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PYRIMIDINES:
BIOLOGICAL IMPORTANCE
AND
CHEMISTRY
PYRIMIDINES : BIOLOGICAL IMPORTANCE AND CHEMISTRY
CONTENTS PAGE
1.1 Biological importance of pyrimidines 3
1.2 Chemistry of pyrimidine ring
1.2.1 Structure of pyrimidine 9
1.2 2 Geometry and electronic structure of pyrimidine ring 10
12.3 pka of pyrimidine 11
oxidation of uric acid.1 Alloxan is known for its diabetogenic action in a number of
animals.2 Uracil, 2, thymine,3 and cytosine,4, are the three important constituents of
the nucleic acids. Amongst these uracil and thymine are important constituents for
3
o
CH 0
Notable amongst the drugs having a pyrimidine nucleus are the barbiturates,
used in the therapy for a long time for their hypnotic, sedative and anticonvulsant
properties. Barbitone (Diethyl barbituricacid, 6) was the first hypnotic to be
9a , R - CHj, X-H
9b. R - X - H
4
the enzyme dihydrofolate reductase (DHFR).9'10 Notable amongst the 2,4-diamino-
DHFR. The very potent, but non selective, DHFR inhibitors, methotrexate,9a, and
10 R1=R2=R=H
11 r 1=c h 3, r = r 2= h
12 R ^ R ^ C H j, R°H
analogs, are used in acute urinary tract infections, cerebrospinal meningitis and for
During the last two decades, several pyrimidine derivatives have been
developed as chemotherapeutic agents and have found a wide clinical applications.
5-Fluorouracil (5-FU, 13a) and its deoxyriboside (5-FUDR) are potent anticancer
5
and 5-thiouracii,13b, exhibits some useful antineoplastic activities.16 2-Thiourcil,
13c, and its alkyl analog, thiobarbital.15, are effective drugs against
O
17
introduced in therapy for its side effects in the treatment of alopecia, male
baldness.22 ,
6
^
NH—
N
<P
Br
18
Besides, there are few examples of pyrimidine antibiotics. The simplest of all
is bacimethrin 4-amino-5-hydroxymethyl-2-methoxypyrimidine,19, active against
against mycobacteria as well as, several Gram positive and Gram negative
bacteria.24 Antibiotic tubercidin,21, is reported to exhibit antitumor activity24.
7
o
present is the only drug receiving wide clinical usage.26"29 Ara-thymidine (ara-T,24),
8
The related orally active fluoroarabino analogue, 1-( 2-deoxy-2-fluoro-p-D-
also been reported to have good anti HIV activity with pharmacokinetics similar to
AZT in monkey.41
X = N O * Halides
27, is reported as a potent Ca-channel blocker with potent and long lasting
symmetry about the 2,5-axis so that three differing pairs of equal bond lengths
result.44
9
4
29
In addition to this, the electronegative "N" atoms constitute high density
centres for the n electrons which are otherwise equally distributed about the ring
the same time, the localization of % - electrons at the two "N" atoms results in
whatever little semblance of aromaticity is left in the system is at the C-5 position.
This decreased stability of pyrimidine which is reflected in the resonance energy of
only 26 Kcal/mole in pyrimidine compared to 36 Kcal/mole in benzene45. Pyrimidine
can be appropriately compared with m-dinitrobenzene, which too has a lower
resonance energy.48
10
+0.054 0 .0 8 2 8 + 0 , 210
N +0.0422
0 .0 0 7 [ s 4 g N -0 .0 9 4 8 f + 0 .0 4 1 4
+ 0 .0 5 4 \ 1 3^ + 0 .0746 :N -0 .0 6 3 2
N
N'
-0 .0 7 4 6
30 31 32
1 .2 .3 p K a o f p y rim id in e
Pyrimidine is a weaker base (pKa 1.31) than pyridine (pKa 5.2) because
the second ring nitrogen shares the available n electrons with the first and tine
system therefore approximate to 3-nitropyridine (pKa 0.8). Its basicity is intermediate
to that of the other two isomeric diazines namely, pyridazine (pKa 2.33) and
pyrazine (pKa 0.6) respectively.48 The insertion of mildly electron releasing methyl
group in the ring partly improves this deficiency so that 2-methyl pyrimidine has a
pKa of 2.0.®
f ^ N N
+
"Ay** *
|
nh2
R R
33 34
R= H+ o r Lewis acid
,11
"N" to attract n electrons. Thus in uracil, 2, for example, both the N atoms are so
involved and protonated that the oxygen atoms are the next available basic
centres.49 On the other hand, the pyrimidinamines are bases of moderate strength
strength.49
and Todd50 in 1957, Ramage and Landquists1 in 1959 and by Brown48,49 in 1966 and
in 1970. Pyrimidine synthesis by the cyclisation of amidines has been reviewed by
12
1) Type IV C-C-C + N-C-N
13
towards the pyrimidine ring construction. It is appropriately termed as the "Principal
synthesis" of pyrimidines.98
N N
C N
The condensation of three carbon fragment with N-C-N fragment donor is,
which are condensed with 1,3-binucleophiles. Thus, 2-alkyl or aryl, 2-amino, 2-oxo
or 2-mercaptopyrimidines,37, have been obtained by employing amidines,
NH
, -A
<2 O
+
m 2n
1■ r3
35 36
c o r , c o o r .o r . c n
IL ,
R1, R2 = Alkyl, Aryl;R3 = Alkyl, Aryl, NH2, SR^, OR 4
Z ■ R, OH, NH2
14
gives the expected pyrimidine 40, while on refluxing in ethanol in presence of base
R = CH3 C H 2C H 2
40 41
NH
li
h2n- c ~ c h 2c o n h 2 c h 2c o n h
o
42
15
h 5 c 2- o - ch= ch- cn (C2H50 ) 2- c h c h 2 c n
45 46
nh2
Cl
1
A n
h 3c = c - c n
47
48
R
i
NC. C -N
NaOEt ' - -** V
x c- ch - o c 2h s -i- h 2 n c n NC— C * CN
NC 2 5 EtOH *
/ Na+
NC
49
50
HCI
or
HBr
v
16
benzoylalkoxyacrylonitrile, 52 (R=H, R =COC 8Hs ) with amidines has been shown to
afford 5-cyano-4-phenylpyrimidine,54.**
R2
17
of alkylidenemalononitrile,58 (X = CN) with cyanamide in the presence of sodium
nh2
«2
NC ¥ " N “v S
h 6c 6 - 7 \ >
H H
62
63
18
Acetylene carboxylic acids have been employed as three carbon
obtained in good yields through the condensation of propiolic acid.66, with urea in
68 R * c h 3, c a 3
the product.123
0 0
X li
X NH
R^ 0 - C—CHjCOjR-j |
<T N R.,0
N *2
68, (X«0)
70,(X*S) 72
71
a-oxo-thioamide,75 with the amidine salt in the presence of a base, such as sodium
ethoxide.124
20
Acylketene 0 ,0 -a c e ta ls have been reacted as 3-C donors with amidines to
H. . C 0 2 C 2 H5
R10 ^ ~ - " 0 R 1
76
12B 127
The condensation of ketene S,S-acetals derived from cyclic ketones, •
oxides or sodium hydride has generally been used as base for the liberation of
amidines from their salts in these reactions. However, in certain cases, the product
formation depends upon the nature and the concentration of the base employed.
2l
NH-
,C N X
NH N aO R , N
H 3 C S ^ ^ 'S C H 3 h 2 n
A .— ^ R20 PT r 1
77 79
X * C N , A ry l
78
v ia th e k e te n e 0 ,S - a c e t a ls 8 1 a n d 8 2 , fo rm e d b y th e initial re a c tio n o f k e te n e S ,S -
g u a n id in e s .127
T h e a -k e to k e te n e S ,S -a c e ta ls 8 3 - 8 5 re a c t w ith g u a n id in e in th e p re s e n c e
o f s o d iu m a lk o x id e to y ie ld th e 2 -a m in o p y rim id in e s 8 6 - 9 0 . 139
22
CfeHs PbHs
H3C ceHSCHZ
LX SCH3
0
'rS>
* jCS^SCH3 HjCST H3CS ^SC H 3
83 84 85
Hs'
<¥%
H3C rA NH2
89
The formation of the pyrimidines 87-90 has been assumed to involve base
intermediate olefin of the type 91, followed by its reaction with guanidine.139"141
23
Ar Ar 0
A A n
NC. JX
Y NH
" 2 ¥
X SCH! r 2R ,N ^
J r 2 r ^h f i^ m 2
92 93 94
Ar Ar
■ A
R2R1N '^ ^ S C H 3
95
24
NH<
Rn^ C N NH RiR2n' NA . R3
*.. .. A . 98
R ^ N ^ '- S C ^ H2N ' 'R 3 NaQEt
O
97 NC
NH
R ■ CgHg, CN, CONH2, C 0 2C2H5
r 1 r 2n ' N' R3
R1 * Alkyl, Aryl
R2 • H, Alkyl, Aryl 99
R3 ■ NH2 , CH3, CgHfi
OR, NH
I 3
h 5c 2 o 2 c ~ c h 2 — c = n c o 2r 2
r 2 o 2c n h N^ r1
100 101
25
+
* 2V
r 3- ^
103
104, was developed by reacting benzotrichloride with various nitriles in the presence
of aluminium chloride.181
Cl
ph R = H, C H 3 , Ph
rh 2c N
104
26
H6c 2° 2 CV / c N HeC<>OoC. XN
105
108
H5C2O2C
a
HN '^N'^'CjHs k J .
ISH
R 109
wA n^ m
i
R 107
27