Indi an Journal of Chemistry Vol. 428, April 2003, pp. 910-9 15

Synthesis and anti-microbial activity of some pyrimidine derivatives

A K Padhy National Institu te of Science & Technology, Palur Hill s, Berhampur-761 008, Orissa, Indi a

and M Bardhan & C S Panda*

Synthetic Organic Laboratory, Deptt of Chemistry, Berhampur Uni versity, Berhampur-760 007 , Orissa. India

Receil•ed 25 July 200 I; accepted (revised) II March 2002

4-Ary l-5-carboethoxy-6- mcthyl- 1 ,2,3,4-tetrahydropyrimidin-2-ones have been synthesized from easily avai labl e start­ing materi als. The carboethoxy group at the C5-position of the pyrimidine ring is converted to corresponding hydrazide which in turn is condensed with cycli sing agents such as aromatic aldehydes, CS2 etc. to give fu sed heterocycles. The fu sed heterocycles are then subjected to phenacylation to g ive Nr phenacylpyrimido-heterocycles in excellent yield. In a slightly modified way, uracil derivatives are condensed with ethy l bromoacetate to give Nrl)-cthoxycarbonyl derivati ves. The hy­drazide derivatives of these Nr l)-ethoxycarbonyl de rivatives subsequently react with 1,2-diketones to give corresponding pyrimido pyridazine derivatives.

Pyrimidines are of great importance in fundamental metabolism, for uracil, thiamine and cytosine are three of the six bases found in the nucleotide 1

• Many derivatives of pyrimidine have been used as therapeu­tic agents2

.3 . Several triazolo and pyrazolopyrimidines are found to possess antifungal and antileishmanial activit/ . Pyrimjdine derivatives are known to possess analgesic and anti-inflammatory activit/. Also some oxadiazolopyrimidines were reported6 to possess fun­gicidal activity . In recent years, pyrimidine deriva­tives have received significant attention owing to their diverse range of biological properties particularly be­ing calcium channel blockers7

• 4-Amino-5-oxopyrido[2,3-d]pyrimidine riboside was found to be very potent inhibitor of cancer cell profilation8

.

The C5 position of pyrimidine nucleus is an attrac­tive site for modification as it is located at the major groove surface in the duplex form and will not di ­rectly inhibit the hydrogen bond in an A : T base pair9

·10

.

The most general and widely employed route to pyrimidines involves the combination of a reagent containing the N-C-N skeleton with C-C-C unit. These syntheses are typical examples of the bi s­nucleophile plus bis-electrophile method of construct­ing heterocycles. Both the nitrogen atoms of the N-C­N reagent act as nucleophiles and both the terminal carbon atoms of C-C-C reagents are electrophiles. Urea, thiourea and guanidine are commonly used as

N-C-N reagents and I ,3-diketones, diesters and dini­triles are typical C-C-C reagents.

Thus, employing a slightly modified method ethyl acetoacetate and cyanoethyl acetate (C-C-C unit) can condense with urea or thiourea (N-C-N unit) in pres­ence of diverse aromatic aldehydes to give pyrimidine derivatives 1 and 2 in appreciable yields. The struc­tural analysis of the product formed retains the car­boethoxy group of ethyl acetoacetate and the cyano group of the cyanoethyl acetate. This suggests that the requisite C-C-C funct ionality for the construction of the pyrimidine ring uses only two carbon centers of these esters and the third carbon being provided by the aldehydic function of the aldehydes employed.

The availability of the carboethoxy group at C-5 of the pyrimidine rings helped us to think of exploring the possible modi fications that can be made at thi s position thereby forming modified bases of significant structural importance. Incidentally, the carboethoxy group of 1 was converted to its hydrazide deri vative 3, which furnishes better reaction site for the con­struction of modified structural units. Thus, the hy­drazides of 1 were condensed with diverse cyclising agents such as aromatic aldehydes, CS2 to give pyrimidotriazoles 4 and pyrimidothiadiazoles 5 re­spectively (Scheme 1).

The structure-activity relationship study of pyrimidines reveals that N-alkyl derivati ves are more potent towards the microorgani sms than that of the

PADHY et al.: SYNTHESIS OF PYRIMIDINE DERIVATIVES 911

CH3COCH2COEt

+ ArCHO+ CJl

X=O, S 2

Ar = Ar'= C6H5 , m-N02C6H4, p-CIC6H4, p-N(CH3)2CsH4 A= C6H5, m-N02CsH4

Scheme I

unsubstituted ones as they increase the toxicity of the molecules. Thus, the synthetic pyrimidines 4 were subjected to phenacylation with the implication that it will increase the potential of the molecules. There are two sites available for the phenacylation N 1- and N3- in those molecules. However, the Nrsite is preferred over the N 1-site as the N3-proton is com­paratively more acidic than N 1, being flanked by a carbonyl group and aromatic nucleus. The question of formation of the mixed product was overruled on the basis that compound 6 is not only having the sharp melting points but also the CH3 peak in the 'H NMR is free from any NOE (Nuclear Overhauser Effect).

Compound 2, which has an analogous nucleus as uracil can therefore be named as uracil derivative, having active site N3-. The proton is being more acidic and therefore can undergo facile alkylation with ethyl bromoacetate to give corresponding N3-~­ethoxycarbonyl derivatives 7. The hydrazides of 7 possess a dinucleophilic locus and thus in turn con­dense with 1,2-diketones to give corresponding fused pyrimidinopyridazine derivatives 8 (Scheme II).

2 7

1

8

a. C 6 H5, X = 0, b . Ar = C 6 Hs . X = S

c. Ar= m-N0 2C 6H4, X=S, d . Ar = p -C IC 6H4, X= O

e. Ar= p-CIC 6 H4, X=S, f. Ar= p-N(CH 3 ) 2 C 6 H4 , X=O

g . Ar= p-N(CH 3 bCsH•, X= S

Scheme II

A disquitening trend after 1950's has been the emergence of more sinister type of fungal infections, which are, to a large extent, inatrogenic. These are associated with the use of broad-spectrum antibiotics,

912 INDIAN J. CHEM .. SEC B, APRIL 2003

corticosteroids, cytotoxic drugs indwelling characters and implants and emergence of AIDS. Looking to the broad spectrum of biological activity, we screened some of these sy nthetic compounds against Staphyllo coccous, E. coli and Candida albicmzs. It has been observed that compounds 6b, 6h and 6v are active against Candida albicans, whereas only 6h is possess­ing significant activity. All these activities were com­pared with the standard drugs chloramphenicol and clotrimazole by measuring the zone of inhibition .

Experimental Sections All the m.ps were measured and uncotTected. IR

spectra were taken in Perkin-Elmer FT-IR spectropho­tometer. 1H NMR was taken in 90MHz Perkin-E lmer spectrophotometer. The microbial screening was done employing cup-plate agar method 11 .

Synthesis of 4-aryl-5-cal"lJOethoxy-6-methyl·2-pyrimidinone 1: General procedure. Urea (0.5 mole), ethyl acetoacetate (0.75mole) and aromat ic aldehyde (0.5 mole) were mixed in ethanol (25 mL). Catalytic amou nt of cone . HCI was added to the mixture, which was then refluxed fo r 3hr. T he contents were kept in refrigerator overnight. The sol id separated out was filtered off. The filtrate was further refluxed on a wa­ter bath for 1.5hr. On cooling a solid separated out was filtered and recrysta lli zed from ethanol to g ive 1. la : IR (v): I 570(C-N), 1650 (am ide), 1730 (ester), 3350(NH) cm·1; 1H NMR (90MHz): 8 1.5 (s, CH 3),

1.8 (t, COOCH2CH3), 2.5 (q, COOCH2CH3), 3.4 (s, C-NH-CO) , 5.4 (s , Ar-Nl-1-CO), 6.4 (s, Ar-CH), 7-8

(m, 5H. ArH); m.p. 21.0°C (72%); Found: C, 64.59; H, 6.14; N, 10.73; Calcd for C 1 ~ H 1 6N203 : C, 64.61; H, 6.14; N, 10.73 %. 1b: m.p. 187°C (75 %); Found: C, 56.91; H, 4.96; N, 9.2. Calcd for C 14H15N20 3CI: C , 57.04; H, 5.09; N, 9.5%. 1c: m.p. 195°C (62 %); Found: C , 63 .3; H, 6.84; N, 13 .81. Calcd for C1 6H21N30 3: C, 63.36; H, 6 .93; N, 13 .86%. 1d: m.p. 220°C (78 %); Found: C, 54.95; H, 4.85; N, 13.65 . Calcd for C14H1sN305: C, 55.08; H, 4.91; N, 13 .77%.

Synthesis of 4-aryl-5-cyanopyrimidin-2, 4-dionc 2: General procedure. To a mixture of urea (0.1 mole), cyanoethyl acetate (0. 1 mole) and aryl aldehyde (O.Imole) in ethanol , K2C03 was added and refluxed for 7 hr on a water bath. On cooling the solid separated out was filtered. The residue was dissolved in hot water and filtered when hot. The filtrate was neutralised with acetic acid and the solid precipitated out was filtered and recrystallised from ethanol. 2a: m.p. 289°C; Found: C, 61.92: H, 3.25; N, 19.67. Calcd for CI1H7N30 2: C, 6 1.97; H, 3.28; N, 19.]1 %. 2b: m.p.

255°C; Found: C, 57.6 1; H, 3.01; N , 18.3. Calcd for C11H7N30S: C, 57.64; H, 3.05; N, 18.34%. 2c: m.p.

179°C; Found: C, 48. 15 ; H, 2. 16; N, 20.41. Calcd for C1IH6N30 3S: C, 48 .17 ; H , 2 .1 8; N, 20.43%. 2d: m.p. 278°C; Found: C, 53.3 L; H, 2.4; N, 16.93. Calcd for C11 H6N30 2CI: C, 53.33; H, 2.42; N. 16.96%; 2e: m.p. 252°C; Found: C, 50.07; H, 2.25; N, 15 .91. Calcd for C IIH6N30SCI: C. 50.09; H, 2.27; N, 15.93%; 2f. m.p.

238°C; Found: C, 60.9 1; H, 4.65; N, 21.86. Calcd for C13H12N402: C, 60.93; H, 4.68; N, 2 1.87%; 2g: m.p. 2 15°C; Found: C, 57.33; H, 4.39; N, 20.54. Calcd for C1 3H1 2N40S: C, 57.35; H, 4.41; N, 20.58%.

Reaction of 1 with hydrazine hydrate: Synthesis of 3. To 1 (0. 1 mole) in ethanol (20mL) was added hydrazine hydrate (0. 1 mol e) followed by the addition of a catalytic amount of cone. H 2SO~ (5clrops). The mixture was refluxed for 2hr. Excess so lvent was re­moved and on cool ing a solid was for med. The solid was crysta ll ised from ethanol to give 3. 3a: IR: 1570(C-N), 1650 (amide), 3350(NH) cm.1; 1H NMR

(90mH z) : 82.5 (d,2 H, NH 1-/2), 3.4 (s, C- H-CO), 5. 1 (s, CO-NH-CO), 4. 1 (t, CONHN), 7-8 (m. 5H ,

ArH), m.p. 196°C, 3b: m.p. 195°C, 3c: m.p. 175°C,

3d: m.p. 190°C.

Synthesis of triazolo-pyrimidinone derivative 4. To a solution of 3 (0. 1 mole) in acetic ac id (20mL) a pinch of ammonium acetate was added followed by the addition of aromatic aldehyde (0.1 mole). The mix­ture was st irred for 2.4 hr at room temperature. The mother liquor on neutralization wi Lh ammonia solu­tion gave a so lid, which was filtered and rec rystailised from ethanol (Table 1). 4b: IR: 1650 (amide), 3350(NH) cm. 1; 1H NMR (90MHz) : 8 I .4 (s, -CH3), 5.2 (s, C-NH-CO), 7-8 (m, 9H, ArH ).

Synthesis of pyrimidinothiadiazole 5. To a solu­tion of KOH (0 .1 5mole) in ethanol and heteroaroyl hydrazide (0. I 5mole) was added CS2 (0. 15mole). This mixture was diluted with ethanol and agitated for a pe­riod of 12- l6hr. Jt was subsequently neutrali zed with HCi and the precipitated solid was filtered, washed with water and recrystalized from ethanol. Sd. IR: 1570(C-N), 1650 (amjcle), 2650(SH), 3350(NH) cm.1; 1H NMR (90MHz) : 81.4 (s,JH, CH3), 3.2 (s, 6H , OCH3), 6.4 (s, ArCH), 7-8 (m, 3H, ArH). Sa: Oi l; Sb· m.p. 200°C; Found: C, 40.84; H, 3.38; N, 17.32. Calcd for C1 3H I IN~S20CI: C, 40.93; H, 3.41; N, 17.36%. Sc: m.p. 2L5°C; Found: C, 39.59; H, 3.27; N, 20.96. Calcd for CuHI1Ns03S2 : C, 39.64; H, 3.3; N, 21.02%. Sd: m.p. l92°C; Found: C, 51.51 ; H, 5.51; N, 15.97. Calcd for C1 sHI 6N40 3S2: C, 51.58; H, 4 .58; N, 16.04%.

PADHY et a/. : SYNTHESIS OF PYRIMIDINE DERIY ATIVES 913

Table 1-Analytical data of 4-ary l-5-(2-aryl-1 ,3,4-triazolo)-6-methyl-1 ,2,3,4-tetrahydropyrimidin-2-ones (4)

Compd Ar Ar' No

4a C6Hs m-N02C6H4

4b C6Hs p -C IC6H4

4c C6Hs p-N,N(CH3hC6H4

4d p -CIC6H4 m-N02C6H4

4e p-CIC6H4 p-CIC6H4

4f p-CIC6H4 p-N,N(CH3)2C6H4

4g p-N ,N(CH3hC6H4 m-N02C6H4

4h p-N,N(CH3hC6H4 p-CIC6H4

4i p-N,N(CH3hC6H4 p-N,N(CH3hC6H4

4j m-N02C6H4 m-N02C6H4

4k m-N02C6H4 p-CIC6H4

41 m-N02C6H4 p-N,N(CH3)2C6H4

Reaction of pyrimidinones 4 with phenacyl bromide: Synthesis of 6. To a solution of 4 (0.1mole) in acetone, potassium carbonate was added followed by the addition of phenacyl bromide (0.1mole). The mixture was stirred for 2 hr at room temperature. Ex­cess solvent was removed and the solid separated out was recrystallised from acetone (Table II). 6c: IR: 1650 (amide), 1690 (-CO-), 3350(NH) cm-1

; 1H NMR

(90MHz) : 8 1.4 (s, -CH3), 3.4 (s, C-NH-CO), 3.6 (s, -COCH2), 7-8 (m, 9H, ArH).

Reaction of 2 with ethyl bromoacetate: Synthe­sis of 7. To a solution of 2 (0.1 mole) in acetone, po­tassium carbonate was added. To this mixture ethyl bromoacetate (0.1mole) was added and the mixture was refluxed for 6hr. On cooling the solid separated out was filtered and recrystallised from acetone. 7a: IR: 1650 (amide), 1730 (ester), 3350(NH) cm-1

; 1H

NMR (90MHz) : 81.8 (t, -COOCH2CH3), 2.3 (s , CH2COOEt), 3.6 (t, -COOCH2), 7-88 (m, 5H, ArH) .

Synthesis of pyridazinopyrimidine derivatives S. To a solution of hydrazides of 7 (0.1 mole) in sodium ethoxide (prepared by dissolving 1g of sodium metal in 20 mL of ethanol) , benzil (0.1mole) was added . The mixture was refluxed for 4hr and then poured into

m.p. Mol. formula Calcd (Found) (DC) c H N

112 C,9 H, 6N60 3 60.63 4.25 22.34 (60.6 4.19 22.3)

85 C,9 H,6NsOCI 62.38 4.37 19. 15 (62.33 4.3 19.1)

95 C21 H22N60 67 .37 5.88 22.45 (67.3 5.85 22.4)

73 C19 H, sN60 3CI 55.54 3.65 20.46 (55.48 3.6 20.4)

52 C 19 H15N50CI2 57.00 3.75 17.5 (56.92 3.71 17 .45)

Oil

124 C21 H21N103 60.14 5.01 23.38 (60.1 4.97 23.3)

78 C21 H21N60CI 61.68 5.14 20.56 (61.6 5.1 20.5)

92 C23 H21N10 66.18 6.47 23 .5 (66.14 6.43 23.47)

86 C,9 H, sN10 s 54.15 3.56 23 .27 (54.1 3.53 23.2)

108 C19 H,sN60 3CI 55.54 3.65 20.46 (55 .5 3.61 20.42)

118 C21 H21N10 3 60.14 5.01 23 .38 (60.09 4.97 23 .35)

crushed ice. The solid separated out was filtered and recrystallized from ethanol to give the desired prod­uct. Sc: IR: 1650 (amide), 3350(NH) cm-1

; 1H NMR

(90MHz) : 8 1.4 (s, -CH3), 3.4 (s, C-NH-CO), 6.1 (d, lH, ArCH), 3.1 (d, 1H, NCH), 6.8-8.5 (m, 15H, ArH). Sa: m.p. 87°C; Found: C, 70.56; H, 3.67 ; N, 15 .23. Calcd for C27H 17N50 3: C, 70.58; H, 3.70; N, 15 .25%. Sb: m.p. 72°C; Found: C, 68.19; H, 3.54; N, 14.71. Calcd for C21H17Ns02S: C, 68.21; H, 3.57; N, 14.73%. Sc: m.p. 78°C; Found: C, 62.28; H, 3.06; N, 16.11. Calcd for CnH,6N604S: C, 62.3; H, 3.07; N, 16.15%. Sd: m.p. 96°C; Found: C, 65.63 ; H, 3.22 ; N, 14.16. Calcd for C21H,6N50 3CI: C, 65.65 ; H, 3.24; N, 14.18%; Se: m.p. 68°C; Found: C, 63.56; H, 3.11 ; N, 13.71. Calcd for Cn H, 6N50 2SCl: C, 63 .59; H, 3. 14; N, 13 .73%; Sf: m.p. 85°C; Found: C, 69.29; H, 4.36; N, 16.71. Calcd for C29H22N603: C, 69 .32; H, 4 .38; N, 16.73%.

Acknowledgement The authors like to thank the authorities of Ber­

hampur University for providing fellowship to MB and Director, NIST for providing facilities to carry out the work.

914 INDIAN J. CHEM., SEC B, APRIL 2003

Table II- Analytical data of 6

Compd R Ar' Ar' m.p. (oC) Mol. formula Calcd % (Fou nd) No c H N

6a C6Hs C6Hs m-N02CoH4 165 C21 H22N604 65.58 4.45 17.00 (65 .56) (4.4) ( 16.96)

6b m-N02C6H4 CoHs III-N02C6H4 89 C21 H2, N10o 60. 11 3.89 18. 18 (60.09) (3 .85) ( 18.16)

6c CoHs CoHs p-CIC6H4 192 C21 H22 Ns0 2CI 67.0 1 4.55 14.47 (66.96) (4.5 1) (14.41)

6d m-N02C6H4 C6Hs p-CIC6H4 70 C21 H2,No04CI 61.3 3.97 15 .89 (6 1.27) (3 .94) ( 15.87)

6c C6Hs C6Hs p-N(CH3)2C6H4 178 C29 H28N602 70.73 5.69 17.07 (70.7) (5.67) (17.02)

6f III-N02C6H4 C6Hs p-N(CH.1hC6H4 72 C29 H21N104 64.8 5.02 18.24 (64.76) (4.98) (18.2)

6g C6Hs p-CIC6H4 m-N02C6H4 182 C21 H2,N604CI 61.3 3.97 15.89 (61.27) (3.94) ( 15.86)

6h m-N02CoH4 p-CIC6H4 m-N02C6H4 80 C21 H2oN106CI 56.49 4.52 17.08 (56.45) (4.51) (17.02)

61 C6Hs p-CIC6H4 p-CIC6H4

6j m-NOzCoH4 p-CIC6H4 p-CIC6H4 85 C21H2oNo04CI2 57.54 3.55 14.92 (57 .51) (3.52) ( 14.89)

6k C6Hs p-CIC6H4 p-N(CH3)2C6H4 116 C29 H21 N602CI 66.09 5.12 15.95 (66.06) (5.08) ( 15.9)

61 m-N02C6H4 p-CIC6H4 p-N(CH3)2C6H4 89 C29 H26N70 4CI 60.89 4 . .54 17.14 (60.82) (4.5 I) ( 17.1)

6m C6Hs p-N(CH3)2C6H4 III-N02C6H4 142 C29 H21N104 64.8 5.02 18.24 (64.76) (4.96) (18.2)

6n m-N02C6H4 p-N(CH.1hC6H4 m-N02C6H4 78 C29 H26Nx06 59.79 4.46 19.24 (59.73) (4.43) ( 19.2)

6o C6Hs p-N(CH.1hC6H4 p-CIC6H4 OIL C21 H2, N60 4CI

6p m-N02C6H4 p-N(CH.1)2Col-14 p-CIC6H4 75 C29 H26N104CI 60.89 4.54 17.14 (60.84) (4.5) ( 17.1 )

6q C6Hs p-N(CH.1hC6H4 p-N(CH3)2C6H4 122 C31 H33N10 2 69.53 6.16 18.3 1 (69.5) (6.15) ( 18.29)

6r III-N02C6H4 p-N(CH3h CoH4 p-N(CH.1hCoH4 80 C.11 H.12 Ns04 64.13 5.51 19.31 (64. I) (5.49) ( 19.28)

6s C6Hs m-N02C6H4 m-N02CoH4 142 C21 H2,N106 60.11 3.89 18. 18 (60.09) (3.85) ( 18.16)

6t m-N02C6H4 m-N02C6H4 m-N02C6H4 69 C21 H2oNsOx 55.47 3.42 19.17 (55.44) (3.4) ( 19.14)

6u CoH5 m-N02C6H4 p-CICoH4 167 C21 H2,N60 4CI 61.3 3.97 15.89 (6 1.28) (:_).94) (15.84)

6v m-N02C6H4 m-N02C6H4 p-CIC6H4 87 C21 HzoN706CI 56.49 3.48 17.08 56.43 3.47 (17.05)

6w C6Hs m-N02CoH4 p-N(CH3)2C6H4 96 C29 H21 N10 4 64.8 5.02 18.24 (64.74) (4.98) ( 18.2)

6x m-N02CoH4 111-N02CoH4 p-N(CH3)2C6H4 77 C29 H26Ns06 59.79 4.46 19.24 (59.73) (4.43) ( 19.2 1)

PADHY et a/.: SYNTHESIS OF PYRIMIDINE DERIVATIVES 915

References I. Joule J & Smith G in Heterocyclic Chemistry (ELBS Low

Price Editio'n, London), 1979, 126 . 2. Wierzehowski K L, Lifonskao E & Surger D, J Am Chem Soc,

87, 1965, 462. 3. Garg H G & Prakash C, J Med Chem, 4, 1971, 175 . 4. Upadhaya D N & Ram Vi shnu J, Indian J Chem, 38B, 1999,

173. 5. Machon Z & Krystyna U, Acta Pol Chem, 42(b), 1985, 516;

Chem Abstr, I 06, 1986, 138388; Sarangan S & Somshekara S, J Indian Chem Soc, 4, 1976, 53; Shishoo C J, Pathak US, Ra­thod I S & Jain K S, Indian J Chem, 38B, 1999, 684.

6. Ni zamuddin, Mishra Madhulika, Srivastava Manoj Kumar & Khan Mukhtar Hussain, Indian J Chem, 40B, 2001, 49.

7. Atwal K S, Swanson B N, Unger S E, Floyd D M, Moreland S, Hedberg A, O'reilly B C & Corrie J E T, J Med Chem, 34, 1991 , 806.

8. Girardet J L, Gunii E, Ester C, Cieslak D, Pietrzkowki Z & Wang G, J Med Chem , 43, 2000, 3704.

9. Cohen J S in Oligonucleotide-Antisense Inhibitors of Gene­Expression (Mcmillan Press Ltd. London), 1989.

10. Beaucage S L & Iyer R P, Tetrahedron, 49, 1993, 6 123. II . Pharmacopoeia of India; Vol II ; 3'd Edn (Government of In­

dia, Mini stry of Health & Family Welfare) , 1985 A-90.