Trisubstituted (E)-alkene dipeptide isosteres as β-turn promoters in the gramicidin S cyclodecapeptide scaffold

Article abstract of DOI:10.1021/ol0617704

(Chemical Equation Presented) A concise synthesis of a gramicidin S analogue with trisubstituted (E)-alkene dipeptide isostere (TEADI) replacements at both D-Phe-Pro positions was realized. Conformational analysis demonstrated that TEADIs can serve as typ

Full text of DOI:10.1021/ol0617704

ORGANIC
LETTERS
2006
Vol. 8, No. 21
4731-4734
Trisubstituted (E)-Alkene Dipeptide
Isosteres as -Turn Promoters in the
â
Gramicidin S Cyclodecapeptide Scaffold
Jingbo Xiao,† Bernard Weisblum,‡ and Peter Wipf*,†
Department of Chemistry and Center for Chemical Methodologies & Library
DeVelopment, UniVersity of Pittsburgh, Pittsburgh, PennsylVania 15260, and
Pharmacology Department, UniVersity of Wisconsin Medical School,
1300 UniVersity AVenue, Madison, Wisconsin 53706
pwipf+@pitt.edu
Received July 18, 2006
ABSTRACT
A concise synthesis of a gramicidin S analogue with trisubstituted (E)-alkene dipeptide isostere (TEADI) replacements at both
D-Phe-Pro
positions was realized. Conformational analysis demonstrated that TEADIs can serve as type II
successfully mimic a proline residue.
â-turn promoters in a cyclic scaffold and
Peptides demonstrate a wide range of diverse physiological
properties as hormones, enzyme inhibitors, growth promoters,
signaling pathway modulators, antimicrobial agents, etc.1 To
overcome the limited bioavailability of peptides,2 we are
studying the synthesis and pharmacological evaluation of
bioisosteric replacements of the amide bond.3 The relatively
rigid trisubstituted (E)-alkene dipeptide isosteres (ψ[(E)-
C(R)dCH], R * H, TEADIs) maintain ω-angle planarity
and represent useful structural surrogates of hydrolytically
labile amide bonds.4 In addition, TEADIs were found to have
potential as â-turn promoters in acyclic sequences in our
previous studies.5 In a continuation of this work, we have
now started to introduce these building blocks into biologi-
cally active cyclic peptide sequences as surrogates of the
powerful turn-inducing D-Phe-Pro sequence6 and evaluate
their potential as â-turn promoters and modulators of
biological and metabolic properties.7
Since its discovery in 1942,8 the cyclodecapeptide anti-
biotic gramicidin S (GS, cyclo-[(Val-Orn-Leu-D-Phe-Pro)2])
(3) (a) Wipf, P.; Fritch, P. C. J. Org. Chem. 1994, 59, 4875. (b)
Henninger, T.; Wipf, P. In Methods in Molecular Biology: Peptidomimetics;
Walker, J. M., Kazmierski, W. M., Eds.; Humana Press: Totowa, 1999;
Vol. 23, pp 125-136. (c) Mu, Y.; Stephenson, C. R. J.; Kendall, C.; Saini,
S. P. S.; Toma, D.; Ren, S.; Cai, H.; Strom, S. C.; Day, B. W.; Wipf, P.;
Xie, W. Mol. Pharmacol. 2005, 68, 403. (d) Wipf, P.; Werner, S.; Woo, G.
H. C.; Stephenson, C. R. J.; Walczak, M. A. A.; Coleman, C. M.; Twining,
L. A. Tetrahedron 2005, 61, 11488. (e) Levinson, N.; Hinman, R.; Patil,
A.; Stephenson, C. R. J.; Werner, S.; Woo, G. H. C.; Xiao, J.; Wipf, P.;
Lynch, K. W. RNA 2006, 12, 925. (f) Wipf, P.; Xiao, J.; Jiang, J.; Belikova,
N. A.; Tyurin, V. A.; Fink, M. P.; Kagan, V. E. J. Am. Chem. Soc. 2005,
127, 12460.
(4) (a) Tamamura, H.; Koh, Y.; Ueda, S.; Sasaki, Y.; Yamasaki, T.; Aoki,
M.; Maeda, K.; Watai, Y.; Arikuni, H.; Otaka, A.; Mitsuya, H.; Fujii, N. J.
Med. Chem. 2003, 46, 1764. (b) Yang, H.; Sheng, X. C.; Harrington, E.
M.; Ackermann, K.; Garcia, A. M.; Lewis, M. D. J. Org. Chem. 1999, 64,
242. (c) Oishi, S.; Miyamoto, K.; Niida, A.; Yamamoto, M.; Ajito, K.;
Tamamura, H.; Otaka, A.; Kuroda, Y.; Asai, A.; Fujii, N. Tetrahedron 2006,
62, 1416.
† University of Pittsburgh.
‡ University of Wisconsin Medical School.
(1) (a) Kazmierski, W. M.; Kenakin, T. P.; Gudmundsson, K. S. Chem.
Biol. Drug Des. 2006, 67, 13. (b) Clark, R. J.; Fischer, H.; Dempster, L.;
Daly, N. L.; Rosengren, K. J.; Nevin, S. T.; Meunier, F. A.; Adams, D. J.;
Craik, D. J. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 13767. (c) Ladner, R. C.;
Sato, A. K.; Gorzelany, J.; De Souza, M. Drug Discuss. Today 2004, 9, 525.
(2) Conradi, R. A.; Hilgers, A. R.; Ho, N. F. H.; Burton, P. S. Pharm.
Res. 1992, 9, 435.
(5) (a) Wipf, P.; Henninger, T. C.; Geib, S. J. J. Org. Chem. 1998, 63,
6088. (b) Wipf, P.; Henninger, T. C. J. Org. Chem. 1997, 62, 1586.
10.1021/ol0617704 CCC: $33.50
© 2006 American Chemical Society
Published on Web 09/21/2006

has served as an inspiration for the design of antibacterial
agents and antimicrobial peptides and as a model system for
conformational mimicry.9 GS is therefore a particularly
significant target for the evaluation of alkene peptide isosteres
as surrogates for the type II′ â-turn inducing sequence.
The D-Phe-Pro reverse turn is a critical feature of the rigid
amphipathic antiparallel â-pleated sheet conformation of
GS.10,11 In earlier work,7 we were able to replace the Leu-
D-Phe peptide bond in GS with a ψ[(E)-C(CF3)dCH] isostere
with minimal perturbation of the secondary structure and
biological activity, whereas the corresponding ψ[(E)-C(CH3)d
CH] isostere failed to maintain the â-pleated sheet conforma-
tion according to CD and NMR analyses. A different
situation presents itself when the D-Phe-Pro peptide bond is
replaced. Because the D-Phe carbonyl group is not involved
in intramolecular H-bonding or dipolar interactions, a ψ-
[(E)-C(CH3)dCH] surrogate should be as effective as a
trifluoromethylated congener in conformationally preorga-
nizing the chain. The restricted backbone rotation imposed
by the A1,3-strain across the trisubstituted alkene and, to a
lesser extent, by the A1,2-strain experienced by substituents
attached to the alkene should be sufficient for both methyl
and trifluoromethyl groups to impose the reverse turn.
Furthermore, neither alkene isostere provides an NH hydro-
gen bond donor group that can lead to the stabilization of
γ-turns or other competitive backbone folding patterns that
would interfere with the desired â-turn motif. These proper-
ties lead, theoretically, to a close match of isostere and D-Phe-
Pro features (Figure 1).5b We now report an experimental
confirmation of this hypothesis.
Scheme 1. Synthesis of
Boc-D-Phe-ψ[(E)-C(CH3)dCH]-Pro-Val-OMe
reaction (Scheme 1).13 Using our hydrozirconation/ZrwZn
transmetalation methodology,14,15 the alkenylzinc species
derived from the chiral internal alkyne 213b was added to 3,
affording the allylic amide 4 in 64% yield as a ∼1:1 mixture
of diastereomers. Deprotection of the TBDPS group with
TBAF provided the primary alcohol 5. The two diastereomers
could not be separated after conversion of 5 to the corre-
sponding acetates;3f,7 however, a two-step oxidation with
Dess-Martin periodinane,16,17 followed by coupling with
valine methyl ester, provided pseudotripeptides 6 and 7 which
were separated by preparative C18 RP HPLC.18
Saponification of pseudotripeptide 7 followed by fragment
coupling with dipeptide H-Orn(Cbz)-Leu-OMe in the pres-
ence of EDC as a coupling reagent afforded the pseudopen-
tapeptide 8 in 96% yield over two steps. We initially
envisioned a one-pot dimerization-cyclization of 8; however,
this approach resulted exclusively in the formation of
cyclized pseudopentapeptide. In contrast, the stepwise cou-
pling proceeded smoothly to give the pseudodecapeptide 9
in excellent yield. Saponification of 9 and stepwise removal
of the Boc protecting group followed by macrolactamization
afforded the desired bis-Cbz-protected GS analogue 10 in
50% yield after preparative C18 RP HPLC purification
(Scheme 2).
The chemical shifts of all amide protons in 10 were
assigned using a combination of COSY, NOESY, HMQC,
(10) (a) Yamada, K.; Unno, M.; Kobayashi, K.; Oku, H.; Yamamura,
H.; Araki, S.; Matsumoto, H.; Katakai, R.; Kawai, M. J. Am. Chem. Soc.
2002, 124, 12684. (b) Doi, M.; Fujita, S.; Katsuya, Y.; Sasaki, M.;
Taniguchi, T.; Hasegawa, H. Arch. Biochem. Biophys. 2001, 395, 85.
(11) (a) Kondejewski, L. H.; Farmer, S. W.; Wishart, D. S.; Hancock,
R. E. W.; Hodges, R. S. Int. J. Pept. Protein Res. 1996, 47, 460. (b)
Kondejewski, L. H.; Farmer, S. W.; Wishart, D.; Kay, C. M.; Hancock, R.
E. W.; Hodges, R. S. J. Biol. Chem. 1996, 271, 25261.
(12) Coˆte´, A.; Boezio, A. A.; Charette, A. B. Proc. Natl. Acad. Sci. U.S.A.
2004, 101, 5405.
Figure 1. GS and its analogue with ψ[(E)-C(CH3)dCH] peptide
bond surrogates.
Because of the lability of phenylacetaldimines, the sulfinyl
adduct 312 was employed in the organometallic allylation
(13) (a) Wipf, P.; Xiao, J.; Geib, S. J. AdV. Synth. Catal. 2005, 347,
(6) Wadhwani, P.; Afonin, S.; Ieronimo, M.; Buerck, J.; Ulrich, A. S. J.
Org. Chem. 2006, 71, 55.
(7) Xiao, J.; Weisblum, B.; Wipf, P. J. Am. Chem. Soc. 2005, 127, 5742.
(8) Gauze, G. F.; Brazhnikova, M. G. Am. ReV. SoViet Med. 1944, 2,
134.
(9) See: Grotenbreg, G. M.; Buizert, A. E. M.; Llamas-Saiz, A. L.;
Spalburg, E.; Van Hooft, P. A. V.; De Neeling, A. J.; Noort, D.; Van Raaij,
M. J.; Van Der Marel, G. A.; Overkleeft, H. S.; Overhand, M. J. Am. Chem.
Soc. 2006, 128, 7559, and references therein.
1605. (b) Wipf, P.; Xiao, J. Org. Lett. 2005, 7, 103.
(14) (a) Wipf, P.; Jahn, H. Tetrahedron 1996, 52, 12853. (b) Wipf, P.;
Kendall, C. Top. Organomet. Chem. 2004, 8, 1.
(15) (a) Wipf, P.; Kendall, C.; Stephenson, C. R. J. J. Am. Chem. Soc.
2001, 123, 5122. (b) Wipf, P.; Kendall, C.; Stephenson, C. R. J. J. Am.
Chem. Soc. 2003, 125, 761.
(16) Dess, D. B.; Martin, J. C. J. Org. Chem. 1983, 48, 4155.
(17) Wipf, P.; Kim, Y.; Goldstein, D. M. J. Am. Chem. Soc. 1995, 117,
11106.
4732
Org. Lett., Vol. 8, No. 21, 2006

coefficients of -1.9 and -1.8 ppb/K, respectively, whereas
Orn-NH and D-Phe-NH were solvent exposed, thus indicating
a hydrogen bonding array typical for an antiparallel â-pleated
sheet conformation.19 Furthermore, NOESY spectra showed
transannular Leu-NH-Val-NH and Val-NH-D-Phe-HR con-
tacts for 10 in agreement with that found for Cbz2GS (Figure
2). The resulting ten-membered intramolecular H-bonding
Scheme 2. Fragment Condensation and Synthesis of
Pseudo-cyclodecapeptide 10
Figure 2. Observed NOEs for 10 and Cbz2GS.
interaction between the valine amide NH and the carbonyl
group of the leucine residue is typical for a type II′ â-turn.20
Further confirmation of the close match between the
secondary structures of 10 and Cbz2GS was provided by
circular dichroism (CD) spectra in EtOH (Figure 3). The
and HMBC data sets collected in DMSO-d6 at 338 K because
some amide H NMR signals were obscured at 298 K.
Variable-temperature NMR was applied to probe the con-
formation of 10 in solution and determine the level of
intramolecular hydrogen bonding (Table 1). Temperature
1
Table 1. Temperature Shift Coefficients (∆δ/∆T) of Amide
Protons in DMSO-d6 (ppb/K) for 10 and Cbz2GS
Orn-NH Leu-NH Orn-δ-NH Val-NH D-Phe-NH
10
Cbz2GS
-4.8
-6.7
-1.9
-3.8
-6.3
-8.6
-1.8
-2.2
-5.9
-11.8
shift coefficients for 10 were in close agreement with the
values for bis-Cbz-protected GS (Cbz2GS).7 The NH shifts
of Leu and Val residues in 10 showed small temperature
(18) The structural assignment of 6 and 7 was based on the ozonolysis
product 12, which was identical to the methylation product obtained from
Boc-D-Phe-OH (11) by chiral HPLC coinjection (Pace, R. D.; Kabalka, G.
W. J. Org. Chem. 1995, 60, 4838).
Figure 3. CD spectra of 10 and Cbz2GS in EtOH.
strong negative band at ∼205-225 nm and a shoulder in
the region of 225-235 nm for both 10 and Cbz2GS are
consistent with a combination of a type II′ â-turn and a
Org. Lett., Vol. 8, No. 21, 2006
4733

â-sheet conformation in these compounds.21 This result,
along with the data from NOESY and variable-temperature
NMR experiments, further confirmed that the methyl (E)-
alkene dipeptide isostere replacements at the former D-Phe-
Pro positions strongly promoted the archetypical architecture
of the parent peptide, gramicidin S. An MMFF-minimized
structure for 1 that is in agreement with all experimental
data is shown in Figure 4.22
Scheme 3. Synthesis of the Hydrochloride Salt of [CH3]2GS
(1‚2HCl)
formational properties of this amino acid residue.23 We have
now demonstrated that a trisubstituted (E)-alkene dipeptide
isostere can serve as a bioisosteric replacement for the D-Phe-
Pro type II′ â-turn in the cyclopeptide antibiotic gramicidin
S. The solution conformational analysis and the biological
assay of analogues 10 and 1, respectively, provide strong
validation of our design principles. Furthermore, the hy-
drozirconation/ZrwZn transmetalation/imine addition meth-
odology was key to a rapid synthetic access to the target
compounds.
Figure 4. Stereoview of the minimized structure of 1 derived from
an MMFF conformational search algorithm.
Our previous biological studies showed that free amine
functions on the ornithine side chains were necessary to retain
the antibacterial, antifungal, and hemolytic activities of GS.7
The Cbz protecting groups in 10 were successfully removed
by hydrogenolysis in the presence of 10% Pd/C in a 0.02 M
HCl/MeOH solution, without concomitant reduction of the
trisubstituted (E)-alkene moieties (Scheme 3). As expected,
the hydrochloride salt of 1 also exhibited functional mimicry
of the natural product, with an MIC of ∼20 µg/mL against
Bacillus subtilis, and thus was equipotent with GS hydro-
chloride (MIC ∼15 µg/mL in the same assay).
Acknowledgment. This work was supported by the NIH/
NIGMS P50 program (GM067082). J.X. gratefully acknowl-
edges an Andrew W. Mellon Predoctoral Fellowship for
support and Dr. Corey R. J. Stephenson (ETHZ) for helpful
discussions.
Supporting Information Available: Experimental pro-
1
cedures and spectral data, including copies of H and 13C
The development of proline mimics is of considerable
current interest due to the helix-breaking and unique con-
NMR spectra for all new compounds, and 2D NMR spectra
of 10 and Cbz2GS. This material is available free of charge
via the Internet at http://pubs.acs.org.
(19) (a) Wipf, P.; Fritch, P. C.; Geib, S. J.; Sefler, A. M. J. Am. Chem.
Soc. 1998, 120, 4105. (b) Imperiali, B.; Fisher, S. L.; Moats, R. A.; Prins,
T. J. J. Am. Chem. Soc. 1992, 114, 3182. (c) Kessler, H. Angew. Chem.,
Int. Ed. 1982, 21, 512.
OL0617704
(20) Ball, J. B.; Hughes, R. A.; Alewood, P. F.; Andrews, P. R.
Tetrahedron 1993, 49, 3467.
(23) (a) Jenkins, C. L.; Vasbinder, M. M.; Miller, S. J.; Raines, R. T.
Org. Lett. 2005, 7, 2619. (b) Cordero, F. M.; Pisaneschi, F.; Batista, K.
M.; Valenza, S.; Machetti, F.; Brandi, A. J. Org. Chem. 2005, 70, 856. (c)
Wang, X. J.; Hart, S. A.; Xu, B.; Mason, M. D.; Goodell, J. R.; Etzkorn,
F. A. J. Org. Chem. 2003, 68, 2343. (d) Halab, L.; Lubell, W. D. J. Am.
Chem. Soc. 2002, 124, 2474. (e) Otaka, A.; Katagiri, F.; Kinoshita, T.;
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Berova, N., Woody, R. W., Eds.; VCH: New York, 1994; Chapter 17, pp
473-496.
(22) A 4300-step conformational equilibrium search was performed
with: Spartan 04; Wavefunction, Inc.: Irvine, CA.
4734
Org. Lett., Vol. 8, No. 21, 2006