Abstract
Indazole nucleus is present in naturally occurring alkaloids and biologically active
molecules. Nigellidine is a natural product containing an indazole nucleus, was isolated
from nigella sativa, which is used for the treatment of various diseases. Commonly
believed to have carminative, stimulatory and diaphoretic properties. Indazole based
heterocycles like indazolo pyrimidines and their derivatives are found to have wide
range of activities. Earlier findings on indazole derivatives specifically known to be
active as protein kinase inhibitors, cancer cell proliferative disorders, alzheimers
disease, viral infections, auto immune and neuro degenerative disorders. In recent
years, some of the indazole ring systems are being evaluated as potential drugs for a
variety of physiological activities with at least few compounds approved for clinical use.
Further, pyrimidine ring in an organic molecule also shows prominent activity against
several diseases. Therefore reactions concerning the synthesis of indazole ring and
their derivatives mainly pyrimidine fused is a part of scaffold are of current interest. In
addition, fluorine or trifluoromethyl group at an appropriate position of molecule
promotes lipophilicity to the molecule as a result increased solubility and transport
mechanism of the drug enhances in lipid system. Therefore the synthesis of new
analogues of indazole based compounds with fluorine or trifluoromethyl group at a
specified position have gained significance to find more potent organic molecules, which
ultimately become drugs. Thus in this research programme, synthesized a number of
novel pyrimido[1,2-b]indazol derivatives and developed novel synthetic methodologies
for important organic compounds. The synthesized compounds were subjected to antibacterial, anti-fungal and anti-cancer activity thereby promising compounds have been
identified. The interesting aspect of this research work is starting from single compound
to a variety of new ring systems. Number of methods adopted in each set of reactions is
discussed in various chapters. The total research contribution will be formatted into
thesis with five chapters, which includes introduction. The research work covered under
each chapter has been briefly outlined below.
Chapter 1
Chapter-I covers overview on the importance of indazoles, pyrimidine fused indazoles,
oxazines, quinolines and their synthetic methods reported in literature so far upto June
2007. It also covers present work in brief which includes number of methods adopted in
synthesis of indazole derivatives, oxazines and quinolines and development of novel
methodologies for important organic compounds and their activity studies.
Chapter 2
This chapter involves
preparation
of 3-trifluoromethyl-5- phenyl-
2, 6-dicyano
aniline 2 and 3-Iodo-5-trifluoromethyl-biphenyl-2, 4-dicarbonitrile 4, 3-amino
-
6-
phenyl-4-trifluoro methyl-1H-indazole-7-carbonitrile 5a, 3-Amino-4-phenyl-6trifluoromethyl-1H-indazole-7-carbonitrile
5b.
Compounds
5a
and
5b
were
independently reacted with various active methylene compounds and obtained
pyrimidine fused indazoles 6, 7, 8, 9 and 10.
a. Preparation of 3-trifluoromethyl-5-phenyl-2,6-dicyanoaniline (2)
1-phenyl-4,4,4-trifluoro-1,3-butanedione was reacted with malononitrile in methanol
and piperidine and obtained 3-trifluoromethyl-5-phenyl-2,6-dicyanoaniline 2 and
oxo-6-phenyl-4-(trifluoromethyl)-1,2-dihydropyridine-3-carbonitrile
3
in
2-
different
proportions. The compound 2 is an interesting trifunctional intermediate is diazotised
followed by reaction with potassium iodide as a result 3-Iodo-5-trifluoromethylbiphenyl-2, 4-dicarbonitrile 4 is formed.
CF3
CF3
CN
CN
piperidine
CF3COCH2COPh + CH2(CN)2
MeOH
rt
1
+
Ph
NH2
Ph
CN
2 (64%)
CF3
O
3 (22%)
CF3
CF3
CN NaNO2 / HCl
CN
CN
KI
CH3CN / 0OC
Ph
N
H
+ N2Cl
Ph
NH2
Ph
I
CN
CN
2
CN
4
Scheme 1
Compound 4 was reacted with hydrazine hydrate in refluxing ethanol resulted two
regioisomers
such
as
3-amino-6-phenyl-4-trifluoromethyl-1H-indazole-7-
carbonitrile 5a, 3-amino-4-phenyl-6-trifluoromethyl-1H-indazole-7-carbonitrile
5b
in
definite proportions. Each regioisomer is separated and identified based on spectral
data followed by single crystal X-ray data.
CF3
CF3
Ph
NH2
NH2
CN
N2H4.8H2O / EtOH
Ph
I
CN
4
reflux, 2hrs
N
N
H
Ph
N
+
N
H
F3C
CN
CN
5a (55%)
5b (45%)
Scheme 2
b. Synthesis of Indazolo pyrimidines
The indazole regioisomers 5a and 5b were independently reacted with 1,3-diketones
(symmetrical and unsymmetrical) in a sealed tube under microwave irradiation
conditions obtained pyrimido[1,2-b]indazole derivatives in
single step. The role of
substituents in 1,3-diketones and compounds 5a, 5b on formation of products 6 is
studied in detail. In case of reaction of unsymmetrical 1,3-diketones with compounds
5a/5b resulted exclusively one regioisomer 6a / 6b respectively.
R
CF3
NH2
R
O
N
CH3COOH / 90 sec
O
N
R'
N
Ph
R'
CN
N
sealed tube / MW / 450w
+
N
Ph
CF3
CN
6a
5a
R
Ph
NH 2
N
N
F3C
CN
5b
Ph
R
O
sealed tube / MW / 450w
O
CH3COOH / 90 sec
+
R'
N
N
N
F3C
R'
CN
Scheme 3
6b
Compound 5a, 5b were also independently reacted with EMMN/EMCA in sealed tube
under microwave irradiation conditions at 450MW gave pyrimido[1,2-b]indazole 7. The
1H
NMR of compounds 7a and 7b is quite interesting in a way that the NH2 protons in
each of compounds appeared as two broad singlets with different chemical shifts. This
is due to extended conjugation with ester carbonyl as a result proton became nonequivalent.
CF3
CF3
NH2
EtO
N
N
CH3COOH / 90 sec
R'
H
CN
NH2
N
Ph
CN
R' = CN, CO2Et
5a
7a
Ph
NH2
Ph
EtO
N
R'
sealed tube / MW / 450W
R'
H
R' = CN, CO2Et
CN
N
CN
+
N
H
F3C
R'
sealed tube / MW / 450W
+
N
H
Ph
CN
N
N
CH3COOH / 90 sec
5b
N
F3C
NH2
CN
7b
Scheme 4
The compound 5a and 5b were similarly reacted with -ketoesters/ DMAD in sealed
tube under microwave irradiation conditions at 450MW gave pyrimido[1,2-b]indazole
8a and 8b respectively. In case of -ketoester the reaction is initiated by nucleophilic
attack on carbonyl carbon followed by cyclisation whereas with DMAD, the reaction is
addition f ollowed by cyclisation.
CF3
CF3
NH2
MeO2 C
CO2 Me
N
N
N
H
Ph
OEt
H3 C
CN
sealed tube / MW / 450w
5a
O
N
Ph
O
O
CN
CO2CH3/CH3
H
N
8a
150 sec
Ph
Ph
NH2
MeO2 C
H
N
CO2 Me
N
N
N
H
F3C
CN
5b
.
CO2CH3 / CH3
OEt
H3 C
O
O
N
F3C
CN
sealed tube / MW / 450w
150 sec
Scheme 5
8b
O
Compound 5a and 5b were further reacted with ethoxymethylene diethylmalonate
(EMME) or dimethylamino diethyl malonate (DAMM) in sealed tube under microwave
irradiation conditions and obtained exclusively an uncyclised intermediate 9a/9b. They
are cyclised in sealed tube under microwave irradiation conditions resulted pyrimido
[1,2-b] indazole derivatives 10a, 10b respectively. The mode of reaction is initially the
substitution of the ethoxy or dimethylamino group in EMME or DAMM followed by
cyclisation on to nitrile or ester carbonyl group. The cyclisation depends on the
nucleophilic nature of nitrile carbon (CN) verses ester carbonyl (CO2Et) and ester
carbonyl is found to be sluggish.
R
NH2
N
R
COOEt
sealed tube
MW / 450W
H
COOEt
CH3COOH
+
N
H
R'
R"
CN
R" = OEt, N(CH3)2
60 sec
N
COOEt
COOEt
N
H
R'
CN
9
5
a) R = CF3, R' = Ph
b) R = Ph, R' = CF3
R
H
N
a) R = CF3, R' = Ph
b) R = Ph, R' = CF3
N
COOEt
CH3COOH
sealed tube
MW / 500W
120 sec
N
N
R'
OH
CN
10
a) R = CF3, R' = Ph
b) R = Ph, R' = CF3
Scheme 6
Chapter 3
Synthesis of trifluoromethyl tetrahydro-pyrimido [1,2-b] indazole carbonitrile
derivatives.
Compound 5a and 5b were treated with formaldehyde followed by various electron
rich alkenes in acetonitrile in presence of one equivalent of GdCl3 at room temperature
to give the corresponding adducts 11. The reaction proceeds probably by a concerted
mechanism is evidenced by the fact that there were no intermediates observed in
study. The synthesized adducts were characterized and structures were established
based on 1H-NMR data. The low coupling constant (J) of the ring junction protons in
the adducts suggests cis ring fusion. The formation of single cis ring fused product
indicates that the cyclisation is regioselective.
CF3
CF3
NH2
N
CN
N
CN
11a
rt
N
H
CF3
CN
Ph
NH2
N
H
N
Ph
5a
Ph
H
HCHO/CH3 CN/GdCl3
N
H
Ph
H
N
H
N
HCHO/CH3CN/GdCl3
N
N
CF3
rt
H H
CN
11b
5b
Scheme 7
Compound 5a and 5b were similarly treated with benzaldehyde followed by various
electron rich alkenes in acetonitrile in presence of one equivalent of GdCl 3 at room
temperature to give the corresponding adducts 12. The synthesized adducts were
characterized and structures were established based on
1H-NMR
and X-ray
crystallographic data. The low coupling constant (J) of the ring junction protons in the
adducts suggests cis ring fusion. The formation of single cis ring fused product
indicates that the cyclisation is regioselective.
CF3
NH2
N
PhCHO/CH3 CN/GdCl3
N
N
H
Ph
N
Ph
CN
5a
CN
12a
Ph
CF3
NH2
N
N
N
Ph
CN
5b
Ph
H
N
PhCHO/CH3 CN/GdCl3
N
H
CF3
Ph
H
N
CF3
CN
12b
Scheme 8
Chapter 4
Section A.
Part I: Synthesis of trifluoromethyl substituted Benzoxazines.
Compound 2 on reaction with phenylmagnesium bromide in ether at room temperature
resulted 2-imino derivative 13. Compound 13 is further refluxed in HCl using para
toluene sulphonic acid for 6hrs. to undergo hydrolysis and obtained ketone
14
quantitatively. This ketone on reaction with zinc borohydride in ether resulted optically
pure alcohol 15. This on reaction with pivalaldehyde in acetic acid gave product 16.
CF3
CF3
CF3
Ph
CN
PhMgBr
Ph
NH 2
NH
Ph
NH 2
CN
Zn(BH4)2
ether / 0OC / 2hrs
Ph
Ph
NH 2
13
14
CF3
AcOH /
0OC
Ph
CHO
Ph
CN
Scheme 9
H
O
/ 3hrs
CN
15
NH 2
CN
OH
H
Ph
CN
2
CF3
O
HCl / PTS
reflux / 6hrs
ether
Ph
16
N
H
Part II: Synthesis of trifluoromethyl aminoquinolines/acridines.
Trifluoromethyl substituted Phenyl amino nitrile 2 on reaction with cyclic ketones under
microwave irradiation conditions at 450W gave product 17.
CF3
CF3
O
CN
+
Ph
( )n
ZnCl 2 / 450W
MW
NH2
NH2
Ph
CN
N
( )n
CN
Scheme 10
2
17
Section B: New methodologies for organic synthesis.
Part I: Synthesis of benzylidene derivatives.
Knoevenagel condensation reaction of aromatic aldehydes and active methylene
compounds using ZrOCl2.8H2O in dichloro methane under microwave irradiation
conditions gave substituted benzylidene compounds 18.
R'
R
CHO
R'
ZrOCl2. 8H2O
+
R
CH
600W
R"
R"
18
Scheme 11
Part II. Synthesi of β-acetamido ketones.
Aromatic aldehydes are also treated with substituted benzophenones in acetonitrile
and acetylchloride in presence of silica sulphuric acid on heating at 80
OC
gave β-
acetamido ketones 19.
O
X
CHO +
H3C
CH3CN./ CH3COCl
Y
X
Y
silica-sulphuric acid. 80 oC
Scheme 12
Chapter 5
NHAc O
19
Physiological activity and molecular modeling studies.
The number of compounds synthesized in each chapter is subjected to screening for
anti-bacterial, anti-fungal and anti-cancer activity. Some of the compounds showed
promising activity. The data is also co-related with QSAR, molecular modeling and
docking studies.The details will be discussed in this chapter.
A number of novel compounds such as indazolo pyrimidines, Oxazines and iminotetrahydro-1H-quinolines have been synthesized. Mechanistic paths for each reaction
is formulated in order to have a clear understanding of synthetic sequence. All the
compounds were screened for various activities in order to identify a promising
candidate, which can become a lead molecule in search of potential drug.