Selective recognition of uracil and its derivatives using a DNA repair enzyme structural mimic

Article abstract of DOI:10.1021/jo901862x

(Chemical Equation Presented) During DNA repair, uracil DNA glycosylase (UDG) pulls unwanted uracil into its active site through hydrogen bonding and π-π stacking interactions. The reason why UDG binds only uracil tightly - and not its derivatives, such as thymine - remains unclear. In this study, we synthesized the stable, water-soluble receptor 1a as a structural mimic of the active site in UDG. Compound 1a contains a 2,6-bis(glycylamino)pyridine group, which mimics the amino acid residues of UDG that interact with uracil through a hydrogen-bonding network; it also possesses a pyrene moiety as a π-π stacking interaction element and fluorescent probe that mimics the aromatic groups (phenyl and fluorescent indolyl units) found in the active site ofUDG. Receptor 1a binds selectively to uracil and derivatives (including thymine, 5-formyluracil, 5-fluorouracil, and 5-nitrouracil) and someDNAand RNA nucleosides (including thymidine and uridine) through hydrogen bonding and π-π stacking interactions. Interestingly, a plot of log K_b with respect to the values of pK_a of the N(3)H units of uracil and its derivatives was linear, with a negative slope (β) of -0.24 ± 0.03. Thus, compounds featuring lower values of pK_a for their N(3)H units provided greater apparent binding constants for their complexes with receptor 1a, suggesting acidity-dependent binding of uracil and its derivatives to this receptor; notably, uracil bound more tightly than did thymine. Our study provides some insight into how uracil and its derivatives in DNA are bound by DNA repair enzymes through hydrogen bonding and π-π stacking interactions.

Full text of DOI:10.1021/jo901862x

pubs.acs.org/joc
Selective Recognition of Uracil and Its Derivatives Using a DNA Repair
Enzyme Structural Mimic
Yu Lin Jiang,* Xiaonan Gao, Guannan Zhou, Arpit Patel, and Avani Javer
Department of Chemistry, College of Arts and Sciences, East Tennessee State University,
Johnson City, Tennessee 37614
jiangy@etsu.edu
Received August 27, 2009
During DNA repair, uracil DNA glycosylase (UDG) pulls unwanted uracil into its active site
through hydrogen bonding and π-π stacking interactions. The reason why UDG binds only uracil
tightly—and not its derivatives, such as thymine—remains unclear. In this study, we synthesized the
stable, water-soluble receptor 1a as a structural mimic of the active site in UDG. Compound 1a
contains a 2,6-bis(glycylamino)pyridine group, which mimics the amino acid residues of UDG that
interact with uracil through a hydrogen-bonding network; it also possesses a pyrene moiety as a π-π
stacking interaction element and fluorescent probe that mimics the aromatic groups (phenyl and
fluorescent indolyl units) found in the active site of UDG. Receptor 1a binds selectively to uracil and
derivatives (including thymine, 5-formyluracil, 5-fluorouracil, and 5-nitrouracil) and some DNA and
RNA nucleosides (including thymidine and uridine) through hydrogen bonding and π-π stacking
interactions. Interestingly, a plot of log Kb with respect to the values of pKa of the N(3)H units of
uracil and its derivatives was linear, with a negative slope (β) of -0.24 ( 0.03. Thus, compounds
featuring lower values of pKa for their N(3)H units provided greater apparent binding constants for
their complexes with receptor 1a, suggesting acidity-dependent binding of uracil and its derivatives to
this receptor; notably, uracil bound more tightly than did thymine. Our study provides some insight
into how uracil and its derivatives in DNA are bound by DNA repair enzymes through hydrogen
bonding and π-π stacking interactions.
Introduction
(pinch, push, plug, and pull) to flip the uracil unit out of the
DNA strand and draw it into the active site for cleavage.2 In
the active site, uracil is bound to the enzyme through hydro-
gen bonding and π-π stacking interactions.3 For instance, in
the complex formed between Escherichia coli UDG and
uracil (PDB, 2EUG), UDG uses its asparagine 123 and
histidine 187 residues to hydrogen bond with uracil and its
phenylalanine 77 residue to contact uracil through π-π
Uracil DNA glycosylase (UDG) is a paradigm DNA
repair enzyme that cleaves an unwanted uracil group from
damaged DNA as the first step of the DNA repair process.1
During the reaction, the enzyme uses a four-step mechanism
*Corresponding author. Tel: 1-423-439-6917. Fax: 1-423-439-5835.
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Amzel, L. M.; Stivers, J. T. Nature 2007, 449, 433–437. (c) Stivers, J. T.; Jiang,
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Published on Web 12/17/2009
DOI: 10.1021/jo901862x
r
2009 American Chemical Society

Jiang et al.
JOCArticle
CHART 1. Uracil and Its Derivatives
stacking interactions.3 In addition, because UDG possesses
a tryptophan 164 residue, which is fluorescent and posi-
tioned adjacent to phenylalanine 77 in the active site, fluor-
escence quenching occurs during the binding of UDG with
uracil. In contrast, quenching of this tryptophan fluores-
cence is not observed when titrating with thymine.4 Thus, it
appears that UDG binds uracil selectively, presumably
because of the presence of a gatekeeper residue (tyrosine
66) that allows only uracil to enter the active site.5 Thus, the
steric effect of this tyrosine residue appears to be an im-
portant factor of the binding during DNA repair. It is not
clear whether the acidity of uracil is also important in the
binding and discrimination against thymine during DNA
base flipping. Noticeably, the cleavage of uracil and its
halogenated derivatives by another DNA repair enzyme,
human thymine DNA glycosylase (TDG), is dependent on
the acidity of the N(1)H unit of the uracil derivatives and the
stability of the N-glycosidic bond.6 Studies of this kind of
acidity-dependent specificity for UDG are impossible with-
out mutating the tyrosine residue, because many uracil
derivatives, such as thymine and halogenated uracil, will
not fit in the UDG active site. An alternative approach
toward studying the specificity of the binding of uracil and
its derivatives through hydrogen bonding and π-π stacking
interactions is the use of synthetic structural mimics of the
active site of UDG.
Molecular recognition of uracil and thymine is particu-
larly interesting because they are RNA and DNA bases,
which are directly related to human diseases and cancers
(Chart 1).7 Uracil and 5-formyluracil are well-known da-
maged DNA bases; their study and detection might assist in
the diagnosis of human diseases and aging problems.8 Be-
cause the drug 5-fluorouracil (5-FU) is widely used for the
treatment of cancers, studies of its binding behavior might
assist cancer research.9 5-Nitrouracil and its derivatives
exhibit antiviral effects because they are inhibitors of thymi-
dylate synthetase.10 Therefore, uracil and its derivatives are
attractive targets for molecular recognition studies. Origin-
ally, uracil was found to bind adenine specifically in CHCl3,
as revealed by IR spectroscopy.11 The pattern of hydrogen
bonds between 1-methyluracil and 9-ethyladenine was dis-
covered crystallographically; at the same time, the effect of
substituent groups at the 5-position of uracil was noted, with
greater acidity of the uracil derivatives facilitating their
binding with the adenine derivative 9-ethyladenine.11 Later,
Hamilton and co-workers discovered that the binding be-
tween thymine and 2,6-bis(acylamino)pyridine occurred
through three hydrogen bonds.12 Recently, 2,6-bis-
(acylamino)pyridine receptors have been developed for the
effective binding of uracil derivatives through hydrogen
bonding and π-π stacking interactions;13 because these
receptors are typically insoluble in water, their binding
studies have been performed mostly in organic solvents, in
which the molecular recognition of DNA and RNA bases
and nucleosides is limited because of low solubility.14
Pyrene-containing receptors have been developed for the
effective recognition of nucleobase derivatives, such as
9-butyladenine, through hydrogen bonding and π-π stack-
ing interactions.15,16 By using our recently developed
naphthalene scaffold, 2,6-bis(acylamino)pyridine as an ele-
ment to bind uracil and its derivatives, and pyrene as a
fluorescent probe and π-π stacking interaction element,
we have prepared a water-soluble receptor 1a as an enzyme
structural mimic of the active site of UDG (Scheme 1).17 This
paper describes a molecular recognition study of the hydro-
gen bonding and π-π stacking interactions of receptor 1a
with uracil, its derivatives, other nucleobases, DNA and
RNA nucleosides, and 20-deoxyuridine. We also report the
effects of the acidities of the N(1)H and N(3)H groups of
uracil and its derivatives on their recognition behavior.
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2005, 70, 2729–2738. (d) Takase, M.; Inouye, M. J. Org. Chem. 2003, 68,
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SCHEME 1. Structural Mimicry of the Truncated Complex of
UDG with Uracil (PDB, 2EUG) Using a Synthetic Pyrene
Receptor/Uracil Complex3
at low temperature (40 °C). We suspect that the organo-
boronic acid 3 might be a useful material for the synthesis of
other bioactive receptors and druglike compounds.
Binding of Receptor 1a with Uracil and Derivatives
Revealed by NMR Spectroscopy.24 We performed an NMR
spectroscopic dilution study of 1 at concentrations from 9.0
to 0.28 mM in D2O at 298 K to investigate its dimerization
patterns and monomer structure (Figure 1). In this study, we
employed 1 as a mixture of 1a and 1b. In H2O, 1b is likely to
dissociate to form the neutral pyridine unit because the pKa
of such a group is estimated to be 3.68 (Scheme 4).25 As a
result, the dilution of 1 with water will promote not only the
formation of monomers of 1a and 1b but also the dissocia-
tion of 1b to 1a, which is more efficient in the binding of
uracil because of its neutral pyridinyl moiety. At a concen-
tration of 0.28 mM, we estimate that 1 contains 91% of 1a
and 9% of 1b. Therefore, the truncated top NMR spectrum
in Figure 1 mainly represents that of 1a.
SCHEME 2. Synthesis of 3
Results and Discussion
Dilution of a solution of 1 caused a downfield shift and
splitting of the signal of the pyridinyl hydrogen atoms (from
one to two peaks). This downfield chemical shift was pre-
sumably the result of diminishing π-π stacking interactions
between the pyrenyl groups in the dimers, suggesting their
dissociation into monomers. The concentrations of 1 and the
corresponding chemical shifts were fitted into a nonlinear
regression curve, which provided an averaged dimerization
constant for 1 of 600 ( 40 M-1 (Figure S1, Supporting
Information). Scheme 5 summarizes the plausible dimeriza-
tion patterns for a sample of 1 containing both 1a and 1b. The
homodimer 1a-1a features hydrogen bonding pairs involving
the pyridinyl nitrogen and amide hydrogen atoms of 1a; the
heterodimer 1a-1b features hydrogen bonding pairs invol-
ving the pyridinyl nitrogen and amide hydrogen atoms of 1a
and the amide bond hydrogen and oxygen atoms of 1b; the
homodimer 1b-1b features hydrogen bonding pairs involving
the amide bond hydrogen and oxygen atoms of 1b.26,14c
The splitting of the signal in Figure 1 from one to two can
also be attributed to the monomeric form of 1. Because the
pyrenyl group is not symmetrical in the monomer 1 and
because of its restricted rotation, due to the peri-disubstitut-
ed naphthalene unit, the apparent symmetry of the pyridinyl
ring in either 1a or 1b is destroyed in the monomer, resulting
in the two pyridinyl hydrogen atoms appearing at different
chemical shifts (Schemes 6 and 7). The maximum difference
between chemical shifts of Hp1 and Hp2 of 1, containing
mostly 1a, was 0.04 ppm (Figure 1).
Synthesis of 1a. 4-Bromo-2,6-diaminopyridine18,19 was
benzylated in the presence of NaH to afford compound 2,
which was converted into the boronic acid 3 through se-
quential treatment with n-BuLi and tri(isopropyl) borate
followed by hydrolysis (Scheme 2).20 Compound 3 was
isolated as a colorless or light-yellow oil; because it turned
purple after storage in a refrigerator, it was used directly,
without further purification, in a standard Suzuki coupling
with 1-[10-(80-bromonaphthyl)]pyrene (4) to afford com-
pound 5,15 which was debenzylated through treatment with
trifluoromethanesulfonic acid (TfOH) in the presence of
pyrene (as a carbocation scavenger) in CH2Cl2 under re-
flux.21 The resulting 2,6-diaminopyridine derivative 6 was
then reacted with N-Boc-Gly-OH in the presence of HATU
[O-(7-azabenzotriazol-1-yl)-N,N,N0,N0-tetramethyluronium
hexafluorophosphate] and Et3N to afford compound 7,22
which was deprotected using a solution of hydrogen chloride
in EtOAc for 5 min to afford the solid 1.23 This final product
was purified through recrystallization from water/THF
(Scheme 3). Elemental analysis of the carbon, hydrogen,
and chlorine atom contents of solid 1 revealed a composition
of M(HCl)2.5(H2O)4, where M is the free amine of 1, suggest-
ing that the solid consisted of 50% each of compounds 1a
and 1b. We used solid 1 for studies of the molecular recogni-
tion of uracil and its derivatives. To provide a sample
suitable for NMR and IR spectroscopic characterization,
we removed the residual solvent from solid 1 (<1%) by
dehydrating an aqueous solution of 1 in a spin vacuum
machine.
Next, we used NMR spectroscopy to study the molecular
recognition of uracil with receptor 1a in D2O at 298 K. In this
binding study, we also used 1 as a mixture of 1a and 1b, where
1a is more likely to bind uracil because of its more effective
hydrogen bond network (Scheme 6). In H2O, however, 1b is
likely to dissociate to form the neutral pyridine unit
(Scheme 4).26 As a result, both of the components of 1 will
bind uracil (Scheme 6).
This paper is the first to report the use of benzyl groups to
doubly protect both amino groups of 2,6-diaminopyridine.
All of these benzyl groups were readily removed using TfOH
(18) Nettekoven, M. Synlett 2001, 1917–1920.
(19) Nettekoven, M.; Jenny, C. Org. Proc. Res. Dev. 2003, 7, 38–43.
(20) (a) Masciadri, R.; Kamer, M.; Nock, N. Eur. J. Org. Chem. 2003,
4286–4291. (b) Amann, N.; Pandurski, E.; Fiebig, T.; Wagenknecht, H.-A.
Chem.—Eur. J. 2002, 8, 4877–4883.
(21) Minetti, P.; Tinti, M. O.; Carminati, P.; Castorina, M.; Di Cesare, M.
A.; Di Serio, S.; Gallo, G.; Ghirardi, O.; Giorgi, F.; Giorgi, L.; Piersanti, G.;
Bartoccini, F.; Tarzia, G. J. Med. Chem. 2005, 48, 6887–6896.
(22) Smith, D. K.; Diederich, F. Chem. Commun. 1998, 2501–2502.
(23) Brady, S. F.; Varga, S. L.; Freidinger, R. M.; Schwenk, D. A.;
Mendlowski, M.; Holly, F. W.; Veber, D. F. J. Org. Chem. 1979, 44, 3101–
3105.
(24) All dilution experiments and binding constant measurements were
performed in water without using any buffer, because receptor 1 became
cloudy and precipitated in phosphate buffer at pH 7.
(25) (a) McMurry, J. Organic Chemistry, 7th ed.; Thomson, Brooks/Cole:
Belmont (CA), 2008; pp 921-924. (b) The pKa for 2,6-diacetamidopyridine was
calculated to be 3.68 using Advanced Chemistry Development (ACD/Labs)
Software V8.14 for Solaris in Scifinder Scholar.
(26) Corbin, P. S.; Zimmerman, S. C.; Thiessen, P. A.; Hawryluk, N. A.;
Murray, T. J. J. Am. Chem. Soc. 2001, 123, 10475–10488.
326 J. Org. Chem. Vol. 75, No. 2, 2010

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FIGURE 1. Partial 1H NMR spectra of 1 at various concentrations in D2O at 298 K.
SCHEME 3. Synthesis of 1
Job’s plots, generated to identify the binding stoichiome-
try between uracil and receptor 1a, revealed 1:1 binding
(Figure S2, Supporting Information).15 The variation in
the chemical shifts of the CH protons of uracil (10.0 mM)
were determined on the basis of NMR spectra recorded in the
presence and absence of 1 (8.7 mM). In the presence of 1
(Figure 2), the signals of the C(5)H and C(6)H protons both
moved upfield by 0.13 ppm, suggesting that uracil was bound
to receptor 1a through π-π stacking interactions. The
binding of uracil to the receptor also resulted in splitting of
the signal for the pyridinyl hydrogen atoms Hp1 and Hp2
[difference in chemical shift: 0.03 ppm (similar to that of
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SCHEME 4. Equilibrium between 1b and 1a in Aqueous
Solution
SCHEME 6. Binding of Uracil (10.0 mM) and 1 (8.7 mM) in
D2O at 298 K Resulted in Upfield Shifts of the Signals of the
C(5)H and C(6)H Protons and Splitting of the Signal of Hp1 and
Hp2 by a Chemical Shift Difference of 0.03 ppm
SCHEME 7. Binding of 1-Butylthymine (10 mM) and 7
(10 mM) in CDCl3 at 298 K Resulted in Downfield Shifts of the
Signals for the Protons Ht (by a Chemical Shift Difference of
2.41 ppm) and Ha and Hb (by Chemical Shift Differences of
1.08 and 1.24 ppm, Respectively)
SCHEME 5. Plausible Dimerization of 1 in Water Involving
Both Hydrogen Bonding and π-π Stacking Interactionsa
1-butylthymine (10 mM) with 7 (10 mM) in CDCl3, the
signals of the protons Ht (of 1-butylthymine) and Ha and Hb
(of 7) all moved downfield by 2.41, 1.08, and 1.24 ppm,
respectively (Scheme 7), suggesting strong hydrogen bonding
between 1-butylthymine and the 2,6-bis(glycylamino)-
pyridinyl group in organic solvent27 and, hence, the possibi-
lity of a strong hydrogen bond network between the receptor
1a and uracil in water.
Binding of 1a with Uracil and Derivatives Revealed by
Fluorescence Spectroscopy. The fluorescence emission spec-
trum of 1 in water reveals a signal maximum at 472 nm.
Therefore, we investigated the binding of 1a with uracil using
fluorescence spectroscopy with water as a solvent at room
temperature (298 K). In the binding study, we still used 1 as a
mixture of 1a and 1b, with a total concentration of 0.87 μM.
In this dilute solution, the majority of 1b is likely to dissociate
to form 1a (Scheme 4). The calculated concentration of 1a,
which was available for binding, was 0.869 μM.28
During the measurements, we monitored the change in
fluorescence intensity during the titration of the receptor
with uracil (Figure 3). The molecular recognition of uracil by
1a resulted in a decrease in the fluorescence intensity at
472 nm, providing further evidence for the binding of these
aThe structures 1a-1a and 1b-1b are formed through homodimer-
ization of 1a and 1b, respectively; 1a-1b is the heterodimer formed from
1a and 1b.
(27) Inouye, M.; Hyodo, Y.; Nakazumi, H. J. Org. Chem. 1999, 64, 2704–
2710.
0.04 ppm for the monomer of 1a)], suggesting that they
experienced different chemical environments after dissocia-
tion of the dimer and formation of the complex with uracil
(Scheme 6).
(28) The pH of the solution of 1 was not controlled using any pH buffer.
The calculated value of the pH for 1 (0.87 μM) was 6.4, determined using the
estimated pKa (3.68) of 1b and the concentrations of 1a and 1b (both 0.435
μM). At these concentrations, 99.8% of 1b will dissociate to form 1a. Because
the proton was not involved in the binding, the concentration of protons
from 1b should remain constant. Although the most acidic uracil derivative
that we investigated (5-nitrouracil) would decrease the pH of the solution to a
calculated value of pH 5.4 during the measurement, the concentration of 1a
would barely change because of the decrease in pH.
To study the hydrogen bonding between uracil and recep-
1
tor 1a, we recorded H NMR spectra of mixtures of their
derivatives 1-butylthymine and 7, respectively. After mixing
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FIGURE 2. Partial 1H NMR spectra (D2O, 298 K) of uracil (10 mM, A), a mixture of uracil (10.0 mM) and 1 (8.7 mM, B), and 1 (8.7 mM, C).
TABLE 1. Apparent Binding Constants (Kb) of Uracil and Its Deriva-
tives, Nucleosides of DNA and RNA, and 20-Deoxyuridine with Receptor
1a in Water at 298 K
substrate
Kb (M-1
)
pKa of N(3)H32,b
thymine
uracil
5-formyluracil
5-fluorouracil
5-nitrouracil
thymidine
20-deoxycytidine
20-deoxyadenosine
20-deoxyguanosine
uridine
cytidine
adenosine
61 ( 14
10.04
9.34
7.58
7.26
6.91
110 ( 18
195 ( 22
315 ( 31
446 ( 29
154 ( 21
14 ( 2
n.d.a
n.d.a
273 ( 21
n.d.a
n.d.a
FIGURE 3. Titration of receptor 1 (0.87 μM) with uracil
(0-24.00 μM), monitored using fluorescence spectroscopy at 298 K.
guanosine
20-deoxyuridine
n.d.a
352 ( 97
aNot determined because of the small fluorescence change. Calcu-
b
two species, with π-π stacking interactions between the two
molecules leading to quenching of the fluorescence of 1a. The
apparent binding constant for the complex formed between
the receptor 1a and uracil was 110 ( 18 M-1, determined
from the fluorescence intensities and nonlinear square curve
fitting (Table 1). The binding constant is close to a reported
value of 714 ( 51 M-1 for uracil and the DNA repair enzyme
UDG.29 The binding constant for the complex formed
between the receptor 1a and uracil would be higher if there
were no energetic penalty for breaking the dimers of 1a,
because we estimated the dimerization constant to be 600 (
40 M-1. Nevertheless, the receptor 1a is an effective binding
partner for uracil, as revealed from the NMR and fluores-
cence spectroscopy studies.
lated using the Poisson-Boltzmann continuum-solvation model.
5-fluorouracil, and 5-nitrouracil, determined through fluor-
escence titrations. Thymine was the poorest guest for recep-
tor 1a; 5-nitrouracil was the best. Thus, receptor 1a can
distinguish between uracil and thymine; the apparent bind-
ing constant for uracil was about 1.8-fold greater than that
for thymine (60 M-1).
A plot of the value of log Kb with respect to the value of
pKa of the N(3)H unit of uracil and its derivatives gave a
straight line having a negative slope (β) of -0.24 ( 0.03
(Figure 4). We also plotted the values of pKb of uracil and its
derivatives with respect to the values of pKa of the N(1)H
units (Chart 1), but the plots had a much greater errors and a
smaller absolute negative slope, -0.16 ( 0.05 (Figure S3,
Supporting Information). These findings indicate that only
the N(3)H units of uracil and its derivatives were involved in
significant hydrogen bonding with receptor 1a, providing
Table 1 lists the apparent binding constants for receptor
1a with the uracil derivatives thymine, 5-formyluracil,
(29) Jiang, Y. L.; Cao, C.; Stivers, J. T.; Song, F.; Ichikawa, Y. Bioorg.
Chem. 2004, 32, 244–262.
J. Org. Chem. Vol. 75, No. 2, 2010 329

Jiang et al.
JOCArticle
FIGURE 4. Values of log Kb for the complexes of 1a with uracil
derivatives plotted with respect to the values of pKa of the N(3)H
units of uracil, thymine (Thy), uracil (Ura), 5-formyluracil (5FoU),
5-fluorouracil (5FU), and 5-nitrouracil (5NiU).32
FIGURE 5. Significant quenching of the fluorescence of receptor 1
or 1a (0.87 μM)28 by the DNA nucleoside thymidine (dT, 8 mM) and
small quenching by 20-deoxycytidine (dC, 8 mM) in water at 298 K.
No fluorescence quenching was induced by other DNA nucleosides
(20-deoxyadenosine and 20-deoxyguanosine); for clarity, their spec-
tra are not displayed.
further evidence for the binding mode presented in Scheme 6.
These results are also consistent with the fact that only the
N(3)H unit of uracil is a hydrogen-bonding donor in the
complex with UDG (Scheme 1). Our results also reveal that a
smaller value of pKa for the N(3)H unit of a uracil derivative
will provide a complex with receptor 1a having a greater
apparent binding constant, suggesting acidity-dependent
binding of uracil and its derivatives by the receptor 1a
through the N(3)H group. This result is consistent with
Rich’s earlier observation of uracil derivatives of greater
acidity exhibiting superior binding with 9-ethyladenine.11 It
also suggests that uracil is bound more tightly by the receptor
1a than is thymine because the N(3)H unit of uracil has a
greater value of pKa for than that of thymine.
TABLE 2. Hydrogen-Bonding Distances and Angles in the Complex
Formed between Uracil and the Receptor 1a, Calculated Using the
Spartan’06 Software Package at the RM1 Level33
˚
hydrogen bond
distance (A)
bond angle (deg)
N-Ha OdC
1.754
1.841
1.766
159.5
175.4
163.9
3 3 3
N
H-N
3 3 3
N-Hb OdC
3 3 3
complex formed between uracil with receptor 1a (parts A
and B of Figure 6).33 Table 2 lists the distances and bond
angles for the hydrogen bonds. The hydrogen atoms of the
amide bonds of receptor 1a formed two strong hydrogen
bonds with the carbonyl oxygen atoms of uracil, with
It is possible that a similar phenomenon may explain why
UDG binds uracil more tightly than it binds thymine.1b
A
slight difference between uracil and thymine in the binding
with UDG may contribute to the discrimination of uracil
from thymine by UDG during the early stages of DNA base
flipping.30 Furthermore, the greater efficiency in the hydro-
gen bonding of uracil will eventually facilitate DNA base
flipping by pulling a uracil moiety from a DNA base stack to
the active site of UDG.31
Next, we investigated the molecular recognition of DNA
and RNA nucleosides and 20-deoxyuridine with receptor 1a.
Significant binding occurred between receptor 1a and
20-deoxyuridine, thymidine, and uridine, but there was little
binding with 20-deoxycytidine. The apparent binding con-
stant for thymidine was ca. 11-fold greater than that for
20-deoxycytidine, presumably because 20-deoxycytidine does
not possess the hydrogen bonding donor N(3)H. In addition,
we observed no binding of receptor 1a with the other nucleo-
sides, suggesting that it can selectively recognize thymidine
among the DNA nucleosides and uridine among the RNA
nucleosides (Table 1 and Figure 5).
˚
distances (bond angles) of 1.754 (159.5) and 1.766 A
(163.9°), respectively. The nitrogen atom of the pyridinyl
group of 1a formed a hydrogen bond with the N(3)H unit of
˚
uracil, with a distance of 1.841 A and a bond angle of 175.4°
(Figure 6A). All the bond lengths and angles satisfy the
criteria for strong hydrogen bonding, suggesting that uracil
is bound by receptor 1a tightly.34 Furthermore, the pyrenyl
group is aligned almost parallel to both the pyridinyl group
in receptor 1a and the bound uracil, indicating that the
complex features π-π stacking interactions (Figure 6B).
The vertical distance from the pyrenyl ring to the pyridinyl
˚
ring was ca. 3.78 A. Although the uracil moiety is not
positioned exactly above the pyrenyl ring in Figure 6A, it
eclipses the edge of the pyrenyl group, sitting above the H4
and H5 atoms of the pyrenyl ring (Figure S4, Supporting
Information). Taken together, our results suggest that the
(33) Shao, Y.; Fusti-Molnar, L.; Jung, Y.; Kussmann, J.; Ochsenfeld, C.;
Brown, S. T.; Gilbert, A. T. B.; Slipchenko, L. V.; Levchenko, S. V.; O’Neill,
D. P.; Distasio, R. A., Jr.; Lochan, R. C.; Wang, T.; Beran, G. J. O.; Besley,
N. A.; Herbert, J. M.; Lin, C. Y.; Van Voorhis, T.; Chien, S. H.; Sodt, A.;
Steele, R. P.; Rassolov, V. A.; Maslen, P. E.; Korambath, P. P.; Adamson, R.
D.; Austin, B.; Baker, J.; Byrd, E. F. C.; Daschel, H.; Doerksen, R. J.; Dreuw,
A.; Dunietz, B. D.; Dutoi, A. D.; Furlani, T. R.; Gwaltney, S. R.; Heyden, A.;
Hirata, S.; Hsu, C.-P.; Kedziora, G.; Khalliulin, R. Z.; Klunzinger, P.; Lee,
A. M.; Lee, M. S.; Liang, W.; Lotan, I.; Nair, N.; Peters, B.; Proynov, E. I.;
Pieniazek, P. A.; Rhee, Y. M.; Ritchie, J.; Rosta, E.; Sherrill, C. D.;
Simmonett, A. C.; Subotnik, J. E.; Woodcock, H. L.; Zhang, W.; Bell, A.
T.; Chakraborty, A. K.; Chipman, D. M.; Keil, F. J.; Warshel, A.; Hehre, W.
J.; Schaefer, H. F.; Kong, J.; Krylov, A. I.; Gill, P. M. W.; Head-Gordon, M.
Phys. Chem. Chem. Phys. 2006, 8, 3172–3191.
Binding of Receptor 1a with Uracil and Derivatives Re-
vealed by Structural Calculations. We used Spartan’06 soft-
ware at the RM1 level to calculate the structure of the
(30) Cao, C.; Jiang, Y. L.; Krosky, D. J.; Stivers, J. T. J. Am. Chem. Soc.
2006, 128, 13034–13035.
(31) (a) Parikn, S. S.; Walcher, G.; Jones, G. D.; Slupphaug, G.; Krokan,
H. E.; Blackburn, G. M.; Tainer, J. A. Proc. Natl. Acad. Sci. U.S.A. 2000, 97,
5083–5088. (b) Krosky, D. J.; Song, F.; Stivers, J. T. Biochemistry 2005, 44,
5949–5959.
(32) Jang, Y. H.; Sowers, L. C.; Cagin, T.; Goddard, W. A., III. J. Phys.
Chem. A 2001, 105, 274–280.
(34) Zhao, J.; Khalizov, A.; Zhang, R.; McGraw, R. J. Org. Chem. 2009,
113, 680–689.
330 J. Org. Chem. Vol. 75, No. 2, 2010

Jiang et al.
JOCArticle
FIGURE 6. Two views of the calculated structure of the complex formed between the receptor 1a and uracil. Dotted lines: hydrogen bonding
between 1a and uracil (two chloride ions have been omitted for clarity).
binding of uracil by receptor 1a is stabilized through both
hydrogen bonding and π-π stacking interactions.
relative to other DNA nucleosides (20-deoxycytidine,
20-deoxyadenosine, 20-deoxyguanosine) and uridine relative
to other RNA nucleosides (cytidine, adenosine, guanosine).
We also investigated the binding between the receptor 1a and
uracil through molecular modeling using Spartan’06 at the
RM1 level; we observed effective hydrogen bonding
and π-π stacking interactions between the two molecules.
Receptor 1a is, therefore, an example of a small molecule that
might be able to detect and recognize damaged DNA and
bases, and thereby assist in the better understanding of DNA
repair enzymes.
Conclusions
To determine why UDG binds uracil tightly, but not
thymine, we prepared a novel fluorescent receptor 1a that
structurally mimics the active site of UDG, which cleaves
uracil from DNA strands. Compound 1a features a
2,6-bis(glycylamino)pyridinyl group that mimics the amino
acid residues in UDG that participate in hydrogen bonding;
it also possesses a pyrenyl group, mimicking the phenyl
group that undergoes π-π stacking interactions in the active
site of UDG. The pyrenyl group also mimics the fluorescent
indolyl group of the tryptophan residue in the active site of
UDG; therefore, it undergoes fluorescence quenching during
binding. We obtained 1a in six steps from 4-bromo-
2,6-diaminopyridine. During this synthesis, we employed
two benzyl groups to protect each amino group in 4-bromo-
2,6-diaminopyridine. We suspect that one of the intermedi-
ates in our synthesis, the pyridinylboronic acid 3, might be a
useful compound for the synthesis of biologically active
molecules, such as receptors and drug-like candidates.
We performed a dilution experiment for 1 to investigate its
dimerization. During the dilution experiment, the downfield
shift and the splitting pattern of the signal of the pyridinyl
hydrogens were consistent with dissociation of the dimers
into monomers of receptor 1.
Experimental Section
4-Bromo-N,N,N0,N0-tetrabenzyl-2,6-diaminopyridine (2). A
solution of 4-bromo-2,6-diaminopyridine (1.07 g, 5.69 mmol)
in DMF (5 mL) was added over 15 min to a mixture of NaH
(60% purity, 1.95 g, 44.2 mmol) in DMF (10 mL) in a 50-mL
round-bottom flask cooled to 0 °C in an ice-water bath. Benzyl
bromide (4.0 mL, 5.75 g, 33.6 mmol) was added, and then the
mixture was warmed to room temperature and stirred for an
additional 1.5 h. Water was added, and then the aqueous phase
was extracted with EtOAc. The combined extracts were con-
centrated, and the residue was purified through column chro-
matography [eluent: hexane and then a mixture of CH2Cl2,
EtOAc, and hexane (17:17:66, v/v/v)] to afford compound 2,
which was recrystallized from EtOAc to give a white solid
(1.47 g, 47%): mp 144-146 °C; IR (neat, cm-1) 3029, 2911,
1556, 1494, 1473, 1450, 1360, 1200, 1172, 964, 951, 777, 730, 694;
1H NMR (400 MHz, CDCl3, ppm) δ 4.66 (s, 8 H), 6.04 (s, 2 H),
7.16-7.29 (m, 20 H); 13C NMR (100 MHz, CDCl3, ppm) δ 50.9,
73.9, 96.8, 127.0, 127.2, 128.6, 138.5, 158.1; HR-ESI-TOF calcd
for C33H31BrN3þ (M þ H) 548.170, found 548.170.
1H NMR spectroscopy revealed that π-π stacking inter-
actions occurred between the receptor 1a and uracil in D2O.
The hydrogen bonding network formed between the
2,6-bis(glycylamino)pyridinyl group of 1a and uracil was
revealed in the NMR spectra of the complex formed between
their organic-soluble congeners 7 and 1-butylthymine,
respectively, in CDCl3. We used fluorescence titrations to
determine the apparent binding constants (Kb) of receptor 1a
with uracil and its derivatives (thymine, 5-formyluracil,
5-fluorouracil, 5-nitrouracil) and related nucleosides (uri-
dine, 20-deoxyuridine, thymidine, 20-deoxycytidine). We
found that receptor 1a recognizes uracil with some selectiv-
ity. A plot of the values of logKb of uracil and its derivatives
with respect to the values of pKa of the N(3)H unit of these
uracil derivatives was highly linear, with a slope of -0.24 (
0.03; i.e., the molecular recognition process was dependent
on the acidity of the substrate. This binding study also
revealed that the receptor 1a selectively binds thymidine
4-(10-[80-(100-Pyrenyl)naphthyl)])-N,N,N000,N000-tetrabenzyl-2,6-
diaminopyridine (5). n-BuLi (1.52 mL of 1.6 M in hexane,
2.44 mmol) was added to a solution of 2 (1.20 g, 2.21 mmol) in
anhydrous THF (8 mL) in a 25-mL round-bottom flask that had
been cooled to -78 °C in an dry ice/acetone bath. The reaction
mixture was stirred for 1.5 h at -78 °C before triisopropyl
borate (0.77 mL, 3.33 mmol) was added; the mixture was then
stirred at this temperature for an additional 0.5 h. After the
mixture was warmed to room temperature and stirred for an
additional 1.5 h, saturated aqueous ammonium chloride (8 mL)
was added and the resulting mixture stirred for 2 h. The aqueous
phase was extracted with CH2Cl2, dried (MgSO4), and concen-
trated in vacuo to afford 3 (1.27 g) as a colorless oil, which
turned purple under storage in a refrigerator. This compound
was used without further purification: IR (neat, cm-1) 3391,
2934, 1595, 1541, 1425, 1358, 1240, 1204, 1045, 1028, 970, 729,
J. Org. Chem. Vol. 75, No. 2, 2010 331

Jiang et al.
JOCArticle
694; 1H NMR (400 MHz, CDCl3, ppm) δ 4.58 (s, 8 H), 4.64 (s,
2 H), 7.10-7.18 (m, 20 H); HR-ESI-TOF calcd for C33H33-
BN3O2þ (M þ H) 514.266, found 514.266.
0-5% acetone/CHCl3) to afford a yellow oil, which solidified
after refrigeration (127 mg, 73%): mp 120-122 °C; IR (neat,
cm-1) 3305, 2978, 1690, 1560, 1506, 1417, 1366, 1220, 1166, 848,
776, 731; 1H NMR (400 MHz, CDCl3, ppm) δ 1.48 (s, 9 H), 1.55
(s, 9 H), 3.10 (s, 2 H), 3.95 (ddd, J = 32, 16, 6 Hz, 2 H), 4.49 (s,
1 H), 5.28 (s, 1 H), 6.42 (s, 1 H), 6.87 (s, 1 H), 7.10 (s, 1 H), 7.16 (d,
J = 6.2 Hz, 1 H), 7.42 (d, J = 9.2 Hz, 1 H), 7.49 (t, J = 7.2 Hz, 1
H), 7.64-7.70 (m, 2 H), 7.72 (s, 1 H), 7.78 (t, J = 9.2 Hz, 2 H),
7.90-7.97 (m, 4 H), 8.03-8.11 (m, 4 H); 13C NMR (100 MHz,
CDCl3, ppm) δ 28.5, 28.6, 44.1, 45.1, 80.2, 80.6, 109.6, 111.2,
123.7, 124.3, 124.5, 124.7, 125.1, 125.5, 125.7, 126.2, 127.0,
127.5, 127.6, 129.4, 129.5, 129.9, 130.1, 130.3, 130.7, 131.2,
131.3, 131.4, 134.9, 138.0, 138.5, 146.1, 154.5, 155.7, 156.3,
1-[10-(80-Bromonaphthyl)]pyrene (4, 0.664 g, 1.3 mmol), com-
pound 3 (0.97 g, 1.4 mmol), and 1,2-dimethoxyethane (20 mL)
were added to a three-neck round-bottom flask under a N2
stream. Pd(PPh3)4 (48 mg, 0.042 mmol) was added to the suspe-
nsion, followed by a degassed solution of K2CO3 (0.618 g,
4.48 mmol) in water (2.93 mL). The resulting mixture was heated
under reflux for 13 h under N2. After being cooled to room
temperature, the mixture was extracted with CH2Cl2, and the
combined organic phases were dried (MgSO4). After filtration,
the solvents were evaporated in vacuo, and the residue was
purified through column chromatography (eluent: 0-2%
EtOAc/hexane) to afford 5 as an orange oil, which solidified
after storage in a refrigerator (0.86 g, 83%): mp 102-105 °C; IR
(neat, cm-1) 3038, 2905, 1587, 1571, 1549, 1493, 1467, 1451,
1355, 1200, 1172, 969, 830, 810, 723, 694; 1H NMR (400 MHz,
CDCl3, ppm) δ 3.08 (d, J = 16.4 Hz, 2 H), 3.44 (d, J = 16.4 Hz, 2
H), 4.30 (d, J = 16.4 Hz, 2 H), 4.72 (d, J = 16.4 Hz, 2 H), 4.88 (s,
1 H), 5.58 (s, 1 H), 6.46 (d, J = 6.0 Hz, 4 H), 7.00-7.02 (m, 6 H),
7.12 (d, J = 6.8 Hz, 5 H), 7.23-7.26 (m, 2 H), 7.30-7.34 (m,
4 H), 7.42-7.47 (m, 2 H), 7.53 (d, J = 9.2 Hz, 1 H), 7.60 (t, J =
7.2 Hz, 1 H), 7.67 (d, J = 7.6 Hz, 1 H), 7.82 (d, J = 9.6 Hz, 1 H),
7.91 (d, J = 7.6 Hz, 1 H), 7.94-8.01 (m, 3 H), 8.07-8.12 (m,
3 H), 8.17 (d, J = 7.6 Hz, 1 H); 13C NMR (100 MHz, CDCl3,
ppm) δ 50.0, 50.4, 96.1, 96.3, 123.7, 124.2, 124.6, 124.9, 125.1,
125.16, 125.23, 125.9, 126.0, 126.3, 126.9, 127.1, 127.4, 127.7,
127.9, 128.3, 128.78, 128.85, 128.9, 129.7, 130.0, 130.1, 130.6,
131.1, 131.5, 132.0, 134.9, 138.5, 138.7, 139.0, 139.5, 140.8,
þ
166.4, 167.8; HR-ESI-TOF calcd for C45H44N5O6 (M þ H)
750.329, found 750.329.
4-(10-[80-(100-Pyrenyl)naphthyl])-2,6-diaminopyridine Bis-gly-
camide Bishydrochloride (1a) and Trishydrochloride (1b). A
hydrogen chloride-saturated solution of EtOAc (2 mL) was
added to a solution of 7 (65 mg, 0.087 mmol) in EtOAc
(0.5 mL) in a 25-mL round-bottom flask. After 5 min, the
precipitate was filtered off, washed with EtOAc (2 ꢀ 2 mL),
and dried in vacuo to give a crude product (55 mg), which was
then dissolved in water (0.30 mL) and mixed with THF (5 mL).
The precipitate was filtered off, washed with THF (2 ꢀ 1 mL),
and dried in vacuo. The residual solvent (<1%) was removed by
dissolving the solid in water (0.5 mL) and evaporating the
solvent in a spin-vac system to afford 1 as a light-yellow solid
(35 mg, 64%): mp >260 °C; IR (neat, cm-1) 2861, 1652, 1595,
1558, 1456, 1198, 855, 833, 773, 725, 684; 1H NMR (400 MHz,
D2O, ppm) δ 2.91 (d, J = 16.4 Hz, 1 H), 3.20 (d, J = 16.8 Hz,
1 H), 3.94 (d, J = 16.4 Hz, 1 H), 4.02 (d, J = 16.4 Hz, 1 H), 6.38
(s, 2 H), 7.02 (d, J = 9.2 Hz, 1 H), 7.11 (d, J = 7.2 Hz, 1 H), 7.51
(t, J = 7.6 Hz, 1 H), 7.61 (d, J = 9.2 Hz, 1 H), 7.65-7.75 (m,
2 H), 7.78 (d, J = 7.6 Hz, 1 H), 7.93-7.99 (m, 3 H), 8.03-8.10
(m, 4 H), 8.21 (d, J = 7.2 Hz, 1 H); 13C NMR (100 MHz, D2O,
ppm) δ 40.8, 41.5, 107.8, 110.1, 122.8, 123.5, 124.9, 125.2, 125.6,
126.3, 126.9, 127.3, 128.1, 128.3, 128.7, 129.2, 130.2, 130.4, 130.6,
131.0, 133.8, 136.5, 137.0, 141.0, 141.7, 157.3, 165.4, 166.7; HR-
þ
152.6, 155.79, 155.84; HR-ESI-TOF calcd for C59H46N3
(M þ H) 796.369, found 796.369.
4-(10-[80-(100-Pyrenyl)naphthyl])-2,6-diaminopyridine (6).
TfOH (0.67 mL, 7.58 mmol) was added dropwise to a mixture
of 5 (0.212 g, 0.277 mmol) and pyrene (1.00 g) in anhydrous
CH2Cl2 (7 mL) in a 25-mL round-bottom flask, and then the
resulting mixture was heated under reflux (oil bath) for 6 h.
After the mixture had cooled to room temperature, it was
poured slowly onto saturated NaHCO3 (80 mL) with constant
stirring, causing a color change from green to deep red. The
aqueous phase was extracted with CH2Cl2, the combined or-
ganic phases were concentrated, and the residue was purified
through flash column chromatography (eluents: hexane, 50%
EtOAc/hexane, EtOAc, and then 0-2.5% MeOH/EtOAc). The
fractions containing compound 6 were combined and concen-
trated; the residue was subjected again to column chromatog-
raphy (eluents: CHCl3 and then 10-50% acetone/CHCl3) to
afford 6 as a deep-red oil (73 mg, 67%): IR (neat, cm-1) 3468,
3383, 3184, 3040, 1612, 1554, 1432, 1398, 1244, 1178, 907, 847,
828, 775, 723; 1H NMR (400 MHz, CDCl3, ppm) δ 2.28 (s, 2 H),
3.81 (s, 2 H), 4.75 (s, 1 H), 5.19 (s, 1 H), 7.15 (d, J = 6.8 Hz, 1 H),
7.50 (t, J = 8.0 Hz, 1 H), 7.59 (d, J = 9.2 Hz, 1 H), 7.62-7.70 (m,
3 H), 7.85 (d, J = 9.2 Hz, 1 H), 7.94-8.08 (m, 7 H), 8.15 (d, J =
7.6 Hz, 1 H); 13C NMR (100 MHz, CDCl3, ppm) δ 100.3, 100.8,
123.6, 124.3, 124.5, 124.9, 125.1, 125.2, 125.3, 125.9, 126.2, 126.8,
127.3, 127.6, 128.6, 129.1, 129.3, 129.4, 129.6, 130.5, 130.7, 130.8,
131.4, 131.6, 135.1, 138.4, 139.2, 153.6, 154.8, 155.0; HR-ESI-
TOF calcd for C31H22N3þ (M þ H) 436.181, found 436.181.
4-(10-[80-(100-Pyrenyl)naphthyl])-2,6-diaminopyridine Bis(Boc-
glycamide) (7). A 25-mL round-bottom flask was charged
sequentially with 6 (0.095 g, 0.232 mmol), anhydrous THF
(2.5 mL), Et3N (0.224 mL, 1.62 mmol), N-Boc-Gly-OH
(0.123 g, 0.703 mmol), and HATU (0.263 g, 0.692 mmol), and
then the mixture was heated under reflux for 4 h. After the
mixture was concentrated in vacuo, the residue was purified
through flash column chromatography (SiO2; 0-50% EtOAc/
hexane). The fractions containing 7 were concentrated and the
residue subjected again to column chromatography (SiO2;
þ
ESI-TOF calcd for C35H28N5O2 (M þ H) 550.224, found
550.223; C35H27N5O2Naþ (M þ Na) 572.206, found 572.204.
Anal. Calcd for C35H37.5Cl2.5N5O6 [M(HCl)2.5(H2O)4]: C, 58.97;
H, 5.30; Cl, 12.43. Found: C, 58.68; H, 4.91; Cl, 12.67.
NMR Spectroscopic Dilution Experiment. Solutions of 1 were
prepared in D2O at concentrations of 9.0, 4.5, 2.2, 1.1, 0.55, and
0.28 mM. The 1H NMR spectra of these samples were then
recorded at room temperature.
Fluorescence Titration. Fluorescence spectra were recorded
using a spectrofluorometer [general settings: increment, 1;
integration, 0.3; slit widths, 3 (excitation) and 3 (emission);
equilibration time, 2 min]. All fluorescence spectra were
recorded at 298 K; the temperature was maintained using a
circulating water bath. The 4-mL quartz cuvette contained
solutions at a final volume of 2 mL. The excitation wavelength
was 350 nm. During the titrations and measurements of appar-
ent binding constants, a solution of 1 (0.87 μM) was prepared
first and then increasing amounts of the binding substrates were
added to the solution using gastight syringes. The intensities of
the fluorescence titration curves at 472 nm were analyzed using a
one-site binding model equation and curve fitting software to
evaluate the apparent binding constants.35
Acknowledgment. This study was supported by the
Office of Research and Sponsored Programs (RD09010,
(35) (a) Palde, P. B.; Gareiss, P. C.; Miller, B. L. J. Am. Chem. Soc. 2008,
130, 9566–9573. (b) Ojida, A.; Takashima, I.; Kohira, T.; Nonaka, H.;
Hamachi, I. J. Am. Chem. Soc. 2008, 130, 12095–12101. (c) Butterfield, S.
M.; Goodman, C. M.; Rotello, V. M.; Waters, M. L. Angew. Chem., Int. Ed.
2004, 43, 724–727.
332 J. Org. Chem. Vol. 75, No. 2, 2010

Jiang et al.
JOCArticle
E82016, RS0026) and SFRA Grants (for A.P., A.J., and
Y.L.J.) from the Honors College at East Tennessee
State University. This study is also supported by the
grants from the National Natural Science Foundation of
China (Nos. 20771021, 20371030, and 20335030), and
Shandong Natural Science Foundation (Nos.Y2005B20)
for X.G.
Supporting Information Available: Improved synthesis
of compound 4; Job plots and a plot of logKb values with
respect to the values of pKa of the N(1)H units for uracil,
1
thymine, 5-formyluracil, 5-fluorouracil, and 5-nitrouracil; H
and 13C NMR spectra of compounds 1, 2, and 5-7. This
material is available free of charge via the Internet at http://
pubs.acs.org.
J. Org. Chem. Vol. 75, No. 2, 2010 333