الفهرس 
introduction
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Abstract
Cancer is one of the major health problems as it is one of the most common causes of death worldwide. Development of targeted anticancer therapy has recently received more attention in order to inhibit some overexpressed molecular targets (enzymes and receptors) that are related to the abnormal nature of cancerous cell. Antiangiogenic therapy was introduced as promising anticancer treatment making use of the continuous need of tumor cell to nutrients and oxygen received through activating certain signalling pathways to provide high micro vessel density. Vascular endothelial growth factor (VEGFa) and its receptor VEGFR-2 are identified as key regulators of angiogenesis. Therefore, inhibition of VEGFR-2 tyrosine kinase (also known as kinase insert domain KDR) through design of small molecule inhibitors was the aim of this study.
A novel series of indazole-based compounds was designed, synthesized and biologically evaluated for their antiangiogenic and anticancer activity. The design process was based on comprehensive SAR study of various potent VEGFR-2 kinase inhibitors and supported by a field alignment study using Cresset BMD FieldAlign application.
The thesis describes the process of design, synthesis and biological evaluation of this new series of compounds covering the following topics:
1. Introduction
A brief account on cancer was given, describing the development of the disease, its main hallmarks and different ways of treatment. Also, an overview on tumor angiogenesis as a target for anticancer therapy was given, highlighting the role of VEGFR-2 as a therapeutic target. Additionally, an account on the medicinal chemistry of indazole as a scaffold was included.
2. Rationale and Design
A comprehensive SAR study was performed in order to determine the essential features required for the design of potent VEGFR-2 inhibitors. The process of design was described based on bioisosteric replacement and scaffold hopping approaches. The results of field alignment study was included; supporting the design rationale.
3. Chemistry
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This study involves the synthesis of the following unavailable reported intermediates:
1. N-(2-Chloropyrimidin-4-yl)-1H-indazol-5-amine(IV)
2. N-(1H-Indazol-5-yl)-6,7-dimethoxyquinazolin-4-amine (VIIIb)
3. 1-(6,7-Dimethoxyquinazolin-4-yl)-1H-indazol-5-amine (XII)
Also, it comprises the following new intermediates:
1. 6,7-Dimethoxy-4-(5-nitro-1H-indazol-1-yl)quinazoline (XI)
2. 1-(2-Chloropyrimidin-4-yl)-5-nitro-1H-indazole (XIV)
3. N-(4-Methoxyphenyl)-4-(5-nitro-1H-indazol-1-yl)pyrimidin-2-amine (XVa)
4. N-(4-Chlorophenyl)-4-(5-nitro-1H-indazol-1-yl)pyrimidin-2-amine (XVb)
5. 4-(5-Nitro-1H-indazol-1-yl)-N-(3,4,5-trimethoxyphenyl)pyrimidin-2-amine (XVc)
Moreover, these new target compounds were synthesized:
1. N4-(1H-Indazol-5-yl)-N2-(p-tolyl)pyrimidine-2,4-diamine (Va)
2. N2-(4-Fluorophenyl)-N4-(1H-indazol-5-yl)pyrimidine-2,4-diamine (Vb)
3. N2-(4-Chlorophenyl)-N4-(1H-indazol-5-yl)pyrimidine-2,4-diamine (Vc)
4. N2-(3,4-Dichlorophenyl)-N4-(1H-indazol-5-yl)pyrimidine-2,4-diamine (Vd)
5. N4-(1H-Indazol-5-yl)-N2-(3-methoxyphenyl)pyrimidine-2,4-diamine (Ve)
6. N4-(1H-Indazol-5-yl)-N2-(4-methoxyphenyl)pyrimidine-2,4-diamine (Vf)
7. N-(4-((4-((1H-Indazol-5-yl)amino)pyrimidin-2-yl)amino)phenyl)acetamide (Vg)
8. N-(5-((4-((1H-Indazol-5-yl)amino)pyrimidin-2-yl)amino)-2-ethylphenyl)acetamide (Vh)
9. 4-((4-((1H-Indazol-5-yl)amino)pyrimidin-2-yl)amino)benzenesulfonamide (Vi)
10. N4-(1H-Indazol-5-yl)-N2-(2-methyl-5-nitrophenyl)pyrimidine-2,4-diamine (Vj)
11. 5-((2-Chloropyrimidin-4-yl)amino)-N-phenyl-1H-indazole-1-carboxamide (VI)
12. N-(3-Chloro-4-methylphenyl)-5-(quinazolin-4-ylamino)-1H-indazole-1-carboxamide (IXa)
13. N-(3,4-Dichlorophenyl)-5-(quinazolin-4-ylamino)-1H-indazole-1-carboxamide (IXb)
14. N-(3-Bromophenyl)-5-(quinazolin-4-ylamino)-1H-indazole-1-carboxamide (IXc)
15. N-(5-Chloro-2,4-dimethoxyphenyl)-5-(quinazolin-4-ylamino)-1H-indazole-1-carboxamide (IXd)
Abstract
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16. N-(3-Chloro-4-methylphenyl)-5-((6,7-dimethoxyquinazolin-4-yl)amino)-1H-indazole-1-carboxamide (Xa)
17. N-(3,4-Dichlorophenyl)-5-((6,7-dimethoxyquinazolin-4-yl)amino)-1H-indazole-1-carboxamide (Xb)
18. N-(3-Bromophenyl)-5-((6,7-dimethoxyquinazolin-4-yl)amino)-1H-indazole-1-carboxamide (Xc)
19. N-(5-chloro-2,4-dimethoxyphenyl)-5-((6,7-dimethoxyquinazolin-4-yl)amino)-1H-indazole-1-carboxamide (Xd)
20. 5-((6,7-Dimethoxyquinazolin-4-yl)amino)-N-phenyl-1H-indazole-1-carboxamide (Xe)
21. 5-((6,7-Dimethoxyquinazolin-4-yl)amino)-N-phenyl-1H-indazole-1-carbothioamide (Xf)
22. 1-(1-(6,7-Dimethoxyquinazolin-4-yl)-1H-indazol-5-yl)-3-phenylurea (XIIIa)
23. 1-(3-Chloro-4-methylphenyl)-3-(1-(6,7-dimethoxyquinazolin-4-yl)-1H-indazol-5-yl)urea (XIIIb)
24. 1-(3,4-Dichlorophenyl)-3-(1-(6,7-dimethoxyquinazolin-4-yl)-1H-indazol-5-yl)urea (XIIIc)
25. 1-(3-Bromophenyl)-3-(1-(6,7-dimethoxyquinazolin-4-yl)-1H-indazol-5-yl)urea (XIIId)
26. 1-(5-Chloro-2,4-dimethoxyphenyl)-3-(1-(6,7-dimethoxyquinazolin-4-yl)-1H-indazol-5-yl)urea (XIIIe)
27. 1-(5-Chloro-2,4-dimethoxyphenyl)-3-(1-(2-((4-methoxyphenyl)amino)pyrimidin-4-yl)-1H-indazol-5-yl)urea (XVIIa)
28. 1-(5-Chloro-2,4-dimethoxyphenyl)-3-(1-(2-((4-chlorophenyl)amino)pyrimidin-4-yl)-1H-indazol-5-yl)urea (XVIIb)
29. 1-(5-Chloro-2,4-dimethoxyphenyl)-3-(1-(2-((3,4,5-trimethoxyphenyl)amino) pyrimidin-4-yl)-1H-indazol-5-yl)urea (XVIIc)
4. Biological evaluation
The biological activity of the compounds was evaluated at both molecular and cellular levels. The target compounds were biologically evaluated for their activity against VEGFR-2 kinase. Most of the target compounds exhibited excellent inhibitory activity against the enzyme. Compounds (XIIIb), (XIIIc) and (XIIIe) displayed significant potency against VEGFR-2 kinase; where they showed IC50 of 1.4, 1.3 and 8.1 nM respectively. Compound (Vi) (IC50=24.5 nM) was further evaluated for its cellular antiangiogenic activity against HUVEC cell line showing IC50 of 1.37μM.
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Fourteen compounds were selected by NCI for evaluation of their in vitro anticancer activity against the full NCI panel of cell lines at 10 μM. Compounds (Ve), (Vf), (XIIIa) and (XIIIc) were further selected for 5-dose testing where (Ve) exerted nanomolar GI50 values against MOLT-4 (525 nM) and upper nanomolar GI50 values against CCRF-CEM (901 nM) and CAKI-1 (992 nM) and one digit micromolar activity against the rest of cell lines ranging from 1.05 μM to 2.41 μM. While (Vf) had one digit micromolar activity against the whole panel of cell lines ranging from 1.55 μM to 7.4 μM. These compounds were further tested against several kinases in order to explain their cellular anticancer activity and they showed strong inhibition against aurora-A, CDK-2 and c-kit. Compound (XIIIa) showed nanomolar activity against 23 cancer cell lines of different types where it exerted its highest potency against T-47D breast cancer cell line (GI50 = 183 nM). Also, it had one digit micromolar GI50 on the rest of cell lines ranging between 1.01 to 5.22 μM. Compound (XIIIc) displayed nanomolar GI50 against two cell lines: KM12 colon cancer cell line (50 nM) and SF-539 CNS cancer cell line (612 nM), while it exerted one digit micromolar GI50 on the rest of cell lines panel that ranged from 1.24 to 4.44 μM .
5. Molecular modeling study
Finally, biological results were interpreted by molecular modelling techniques. Molecular docking of target compounds was attempted in order to predict the supposed binding mode of the compounds compared to various lead compounds. Also, selected compounds were compared to the lead compounds through field alignment study to explain their biological activity in terms of similarity or dissimilarity to the lead compounds.