.

Explore

alternative

alternative ways to block inflammatory pathway .

To study the effect of

inhibition of hnpsPLA2

inhibition of hnpsPLA2 in inflammatory pathway.

Identification of the known

3D structure

3D structure of sPLA2 receptors

Listing of current

commercial

commercial drugs towards the inhibition of receptor.

Listing of

predicted inhibitors

predicted inhibitors in QSAR studies based on literature review.

Retrieval

Retrieval of 3D structure of available drugs in market from Pubchem.

10. Molecular

design

design and 3D modeling of predicted drugs of QSAR studies.

11. Comparative

docking

docking studies of both predicted and marketed drugs.

12.

ADME

ADME studies of the selected inhibitory compounds.

13.

Selection of lead

Selection of lead having good Dock Score and optimum ADME
properties

SOFTWARE TOOLS USED

• Operating system used Red Hat Linux 5.
• MDL-ISIS Draw 2.5

•

Used for sketching the molecules

• Discovery Studio 2.1

–

CHARMm

•

Used for Forcefield energy optimization

–

LIGAND-FIT

•

Used for docking study

–

ADMET

•

Used for study of Absorption, Distribution,

Metabolism, Excretion parameters.

ADME Studies

In the ADMET module we studied about the

important Pharmacodynamic parameters

like Absorption, Distribution, Metabolism

and Excretion for all the 126 compounds.

This was done with the help of the following

models of Discovery Studio:

1. Intestinal absorption
2. Aqueous solubility
3. Blood brain barrier penetration
4. Plasma protein binding
5. Cytochrome and P450 2D6 inhibition Model.

ADME Studies

In the ADMET module we studied about the

important Pharmacodynamic parameters

like Absorption, Distribution, Metabolism

and Excretion for all the 126 compounds.

This was done with the help of the following

models of Discovery Studio:

1. Intestinal absorption
2. Aqueous solubility
3. Blood brain barrier penetration
4. Plasma protein binding
5. Cytochrome and P450 2D6 inhibition Model.

RESULTS

• During our study we found that the drugs found

most effective in prior QSAR studies also gave

consistently high scores in our Docking Analysis,

proving the effectiveness of the modern inSilico

Drug-Designing approaches.

• In our study we came across many effective drugs

like 7u, 7i, 13h etc. But

13h

was chosen as the

novel molecule because it showed consistently high

dock score with all three receptors namely

1DCY,

1DB4, 1DB5

– responsible for causing inflammatory

response.

• We also found that Molecule: 13h also showed

optimum ADME

properties. This further proved that

Molecule 13h has a good future potential as a novel

and effective lead in the times to come.

13h Docked In The Active Site

of 1DB5, Dock Score 75.19

13h Docked In The Active Site

of 1DB4, Dock Score 80.47

13h Docked In The Active Site

of 1DCY, Dock Score 69.68

Conclusion

Absorption, Distribution, Metabolism and Excretion parameters of

13h were also found within their optimum ranges as mentioned

below:

–

Blood Brain Penetration

Blood Brain Penetration Level was found to be

extremely low-

extremely low-(4)

(4)

and thus

ensuring a very low brain penetration ensuring minimum drug effect on

CNS and thus

reducing the side effects

reducing the side effects like

sedation

sedation a common in most

of the marketed drugs.

–

Intestinal Absorption

Intestinal Absorption Level was found to be

very good-

very good-(0)

(0)

ensuring that

drug can be taken easily in form of Oral Drug delivery systems like Tablet

and Capsules thus

reducing the overall cost

reducing the overall cost of the final marketed product

as well as

better patient compliance

–

Aqueous Solubility

Aqueous Solubility was within optimal range-(4.028)

(4.028)

and in accordance to

Lipinski Rules ensuring that optimal concentration of drug would be

available in blood ensuring

Good therapeutic efficacy

–

Cytochrome P450 enzyme

Cytochrome P450 enzyme was not found to be inhibited by the drug thus

ensuring good excretion half life of the drug which in turn decreases the

probability of toxicity of the drug. Thus the drug has a

good therapeutic

index

ensuring maximum patient safety against drug over dosage.

–

Plasma Protein Binding

Plasma Protein Binding was found to be greater than 95%- (2).

(2).

This calls

for higher loading dose for the drug but ensures a sustained therapeutic

action even after stoppage of dosage, thus ensuring single tablet per day

dosage regimen, ensuring

better

patient acceptance and

therapeutic

action

Lens regeneration – In silico and In vivo studies

(JPB/Vol.1.2 104-108(2008)/May 2008)

• In vivo studies of lens regeneration
• lens regeneration is the process of

reformation of lens.

• Dorsal iris lens forming cell

            lens vesicle          primary
lens fiber            secondary lens
fiber                  RL

In vivo with help of Vitamin

• Dorsal iris and

cleft

Vitamin A dose effect on

lens regeneration

• Vitamin A doses inducing lens

regeneration

Data Table

Group No. of Operation No of reg
Young Mice

       Control                   20                                           4

      Vit A treated           20                                          18

In silico studies of lens

regeneration

• Rxr alpha receptor-

Mechanism of

action(Drug Bank)

• “

The role of Vitamin A in epithelial differentiation, as well as in

other physiological processes, involves the binding of Vitamin A to
two  families  of  nuclear  retinoid  receptors  (retinoic  acid
receptors,RARs;  and  retinoid-Xreceptors,RXRs).These  receptors
function  as  ligand-activated  transcription  factors  that  modulate
gene transcription.”

• It has been found that expression and role of retinoic acid receptor

alpha was very important in lens regeneration (Tsonis et al, 2002).

• vitamin A and its derivatives were found to accelerate lens

regeneration not only in amphibian frogs but also in mammals like
swiss albino mice, rabbit, guinea pigs and pigs (Shekhawat et al,
2001).

• Vitamin A metabolite 9-cis retinoic acid present endogenously and

works as an agonist (Calberg et al, 1993)

METHODOLGY

• Using Autodock the 1mv9 and 1fby comparatively docking with vitamin A

and 9- cis retinoic acid dock energies was found relatively very closed.

• The docking energy for IMV9 with vitamin A ranges between -11.65 kcal

and -6.88 kcal and for 9-cis retinoic acid it ranges between -11.83 cal and
-6.55 kcal.

• Similarly for 1FBY the docking energy for vitamin A was between -12.19

kcal and -7.30 and for 9-cis retinoic acid it was between -12.14 kcal and
-4.10 kcal.

• The result showed that the docking energies of highest ranked conformer

for Rxr alpha receptor of human with vitamin A and 9-cis retinoic acid
were very close and similar was in case of mice. The structural and
docked energy similarity of both receptors gives clear evidence why
exogenous vitamin A proved beneficial for lens regeneration.

9-cis retinoic
acid

Vitamin A with 1FBY

conclusion

• It has been reported that vitamin A doses enhance

9-cis retinoic acid concentration in the plasma of

preruminant calves (Brian J. Nonnecke1 et al,

2000) can prove this theory that vitamin A can

convert to its derivative 9-cis retinoic acid.

Thanks!!!

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