Unusually strong binding of a designed transition-state analog to a base-excision DNA repair protein

Full text of DOI:10.1021/ja970828u

J. Am. Chem. Soc. 1997, 119, 7865-7866
Unusually Strong Binding of a Designed
7865
Transition-State Analog to a Base-Excision DNA
Repair Protein
Li Deng, Orlando D. Scha¨rer, and Gregory L. Verdine*
Department of Chemistry and Chemical Biology
HarVard UniVersity, Cambridge, Massachusetts 02138
Figure 1. (A) Structural analogy between the proposed transition state
for glycosidic bond cleavage catalyzed by base-excision DNA repair
protein and inhibitors 1 and 2; and (B) sequence of the double-stranded
25-mer (ds 25-mer) containing a single/centrally located phA/OG pair.
Asterick indicates 5′-32P-label.
ReceiVed March 14, 1997
DNA repair enzymes are responsible for maintaining the
integrity of heritable genetic information. One class of such
proteins, base-excision DNA repair (BER) enzymes, recognizes
and removes from DNA aberrant bases that have arisen through
the attack of exogenous or endogenous agents or through errors
in replication.1 Left unrepaired, these lesions have profound
effects on cell viability and proliferation.2 A major challenge
is to identify how BER enzymes recognize their substrates,
which often differ only subtly from their normal counterparts.3
However, efforts along these lines have been hampered by the
fleeting nature of the association between repair enzymes and
their DNA substrates. In principle, this problem could be solved
by structural alteration of either the enzyme or the substrate, so
as to stall the normal reaction process and thereby generate a
long-lived protein-DNA complex. Indeed, mutant versions of
bacteriophage T4 endonuclease V and the human uracil DNA
glycosylases have been found to bind tightly to DNA containing
thymine dimer4 and uracil, respectively.5 X-ray crystallographic
analyses of these complexes have yielded the first glimpses into
the origin of substrate specificity of BER enzymes. We and
others6-8 have pursued an alternate approach based on the
modification of the DNA substrate. We have focused our
attention on members of a recently identified superfamily of
BER enzymes, for which no cocrystal structures are yet
available.9 Our strategy for the design of altered DNA substrates
that are capable of being recognized but not repaired centers
on two distinct concepts, either mimicry7 or electronic desta-
bilization of the transition state8,9 for the glycosyl transfer
reaction leading to base excision (Figure 1).10 Of particular
relevance to the present study is the finding that pyrrolidine 1,
a transition-state mimic, binds with exceedingly high affinity
and specificity to a variety of BER enzymes.7 However, because
1 lacks a base moiety, it is unsuitable for studies aimed at
elucidating the specific interactions between the substrate base
and the enzyme active site. Here we report the design and
synthesis of a new class of pyrrolidine-based inhibitors contain-
ing an attached base. Biochemical analysis of one such inhibitor
reveals that it binds a DNA glycosylase with a dissociation
constant below 1 picomolar.
We reasoned that appropriate attachment of a DNA base to
the pyrrolidine ring in 1 should lead to inhibitors possessing
even stronger binding affinity and greater specificity than 1
itself. Attaching the base directly to the 1′-carbon in 1 would
be expected to generate an unstable linkage,11 thus ruling out
this option. To ensure appropriate stability, we inserted a
-CH2- unit between the C-1′ and the base, thus generating
the pyrrolidine homonucleoside containing inhibitor 2. Al-
though this formal insertion of a -CH2- unit into the glysosidic
bond lengthens the separation between the base and the
pyrrolidine ring relative to that in the substrate, this bond is
likewise elongated in the transition state.10,11 Inhibitors designed
along similar lines have been shown to be effective agents for
glycosylases that act on monomeric nucleoside and simple
carbohydrate substrates.12 As a test system for these concepts,
we decided to examine the ability of an adenine pyrrolidine
homonucleoside in DNA (phA, 2a) to inhibit the adenine DNA
glycosylase MutY.13 One component of a repair pathway
specific for oxidatively damaged DNA,14 MutY recognizes A
inappropriately paired to the lesion 8-oxoguanine (OG), and
selectively cleaves the A residue.
The synthesis of inhibitor 2a (Scheme 1) began with D-serine
(3), which was converted in four steps and 60% overall yield
to aldehyde 4.15 Allylboration of aldehyde 4 using a chiral
boron reagent proceeded with excellent diastereoselectivity (94%
de) to yield 5.16 Cleavage of the Boc-protected oxazolidine ring
followed by TBS protection yielded 6. Reaction of 6 with
mCPBA in methylene chloride gave the corresponding epoxide
as a mixture of diastereomers (5:1) favoring the desired
stereoisomer. Acid-catalyzed intramolecular cyclization of
epoxide 7 led to the formation of the key intermediate 8.
Attachment of the 6-chloropurine base to the pyrrolidine scaffold
proceeded most effectively under Mitsunobu conditions17 to
afford the fully protected pyrrolidine homonucleoside 9. Rou-
tine protecting group manipulations furnished cyclic diol 10.
Tritylation of the primary alcohol followed by phosphitylation
* To whom correspondence should be addressed.
(1) Lindahl, T. Nature 1993, 362, 709-715.
(2) Friedlberg, E. C.; Walker, G. C.; Siede, W. (1995). DNA Repair and
Mutagenesis; ASM Press: Washington, DC, 1995.
(3) Brunner, S. D.; Verdine, G. L. Chem. Biol. 1997, 4, 329-334.
(4) Vassylyev D. G.; Kashiwagi, T.; Mikami, Y.; Ariyoshi, M.; Iwai S.;
Ohtsuka, E.; Morikawa, K. Cell 1995, 83, 773-782.
(10) Horenstein, B. A.; Schramm, V. L. Biochemistry 1993, 32, 7089-
7097. Horenstein, B. A.; Schramm, V. L. Biochemistry 1993, 32, 9917-
9925. Horenstein, B. A.; Zabinski, R. F.; Schramm, V. L. Tetrahedron Lett.
1993, 34, 7213-7216.
(11) Altmann, K. H. Tetrahedron. Lett. 1993, 34, 7721-7724
(12) Liu, P. S. J. Org. Chem. 1987, 52, 4717-4721. Wong, C-H.;
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R.; Steensma, D. H. J. Org. Chem. 1995, 60, 1492-1501.
(13) Michaels, M. L.; Pham, L.; Nghiem, Y.; Cruz, C.; Miller, J. H.
Nucleic Acid Res. 1990, 18, 3841-3845.
(5) Slupphaug, G.; Mol, C. D.; Kavli, B.; Arvai, A. S.; Krokan, H. E.;
Tainer, J. A. Nature 1996, 80, 87-92.
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10782. Scha¨rer, O. D.; Kawate, T.; Gallinari, P.; Jiriciny, J.; Verdine, G.
L. Proc. Natl. Acad. Sci. U.S.A., in press.
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J.-J.; Cillo, J. J. Biol. Chem. 1995, 270, 23582-23588. Varaprasad, C. V.;
Bulychev, N. Y.; Dorman, G.; Miller, J. H.; Eisenberg, M.; Grollman, A.
P.; Johmson, F. Biochemistry 1996, 35, 13147-13156.
(9) Nash, H. M.; Bruner, S. D.; Scha¨rer, O. D.; Kawate, T.; Addona, T.
A.; Spooner,E.; Lane, W. S.; Verdine, G. L. Curr. Biol. 1996, 6, 1230-
1233. Labahn, J.; Scha¨rer, O. D.; Long, A.; Ezaz-Nikpay, K.; Verdine, G.
L.; Ellenberger, T. E. Cell 1996, 86, 321-329.
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Genet. 1993, 9, 246-249. Tajiri T.; Maki, H.; Sekiguchi, M. Mutat. Res.
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A. P.; Miller, J. H. Biochemistry 1992, 31, 10964-10968.
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S0002-7863(97)00828-7 CCC: $14.00 © 1997 American Chemical Society

7866 J. Am. Chem. Soc., Vol. 119, No. 33, 1997
Communications to the Editor
Scheme 1a
Reagents and conditions: a) allylB(lpc)2, Et2O; b) TsOH, MeOH, 52% 2 steps; c) TBSCl, DMF; d) mCPBA, CH2Cl2; e) AcOH; f) 6-chloropurine,
DEAD, THF, 34% 4 steps; g) TBAF, THF; h) TFA, CH2Cl2; i) FmocCl, CH2Cl2/MeOH, 56% 3 steps; j) DMTrCl, DMAP, Et3N, CH2Cl2; k)
iPr2NP(Cl)OC2H4CN, iPr2NEt, CH2Cl2, 48% 2 steps; l) solid phase DNA synthesis; m) NH3 55 °C.
Figure 2. (A, left) EMSA assay to detect binding of 2a to MutY. 32P-labeled oligonucleotide concentration (single- plus double-stranded forms)
) 3.0 pM. MutY concentrations are as indicated. (B, right) Competition EMSA assay to determine the specificity of 2a to MutY: concentration
of 32P-labeled ds 25-mer, 0.2 nM; concentration of MutY, (lane 1) no protein, (lanes 2-4), 1.0 nM; concentration of unlabeled ds-25mer in lane
3, 20 nM; concentration of unlabeled non specific competitor in lane 4, 20 nM.
of the secondary alcohol provided the phosphoramidite 11.
Using phosphoramidite 11, we synthesized a 25-mer oligo-
nucleotide containing a centrally modified phA unit (5′-GGA
TAG TGT CCA phA GTT ACT CGA AGC-3′). Deprotection
of the oligonucleotide and concomitant conversion of the
6-chloropurine into adenine were accomplished by incubation
of the oligonucleotide with aqueous ammonia at 55 °C for 12
h.18 The phA-containing 25-mer was 5′-32P-end labeled and
annealed to a complementary 25-mer having one OG residue,
thereby generating a duplex 25-mer containing a singly, centrally
located phA/OG pair (ds 25-mer, Figure 1B).
The binding affinity of MutY for the ds 25-mer containing
phA/OG was investigated with the use of the electrophoretic
mobility shift assay (EMSA).19 This assay detects the difference
in electrophoretic mobility of the free ds 25-mer and the
MutY‚ds 25mer complex (Figure 2A). With the ds 25-mer
present at a concentration of less than 3 pM, addition of 1 equiv
of MutY resulted in virtually complete formation of the ds 25-
mer‚MutY complex (Figure 2A), thus indicating that the Kd for
the protein-DNA interaction is well below 3 pM, and certainly
below 1 pM.20 By contrast, the Kd of MutY for the congener
of the ds 25-mer bearing the simple pyrrolidine 1 in place of
2a was determined to be 65 ( 11 pM. Thus, the binding of
MutY is stimulated at least ∼50-fold by the presence of the
-CH2-adenine unit in 2a. A high degree of specificity for
the inhibitor in this binding interaction was inferred on the basis
of competition assays (Figure 2B), in which a 100-fold excess
of nonradioactive counterpart of the ds 25-mer completely out-
competed complex formation with the radiolabeled ds 25-mer
(lane 3), whereas a 100-fold excess of nonspecific DNA had
no effect (lane 4). In competition cleavage assays (data not
shown), we determined that the addition of an equivalent amount
of phA/OG-containing DNA inhibited, by greater than 50%,
MutY-catalyzed cleavage of a native A/OG substrate, even when
the enzyme was present in 50-fold excess over substrate.
Here we have reported a new class of mechanism-based
inhibitors that bind with unprecedented strength (Kd < 1 pM)
to a base-excision DNA repair protein, MutY.21 We expect
variants of 2a, having a different base moiety, will bind
specifically to other BER enzymes, especially those belonging
to a recently identified superfamily of DNA glycosylases.9 This
new class of pyrrolidine homonucleosides should thus prove
valuable in structural studies aimed at elucidating the molecular
basis of DNA damage recognition and repair.
Acknowledgment. We thank Professor Stephen Lloyd for providing
the MutY protein and H. M. Nash and S. D. Bruner for discussions.
This work was supported by NIH (GM51330). L.D. is an American
Cancer Society postdoctoral fellow (PF-4229).
Supporting Information Available: General methods and analyses
for the compounds discussed in this communication (11 pages). See
any current masthead page for ordering and Internet access instructions.
JA970828U
(20) Under conditions in which [DNA] , Kd, the concentration of protein
that affords 50% formation of a protein-DNA complex is approximately
equal to Kd. As 1 equiv of MutY is sufficient to drive formation of a ds
25mer‚MutY complex essentially to completion in Figure 2A, we conclude
that the binding observed under these conditions is controlled by stoichi-
ometry rather than Kd. This necessarily means that the DNA concentration
in Figure 2A (3 pM) is will above Kd, hence Kd can safely be assumed to
be less than 1 pM. Attempts to determine the Kd more precisely have been
frustrated by the tendency of DNA to favor the single-stranded state at
very low concentrations, and by the vanishingly small amounts of radioactive
counts present under conditions in which binding is Kd controlled.
(21) Other known MutY inhibitors containing a base moiety bind the
enzyme no more tightly than 0.2 nM.7
(17) Mitsunobu, O. Synthesis 1981, 1-54. Iwakawa, M.; Pinto, B. M.;
Szarek, W. A. Can. J. Chem. 1978, 56, 326-335.
(18) Additional details are provided in the Supporting Information.
(19) Fried, M. G.; Crothers, D. M. J. Mol. Biol. 1984, 172, 263-282.