Peptide Quinoline Conjugates: A New Class of RNA-Binding Molecules

Article abstract of DOI:10.1021/ol036094+

(Equation presented) A synthesis of 4,8-disubstituted 2-phenylquinoline amino acids is reported with the incorporation of one example into a peptide by solid-phase synthesis. The phenylquinoline-containing peptide binds an RNA target with nanomolar affini

Full text of DOI:10.1021/ol036094+

ORGANIC
LETTERS
2004
Vol. 6, No. 1
63-66
Peptide Quinoline Conjugates: A New
Class of RNA-Binding Molecules
Malathy Krishnamurthy, Barry D. Gooch, and Peter A. Beal*
Department of Chemistry, UniVersity of Utah, Salt Lake City, Utah 84112-0850
beal@chemistry.utah.edu
Received October 27, 2003
ABSTRACT
A synthesis of 4,8-disubstituted 2-phenylquinoline amino acids is reported with the incorporation of one example into a peptide by solid-
phase synthesis. The phenylquinoline-containing peptide binds an RNA target with nanomolar affinity (KD ) 208 nM). The strategy can be
used to prepare a variety of 2-substituted quinoline amino acids for alteration of affinity in intercalator peptides. Since quinolones represent
an important class of antibacterials, these compounds may be useful in the discovery of new antibacterial agents.
The appreciation of RNA as a target for new antibiotic drugs
has increased interest in the development of low molecular
weight compounds that bind RNA selectively.1-5 Early
studies indicate the major challenge in developing small
molecule ligands for RNA is making them specific for a
given RNA target.6,7 Compounds that bind an RNA structure
and make contacts at several sites using a variety of binding
modes (e.g., π-stacking, H-bonding, van der Waals contacts,
charge-charge interactions, etc.) will likely be the most
selective, since other RNAs will not have the requisite
arrangement of complementary functional groups. A par-
ticularly attractive binding mechanism that allows for
multiple points of contact between ligand and RNA is
threading intercalation.8-11 Threading intercalation involves
insertion of an intercalator between base pairs of a nucleic
acid duplex and localization of distinguishable substituents
on the heterocycle in opposite grooves of the helix. We have
reported a solid-phase synthesis approach to threading
intercalator peptides with an acridine chromophore intro-
duced into the peptide backbone such that the N- and
C-termini lie in opposite grooves in an intercalation com-
plex.12 This design allows the groove-localized substituents
to be varied via combinatorial peptide synthesis.
Importantly, for selective binding to be achieved, the
relative contribution to the binding affinity of functional
groups in the ligand must be balanced to prevent nonspecific
binding to imperfectly matched sites. In the case of threading
intercalators, if the affinity of the intercalating group is too
large relative to other groups in the ligand, additional nucleic
acids with accessible π-stacking surfaces may also be bound
with similar affinities. Thus, controlling the binding affinity
of the intercalating group will become increasingly important
as threading intercalators are developed for selective RNA
binding. In this Letter, we describe a new threading inter-
(1) Gallego, J.; Varani, G. Acc. Chem. Res. 2001, 34, 836-843.
(2) Hermann, T.; Westhof, E. Curr. Opin. Biotechnol. 1998, 9, 66-73.
(3) Pearson, N. D.; Prescott, C. D. Chem. Biol. 1997, 4, 409-414.
(4) Wilson, W. D.; Li, K. Curr. Med. Chem. 2000, 7, 73-98.
(5) Xavier, K. A.; Eder, P. S.; Giordano, T. TIBTECH 2000, 18, 349-
356.
(6) Carlson, C. B.; Spanggord, R. J.; Beal, P. A. ChemBioChem 2002,
3, 859-865.
(7) Luedtke, N. W.; Liu, Q.; Tor, Y. Biochemistry 2003, 42, 11391-
(10) Jourdan, M.; Garcia, J.; Lhomme, J. Biochemistry 1999, 38, 14205-
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11403.
(8) Caceres-Cortes, J.; Sugiyama, H.; Ikudome, K.; Saito, I.; Wang, A.
H.-J. Biochemistry 1997, 36, 9995-10005.
(9) Guelev, V.; Lee, J.; Ward, J.; Sorey, S.; Hoffman, D. W.; Iverson,
B. L. Chem. Biol. 2001, 8, 415-425.
(11) Liaw, Y.-C.; Gao, Y.-G.; Robinson, H.; van der Marel, G. A.; van
Boom, J. H.; Wang, A. H.-J. Biochemistry 1989, 28, 9913-9918.
(12) Carlson, C. B.; Beal, P. A. Bioorg. Med. Chem. Lett. 2000, 10,
1979-1982.
10.1021/ol036094+ CCC: $27.50 © 2004 American Chemical Society
Published on Web 12/09/2003

calator design: the peptide quinoline conjugate (PQC). A
solid-phase synthesis scheme is reported for the preparation
of 2-phenylquinolines with peptide substituents at the 4- and
8-positions. Furthermore, the ability of the intercalator to
π-stack can be readily modulated by altering the polarity of
the π-aromatic system through substitution of the 2-phenyl
group. The RNA binding properties of a prototypical PQC
are also evaluated.
Scheme 1a
To generate quinoline-based threading intercalator pep-
tides, we prepared compounds 1 and 2, each with an Alloc-
protected 4-aminobenzylamine appendage at the quinoline
4-position and a carboxyl group at the 8-position (Figure
1). A phenyl group is present at position 2, since 2-phenyl-
a (a) (i) CH3SO3H/benzene reflux, (ii) Ph2O/255 °C; (b) PPh3/
NBS/CH3CN reflux; (c) allyl 4-aminobenzyl-amino carbamate12/
CH3CN reflux; (d) LiOH‚H2O/THF-H2O rt.
Figure 1. Amino acids synthesized for incorporation into peptide
quinoline conjugates via SPPS.
weakly nucleophilic aniline derivatives.18 Indeed, compound
4 is readily converted to 4-anilino derivative 5 in acetonitrile
at reflux in excellent yield. Saponification of the methyl ester
gave N-Alloc-protected amino acid 1 ready for activation
and coupling in SPPS. This same strategy can be extended
to prepare quinoline amino acids with a substituted phenyl
group of varying π-system polarity, as indicated by the
synthesis of nitro compound 2 (Scheme 1). The synthesis of
2 was initiated by condensation of ethyl(4-nitrobenzoyl)-
acetate and methylanthranilate followed by cyclization to
give quinolone 6. Bromination to 7, substitution with Alloc-
protected amine to give 8, and saponification produced 2-(4-
nitrophenyl)quinoline amino acid 2.
To demonstrate that these 2-phenylquinoline amino acids
can be used in SPPS, the peptide sequence N-Abu-Ser-Val-
PheQ-Arg-C was prepared, where Abu is aminobutyric acid
and PheQ refers to the 4,8-disubstituted 2-phenylquinoline
amino acid. Amino acid 1 was activated as the N-hydroxy-
succinimide (NHS) ester and coupled to the solid-supported
primary amino group of Pbf-protected arginine. The Alloc
group was removed using Pd(PPh3)4/PhSiH3 in CH2Cl2 at
room temperature for 30 min to reveal the benzylamine for
subsequent elaboration by peptide synthesis.19 The additional
amino acid residues were introduced via standard protocols.
Upon completion of the solid-phase synthesis, the peptide
was released and the side chains were deprotected by
treatment of the resin with TFA/TIS/PhOH/H2O (88:5:5:2)
to give peptide 9 (Figure 2). The structure of 9 was confirmed
by fast atom bombardment and electrospray ionization mass
spectrometry.
quinolines are known intercalators. Furthermore, the π-stack-
ing ability of the 2-phenyl group present in compound 2 is
modulated by the polarizing nitro substituent. In analogy to
the acridine-containing amino acid previously described by
us, these compounds are likely to be compatible with solid-
phase peptide synthesis (SPPS) with Fmoc-protected amino
acids.12,13 2-Phenyl-4-aminoquinoline derivatives and 2-
phenylquinoline-8-carboxamides have been shown to bind
nucleic acids by intercalation.14,15 However, there are no prior
reports of 2-phenylquinolines simultaneously modified at
positions 4 and 8 in this manner. This substitution pattern
creates molecules with substituents on opposite edges of the
quinoline heterocycle and, thus, potential threading interca-
lators.
Our synthesis of 1 begins with 8-methoxycarbonyl-2-
phenyl-4(1H)-quinolone 3, which is prepared as described
by Denny via condensation of methyl anthranilate and
ethylbenzoyl acetate followed by thermal cyclization of the
condensation product (Scheme 1).16 Bromination of 3 by
treatment with triphenylphosphine and N-bromosuccinimide
in acetonitrile gave 4 in good yield.17 Given our recent
experience with simple substitution reactions involving
acetyl-protected bromopurine ribonucleosides, we anticipated
that bromoquinoline 4 would react selectively at the 4-posi-
tion under mild conditions with nitrogen nucleophiles, even
(13) Carlson, C. B.; Beal, P. A. Org. Lett. 2000, 2, 1465-1468.
(14) Zhou, M.; Janda, L.; Nguyen, J.; Strekowski, L.; Wilson, W. D.
Biopolymers 1994, 34, 61-73.
The threading peptide N-Abu-Ser-Val-Acr-Arg-C (10),
where Acr is a 4,9-disubstituted acridine amino acid, binds
(15) Denny, W. A.; Atwell, G. J.; Baguley, B. C. Anti-Cancer Drug Des.
1987, 2, 263-270.
(16) Atwell, G. J.; Baguley, B. C.; Denny, W. A. J. Med. Chem. 1989,
32, 396-401.
(18) Ve´liz, E. A.; Beal, P. A. J. Org. Chem. 2001, 66, 8592-8598.
(19) Thieriet, N.; Alsina, J.; Giralt, E.; Guibe´, F.; Albericio, F.
Tetrahedron Lett. 1997, 38, 7275-7278.
(17) Sugimoto, O.; Mori, M.; Tanji, K.-i. Tetrahedron Lett. 1999, 40,
7477-7478.
64
Org. Lett., Vol. 6, No. 1, 2004

Figure 2. (a) Quantitative ribonuclease V1 footprinting with AbuSVPheQR (9) and an in vitro selected RNA. Shown is a partial storage
phosphor autoradiogram of a 10.5% denaturing polyacrylamide gel separating 5′-32P-labeled RNA cleavage products. First three lanes,
from left to right: Alone, RNA in buffer only; OH, alkaline hydrolysis; T1, RNase T1. The remaining lanes contain increasing concentrations
of 9 (from left to right, 0, 0.001, 0.01, 0.1, 1, 10, 50 µM) in the presence of RNase V1. The footprinted region (C42-A46) is bracketed,
as well as the constant V1-dependent nucleotide (U54) used to normalize for differential loading of the gel. (b) Secondary structure of
nucleotides C22-G56 of the RNA aptamer as predicted by mfold.20,21 The binding site for 9 is indicated. (c) Plot of fraction bound versus
concentration of 9 (red) and 1022 (blue) as determined by RNase V1 footprinting.
preferentially to base-paired 5′-CpG-3′ sites in RNA flanked
by non-Watson-Crick structural elements (Figure 2).22 We
determined the extent to which 9 bound to an in vitro selected
RNA containing such a site using ribonuclease V1 footprint-
ing (Figure 2a). Peptide 9 bound this stem-loop structure to
give a footprint similar to that observed with 10, indicating
peptides 9 and 10 bind the same site on this RNA.22
Quinoline peptide 9 binds with a KD ) 208 nM, whereas
acridine peptide 10 bound with a KD ) 20 nM (Figure 2c).
Interestingly, this difference in affinity is similar to that
observed for a 2-phenylquinoline substitution for acridine
in a known DNA intercalator.15 Thus, the decreased binding
affinity of peptide 9 compared to that of 10 likely arises from
a decrease in efficacy of intercalation.
In summary, the synthesis of 2-phenylquinoline amino
acids compatible with SPPS with Fmoc-protected amino
acids has been accomplished. A peptide prepared with a
2-phenylquinoline amino acid binds an RNA stem-loop
structure at the same site as the corresponding acridine-based
threading peptide with an approximately 10-fold lower
affinity. The strategy developed is applicable to the prepara-
tion of a variety of 2-substituted quinoline amino acids for
systematic alteration of intercalator affinity in threading
intercalator peptides. Since quinolones represent an important
class of antibacterials, these compounds (conjugates and/or
libraries) may also be useful in the discovery of new
antibacterial agents.
(20) Mathews, D. H.; Sabrina, J.; Zuker, M.; Turner, D. H. J. Mol. Biol.
1999, 288, 911-940.
(21) Zuker, M.; Mathews, D. H.; Turner, D. H. Algorithms and
Thermodynamics for RNA Secondary Structure Prediction: A Practical
Guide in RNA Biochemistry and Biotechnology; Kluwer Academic Publish-
ers: Dordrecht, 1999.
Acknowledgment. P.A.B. acknowledges support from the
NIH (AI-49062) and a Camille Dreyfus Teacher Scholar
(22) Carlson, C. B.; Vuyisich, M.; Gooch, B. D.; Beal, P. A. Chem. Biol.
2003, 10, 663-672.
Org. Lett., Vol. 6, No. 1, 2004
65

Award. B.D.G. was supported by a National Institutes of
Health training grant (GM-08573).
of 9 and its biochemical analysis, including RNA syn-
thesis and labeling and ribonuclease footprining. This ma-
terial is available free of charge via the Internet at
http://pubs.acs.org.
Supporting Information Available: Experimental pro-
cedures and NMR and mass spectral data for compounds
listed in Scheme 1 and general procedure for the synthesis
OL036094+
66
Org. Lett., Vol. 6, No. 1, 2004