Table of Contents 1. SUMMARY .......................................................................................................... 8  2. ABBREVIATIONS ........................................................................................... 13  3.

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Table of Contents

1. SUMMARY ... 8 

2. ABBREVIATIONS ... 13 

3. INTRODUCTION AND THE OBJECTIVES OF THE STUDY ... 17 

4. DRUG DISCOVERY AND RATIONAL DRUG DESIGN ... 20 

4.1.

I

... 20 

4.1.1. Drug discovery process... 21 

4.1.1.1. Target identification ... 21 

4.1.1.2. Target validation ... 23 

4.1.1.3. Lead identification:... 23 

4.1.1.4. Lead optimization: ... 25 

4.1.1.5. Preclinical and clinical development: ... 26 

4.2.

R

... 27 

4.2.1. Computer-assisted drug Design (CADD) ... 29 

4.2.1.1. Ligand-Based Drug Design (LBDD)... 30 

4.2.1.2. Structure-Based-Drug Design (SBDD) ... 31 

4.2.1.3 Docking and scoring ... 35 

4.2.1.4 Virtual screening (VS), High throughput virtual screening (HTVS) ... 45 

5. MYELOPEROXIDASE AS A TARGET FOR DRUG DISCOVERY ...

55

5.1.

MPO

... 56 

5.2.

MPO

... 58 

5.3.

MPO

... 60 

5.4.

MPO

... 60 

5.5.

MPO

... 61 

5.6.1. Introduction to X-ray Crystallography ... 62 

5.6.2. MPO structure and its Crystallography data ... 66 

5.6.2.1. The first published X-ray structures of MPO (1992-1995, Fenna and Zeng work). ... 72 

5.6.2.2. The X-ray structures of MPO with Cl-_{, Br}- _CN-_{, SCN}- _{ligands ... 73} 

5.6.2.3. The x-ray structure of MPO and the proximal histidine (His336) orientation ... 76 

5.6.2.4. The X-ray structure of MPO inactivated by thioxanthine derivatives and Ceruloplasmin. ... 78 

5.6.2.5. The X-ray structure of MPO complexed with aromatic hydroxamates. ... 82 

5.6.2.6. The X-ray structure of MPO of the highest resolution (5FIW) ... 84 

5.6.2.7. Comments on MPO structure: ... 84 

5.7.

M

MPO ... 86 

5.8.

I

MPO

... 90 

5.9.

MPO

. ... 91 

5.9.1. Random screening: tests and MPO inhibitors. ... 91 

5.9.1.1. Screening tests ... 91 

5.9.1.2. Random screenings ... 95 

5.9.1.2.1. Natural compounds ... 95 

5.9.1.2.1.1. Flavonoids, Polyphenols and Chalcones ... 95 

5.9.1.2.1.2. Indole derivatives ... 98 

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5.9.2. Pharmacomodulation approaches of hits that inhibit MPO ... 99 

5.9.2.1. Benzoic acid hydrazide ... 99 

5.9.2.2. Aromatic hydroxamic acids ... 100 

5.9.2.3. Flufenamic acid derivatives ... 102 

5.9.3.4. Tryptamine derivatives ... 103 

5.9.2.5. Indazole and indazolone derivatives ... 104 

5.9.2.6. Naphthalene derivatives ... 105 

5.9.2.7. Nitroxide derivatives. ... 106 

5.9.2.8. Thioxanthines, 2-Thiopyrimidinone, 2- Thio-2,3-dihydroquinazolin-4-one derivatives 106 

5.10.

D

HTVS

MPO

. ... 109 

6. MATERIALS AND METHODS ... 115

6.1.

M

. ... 115 

6.2.

I

... 118 

7. RESULTS AND DISCUSSION ... 123

7.1.

E

N

S

M

I

R

D

C

H

-T

V

S

... 123 

7.1.1. Introduction ... 123 

7.1.2. Results ... 124 

7.1.2.1. In vitro tests and best docking experiments poses of the best MPO inhibitors ... 125 

7.1.3. Discussion and Conclusion ... 131 

7.2.

N

B

-A

M

I

:

D

,

S

,

S

-

R

S

... 144 

7.2.1. Introduction ... 144 

7.2.2. Results ... 145 

7.2.2.1. Docking experiments ... 145 

7.2.2.2 Chemistry. ... 156 

7.2.2.3 Inhibition of chlorination activity of myeloperoxidase ... 158 

7.2.2.3 Transient-state kinetics between MPO compound I and compound II with inhibitors .... 158 

7.2.2.4 Serotonin reuptake inhibition, electron density maps and determination of redox potentials ... 159 

7.2.3. Discussion and Conclusion ... 159 

8. FUTURE WORK ... 179

9. APPENDIXES ... 180

9.1.

S

... 180