A carbocyclic 7-deazapurine-pyrimidine hybrid nucleoside

Article abstract of DOI:10.1135/cccc20061161

The design, synthesis and rationale for the first example of a carbocyclic 7-deazapurine-pyrimidine hybrid nucleoside is described. The marriage of key structural features from the purine and pyrimidine nucleobase scaffolds has given rise to novel hybrid

Full text of DOI:10.1135/cccc20061161

7-Deazapurine–Pyrimidine Hybrid Nucleoside
1161
A CARBOCYCLIC 7-DEAZAPURINE–PYRIMIDINE HYBRID
NUCLEOSIDE
1
2
3,
Naresh K. SUNKARA , Sylvester L. MOSLEY and Katherine L. SELEY-RADTKE *
Department of Chemistry and Biochemistry, University of Maryland,
Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, U.S.A.;
1
2
3
e-mail: naresh1@umbc.edu, smosley1@umbc.edu, kseley@umbc.edu
Received March 13, 2006
Accepted July 10, 2006
Dedicated to Professor Antonín Holý on the occasion of his 70th birthday in recognition of his
outstanding contributions to the area of nucleic acid chemistry.
Th e design , syn th esis an d ration ale for th e first exam ple of a carbocyclic 7-deazapurin e–
pyrim idin e h ybrid n ucleoside is described. Th e m arriage of key structural features from th e
purin e an d pyrim idin e n ucleobase scaffolds h as given rise to n ovel h ybrid n ucleobases de-
sign ed to be recogn ized by biologically relevan t purin e- an d pyrim idin e-m etabolizin g en -
zym es. Pairin g th ese h ybrid bases with ch em oth erapeutically ben eficial carbocyclic “sugars”,
in addition to utilizin g th e h igh ly effective 7-deaza rin g system , sh ould result in ch em o-
th erapeutically useful n ucleosides. Th e approach to realize th e first 7-deazapurin e–pyrim idin e
h ybrid n ucleoside 3 is presen ted h erein .
Keyw ord s: Carbocyclic n ucleosides; Carban ucleosides; Isoaden osin e; 7-Deazapurin es;
Pyrrolopyrim idin es; Pyrim idin es; Nucleobases.
Recen t efforts in our laboratories h ave focused on th e strategic m an ipula-
tion of key aspects of th e n ucleoside scaffold in an effort to probe structure,
fun ction , an d ch em oth erapeutic activity. In creasin g reports of viral an d an -
tibacterial resistan ce h ave ren dered m an y of th e curren t ch em oth erapeutics
less effective, th us th e design of an in h ibitor th at could be recogn ized by
eith er a purin e- or a pyrim idin e-m etabolizin g en zym e m igh t lead to a dual
in h ibitor capable of disruptin g two differen t en zym atic steps in th e sam e
m ech an istic path way, or in differen t path ways. Th is could prove to be a
h igh ly effective approach for overcom in g resistan ce m ech an ism s in volvin g
bin din g site m utation s.
In th at regard, exploitation of th e n on stan dard con n ectivity of th e pu-
rin e n ucleoside isoaden osin e (1; IsoA, Fig. 1) was en vision ed as a startin g
poin t for con structin g h ybrid n ucleosides th at resem ble both purin es an d
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© 2006 Institute of Organic Chemistry and Biochemistry
doi:10.1135/cccc20061161

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Sunkara, Mosley, Seley-Radtke:
pyrim idin es. IsoA is a structural isom er of aden osin e wh ere th e purin e rin g
is con n ected to th e sugar m oiety at N3 (purin e n um berin g), rath er th an th e
tradition al N9 (refs1,2). In terestin gly, N3-glycosolated purin es can be viewed
as 5,6-disubstituted pyrim idin es, an d con versely, 5,6-disubstituted pyrim i-
din es are often con sidered as purin e m im ics, th us providin g im petus for
our goal3,4
.
FIG. 1
Isoaden osin e an d (–)-3-(2′,3′-dih ydroxycyclopen t-4′-en yl)aden in e
Next, in corporation of th e carbocyclic n ucleoside scaffold was also
viewed as strategic, sin ce as a class, carbocyclic purin e n ucleosides are
kn own in h ibitors of S-aden osylh om ocystein e h ydrolase (SAHase), an d in di-
rectly, DNA m eth yltran sferase (DNA MeTase), both critical en zym es in th e
replication cycle of m an y viruses, parasites, an d can cers5,6. In addition ,
som e carbocyclic pyrim idin es h ave proven to be poten t in h ibitors of CTP
syn th etase7,8, wh ile m an y 5- an d 6-substituted pyrim idin e n ucleosides h ave
exh ibited poten t broad-spectrum ch em oth erapeutic activity9, as well as in -
h ibition of th ym idin e ph osph orylase an d th ym idin e syn th ase10,11. Drawin g
upon th ese leads, it appeared th at a h ybrid of th e pyrim idin e an d purin e
rin g system s m erged with th e carbocyclic scaffold m igh t offer forth a suc-
cessful strategy for th e design of dual in h ibitor an alogues.
Wh ile our in itial syn th etic efforts h ad begun with th e con struction of th e
paren t carbocyclic isoA an alogue (2; DHCe-IsoA, Fig. 1)12 as an en try in to
th e N3-glycosylated series, our ultim ate goal was to con struct a h ybrid of
th e pyrim idin e an d purin e rin g system s, th us th e n ext targets con sidered
were th e fused uridin e-im idazole an alogues depicted in Fig. 2. Prelim in ary
ab in itio calculation s (data n ot sh own ) in dicated th at th e im idazole proton
th at tautom erizes between N7 an d N9 preferred to reside on N7. Un fortu-
n ately, th is also suggested th at an in tram olecular h ydrogen bon d (Fig. 3)
due to th e form ation of a five-m em bered pseudo cyclic structure was h igh ly
favorable. Th is was un desirable, sin ce it would deactivate two key structural
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7-Deazapurine–Pyrimidine Hybrid Nucleoside
1163
FIG. 2
Carbocyclic purin e–pyrim idin e h ybrid n ucleosides
FIG. 3
In tram olecular H-bon din g in a carbocyclic n ucleoside
con tacts critical for recogn ition in en zym e bin din g sites. To in vestigate th e
im plication s of th is, th e isosteric exch an ge of a m eth in e group for th e N7
n itrogen to afford a 7-deazapurin e-like or pyrrolopyrim idin e n ucleoside was
con sidered (Fig. 4). Th is structural m odification would allow for reten tion
of th e arom aticity desired for th e h eterocyclic base wh ile rem ovin g th e
proton in volved. In addition , given th e rich h istory of biological activity
for m an y 7-deaza carbocyclic n ucleosides13–16, th e pursuit of th is target was
deem ed especially attractive.
FIG. 4
Carbocyclic pyrrolopyrim idin e h ybrid n ucleosides
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Th e route to our previously reported12 isoA an alogue 2 (an d its corre-
spon din g en an tiom er) h ad relied upon n ucleoph ilic displacem en t of an ac-
tivated alcoh ol or h alide by aden in e in th e absen ce of base. Th is approach
h ad proven un satisfactory due to disappoin tin gly low yields. In th e absen ce
of base th e N3-glycosylated product was th e m ajor isom er obtain ed, h ow-
ever, th e N7, N9 an d N1 isom ers were also form ed, th ereby sign ifican tly
lowerin g th e yield of th e desired N3 isom er. As a result, a n ew, m ore effi-
cien t couplin g procedure, was sough t. In th at regard, Mitsun obu couplin g17
h as been on e of th e tradition ally used m eth ods in th e syn th esis of
carbocyclic n ucleosides, alth ough it is gen erally h igh er yieldin g for purin e
n ucleosides, sin ce th e pyrim idin es suffer from com petition between O- an d
N-alkylation . Fortun ately, a recen t study in th e literature18 provided a valu-
able in sigh t on h ow to tip th e scales to favor alm ost exclusive form ation of
th e desired N-alkylated product by usin g th e ben zoyl protectin g group for
th e N3 of uracil.
As sh own in Sch em e 1, N3-ben zoyl uracil19 was coupled to th e kn own
4
14,20, wh ich , after rem oval19 of th e ben zoyl group gave 5 in a 65% yield
for th e two steps. Reduction of th e double bon d of th e cyclopen ten e rin g
was th en n ecessary, as we h ave foun d th at direct iodin ation of th e base re-
sults in a sign ifican t am oun t of cleavage of th e base, probably due to th e
form ation of an allylic carbocation . Th e reduction was accom plish ed in
quan titative yield usin g m ild palladium -catalyzed h ydrogen ation 15 to af-
ford 6, wh ich , followin g iodin ation with LDA 10,21 gave 7 (60%). Next, dis-
SCHEME 1
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7-Deazapurine–Pyrimidine Hybrid Nucleoside
1165
placem en t of th e iodo fun ction ality with sodium azide provided 8 (82%),
followed by reduction to the 6-aminopyrimidine intermediate 9 in quantitative
yield10. Man ipulation of th e am in e fun ction ality of 9 to form th e pyrrole
rin g (Sch em e 2) of 10 was accom plish ed by refluxin g 9 with ch loro-
acetaldeh yde an d sodium acetate for 1 day22, albeit in on ly a m oderate
yield (40%). Fin ally, stan dard deblockin g of th e isopropyliden e group on
th e 2′- an d 3′-h ydroxyl groups of 10 (quan titative) gave th e desired 7-deaza
target 3 in 7 steps with an overall yield of 9.6%. Efforts are curren tly un der-
way to optim ize th is route so th at m ore exten sive biological studies of 3
can be un dertaken . In th e m ean tim e, th e in itial broad-screen biological
testin g on 3 h as begun an d th e results will be described in due course.
SCHEME 2
In sum m ary, a sh ort an d reason ably efficien t syn th etic route to a n ew
class of 7-deazapurin e–pyrim idin e h ybrid n ucleosides h as been in troduced.
Wh ile it rem ain s to be seen if th ey will ultim ately act as dual in h ibitors, th e
sign ifican t biological activity of a variety of 7-deaza n ucleosides in cludin g
7-deazaaristerom ycin , 7-deaza-5′-n oraristerom ycin 13,16, tubercidin , toyoca-
m ycin an d san givam ycin 14,23–25 certain ly offers forth stron g im petus for th e
pursuit of th e correspon din g h ybrid an alogues of th ese poten t n ucleosides.
Efforts are curren tly un derway to realize th ese, an d reports of th eir syn th e-
sis will be forth com in g as th ey becom e available.
EXPERIMENTAL
Gen eral
Meltin g poin ts are un corrected. 1H an d 13C NMR spectra (δ, ppm ; J, Hz) were operated at
400 an d 100 MHz, respectively, all referen ced to in tern al tetram eth ylsilan e (TMS) at 0.0 ppm .
Reaction s were m on itored by th in -layer ch rom atograph y (TLC) usin g 0.25 m m Wh atm an
Collect. Czech. Chem. Commun. 2006, Vol. 71, No. 8, pp. 1161–1168

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Sunkara, Mosley, Seley-Radtke:
Diam on d silica gel 60-F254 precoated plates. Colum n ch rom atograph y was perform ed on
Wh atm an silica, 200–400 m esh , 60 Å an d elution with th e in dicated solven t system . Yields
refer to ch rom atograph ically an d spectroscopically (1H an d 13C NMR) h om ogen eous m aterials.
Preparation of 1-[(4,5-(Propan e-2,2-diyldioxy)cyclopen t-2-en -1-yl]uracil (5)
To (+)-4,5-(propan e-2,2-diyldioxy)cyclopen t-2-en -1-ol14,20 (4) (6.50 g, 41.67 m m ol), N3-ben z-
oyluracil19 (18.02 g, 83.33 m m ol) an d PPh 3 (21.88 g, 83.33 m m ol) in an h ydrous CH3CN
(500 m l) at 0 °C was added dropwise diisopropylazodicarboxylate (16.85 g, 83.33 m m ol,
16.52 m l). After stirrin g at room tem perature for 15 h , th e m ixture was con cen trated an d
purified by colum n ch rom atograph y (EtOAc/h exan e, 3:1) to afford 9.74 g of th e coupled
product as a wh ite solid, 66% yield. 1H NMR (400 MHz, DMSO-d6): 1.23 (3 H, s); 1.32
(3 H, s); 4.71 (1 H, d); 5.27 (1 H, s); 5.29 (1 H, d); 5.81 (1 H, d); 5.84 (1 H, dd); 6.23 (1 H,
dt); 4.71 (1 H, d); 5.29 (2 H, d); 5.84 (1 H, d); 5.85 (1 H, d); 6.22 (1 H, m ); 7.51 (1 H, d);
7.57 (2 H, t); 7.78 (1 H, t); 7.97 (2 H, m ). 13C NMR (75 MHz, DMSO-d6): 24.5, 26.2, 69.2,
83.2, 84.6, 101.1, 111.8, 128.9, 129.1, 130.2, 131.6, 135.0, 139.0, 143.0, 145.0, 163.0, 168.8.
NaOH (10 m l, 1% in MeOH) was added to th e coupled product (0.45 g, 1.27 m m ol) an d
th e m ixture allowed to stir at room tem perature for 12 h , th en n eutralized with 1 M HCl 19
.
Th e m ixture was evaporated an d th e resultin g residue dissolved in EtOAc (50 m l), wash ed
with H2O (25 m l), dried (an h ydrous MgSO4), an d th e solven t evaporated un der vacuum . Th e
residue was th en purified by colum n ch rom atograph y (EtOAc/h exan e, 4:1) to afford 0.25 g
of 5 as a wh ite solid, 79% yield. 1H NMR (400 MHz, CD3OD): 1.22 (3 H, s); 1.31 (3 H, s);
4.53 (1 H, d); 5.27 (2 H, m ); 5.52 (1 H, dd); 5.77 (1 H, dd); 6.19 (1 H, d); 7.23 (1 H, d); 11.3
(1 H, s). 13C NMR (75 MHz, CD3OD): 24.5, 26.2, 68.4, 83.4, 84.6, 101.2, 111.7, 129.4, 138.6,
142.5, 151.3, 165.0.
Preparation of 1-[(2,3-(Propan e-2,2-diyldioxy)cyclopen tyl]uracil (6)
To 5 (0.25 g, 1.0 m m ol) in MeOH (10 m l) was added Pd/C (10%, 0.025 g) an d th e m ixture
subjected to h ydrogen ation at a pressure of 0.17 MPa for 20 m in 14. Th e m ixture was filtered
an d th e filtrate con cen trated to afford 0.26 g of 6 as a wh ite solid (quan titative). 1H NMR
(400 MHz, DMSO-d6): 1.20 (3 H, s); 1.35 (3 H, s); 1.65–1.82 (2 H, m ); 1.95–2.15 (2 H, m );
4.63 (1 H, m ); 4.64 (1 H, m ); 4.71 (1 H, dd); 5.52 (1 H, d); 7.58 (1 H, d); 11.3 (1 H, s).
13C NMR (75 MHz, DMSO-d6): 24.5, 27.3, 29.1, 31.2, 63.9, 80.4, 84.4, 101.8, 110.0, 143.9,
152.6, 163.8
Preparation of 6-Iodo-1-[(2,3-(propan e-2,2-diyldioxy)cyclopen tyl]uracil (7)
To a flam e-dried flask un der an Ar atm osph ere was added an h ydrous THF (5 m l) an d fresh ly
distilled diisopropylam in e (0.23 g, 2.27 m m ol). Th e tem perature was lowered to –78 °C an d
n -BuLi added dropwise (2.5 M in h exan es, 2.27 m m ol, 0.21 m l). Main tain in g th e tem pera-
ture at –78 °C, th e m ixture was stirred for 15 m in , th en a solution of 6 (0.26 g, 1.03 m m ol)
in an h ydrous THF (10 m l) added an d th e m ixture stirred for an addition al 30 m in . Still
m ain tain in g th e tem perature at –78 °C, a solution of I2 (0.58 g, 2.27 m m ol) in an h ydrous
THF (5 m l) was added an d th e m ixture stirred for an addition al 2 h 10,21. Th e reaction was
th en quen ch ed with acetic acid (10 drops) an d NaHCO3 (1 m l), th e solven t rem oved by
evaporation , an d th e resultin g residue dissolved in EtOAc (50 m l), wash ed with sodium
th iosulfate (25 m l) an d brin e (25 m l), dried (an h ydrous MgSO4), an d th e solven t rem oved
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7-Deazapurine–Pyrimidine Hybrid Nucleoside
1167
by evaporation . Th e residue was purified by colum n ch rom atograph y (EtOAc/h exan e, 4:1) to
afford 0.23 g of 5 as a wh ite solid, 60% yield. 1H NMR (400 MHz, CD3OD): 1.26 (3 H, s);
1.46 (3 H, s); 1.81–1.88 (1 H, m ); 1.92 (1 H, m ); 2.31 (2 H, m ); 4.99 (2 H, s); 5.01 (1 H, m );
6.38 (1 H, s). 13C NMR (75 MHz, CD3OD): 23.6, 26.4, 29.2, 31.7, 74.9, 82.2, 84.7, 110.8,
115.1, 118.1, 148.3, 162.9.
Preparation of 6-Azido-1-[(2,3-(propan e-2,2-diyldioxy)cyclopen tyl]uracil (8)
A solution of 7 (0.10 g, 0.29 m m ol) an d NaN3 (0.094 g, 1.45 m m ol) in an h ydrous DMF (3 m l)
was stirred at room tem perature for 30 m in 10. H2O (20 m l) was added an d th e m ixture ex-
tracted with EtOAc (3 × 50 m l), wash ed with brin e (50 m l), dried (an h ydrous MgSO4), an d
con cen trated to yield 0.066 g of 8 as a wh ite solid, 85% yield. 1H NMR (400 MHz, CD3OD):
1.25 (3 H, s); 1.43 (3 H, s); 1.79–1.83 (1 H, m ); 1.95 (1 H, m ); 2.29 (2 H, m ); 4.83 (2 H, m );
4.97 (1 H, dd); 5.52 (1 H, s). 13C NMR (75 MHz, CD3OD): 23.8, 26.2, 28.5, 31.8, 62.2, 81.9,
84.4, 87.9, 111.5, 146.2, 151.7, 163.1.
Preparation of 6-Am in o-1-[(2,3-(propan e-2,2-diyldioxy)cyclopen tyl]uracil (9)
To a solution of 8 (0.066 g, 0.23 m m ol) in absolute EtOH (50 m l) was added Pd/C (10%,
10 m g). Th is m ixture was subjected to h ydrogen ation at a pressure of 0.17 MPa for 20 m in .
Th e reaction m ixture was filtered an d th e filtrate con cen trated to afford 0.060 g of 9 as a
wh ite solid (quan titative yield). 1H NMR (400 MHz, CD3OD): 1.23 (3 H, s); 1.43 (3 H, s);
1.91 (2 H, m ); 2.32 (2 H, m ); 4.39 (1 H, m ); 4.81 (1 H, s); 4.88 (1 H, m ); 5.06 (1 H, dd).
13C NMR (75 MHz, CD3OD): 23.5, 26.1, 29.6, 32.6, 62.2, 76.3, 82.1, 84.9, 110.5, 151.5,
157.8, 164.9.
Preparation of 1-[(2,3-(Propan e-2,2-diyldioxy)cyclopen tyl]-7H-pyrrolo[2,3-d]pyrim idin e-
2,4-(1H,3H)-dion e (10)
To a stirred suspen sion of 9 (0.06 g, 0.22 m m ol) in EtOH (10 m l) was added NaOAc (0.07 g,
0.51 m m ol) an d th e m ixture was h eated to 70 °C. Ch loroacetaldeh yde (0.02 m l, 0.31 m m ol)
an d NaOAc (0.07 g, 0.51 m m ol) were th en added an d th e m ixture was stirred at 70 °C for an
addition al 24 h 22. Th e EtOH was rem oved un der vacuum an d th e product was dissolved in
EtOAc (25 m l), wash ed with H2O (2 × 10 m l) an d brin e (2 × 10 m l), dried (an h ydrous
MgSO4), an d con cen trated. Th e residue was purified by colum n ch rom atograph y
(EtOAc/h exan es, 4:1) to afford 0.028 g of 10 as a wh ite solid, 51% yield. 1H NMR (400 MHz,
CD3OD): 1.24 (3 H, s); 1.44 (3 H, s); 1.89 (2 H, m ); 2.34 (2 H, m ); 3.28 (1 H, m ); 4.44 (1 H,
s); 4.89 (1 H, s); 5.21 (1 H, s); 6.43–6.47 (1 H, m ); 6.63 (1 H, m ); 9.98 (1 H, s). 13C NMR (75
MHz, CD3OD): 23.2, 25.8, 29.5, 32.1, 64.0, 81.9, 84.2, 99.8, 103.8, 110.5, 117.2, 140.5,
150.8, 160.9.
Preparation of 1-(2,3-Dih ydroxycyclopen tyl)-7H-Pyrrolo[2,3-d]pyrim idin e-
2,4-(1H,3H)-dion e (3)
Com poun d 10 (0.028 g, 0.09 m m ol) was dissolved in a 1:1 m ixture of TFA an d H2O (25 m l)
an d th e reaction m ixture was stirred at room tem perature for 12 h . Th e resultin g solution
was con cen trated an d th e residue was purified by colum n ch rom atograph y (CH2Cl2/MeOH,
5:1) to afford 0.012 g of 3 as a wh ite solid 70.5% yield. 1H NMR (400 MHz, CD3OD): 1.71
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(1 H, m ); 2.14 (3 H, m ); 4.12 (1 H, m ); 4.54 (1 H, m ); 4.76 (1 H, m ); 6.42 (1 H, d); 6.71
(1 H, d). 13C NMR (75 MHz, CD3OD): 22.9, 29.3, 62.8, 72.1, 74.1, 99.9, 103.5, 116.9, 141.4,
150.6, 161.1. For C11H13N3O4·0.3H2O calculated: 51.48% C, 5.35% H, 16.38% N; foun d:
51.39% C, 5.20% H, 16.26% N.
This work was supported by the National Institutes of Health (NIH) RO1 CA 97634.
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