Abstraction

Bacterial DNA Gyrase is considered as one of the mark against the Anti-Tuburcular agent through the assorted.They are the enzyme responsible for the reproduction of theMycobacteria TBand hence the growing of it. Therefore Targeting these enzyme will non hold any side effects in the Humans since it is absent in the human existences. Deoxyribonucleic acid Gyrase is a tetramer A2B2 protein. The Deoxyribonucleic acid Gyrase fractional monetary unit A is responsible for the breakage-reunion active site, whereas the DNA Gyrase fractional monetary unit B promotes ATP hydrolysis.Targeting DNA Gyrase is one of disputing undertaking since its binding site is non easy accessible, so the undertaking focuses on aiming DNA Gyrase.

Choice of Target Protein PDB was done based on the X-ray declaration and nucleus construction of Ligand. Pose duplicability is one of the proof surveies which were a failure for selected mark protein PDB ; therefore the Homology analysis was carried out. Through this survey two promising receptor for DNA Gyrase Subunit A and Subunit B ( 3IFZ.pdb and 3ZM7.pdb ) was identified. Since it is really hard for any of experts to place active site in progress for any of protein even if the protein construction is available, hence Sitemap was carried out. Grid Coevals for receptors was carried out through GLIDE so that appropriate airss will be produced after docking. Since the identified hits didn’t contain any Ligand, so edifice of fresh library of compounds was done by analysing different Ligand databases.ChemblLigand database was selected, prepared and analyzed. Virtual showing was carried through molecular moorageChemblLigand database with each promising receptors.

There were 5 sites produced through Sitemap, site 1 was selected which produced highest D mark of 1.019 and 1.030 severally. There were one hundred thousand docked molecule produced for each fractional monetary units through Molecular moorage, out of which top 100 docked constructions of both Hits were selected based on Lipskin regulation of five and computation of Average docking Mark followed with the bunch was carried out.13 and 4 bunchs for fractional monetary unit A and Subunit B was obtained severally which are see to be assuring compounds against Tuberculosis. Chemo information sciences analysis for the obtained bunchs were carried out to analyse the customized nucleus for the bunchs. The bunch 2 was selected for readying of complex since it had highest mean docking mark of -8.997.Molecular kineticss was carried for complex and different secret plans and per centum interaction was analyzed. ThereforeM. TBDeoxyribonucleic acid Gyrase is one of the mark for anti-tubercular drug find.

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List OF CONFERENCE PRESENTATION

1. Oral Presentation on “Modeling of Mycobacterial DNA Gyrase Subunit A” in the conference on Progresss in Research and Development and Dissemination of Interdisciplinary Developments for Sustainability” .

Table OF CONTENTS

Chapter no. Title Page no.

Recognitionfour

AbstractionV

List of Conference Presentationsix

Table of Contentssseven

Abbreviationsten

List of Figureseleven

List of Tablesfourteen

1 Introduction1

1.1Background1

1.1.1 Introduction to Computational Approach 2

1.1.2 Insilico Drug Designing 3

1.1.3 Introduction to Topoisomerase 5

1.2 Motivation7

1.3 Review of Literature7

1.3.1 Introduction to DNA Gyrase 8

1.3.2 Structure and Mechanism of Action9

1.3.3 Bacterial DNA Gyrase as Drug mark 12

1.4 Objective14

1.5 Organization of Report14

2 METHODOLOGY15

2.1 Workflow for the Undertaking15

2.2 Flow chart for Homology Analysis16

2.3 Flowchart for Protein Preparation16

2.4 Flowchart for Chemo information sciences Analysis17

3 TOOLS AND TECHNIQUES 18

3.1 Maestro 18

3.1.1 GLIDE 19

3.1.2 QIKPROP 21

3.1.3 Premier 26

3.1.4 SITEMAP 27

3.1.5 DESMOND 29

Techniques 31

3.2 Molecular Docking 31

3.3 Molecular Dynamicss 32

3.4 Databases 33

3.4.1 Protein Databank 33

3.4.2 UNIPROT 34

4 MATERIALS AND METHODS

4.1 Designation of PDB for Target Protein37

4.2 Designation of best PDBs for Screening 37

4.2.1 Pose Reproducibility 37

4.2.2 Homology Analysis 37

4.3 Selection and readying of protein 38

4.4 Active Site designation 39

4.5 Receptor Grid Generation 40

4.6 Ligand Database 40

4.6.1 Ligand Preparation 42

4.7 Chemo information sciences Analysis 43

4.8 Molecular Docking 43

4.8.1 Docking Protocol 43

4.8.2 Virtual Screening 43

4.8.3 Generation of Average Score 44

4.8.4 Postulation of ADMET belongings 44

4.9 Molecular Dynamicss44

5 RESULTS AND DISCUSSION46

5.1 STRUCTURE OF DNA GYRASE 46

5.2 Designation of PDB for Target 46

5.3 Designation of Best PDBs for Screening through 48

Validation surveies

5.4 Sequence analysis and comparing for DNA Gyrase 51

5.4.1 Sequence comparing 55

5.5. Choice and Preparation of Protein 56

5.5.1 Resolution 57

5.5.2 Ramchandran Plot 58

5.6. Protein Preparation 59

5.7 Site Map Analysis 60

5.7.1 Receptor Grid Generation 64

5.8. Ligand Database 65

5.8.1Property Analysis from Ligand Database 66

5.9 Docking Analysis 68

5.9.1 Interaction analysis of Ligand with the Promising Hits 69

5.9.2 Interaction of proteins with the Amino acid residue 71

Of Best bunch

5.9.3 Graphs for Interaction Fingerprint Analysis for 72

Subunit A ( 3IFZ.pdb )

5.9.4 Graphs for Interaction Fingerprint Analysis for 76

Fractional monetary unit B ( 3ZM7.pdb )

5.9.5 ADMET Property 79

5.10 Molecular Dynamicss 82

6 CONCLUSION AND FUTURE SCOPE 96

Mentions 98

Abbreviation

Deoxyribonucleic acid Deoxyribonucleic acid

Deoxyribonucleic acid Gyr DNA Gyrase

Deoxyribonucleic acid Gyr A DNA Gyrase subunit A

Deoxyribonucleic acid Gyr B DNA Gyrase fractional monetary unit B

M.tbMycobacteria TB

OPLS Optimized potency for Liquid Simulation

CTD C-terminal Domain

QSAR Quantity Structural Activity Relationhip

QRDR Quinolone opposition finding part

NTD N-terminal Sphere

PA Primary booster for Gyrase A

PB Primary Promoter for Gyrase B

?-factor Isotropic temperature factor

PDB Protein Databank

Alogp Partition Coefficient

HBD Hydrogen Bond acceptor

MW Molecular weight

List OF FIGURES

Figure no. Title Page no.

1. 1 Stairss in planing and marketing the drug 3

1.2 Docking procedure in Drug Designing 4

1.3 Mechanism of action of Topoisomerase 5

1.4 Strand transition by Topoisomerase 6

1.5 Structure of Topoisomerase 6

1.6 Structure of DNA Gyrase 9

1.7 QRDR part for fractional monetary unit A 10

1.8 Action of DNA Gyrase 11

1.9 Mechanism of action 12

3.1 Outline of tools used 18

3.2 The Application tree and undertaking panel tree 19

3.3 Glide Docking Hierarchy 21

3.4 Hydrophobic, Donor, Acceptor map, 28

Exterior of Pocket

3.5 Hydrophobic, Donor, Acceptor map, 28

Interior of Pocket

3.6 The Top-Ranked Site with Ligand for 1KE8 29

3.7 Basic Outline of a Desmond Simulation 30

3.8 Flowchart for different phases of Docking 31

3.9 Multi-stage testing workflow 32

3.10 Simulation as a span between

a ) Microscopic and Macroscopic 33

B ) Theory and Experiment

3.11 UNIPROT web page 36

3.12 Beginning and Flow of Data UNIPROT-GOA 37

4.1 Workflow for Lead designation and optimisation 42

4.2 Panels used in the practical combinatorial testing 43

4.3 Stairss in the Molecular kineticss 46

5.1 Sequence analysis consequences for Targets 53

5.2 Consensus sequence analysis for mark 54

5.3 ?-Factor analysis for Target 55

5.4 Sequence Comparison for Target 56

5.5 ( A ) 3D position of Subunit A ( 3IFZ.pdb ) 57

5.5 ( B ) 3D position of Subunit B ( 3ZM7.pdb ) 58

5.6 ( A ) Ramchandran Plot of Subunit A ( 3IFZ.pdb ) 60

5.6 ( B ) Ramchandran Plot of Subunit B ( 3ZM7.pdb ) 60

5.7 Site ( S1 ) View of Subunit A ( 3IFZ.pdb ) 63

5.7 ( A ) Site Map View Subunit A ( 3IFZ.pdb ) 63

5.8 Site ( S1 ) position of Subunit B ( 3ZM7.pdb ) 64

5.8 ( A ) Site Map View Subunit B ( 3ZM7.pdb ) 64

5.9 ( A ) Receptor Grid Generated in Subunit A 65

5.9 ( B ) Receptor Grid Generated in Subunit B 66

5.10 Bar Diagram for Number of Clusters v/s 67

Frequency of Molecule

5.11 Scatter Plot for HBA v/s MW 68

5.12 Scatter Plot for Alogp v/s MW 68

5.13 Bar diagram for Top 100 Clusters v/s 69

Frequency of docked Molecules

5.14 Hierarchical Clustering of top 100 docked 70

Molecule

5.15 ( A ) Different Interaction of Ligand with Subunit A 71

5.15 ( B ) Different Interaction of Ligand with Subunit B 71

5.16 ( A ) Interaction Matrix Analysis for 3IFZ.pdb 73

5.16 ( B ) Aromatic residue Analysis for 3IFZ.pdb 74

5.16 ( C ) Charge residue Analysis for 3IFZ.pdb 74

5.16 ( D ) Hydrogen Bond Donor residue Analysis 75

for 3IFZ.pdb

5.16 ( E ) Hydrophobic residue Analysis for 3IFZ.pdb 75

5.16 ( F ) Polar residue Analysis for 3IFZ.pdb 76

5.16 ( G ) Side concatenation residue Analysis for 3IFZ.pdb 76

5.17 ( A ) Interaction Matrix Analysis for 3ZM7.pdb 77

5.17 ( B ) Aromatic residue Analysis for 3ZM7.pdb 77

5.17 ( C ) Charge residue Analysis for 3ZM7.pdb 78

5.17 ( D ) Hydrogen Bond Donor residue Analysis 78

for 3ZM7.pdb

5.17 ( E ) Hydrophobic residue Analysis for 3ZM7.pdb 79

5.17 ( F ) Polar residue Analysis for 3ZM7.pdb 79

5.17 ( G ) Side concatenation residue Analysis for 3ZM7.pdb 80

5.18 Simulation Graph of Protein 84

Subunit A v/s Ligand RMSD

5.18 ( A ) Simulation Graph of Protein 84

Subunit B v/s Ligand RMSD

5.19 Graph of Protein ( Subunit A ) -Ligand Contact 85

5.19 ( A ) Graph of Protein ( Subunit B ) -Ligand Contact 86

5.20 Ligand –Protein Subunit A contacts 87

5.20 ( A ) Ligand –Protein Subunit B contacts 88

5.21 ( A ) Bunch 2 for fractional monetary unit A used in readying of 89

Complex

5.21 ( B ) Cluster 2 for fractional monetary unit B used in readying of 89

Complex

List OF TABLE

Table no. Title Page no.

3.1 Descriptor Used for ADME Property 22

3.2 PDB keeping lists 34

5.1 Structure of DNA Gyrase 47

5.2 Detailss of screened PDBs 48

5.3 FASTA sequence DNA Gyrase Subunit A 50

5.3.1 3D construction Database for DNA Gyrase 50

Fractional monetary unit A

5.4 FASTA sequence DNA Gyrase Subunit B 50

5.4.1 3D construction Database for DNA Gyrase 51

Fractional monetary unit B

5.5 Promising Hits for DNA Gyrase 51

Subunit A and Subunit B

5.6 RMSD and Alignment Score for Protein 52

Structure Alliance

5.7 Site Map consequences for Screened PDBs 61

5.7.1 Site Map consequences for mark receptor 62

Fractional monetary unit B ( 3ZM7.pdb )

5.7.2 Site Map consequences for mark receptor 62

Subunit A ( 3IFZ.pdb )

5.8 Important Interaction of protein with the 72

Amino Acid of selected Bunch

5.9 Qikprop belongings computation for 81

Antituburcular activity

1

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