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INTRODUCTION

Drug design is the approach of finding new drugs , based on the biological targets (the

protein). Typically a drug target is a key molecule involved in a particular metabolic or signalling pathway that is specific to a disease condition or pathology, or to the

infectivity or survival of a microbial pathogen.

Rational Drug Design (RDD) is a process used in the biopharmaceutical industry to

discover and develop new drug compounds. RDD uses a variety of computational

methods to identify novel compounds, design compounds for selectivity, efficacy and

safety, and develop compounds into clinical trial candidates. These methods fall into

several natural categories structure-based drug design, ligand-based drug design, de

novo design and homology modeling depending on how much information is available

about drug targets and potential drug compounds.

In this project main emphasis is on Cyclooxygenase 2 which is an enzyme which is

present in human body and is responsible for inflamatory response of the immune system

of human body.The cyclooxygenase is naturally occuring enymes and produces

hormones called protaglandins.E.C number of cyclooxygenase is 1.14.99.1 .There aretwo isoforms of cyclooxygenase .Cyclooxygenase-1(Cox-1) & cyclooxygenase-2(Cox-

2). The genes for cox-1 and cox-2 are located on chromosomes 9 and 1. The human cox-

2 gene is 8.3 kilobases (kb) whereas the cox-1 gene is much larger 22 kb . In terms of

their molecular biology, COX-1 and COX-2 are of similar molecular weight (67 and 72

k Da respectively), and having 65% amino acid sequence homology and near-identical

catalytic sites.

Cox-1 Is a House Keeping Enzyme and Is Normally Present in a Variety of Area of the

Human Body Including Stomach.The cox-1 enzyme of the stomach produces certain

chemical messanger called prostaglandins that ensure the natural mucus lining which

protects the inner stomatch, mediate normal platelet function and regulate renal blood

flow.

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Cox 2 is 74 kD protein,Cox 2 contains 604 amino acids, it is located at chromosome

number 1,TATA box is present upstream of the start codon,it is usually absent in a cell

under normal condition and is expressed only in response to inflammatio,its over

expression in our system is a matter of concern as it may cause tumor formation.The

tumor formed may,under the influence of mitogens and other carcinogens, lead to cancer

formation.

There are many differences between cox 1 and cox 2.COX 1 is detectable under normal

conditions while COX 2 is not.COX 1 is located on chromosome number 9 while COX 2

is located on chromosome number 1 in human DNA.In COX 1 TATA Box is is ABSENT

while in COX 2 it is present.The lumen of COX 1 is thinner while that of COX 2 is

wider,so sometimes antibodies for COX 2 tend to affect COX 1 as well.The gene for COX 1 is longer as compare to COX 2. COX 1 is found in most mammalian cells while

COX 2 is abundant only in macrophages and other sites of inflammation.At position

523,in the gene,COX 1 has isoleucine while COX 2 has valine.

1.2 Pathways Of Formation And Action Of Cox-1 And Cox-2

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1.3 Production And Action Of Prostagladin

Arachidonic acid(a 20 carbon FA containing 4 double bonds) is liberated from the

membrane phospholipids by phospholipase A2, Which is activated by diverse stimuli.

Arachidonic acid is converted by cyclooxygenase to the unstable intermediate

prostaglandinH2 .

Prostaglandin H2 is converted by tissue specific isomerases to multiple prostaglandin

such as prostacyclin, thromboxane,prostaglandinD,E,F.

FIG. . The arachidonic acid cascade

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While initial studies upheld the concept that COX-2 is mainly an inflammatory, inducible

enzyme, more recent studies are beginning to reveal additional functions. We will now

turn our attention to the various organ systems and disease states where COX-2 appears

to have functional significance.

Prostaglandins are known to serve as important physiologic modulators of vascular tone

and sodium and water homeostasis in the mammalian kidney, including modulation of

glomerular hemodynamics, tubular reabsorption of sodium and water, and regulation of

renin secretion.

COX-2 seems to have some role in regulating brain function. PGs have long been knownas mediators of fever, of inflammatory reactions in neural tissue, and, more recently, of

brain function. The recognition that each of these processes involves induction of PG

synthesis has led to an appreciation of the role COX-2 plays in the PG-mediated

functions. In turn, COX-2 inhibition by an isoform-specific NSAID can effectively block

fever . Communication between local inflammatory sites and the brain endothelium is

mediated by cytokines such as IL-1, which can directly induce COX-2 expression in

these cells .

The use of NSAIDs causes a variety of problems in the gastrointestinal tract including

irritation and ulceration of the stomach lining . In animal studies, COX-2 is not induced

after exposure to radiation, and its presence is not essential for crypt cell survival . Under

these circumstances, COX-1 appears to play a major role, as it does in the stomach, in

maintaining proper glandular architectureIn addition, COX-2 is expressed during

inflammation and wound healing, and in animal models, treatment with COX-2 inhibitors

can exacerbate inflammation and inhibit healing. Nevertheless, COX-2 selective

inhibitors appear to be associated with less gastrointestinal damage than conventional

NSAIDs .

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Evidence provided by animal models of inflammatory arthritis strongly suggests that

increased expression of COX-2 is responsible for increased PG production seen in

inflamed joint tissues . COX-2 induction has been observed in both human osteoarthritis-

affected cartilage as well as in synovial tissue taken from patients afflicted with

The pro-inflammatory agents IL-1, TNF-, and LPS, as well as the growth factors TGF-,

EGF, PDGF, and FGF, have all been shown to induce COX-2 expression in this system.

On the other hand, the antiinflammatory cytokines IL-4 and IL-13, as well as the

immunosuppresive glucocorticoids, were shown to decrease COX-2 levels . Although the

synovial tissues of patients with osteoarthritis express lesser amounts of COX-2, primary

explant cultures of human osteoarthritis-affected cartilage spontaneously express large

amounts of COX-2 and PGs .The rapid expansion of knowledge about the role of COX-2in inflammation led to drug screens attempting to identify antiinflammatory agents

selective for COX-2 as well as to the rational design of highly selective COX-2

inhibitors.

COX-2 is induced in both local and central sites , and the question of whether COX-2

mediates pain reception or transmission is being investigated, primarily through the use

of COX-2 specific NSAIDs.. In fact, the COX-2 specific inhibitor Celecoxib was shown

in short-term human studies to effectively suppress the pain associated with dental work,

osteoarthritis, or rheumatoid arthritis without causing any significant gastroduodenal

lesions .

NSAID use reduces risk for Alzheimer's Disease (AD), with users of these agents having

as little as one half the risk of acquiring AD as those not taking NSAIDs. Several

population-based studies have detected a 4050% decrease in relative risk for colorectal

cancer in persons who regularly use aspirin and other NSAIDs .

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REVIEW OF LITERATURE

Barbara et-al , 2007 reported recently that changes in expression level of COX-2 are

correlated with development and progression of human melanoma. In this study, weinvestigated whether the COX-2 expression level might be a useful immunohistochemical

marker for distinguishing cutaneous melanomas from benign melanocytic lesions. Up to

now, immunohistochemical markers have not ensured satisfactory sensitivity and

specificity of differential pathologic diagnosis of melanoma. The expression of COX-2

was determined immunohistochemically in formalin-fixed, paraffin-embedded specimens

of 33 early Clark I/II melanomas and 58 naevi. Mean COX-2 expression in melanomas

was significantly stronger than in naevi (P[almost equal to]10-13). A simple diagnostic

algorithm using threshold values of the COX-2 expression level allows for differentiation

between early melanomas and naevi with high sensitivity (Se) and specificity (Sp) (for Se

between 91 and 100%, Sp values change between 96.5 and 51.7%). Areas under the

receiver operating characteristic curves were, respectively, 0.97+/-0.02 and 0.86+/-0.04

for the COX-2 expression in central and border regions of the lesions. For all the

melanomas (not only the early ones),the respective areas under the ROC curve values

were 0.98+/-0.01 and 0.97+/-0.02. In conclusion, COX-2 is the first

immunohistochemical marker that allows the distinguishing of early melanomas frombenign melanocytic lesions with both high sensitivity and specificity

Jeroen , et-al , 2005 worked on neuronal expression of cyclooxygenase-2 (COX-2) and

cell cycle proteins is suggested to contribute to neurodegeneration during Alzheimer's

disease (AD). The stimulus that induces COX-2 and cell cycle protein expression in AD

is still elusive. Activated glia cells are shown to secrete substances that can induce

expression of COX-2 and cell cycle proteins in vitro . Using post mortem brain tissue we

have investigated whether activation of microglia and astrocytes in AD brain can be

correlated with the expression of COX-2 and phosphorylated retinoblastoma protein

(ppRb). The highest levels of neuronal COX-2 and ppRb immunoreactivity are observed

in the first stages of AD pathology (Braak 0II, Braak A). No significant difference in

COX-2 or ppRb neuronal immunoreactivity is observed between Braak stage 0 and later

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Braak stages for neurofibrillary changes or amyloid plaques. The mean number of COX-

2 or ppRb immunoreactive neurons is significantly decreased in Braak stage C compared

to Braak stage A for amyloid deposits. Immunoreactivity for glial markers KP1, CR3/43

and GFAP appears in the later Braak stages and is significantly increased in Braak stage

V-VI compared to Braak stage 0 for neurofibrillary changes. In addition, a significant

negative correlation is observed between the presence of KP1, CR3/43 and GFAP

immunoreactivity and the presence of neuronal immunoreactivity for COX-2 and ppRb.

These data show that maximal COX-2 and ppRb immunoreactivity in neurons occurs

during early Braak stages prior to the maximal activation of astrocytes and microglia. In

contrast to in vitro studies, post mortem data do not support a causal relation between the

activation of microglia and astrocytes and the expression of neuronal COX-2 and ppRb in

the pathological cascade of AD

Anna , et-al , 2007 work showed that Cyclooxygenase-2 (COX-2) is the inducible form of

the enzyme involved in the first steps of the prostaglandins and thromboxane synthesis.

COX-2 up-regulation is demonstrated in tumors where it can modulate tumoral

progression, metastasis, multidrug resistance, and angiogenesis. Experimental data

suggest a possible therapeutic use of the COX-inhibitors nonsteroidal antiinflammatory

drugs (NSAIDs). NSAIDs can block tumor growth through many mechanisms, especially

through antiangiogenic and proapoptotic effects. Moreover, NSAIDs can also improve

the efficacy of radiotherapy, chemotherapy, and hormonal therapy. This study reviews

the COX-2 expression as evaluated through immunohistochemistry and real time

polymerase chain reaction (RT-PCR) in 23 meningiomas [14 World Health Organization

(WHO) grade I; 5 WHO grade II; 3 WHO grade III; 1 oncocytic meningioma]. At

immunohistochemistry all the lesions but 4 (83%) were COX-2 positive. At RT-PCR 9

meningiomas, 8 WHO grade I and 1 WHO grade II, showed a COX-2 expression greater

than the reference value (average expression of all meningiomas that we studied). Theassociation between tumor grade and immunohistochemical or RT-PCR COX-2

expression was not significant (P=0.427 and P=0.251, respectively). In conclusion, even

if further studies on larger series are necessary, the common COX-2 overexpression in

meningiomas may suggest considering the COX-2 inhibitors, alone or in combination

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with radiotherapy, a potential area of therapeutic intervention in some selected

meningiomas.

Marco , et-al, 2005 work showed that Cyclooxygenase 2 (COX-2) is an inflammation-

associated enzyme involved in the pathogenesis of many solid tumors, but little is known

about its presence and role in hematologic neoplasms. Multiple myeloma (MM) is known

to involve a deregulated cytokine network with secretion of inflammatory mediators. We

thus decided to investigate the involvement of COX-2 in this neoplasm. Western blotting

(WB) was used to evaluate 142 bone marrow (BM) specimens, including MM and

monoclonal gammopathy of undetermined significance (MGUS). Selected cases under-

went further evaluation by WB on purified CD138 + cells, immunohistochemistry (IC),

and real-time

polymerase chain reaction (PCR) for mRNA expression. COX-2 wasexpressed in 11% (2 of 18) of MGUS specimens, 31% (29 of 94) of MM at diagnosis, and

47% (14 of 30) of MM with relapsed/refractory disease. COX-2 positivity was associated

with a poor outcome in terms of progression-free (18 vs 36 months; P < .001) and overall

survival (28 vs 52 months; P < .05). Real-time PCR showed COX-2 mRNA

overexpression. IC and cell separation studies demonstrated COX-2 expression to be

restricted to malignant plasma cells. This is the first report of the presence and prognostic

role of COX-2 expression in MM. Future studies will assess COX-2 involvement in other

hematologic tumors and its potential use as a therapeutic or chemo-preventive target in

onco-hematology.

Phuong, et-al, 2002 Their studies were performed to ascertain the relative abundance of

E prostaglandin (EP) receptor mRNAs in tissues that are major targets, or major

degradative sites, of insulin; to identify which EP receptor type mediates PGE 2 inhibition

of insulin secretion in pancreatic islets; and to examine possible sites of action through

which sodium salicylate might affect IL-1/PGE 2 interactions. Real-time fluorescence-

based RT-PCR indicated that EP3 is the most abundant EP receptor type in islets, liver,

kidney, and epididymal fat. EP3 mRNA is the least, whereas EP2 mRNA is the most,

abundant type in skeletal muscle. Misoprostol, an EP3 agonist, inhibited glucose-induced

insulin secretion from islets, an event that was prevented by preincubation with pertussis

toxin, by decreasing cAMP. Electromobility shift assays demonstrated that sodium

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recurrent neoplastic polyps of the large bowel in patients with a history of colorectal

adenomas.A total of 2586 patients with a history of colorectal adenomas underwent

randomization: 1287 were assigned to receive 25 mg of rofecoxib daily, and 1299 to

receive placebo. All investigator-reported serious adverse events that represented

potential thrombotic cardiovascular events were adjudicated in a blinded fashion by an

external committee. A total of 46 patients in the rofecoxib group had a confirmed

thrombotic event during 3059 patient-years of follow-up (1.50 events per 100 patient-

years), as compared with 26 patients in the placebo group during 3327 patient-years of

follow-up (0.78 event per 100 patient-years); the corresponding relative risk was 1.92 (95

percent confidence interval, 1.19 to 3.11; P=0.008). The increased relative risk became

apparent after 18 months of treatment; during the first 18 months, the event rates were

similar in the two groups. The results primarily reflect a greater number of myocardialinfarctions and ischemic cerebrovascular events in the rofecoxib group. There was earlier

separation (at approximately five months) between groups in the incidence of

nonadjudicated investigator-reported congestive heart failure, pulmonary edema, or

cardiac failure (hazard ratio for the comparison of the rofecoxib group with the placebo

group,4.61;95percent confidence interval, 1.50 to 18.83). Overall and cardiovascular

mortality was similar in the two groups. CONCLUSIONS: Among patients with a history

of colorectal adenomas, the use of rofecoxib was associated with an increased

cardiovascular risk

Jana, et-al , 2002 worked on Dexamethasone and concluded that it is very effective for

controlling peritumoral cerebral edema, it is associated with distressing side effects that

decrease the quality of life for many patients. One potential mechanism to explain the

ability of dexamethasone to repair blood-brain barrier dysfunction is through the

inhibition of cyclooxygenase-2 (COX-2). The purpose of this study was to determine in a

rat brain tumor model whether SC-236, a selective COX-2 inhibitor, is as effective asdexamethasone. Twenty-nine adult male Fischer 344 rats were implanted with

intracerebral 9L gliosarcomas and divided into 3 treatment groups. One group ( n = 9)

served as controls, another ( n = 9) was treated with dexamethasone (3 mg/kg p.o. daily),

and a third group ( n = 11) received SC-236 (3 mg/kg p.o. daily). A survival study was

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performed. The median survival in the control group was 16 days, compared with 23 days

for the dexamethasone group and 23 days for the COX-2 inhibitor group. Kaplan-Meier

analysis on pairwise group comparisons showed improved survival that was statistically

significant for each treatment group compared with the control group (log-rank test P =

0.009 for dexamethasone to control and P = 0.005 for COX-2 to control), and no

significant difference in survival for the COX-2 compared with dexamethasone (log-rank

test P = 0.2). These results suggest that a selective COX-2 inhibitor appears to be as

effective as dexamethasone in prolonging survival in a rat brain tumor model

Lisa, et-al , 2002 indicated that prostanoids, such as prostaglandins, play a regulatory role

in several forms of neural plasticity, including long-term potentiation, a cellular model for

certain

forms of learning and memory. In these experiments, the significance

of the COXisoforms cyclooxygenase-1 (COX-1) and cyclooxygenase-2 (COX-2) in post-training

memory processes was assessed. Adult male Long-Evans rats underwent an eight-trial

(30-sec intertrial interval) training session on a hippocampus-dependent (hidden platform)

or dorsal striatal-dependent (visible platform) tasks in a water maze. After the

completionoftraining, rats received an intraperitoneal injection of the nonselective COX

inhibitor indomethacin, the COX-1-specific inhibitor piroxicam, the COX-2-specific

inhibitor N -[2-cyclohexyloxy-4-nitrophenyl]-methanesulfonamide (NS-398), vehicle

(45% 2-hydroxypropyl- -cyclodextrin in distilled water), or saline. On a two-trial

retention test session 24 h later, latency to mount the escape platform was used as a

measure of memory. In the hidden platform task, the retention test escape latencies of rats

administered indomethacin (5 and 10 mg/kg) or NS-398 (2 and 5 mg/kg) were

significantly higher than those of vehicle-treated rats, indicating an impairment in

retention. Injections of indomethacin or NS-398 that were delayed 2 h post-training had

no effect on retention. Post-training indomethacin or NS-398 had no influence on

retention of the visible platform version of the water maze at any of the dosesadministered. Furthermore, selective inhibition of COX-1 via post-training piroxicam

administration had no effect on retention of either task. These findings indicate that COX-

2 is a required biochemical component mediating the consolidation of hippocampal-

dependent memory

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MATERIALS AND METHODS

3.1. Retrieval of Protein Sequence of Cox 2 in Homo sapiens:

Protein sequence of cox 2 in Homo sapiens was done from National Center Of Biotechnology information( www.ncbi.nlm.nih.gov/). The sequence of protein was in

fasta formet.

3.2 Homology Modelling :

Homology modelling is required when the exact structure of the protein is not

available.The structure of cyclooxygenase 2 was also unavailable,so homology modeling

was required.It is also known as comperative modelling.Here we model themolecule(protein) from amino acid sequence by following a protocol to model.The amino

acid sequence is query or target sequence.Homo;ogy modeling techniques depend on

identificatiction of one or more stuctures known as template,which resembles the

sructure of query sequence.The sequence alignment and template stucture are used to

produce a structural model of the target.Usually sequence similarity corresponds to high

structural similarity.

Different softwares are used for Homology Modelling such as SWISS MODEL

SERVER.,CPH MODEL SERVER.,MODELLER etc. In this project Swiss Model server

is used for Homology Modelling.The methodology for homology modeling with swiss

Model Server is:

3.2.1. BLAST

BLAST (Basic Local Alignment Search Tool),( www.ncbi.nlm.nih.gov/BLAST)is a tool by

which we can find alignment between our query in form of nucleotide or protein

sequence,against the database of BLAST.The results show us the extent to which our

query sequence matches the sequences stored in the BLAST database.In case our

sequence is a novel entry,it does not show any results.Here I carried out protein-protein

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BLAST of my query sequence,against pdb(protein data bank);which consists of amino

acid sequences of the proteins submitted in pdb .The results generated by BLAT were

furthur used for the modeling of the protein. After we get BLAST results we carry out

CLUSTAL W.

3.2.2. CLUSTAL W

CLUSTAL-W (www.ebi.ac.uk/clustalw/) is a multiple sequence alignment programme

for DNA or proteins.It provides multiple sequence alignment forgiven sequence.It gives

the match between the query sequences and allows us to have the idea of best match

between our target sequence and template.This informationis furthur used in swiss

model.Evolutionary relationships can be viewed by cladograms or phylograms.

3.2.3. Swiss Model:

It is totally automated protein structure homology modeling server ,accessible via

ExPASy web server or from swiss pdb viewer.(www.swissmodel.expasy.org//SWISS-

MODEL.html).

SWISS MODEL SERVER: It is used for final modeling of protein,using results of

CLUSTAL-W.Basically there are three moes os SWISS MODEL,which are:

1. First approach mode:it only requires a single amino acid sequence information as input

data.The server automatically selects suitable template.However the user may specify

upto five template structures either from ExPDB library,or opload co-ordinate files.The

process starts if atleast one template sequence has a identity of more than 25% with

submitted target sequence.The reliability of model decreases as sequence identity

decreases.

2. Alignment Mode:it is done by submitting a sequence alignment.The ser predicts the

target sequence and the one ,which is structurally known protein FROM ExPDB

library.The server builds yhe model according to given alignment.

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3. Project Mode:here user submits a manually optimized modeling request to SWISS

MODEL server The starting moe is a Deep View project file.It contains superposed

template structures and alignment between target and template.It allows template

selection or gap placement in the alignment.It can also be used to improve the output of

first approach mode.

Here alignment mode of SWISS MODEL was used to predict structure of cox 2 model.

There are certain steps to be followed in this process,which are:

Retrieval of protein seuence from NCBI in FASTA format.

Protein BLAST of protein sequence obyained in last step against pdb(protein databank).

Selecting the second,third,fourth match results and obtaining their FASTA format of

sequence.

Puting the results obtained in last step alongwith target protein sequence of protein

in a notepad.The sequences obtained in last steo are pot\entail te,plates.

Open CLUSTAL W page and paste the sequence obtained in last step in window

displayed and submit.

Open SWISS MODEL SERVER page and paste the sequence in window and

submit.

The results are obtained,asve the result file with (.pdb) extension,to save a pdb file.

Open the saved file with rasmol viewer to view 3-D image of the modeled protein.

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3.3 Retrieval of inhibitor against Cox-2:

Inhibitor against Cox-2 protein retrieved through two major sources.

1. BRENDA (www.brenda.uni-koeln.de) is the main collection of enzyme functionaldata available to the scientific community.BRENDA is maintained and developed at the

institute of Biochemistry at the University of Cologne

2. NCBI Pubchem Compound : PubChem Structure Search allows PubChem

Compound Database to be queried using a chemical structure. Chemical structure queries

may be sketched using the PubChem Sketcher. You may also specify the structural query

input by PubChem Compound Identifier (CID), SMILES, SMARTS, InChI, Molecular

Formula, or by upload of a supported structure file format.

This standardizing allows NCBI to compute chemical parameters and similarity

relationships between compounds. The compounds are grouped into levels of chemical

similarity from most general to most specific: same bonding connectivity and any

tautomer; same bonding connectivity; same stereochemistry; same isotopes; and same

stereochemistry and isotopes. PubChem Compound also indexes these chemicals using

34 fields, many of which represent computed chemical properties such as the number of

chiral centers, the number of hydrogen bond donors/acceptors, molecular formula and

weight, total formal charge, and octanol-water partition coefficients (XlogP). These

groups are provided as Entrez links that allow similar compounds to be retrieved quickly

3.3 Building of 3d structure (PDB file) of Inhibitors:

2D structure of potent inhibitors are obtained by submitting the CID no to the NCBIs

Pubchem compound and convert it into SDF format then convert it into PDB format to

get the 3D-structure.

Procedure of converting 2D-structure into 3D-structure

1) To select SDF format from NCBI.

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Open google and enter NCBI home page.

Choose pubchem compound from search drop-down menu.

Type CID no.

When answers come ,Change display format to SDFand save it

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3.5 Docking Of Flexible Ligands to the Receptors

For docking the flexible ligands to the receptors following softwares can be used whichare listed below :

SN Name License Term Platform Keyword1 Autodock Commercial UNIX,LINUX,SGI GA/LGA,MC2 Affinity Commercial SGI Monte Carlo

method3 Dock Vision Commercial LINUX.IRIS MC,GA4 DOT(Daughter

of Turnip)

Free Supercomputers,UNIX

5 Flex X Commercial UNIX Fragnent Based6 Shape E-mail request UNIX Structure and

chemistry of

molecular

surface7 LEAPFROG Commercial SGI ligand design8 Q site Commercial UNIX,LINUX,SGI Mixed

quantum and

molecular

mechanics9 HINT Commercial Windows

2000,SGI,LINUX

Hydropathic

interaction10 GOLD Free evaluation UNIX GA

3.3.2 Cygwin : It is a collection of free software tools originally developed from

Cygnus solutionsto allow various versions of Microsoft windows to act similarto a

Linux operating system.As Autodock is programmed to run on Linux operating system,so

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for those systems which run on windows,cygwin is a must.It can be freely downloaded

from the internet.

3.3.3. AUTODOCK: Autodock is a suite of automated docking tools. It is designed to

predict how small molecules, such as substrates or drug candidates, bind to a receptor of

known 3D structure. AutoDock actually consists of two main programs: AutoDock

performs the docking of the ligand to a set of grids describing the target protein; Auto

Grid pre-calculates these grids. In additions to using them for docking, the atomic affinity

grids can be visualized. This can help, for example, to guide organic synthetic chemists

design better binders .

1.Autogrid.

2.Autodock.

3.3.3.1 . AUTOGRID :

A.Peparing a Ligand for Autodock :

i.In autodock page,go to ligand and in it click on input.

ii.In input click on open AD3.

iii.Go to your folder and open the (.pdb) file of the inhibitor.

iv.Go to Ligand again in autodock window and in it Torsion Tree and click ondetect

route.

v.In Ligand select Torsion Tree and click on Choose Torsionand click on done.

vi.Go to Ligand again and select Torsion Tree and select Set number Of

Torsions.The number of torsions

vii.Set number of torsions less than or equal to 6 and click on Dismiss.

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viii.Go to Logand and in it to Output and then click on Save As PDBQ.Then go to

your folder a save your this file as (inhibitor name.out.pdbq).

B. Preparing A Macromolecule For Autodock:

i.Go to Grid and in it click on Macromolecule and in it click on Open AG3.

ii.Open the (.pdb) file from your folder and click on OK.

iii.Now save this file as protein name.pdbqs.

iv.Come back to autodock window and press shift key+n to visualize the protein on

screen.

C.Preparing The Grid Parameter File:

i.Go to Grid and select Set Map Types and in it select Choose Ligand AG3.

ii.Now select the inhibitor file.

iii.Now click on Ligand and then click on Accept.

iv.Go to Grid and selectGrid Box.

v.On the window that opens,set x,y,z co-ordinate axes so that the macromolecule is

completely covered.You can rotate the molecule by pressing shift+right click of mouse.

vi.On the same window,click on File and there click on Saving Current Setting.

vii.Go to Grid again and in it go to Output,then click on SaveGPF(AG3)

viii.Save this file in your folder as protein name.gpf.

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ix.Go to Grid and in it go to Edit Grid and clik it,then click on Accept.

x.Go to your folder and copy the path of your folder eg(C:\probir) and open the (.gpf) file

in your folder wit wordpad and paste this path followed by \ on left of wherever you

find protein name in this file.It is to be noted that there should not be any gap between

path and protein name.

xi.Click on Save in this window after you finish.

3.3.3.2.AUTODOCK :

A.Startimg Autodogrid:

i.Go to Run and in it click on Run Autogrid.

ii.On the window that opens on the first Browse option click and select autogrid.exe

file.

iii.Then in second Browse option click and go to your folder and open the (.gpf) file.

iv.Back to autogrid, select the entire bottom line(i.e. the path) of the Browse window

and press cntrl+c.

v.Open Cygwin and in it go to Edit and Paste the path copied and press Enter.

B.Preparing A docking Parameter For Autodock:

i.Click on Docking on the the autodock window.

ii.In it select on Macromolecule and in it click on Choose AD3.

iii.Select your protein in the window that opens and click on OK.

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iv.Click on Select Macromolecule and click on window that opens twice.

v.Go to Docking and in it go to Ligand and in it click on Choose (AD3).

vi.On the window that opens click and select the ligand.

vii.Click on Select Ligand and click on Accept on the window.

viii.Go to docking again and selectSearch Parameterand in it click on Genetic

Algorithm.Click Accept on yhe window that opens.

ix.Go to Docking again and in it click on Docking Parameters.Click on Accept on

the window that opens.

x.Go to Docking again and in it select Output and in it click on Lamarkian

GA(AD3).Then go to your folder and save the file as (inhibitor name.dpf).

xi.Go to your folder and copy the path of (.dpf) file.

xi.Open this (.dpf) file in wordpad and paste the copied path everywhere you find

inhibitor name,followed by \ i.e.path+\,on left of the inhibitor name.Continue till you

reach on yhe line with move and here do the same.

xii.Save the page.

C.Starting Autodock:

i.Back to autodock,click on Run and in it click on Run Autodock.

ii.On the window that opens on first Browse option,click it and open the autodock.exe

file.

iii.On the second Browse option,click and go to your folder and open the the (.dpf) file.

iv.Come back to Browse window and copy the path at the bottom by selecting it and

then pressing cntrl+c.

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v.Open Cygwin and go to Edit and click on Paste .

vi.Press Enter to run Autodock.

D.Analysing Autodock Results:

i.Click on Analyse on the autodock window and in it click on Docking.

ii.Go to your folder and open the (.dlg) file. And click ok.

iii.Now go to Macromolecule in Analyse and go to your folder and open the (.pdbqs)

file of the target.

iv.Press Shift+n to visualize the macromolecule on the screen.

v.Go to Conformation in Analyse and in it click on Load,a box appears.

vi.Go to Conformation again and click on Play,another window opens.

vii.In the Play window,click on (&) sign ,a new window opens.

viii.Now on the first window that came on pressing Load go to its second line and click

it.It shows the docking energy and various other docking parameters.Note it.The more

negative dock energy,the better inhibitor is;positive dock energies(if found) are neglected

as it is not a proper result.

ix.Now go to the window which came in Play,in it click on the direction buttons to

analyse each of the ten active sites.It gives information about various parameters on a

particular active site.Here we also search for hydrogen bonds which are shown on the

bottom of that window and we can also find the amino acid to which the ligand binds.

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x.Expand the bottom of the box which we got on clicking Load.

xi.Click on Write Current Coords and go to your folder and save this file as

(inhibitor.docked.pdbq).

xii.Record the results.

3.4. PMV (Python Molecular Viewer):

Python Molecular Viewer is a tool to view the binding of hydrogen bonds in the target

molecule.It helps to visualise and analyse the hudrogen bonds.The process of operation of PMV is enlisted below:

Procedure For Operation Of PMV:

i.Open PMV.

ii.Go to File and click on Browse Command.

iii.In the window that opens,click on pmv

.

iv.In the adjacent window click on trace command,then click on Load.Again in the

adjacent window of pmv click on hbond command and load this too.

v.Go to file in PMV and click on Read Molecule nad go to your folder and open

(protein name.pdbqs) file.

vi.Go to Compute and in it go to Trace.

vii.Here click on Compute Extrude Trace.

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xxiii.Click ok.

xxiv.Go to File and in it go to Read Molecule.

xxv.By last step go to your folder and open the (inhibitor.docked.pdbq) file and open it.

xxvi.Go to Select and in it click on Direct Select.

xxvii.In the window that opens click on Molecule and in it click on your

macromolecule.

xxviii.Click on Molecule again and now click on the ligand or the inhibitor.

xxix.Click on Dismiss.

xxx.Go to Display.

xxxi.In it click on Stick and Balls.

xxxii.In the window that opens set Stick Quality to 15 and set Ball Quality to 15.

xxxiii.Click ok.

xxxiv.Go to Color and click on By Atom Type.

xxxv.In the next window click on Stick and Balls.

xxxvi.Click ok.

xxxvii.Go to Hydrogen Bond.

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xxxvii.In it go to Build.

xxxviii.In it click on Set Parms+Build.

xxxix.In the window that opens click on specify two sets.

xxxx.In the next window click on,in the top list under Molecule List click it and select

macromolecule.

xxxxi.I the bottom Molecule List,click it and select the ligand.

xxxxii.Click ok.

xxxxiii.Go to H bond and in it click on Display.

xxxxiv.In it click on as lines.

xxxxv.Click Dismiss in the window that opens.

xxxxvi.Again go to Display and click on Cylinders.

xxxxvii.In the window that opens adjust bond length and bond radius of the hydrogen

bond by using mouse,to a suitable size.

xxxxviii.Go to Dj vu GUI and click on camera in the lower window.

xxxxix.On the window which lengthens, click on Set Background Color.

xxxxx. Click on SW and then click on S.

xxxxxi.Go to File of PMV and click on save as.

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RESULTS AND DISCUSSION

Retrieval of protein sequence of COX2 (cyclooxygenase2).

>gi|3915797|sp|P35354|PGH2_HUMAN Prostaglandin G/H synthase 2 precursor(Cyclooxygenase-2) (COX-2) (Prostaglandin-endoperoxide synthase 2)(Prostaglandin H2 synthase 2) (PGH synthase 2) (PGHS-2) (PHS II)

MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPT

PNTVHYILTHFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPP

VPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPDPQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGL

GHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVGQEVFGL

VPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPE

LLFNKQFQYQNRIAAEFNTLYHWHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRV

AGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGEKEMSAELEALYGDIDAVELY

PALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKG

CPFTSFSVPDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL

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BLAST Result:-

Fig4.1: BLAST RESULT

4.2.ClustalW Results:

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Results of searchNumber of sequences 4Alignment score 20349Sequence format PearsonSequence type aaClustalW version 1.83JalView Output file clustalw-20070718-12352061.outputAlignment file clustalw-20070718-12352061.alnGuide tree file clustalw-20070718-12352061.dndYour input file clustalw-20070718-12352061.input

.

Scores Table

SeqA Name Len(aa) SeqB Name Len(aa) Score

1 seq1 604 2 seq2 587 861 seq1 604 3 seq3 552 88

1 seq1 604 4 seq4 552 87

2 seq2 587 3 seq3 552 99

2 seq2 587 4 seq4 552 99

3 seq3 552 4 seq4 552 99

CLUSTAL W (1.83) multiple sequence alignment

seq2 -----------------ANPCCSNPCQNRGECMSTGFDQYKCDCTRTGFYGENCTTPEFL 43



seq1 MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFL 60

seq2 TRIKLLLKPTPNTVHYILTHFKGVWNIVNNIPFLRSLIMKYVLTSRSYLIDSPPTYNVHY 103



seq1 TRIKLFLKPTPNTVHYILTHFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADY 120

seq2 GYKSWEAFSNLSYYTRALPPVADDCPTPMGVKGNKELPDSKEVLEKVLLRREFIPDPQGS 163


313
http://www.ebi.ac.uk/jalview2/http://www.ebi.ac.uk/cgi-bin/jobresults/clustalw/clustalw-20070718-12352061.outputhttp://www.ebi.ac.uk/cgi-bin/jobresults/clustalw/clustalw-20070718-12352061.alnhttp://www.ebi.ac.uk/cgi-bin/jobresults/clustalw/clustalw-20070718-12352061.dndhttp://www.ebi.ac.uk/cgi-bin/jobresults/clustalw/clustalw-20070718-12352061.inputhttp://www.ebi.ac.uk/jalview2/http://www.ebi.ac.uk/cgi-bin/jobresults/clustalw/clustalw-20070718-12352061.outputhttp://www.ebi.ac.uk/cgi-bin/jobresults/clustalw/clustalw-20070718-12352061.alnhttp://www.ebi.ac.uk/cgi-bin/jobresults/clustalw/clustalw-20070718-12352061.dndhttp://www.ebi.ac.uk/cgi-bin/jobresults/clustalw/clustalw-20070718-12352061.input


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seq1 GYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVGKLLLRRKFIPDPQGS 180

seq2 NMMFAFFAQHFTHQFFKTDHKRGPGFTRGLGHGVDLNHIYGETLDRQHKLRLFKDGKLKY 223

seq4 NMMFAFFAQHFTAQFFKTDHKRGPGFTRGLGHGVDLNHIYGETLDRQHKLRLFKDGKLKY 223

seq3 NMMFAFFAQHFTHQFFKTDHKRGPGFTRGLGHGVDLNHIYGETLDRQHKLRLFKDGKLKY 223

seq1 NMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKY 240

seq2 QVIGGEVYPPTVKDTQVEMIYPPHIPENLQFAVGQEVFGLVPGLMMYATIWLREHQRVCD 283

seq4 QVIGGEVYPPTVKDTQVEMIYPPHIPENLQFAVGQEVFGLVPGLMMYATIWLREHQRVCD 283

seq3 QVIGGEVYPPTVKDTQVEMIYPPHIPENLQFAVGQEVFGLVPGLMMYATIWLREHNRVCD 283

seq1 QIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVGQEVFGLVPGLMMYATIWLREHNRVCD 300

seq2 ILKQEHPEWGDEQLFQTSKLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNQQFQYQ 343

seq4 ILKQEHPEWGDEQLFQTSKLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNQQFQYQ 343seq3 ILKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNQQFQYQ 343

seq1 VLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQ 360

seq2 NRIASEFNTLYHWHPLLPDTFNIEDQEYSFKQFLYNNSILLEHGLTQFVESFTRQIAGRV 403



seq1 NRIAAEFNTLYHWHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRV 420

seq2 AGGRNVPIAVQAVAKASIDQSREMKYQSLNEYRKRFSLKPYTSFEELTGEKEMAAELKAL 463

seq4 AGGRNVPIAVQAVAKASIDQSREMKYQSLNEYRKRFSLKPYTSFEELTGEKEMAAELKAL 463seq3 AGGRNVPIAVQAVAKASIDQSREMKYQSLNEYRKRFSLKPYTSFEELTGEKEMAAELKAL 463

seq1 AGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGEKEMSAELEAL 480

seq2 YSDIDVMELYPALLVEKPRPDAIFGETMVELGAPFSLKGLMGNPICSPQYWKPSTFGGEV 523



seq1 YGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEV 540

seq2 GFKIINTASIQSLICNNVKGCPFTSFNVQDPQPTKTATINASASHSRLDDINPTVLIKRR 583

seq4 GFKIINTASIQSLICNNVKGCPFTSFNVQ------------------------------- 552

seq3 GFKIINTASIQSLICNNVKGCPFTSFNVQ------------------------------- 552

seq1 GFQIINTASIQSLICNNVKGCPFTSFSVPDPELIKTVTINASSSRSGLDDINPTVLLKER 600

seq2 STEL 587

seq4 ----

seq3 ----

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seq1 STEL 604

4.3 SWISS MODEL Result: _________________

4.4. INHIBITOR TABLE:

Table 4.1 : List of inhibitors against COX2(cyclooxygenase2).

Inhibitor

Name

Structure IUPAC Name IC50

Value

Side

effects

Clinical

phase

Sodium

Parecoxib

sodium N-[4-(5-

methyl-3-phenyl-1,2-

oxazol-4-

yl)phenyl]sulfon

ylpropanimidate

0.005

+/-0.1

micro

moles

/L

Gastro

-

intesti

nal

infecti

on

Phase IV

celecoxib 4-[5-(4-methylphenyl)-

3-

(trifluoromethyl)pyrazol-1-

yl]benzenesulfon

amide

4.8

+/-0.4

nmol/

L

Gastro

intesti

nal

infecti

on,ulc

ers

Phase III

Valdecoxi

b

4-(5-methyl-3-

phenyl-1,2-

oxazol-4-

yl)benzenesulfon

amide

0.001

+/-

0.3mi

croM

Hyper

algesia

:increa

sed

sensitivity to

pain

Phase III

333
http://%20void%20window.open%28%27../image/structurefly.cgi?cid=119607&width=400&height=400%27,%20%27StructureFly%27,%20%27resizable=yes,%20scrollbars=yes,%20WIDTH=620,%20HEIGHT%20=%20620%27)


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Rofecoxib 4-(4-methylsulfonylp

henyl)-3-phenyl-

5H-furan-2-one

(4.7+/

-0.5)

nmol/

L

headac

he,ble

eding

Phase III

Doxorubic

in

(7S,9R)-7-

[(2S,4S,5S,6S)-

4-amino-5-

hydroxy-6-

methyl-oxan-2-

yl]oxy-6,9,11-trihydroxy-9-(2-

hydroxyacetyl)-

4-methoxy-8,10-

dihydro-7H-

tetracene-5,12-

dione

0.42+/

-0.3

micro

M

Hair

loss,fa

tigue

Phase II

Etoricoxib 5-chloro-2-(6-methylpyridin-3-

yl)-3-(4-methylsulfonylp

henyl)pyridine

1.1+/-

0.1

micro

M

Fatigu

e and

dizines

s

Phase III

Lumiracox

ib

2-[2-[(2-chloro-

6-fluoro-

phenyl)amino]-

5-methyl-

phenyl]acetic

acid

0.06+/

-0.3

micro

M

dizzine

ss or

sleepin

ess

Phase III

343
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Nimesulid

e

N-(4-nitro-2-

phenoxy-

phenyl)methanes

ulfonamide

0.071

+/-0.5

micro

M

Liver

enlarg

ement,

liver

toxific

ation

Phase III

Dipyrone sodium [(1,5-dimethyl-3-oxo-

2-phenyl-

pyrazol-4-yl)-

methyl-

amino]methanes

ulfonate

4.6+/-

0.3

micro

M

agranulo

cytosis

Phase II

Thalidomi

de

2-(2,6-dioxo-3-

piperidyl)isoindo

le-1,3-dione

3.1+/-

0.3

micro

M

constipa

tion,

dizzines

s

Phase III

Etodolac 1,8-diethyl-1,3,4,9-

tetrahydropyrano

-[3,4-b]indole-1-

acetic acid.

2.9+/-

0.4

micro

M

allergi

c

reactio

n

Phase II

(8E)-8-

[hydroxy-[(5-

methyl-1,3-

thiazol-2-

yl)amino]methyl

idene]-9-methyl-

10,10-dioxo-

10 6-thia-9-

azabicyclo[4.4.0

]deca-1,3,5-

trien-7-one

4.51+/

-0.8

micro

M

headach

e,

fatigue

related

to

anemia

Phase III

353
http://%20void%20window.open%28%27../image/structurefly.cgi?cid=5281106&width=400&height=400%27,%20%27StructureFly%27,%20%27resizable=yes,%20scrollbars=yes,%20WIDTH=620,%20HEIGHT%20=%20620%27)http://%20void%20window.open%28%27../image/structurefly.cgi?cid=3308&width=400&height=400%27,%20%27StructureFly%27,%20%27resizable=yes,%20scrollbars=yes,%20WIDTH=620,%20HEIGHT%20=%20620%27)http://%20void%20window.open%28%27../image/structurefly.cgi?cid=5426&width=400&height=400%27,%20%27StructureFly%27,%20%27resizable=yes,%20scrollbars=yes,%20WIDTH=620,%20HEIGHT%20=%20620%27)http://%20void%20window.open%28%27../image/structurefly.cgi?cid=6236&width=400&height=400%27,%20%27StructureFly%27,%20%27resizable=yes,%20scrollbars=yes,%20WIDTH=620,%20HEIGHT%20=%20620%27)http://%20void%20window.open%28%27../image/structurefly.cgi?cid=4495&width=400&height=400%27,%20%27StructureFly%27,%20%27resizable=yes,%20scrollbars=yes,%20WIDTH=620,%20HEIGHT%20=%20620%27)


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ibuprofen 2-[4-(2-methylpropyl)ph

enyl]propanoic

acid

3.8

+/-0.7

micro

M

ulcerati

ons,

abdomi

nal pain

Phase III

Naproxen sodium (2S)-2-(6-

methoxynaphtha

len-2-

yl)propanoate

3.4

+/-0.4

micro

M

headach

e, and

dizzines

s

Phase II

Table4.4 shows the chemical formula, molecular weight, chemical structure and IUPAC

name of different inhibitors which show interaction with COX2(cyclooxygenase2).

protein. The IUPAC name of the inhibitor is further used in making pdb file of that

inhibitor.

4.5 Docking of ligand to receptor

4.5.1 AUTODOCK RESULTS

Table 4.2: Docked energies and other parameters of the inhibitors using Auto Dock

docking program.

363
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Table 4.2 shows the results displayed by Autodock docking program displaying Free-energy, Intermolecular-energy, Internal-energy and finally Docked energy of the COX2

(cyclooxygenase2) with its inhibitor. Autodock docking results show that Bellnamine

inhibitor of COX2 (cyclooxygenase2) shows best interaction with the

COX2(cyclooxygenase2), with its docked energy of 19.79.

4.6 Python Molecular Viewer (PMV) Results:

SN Inhibitor

Name

Docked

Energy

Ref

RMS

Free

Energy

Intermolecular

Energy

Internal

Energy1 Etodolac -15.1 37.3 -16.4 -17.67 2.572 Nimesulide -2.01 35.3 -1.73 -2.98 0.96

3 Etoricoxib -15.1 37.3 -16.74 -17.67 2.574 Melocoxib -17.49 55.47 -16.56 -18.12 0.635 Valdecoxib -19.3 31.18 -11.04 -19.13 0.06 Doxorubicin -16.78 24.05 -18.97 -19.9 3.127 Thalidomide -11.84 36.61 -11.22 -11.84 0.08 Ibuprofen -8.87 25.68 -9.49 -10.74 1.879 Naproxene -19.79 32.53 -11.7 -19.79 0.010 Rofecoxib -19.1 28.56 -16.92 -19.1 0.0

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Fig 4.6.1.: Hydrogen Bond Formed Between Proteins Active Site and Inhibitor

Etorocoxib

383


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Fig 4.6.2.: Hydrogen Bond Formed Between Proteins Active Site and Inhibitor Etodolac

393


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Fig 4.6.3.: Hydrogen Bond Formed Between Proteins Active Site and Inhibitor Nimesulide

404


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Fig4.6.4.: Hydrogen Bond Formed Between proteins Active Site and Inhibitor Doxorubicin

414


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Fig4.6.5.: Hydrogen Bond Formed Between Proteins Active Site and Inhibitor

Melocoxib

424


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Thalidomide

434


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Rofecoxib

444


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Fig 4.6.8.: Representation Of The Interaction between the protein and Valdecoxib

454


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Fig 4.6.9.: Representation Of The Interaction between the protein and Ibuprofen

464


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Fig 4.6.10.: Representation Of The Interaction between the protein and Naproxene

DISCUSSION

Rational Drug Designing Strategies reduce a lot of time ,money and energy as compared

to other hit and trial methods.According to recent trends mathematical modelling has

become very valuable.The use of sophasticated softwares and tools greatly help in this

process,helping furthur development in research and development in this field. The

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main concern in AutoDock is computation of docking energy,which essentially should be

less than zero.The more negative the docking energy,the better it is.

Fig 4.7. Shows the relative docked energies of various inhibitors with the target protein.

From the figure we can conclude that Naproxene has the minimum docked

energy,hence the best inhibitor

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CONCLUSION

After the project work on rational drug design for COX 2,the conclusion is that out of all

the inhibitors chosen for the docking,naproxene emerged to be be the best inhibitor for the protein COX 2.The precise reason for it was its docking energy which was the

lowest(docked energy=-19.79),among all other inhibitors used.Hence the conclusion is

that naproxene is the best inhibitor,for COX 2.Hence the task was completed

successfully.

Cancer is a major threat to the worlds health.There are many reasons and factors

responsible for induction of cancer.COX 2 is also one of those factors responsible for the

induction of cancer.Basically COX 2 is an enzyme present in our body which is anintegral part of the inflamatory responses of our immune system.If due to any reason the

secretion of this enzyme crosses a perticular threshold,it can cause tumor formation.This

tumor may under the influence of mitogens and other carcinogens can cause cancer.The

threat if cancer bein cause by COX 2 has spread globally and many bio-pharma giants

have launched several medicines eg:Celebrex,Vioxx etc.The main concern is to reduce

the over-expression of COX 2 and not to terminate its secretion completely.There are

many inhibitors which are used for the inhibition of over secretion of COX 2.Out of

many inhibitors,some are rejected due to their side effects,as gastric ulcer in case of

aspirin.However there is no inhibihitor which is fully perfect and without any

sideeffects.Nevertheless we try to reduce the burden on the general health of the patient

to the maximum extent possible.Hence ,newer drugs are required which have the same

efficacy as the older one but are having fewer side effects.The intial phase of discovering

a new drug nowadays is by using CADD.This method has greately reduced the time

,energy and money involved in the traditional methods.After a drug has been designined

in-silico,its furthur verification is done,as stated earlier in laoratories.This method of

using computer to design the drugs has indeed hastened the process of drug discovery.

Rational Drug Designing Strategies reduce a lot of time ,money and energy as compared

to other hit and trial methods.According to recent trends mathematical modelling has

494


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51/55

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rofecoxib in a colorectal adenoma chemoprevention trial, New England Journal of

Medicine, , 11: 1092-1102.

Commonly used websites:

www.ncbi.nlm.nih.gov/

www.pdb.org

http://redpoll.pharmacy.ualbarta.ca/drugbank. http//:Swissmodel.expasy.org/workspace

Journals:

Applied Immunochemistry And Molecular Morphology.

Blood

Cancer Biology

Diabetes

Health Affairs

Journal Of Neuroinfllammation.

Learning Memory

Melanoma Research

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Nuero Oncology

The New England Journal of Medicine

Neuro Oncology

The New England Journal Of Medicine

Thieme Docking

Abbreviations:

NCBI-National Center Of Biotechnology Information.

COX-Cyclooxygenase.

PDB-Protein Data Bank.

BLAST-Basic Local Alignment Search Tool.CADD-Computer Aided Drug Designing.

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.

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Documents

probir project