Design, synthesis, and structural analysis of D, L -mixed polypyrrolinones. 1. from nonpeptide peptidomimetics to nanotubes

Article abstract of DOI:10.1021/ol101007n

To expand the potential conformational space available to the polypyrroline structural motif, an open chain, d,l-alternating hexapyrrolinone was designed and synthesized. Structural studies, including solution NMR and X-ray crystallographic analysis, revealed that the hexapyrrolinone adopts a turn conformation both in solution and in the solid state, with aggregation in solution and a nanotube-like quaternary structure in the crystal.

Full text of DOI:10.1021/ol101007n

ORGANIC
LETTERS
2010
Vol. 12, No. 13
2990-2993
Design, Synthesis, and Structural Analysis
of D,L-Mixed Polypyrrolinones. 1. From
Nonpeptide Peptidomimetics to Nanotubes
Amos B. Smith, III,* Wenyong Wang, Adam K. Charnley, Patrick J. Carroll, Craig
S. Kenesky, and Ralph Hirschmann*,‡
Department of Chemistry, UniVersity of PennsylVania, Philadelphia, PennsylVania 19104
smithab@sas.upenn.edu
Received May 2, 2010
ABSTRACT
To expand the potential conformational space available to the polypyrroline structural motif, an open chain, D,L-alternating hexapyrrolinone was
designed and synthesized. Structural studies, including solution NMR and X-ray crystallographic analysis, revealed that the hexapyrrolinone adopts
a turn conformation both in solution and in the solid state, with aggregation in solution and a nanotube-like quaternary structure in the crystal.
A major achievement in the field of nonpeptide peptidomi-
metics would comprise the design and synthesis of biologi-
cally relevant mimics, capable of adopting conformations
similar to the three principal secondary structures accessible
to peptides and proteins (e.g., ꢀ-turns, ꢀ-strands, or R-heli-
ces), with conformational control manifested simply via
structural modification of the side-chains and/or the stereo-
genicity of the constituent monomers. To date, only a limited
number of conformationally versatile nonpeptide peptido-
mimetics have been reported.1
structures of peptides and proteins.2,3 As such, the polypyr-
rolinones constituted early examples of foldamers as defined
by Gellman4,1a,b and elegantly demonstrated for ꢀ-peptides
by both Seebach5,1c and Gellman.4b,1a,b Pleasingly, initial
studies demonstrated that homochiral polypyrrolinones (e.g.,
all D),6 such as (-)-1, can adopt extended parallel (1a, Figure
1) or antiparallel (1b) ꢀ-strand/ꢀ-sheet mimics, depending
on the presence or absence of a Boc C-terminus.2,3,7 This
observation led to the design and synthesis of a series of
potent pyrrolinone-based enzyme inhibitors,8 requiring the
In 1992, the Hirschmann-Smith collaboration reported
the design and synthesis of a new class of peptidomimetics
based on the pyrrolinone scaffold (Figure 1).2 Computational
studies suggested that oligomers based on this repeating
vinylogous amide motif held the promise of adopting
structures similar, but not identical, to the three secondary
(2) Smith, A. B., III; Keenan, T. P.; Holcomb, R. C.; Sprengler, P. A.;
Guzman, M. C.; Wood, J. L.; Carrol, P. J.; Hirschmann, R. J. Am. Chem.
Soc. 1992, 114, 10672
.
(3) (a) Smith, A. B., III; Guzman, M. C.; Sprengler, P. A.; Keenan,
T. P.; Holcomb, R. C.; Wood, J. L.; Carrol, P. J.; Hirschmann, R. J. Am.
Chem. Soc. 1994, 116, 9947. (b) Smith, A. B., III; Favor, D. A.; Sprengler,
P. A.; Guzman, M. C.; Carrol, P. J.; Furst, G. T.; Hirschmann, R. Bioorg.
Med. Chem. 1999, 7, 9. (c) Smith, A. B., III; Wang, W.; Sprengler, P. A.;
Hirschmann, R. J. Am. Chem. Soc. 2000, 122, 11037
.
‡ May 6, 1922-June 20, 2009.
(4) (a) Dado, G. P.; Gellman, S. H. J. Am. Chem. Soc. 1994, 116, 1054.
(b) Appella, D. H.; Christianson, L. A.; Karle, I. L.; Powell, D. R.; Gellman,
S. H. J. Am. Chem. Soc. 1996, 118, 13071. See also ref 1.
(5) (a) Seebach, D.; Overhand, M.; Ku¨hnle, F. N. M.; Marinoni, B.;
Oberer, L.; Hommel, U.; Widmer, H. HelV. Chim. Acta 1996, 79, 913. (b)
Seebach, D.; Ciceri, P. E.; Overhand, M.; Jaun, B.; Rigo, D.; Oberer, L.;
Hommel, U.; Amstutz, R.; Widmer, H. HelV. Chim. Acta 1996, 79, 2043.
(c) Seebach, D.; Matthews, J. L. Chem. Commun. 1997, 2015. See also ref
1.
(1) (a) Gellman, S. H. Acc. Chem. Res. 1998, 31, 173. (b) Horne, S. W.;
Gellman, S. H. Acc. Chem. Res. 2008, 41, 1399. (c) Seebach, D.; Hook,
D. F.; Glattli, A. Biopolymers (Pept. Sci.) 2006, 84, 23. (d) Stigers, K. D.;
Soth, M. J.; Nowick, J. S. Curr. Opin. Chem. Biol. 1999, 3, 714. (e) Hill,
D. J.; Mio, M. J.; Prince, R. B.; Hughes, T. S.; Moore, J. S. Chem. ReV.
2001, 101, 3893. (f) Foldamers: Structure, Properties and Applications;
Hecht, S., Huc, I., Eds.; Wiley-VCH Verlag GmbH & Co. KGaA:
Weinheim, Germany, 2007. (g) Angelo, N. G.; Arora, P. S. J. Am. Chem.
Soc. 2005, 127, 17134. (h) Goodman, C. M.; Choi, S.; Shandler, S.;
DeGrado, W. F. Nat. Chem. Biol. 2007, 3, 252, and references cited therein.
(6) While D,L descriptors are not directly applicable to the pyrrolinone
units, their use simplifies comparison with peptidal structures.
10.1021/ol101007n  2010 American Chemical Society
Published on Web 06/02/2010

Ghadiri,16 and Ciufolini17 laboratories, demonstrating that
peptides embodying alternating D- and L-amino acids can
adopt turn conformations, and in some cases assemble into
nanotubes, suggested that a sequence of alternating D,L-linked
pyrrolinones might also preferentially adopt a turn structure.
That this scenario proved correct was demonstrated by the
synthesis of the alternating D,L-tetra-pyrrolinone (-)-2,
shown by NMR studies, in conjunction with molecular
modeling, to adopt a low-energy turn conformation in
solution.3c Importantly, control over the conformation of
(-)-2 was achieved by alternating the building block
configuration along the sequence. An equally important issue
concerned the biological relevance of such polypyrrolinone
turn mimics. Toward this end, we designed and synthesized
several mimics [cf. (-)-3] of the neuropeptide hormone
somatostatin-14 (SRIF), known to incorporate a ꢀ-turn as
the pharmacophore structural element.18 Importantly, a
heterochiral tetrapyrrolinone proved to be a functional mimic
of SRIF.19
Having achieved both bioactive ꢀ-strand and ꢀ-turn
mimics with designed polypyrrolinones, we turned to larger
congeners, with an eye toward the possibility of helix
mimics.3b We first selected alternating D,L-hexapyrrolinone
(-)-4 (Figure 1) and carried out a 10 000-step Monte Carlo
conformational search20 employing the MMFFS force field.21
The calculations rendered a set of low energy conformations,
typified by a turn motif with four intramolecular hydrogen
bonds among neighboring residues and one hydrogen bond
spanning the cleft between the terminal residues (Figure 2a).
The computationally predicted ability of the pyrrolinone-
derived turn to draw the termini of the hexapyrrolinone
oligomer close together confirmed our interest in 4 as a
Figure 1. Designed ꢀ-strand/ꢀ-sheet trispyrrolinones (-)-1a,b; ꢀ-turn
tetrapyrrolinones (-)-2 and (-)-3; and hexapyrrolinone (-)-4.
ꢀ-strand/ꢀ-sheet motif, including metalloproteases,9 and
orally bioavailable HIV-1 protease inhibitors,10 as well as a
peptide-pyrrolinone hybrid ligand for the class II MHC
protein HLA-DR1.11
With these initial achievements, a central theme of the
pyrrolinone-based peptidomimetic program became the
expansion, by design, of the diverse conformational space
accessible to the polypyrrolinone structural motif for peptide/
protein mimicry. We recognized that the ability to control
the various possible conformations, via simple modulation
of the side-chain structure and/or R-stereogenicity, would
significantly enhance the opportunities for the polypyrroli-
none construct in biologically relevant mimics.
(13) (a) Karle, I. L.; Handa, B. K.; Hassall, C. H. Acta Crystallogr.
1975, B31, 555. (b) Chiang, C. C.; Karle, I. L. Int. J. Pept. Protein Res.
1982, 20, 133.
(14) De Santis, P.; Morosetti, S.; Rizzo, R. Macromolecules 1974, 7,
52.
(15) (a) Tomasic, L.; Lorenzi, G. P. HelV. Chim. Acta 1987, 70, 1012.
(b) Pavone, V.; Benedetti, E.; Di Blasio, B.; Lombardi, A.; Pedone, C.;
Tomasich, L.; Lorenzi, G. P. Biopolymers 1989, 28, 215. (c) Saviano, M.;
Zaccaro, L.; Lombardi, A.; Pedone, C.; Di Blasio, B.; Sun, X.; Lorenzi,
G. P. J. Inclusion Phenom. 1994, 18, 27. (d) Sun, X.; Lorenzi, G. P. HelV.
Chim. Acta 1994, 77, 1520.
The well-recognized principle that D-amino acids stabilize
ꢀ-turns,12 in conjunction with the pioneering reports by
Karle13 and De Santis,14 later extended by the Lorenzi,15
(16) (a) Ghadiri, M. R.; Granja, J. R.; Milligan, R. A.; McRee, D. E.;
Khazanovich, N. Nature 1993, 366, 324. (b) Ghadiri, M. R.; Kobayashi,
K.; Granja, J. R.; Chadha, R. K.; McRee, D. E. Angew. Chem., Int. Ed.
Engl. 1995, 34, 93. (c) Hartgerink, J. D.; Granja, J. R.; Milligan, R. A.;
Ghadiri, M. R. J. Am. Chem. Soc. 1996, 118, 43. (d) Clark, T. D.; Buriak,
J. M.; Kobayashi, K.; Isler, M. P.; McRee, D. E.; Ghadiri, M. R. J. Am.
Chem. Soc. 1998, 120, 8949.
(7) (a) Smith, A. B., III; Holcomb, R. C.; Guzman, M. C.; Keenan, T. P.;
Sprengeler, P. A.; Hirschmann, R. Tetrahedron Lett. 1993, 34, 63. Guzman,
M. C. Ph.D. Thesis, University of Pennsylvania, 1995.
(17) Xi, N.; Alemany, L. B.; Ciufolini, M. A. J. Am. Chem. Soc. 1998,
120, 80.
(8) Smith, A. B., III; Akaishi, R.; Jones, D. R.; Keenan, T. P.; Guzman,
M. C.; Holcomb, R. C.; Sprengeler, P. A.; Wood, J.; Hirschmann, R.;
Holloway, M. K. Biopolymers (Pept. Sci.) 1995, 37, 29.
(18) (a) Nutt, R. F.; Colton, C. D.; Saperstein, R.; Veber, D. F.
Somatostatin; Reichlin, S., Ed.; Plenum: New York, NY, 1987; p 83. (b)
Veber, D. F. Peptides-Chemistry and Biology: Proceedings of the 12th
American Peptide Symposium; Smith, J. A., Rivier, J. E., Eds.; ESCOM:
Leiden, 1992; p 3.
(9) Smith, A. B., III; Nittoli, T.; Sprengeler, P. A.; Duan, J. W.; Liu,
R.-Q.; Hirschmann, R. Org. Lett. 2000, 2, 3809.
(10) (a) Smith, A. B., III; Cantin, L.-D.; Pasternak, A.; Guise-Zawacki,
L.; Yao, W. Q.; Charnley, A. K.; Barbosa, J.; Sprengeler, P. A.; Hirschmann,
R.; Munshi, S.; Olsen, D. B.; Schleif, W. A.; Kuo, L. C. J. Med. Chem.
2003, 46, 1831, and references cited therein. (b) Smith, A. B., III; Charnley,
A. K.; Harada, H.; Beiger, J. J.; Cantin, L.-D.; Kenesky, C. S.; Hirschmann,
R.; Munshi, S.; Olsen, D. B.; Stahlhut, M. W.; Schleif, W. A.; Kuo, L. C.
Bioorg. Med. Chem. Lett. 2006, 16, 859.
(19) Smith, A. B., III; Charnley, A. K.; Mesaros, E. F.; Kikuchi, O.;
Wang, W.; Benowitz, A.; Chu, C.-L.; Feng, J.-J.; Chen, K.-H.; Lin, A.;
Cheng, F.-C.; Taylor, L.; Hirschmann, R. Org. Lett. 2005, 7, 399.
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111, 4379.
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T. A. J. Comput. Chem. 1996, 17, 520. (c) Halgren, T. A. J. Comput. Chem.
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synthetic target. To access 4, we turned to our iterative
pyrrolinone synthetic protocol, beginning with aldehyde
(-)-5 (Figure 2c) and building the pyrrolinone chain in the
C to N direction (see Supporting Information). Yields for
the two-step iterative sequences were in general good.
To establish the solution conformation of (-)-4, a series
of ROESY NMR experiments in CDCl3 [1 mM in (-)-4],
similar to those exploited with (-)-2,3c were conducted. Ten
critical long-range NOEs were observed (Figure 2d). The
ROE NMR data were then employed as a constraint file in
a 10 000-step Monte Carlo conformational search; the result
revealed (-)-4 to exist in solution in a flat, G-shaped turn
conformation similar to that previously reported for (-)-2
(Figure 2b).3c
Crystallization of (-)-4 from CHCl3 via vapor-phase
equilibration with hexane furnished single crystals (mp
195-197 °C) suitable for X-ray analysis.22 Pleasingly, the
derived ORTEP diagram (Figure 3a) reveals a flat G-shaped
structure similar to the low energy conformation observed
in solution. Importantly, overlay of the solution structure with
the crystal structure provided excellent atom-to-atom cor-
respondence (Figure 3b; root-mean-square value of 0.508
Å). Of equal importance, the unit cell structure possesses
four (-)-4 monomers that self-assemble into a nanotube-
like quaternary structure (Figure 3c-e), with the monomers
arrayed in an antiparallel fashion.
A crystallographic 3-fold rotation axis, parallel to the c
axis, passes through the center of the best molecular plane.
The tubular structure is best revealed by removing the
internal and external side-chains (Figure 3e). In this way,
the intermolecular hydrogen bonds, which stabilize the
molecular assembly, are more clearly visible. To ascertain
the possibility of self-assembly of (-)-4 in solution, we
Figure 2. (a) Computational model of (-)-4 in CHCl3 arising from a
10 000-step Monte Carlo conformational search. (b) The solution
structure of the alternating D,L-hexapyrrolinone (-)-4. (c) Synthesis
of hexapyrrolinone (-)-4. (d) Ten critical long-range NOEs, color
coded by their interactions with the prenyl side chain.
Figure 3. (a) ORTEP diagram of the D,L-mixed hexapyrrolinone (-)-4. (b) Overlay of the crystal structure (blue) and the solution structure (red)
of (-)-4. (c) and (d) Stereoviews illustrating the nanotube-like assembly of (-)-4 in the crystal packing diagram, side view and top view, respectively,
with intermolecular hydrogen bonding illustrated. (e) Stereoview with side-chains removed to highlight the nanotube-like assembly.
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1
performed a variable concentration H NMR analysis to
[NH(1-5)], which resonate in the hydrogen bonded N-H
region (ca. δ 6.95-8.00 ppm), displayed modest shifts
(0.06-0.41 ppm, 3.5 × 10-3 M to 2.6 × 10-2 M) consistent
with self-assembly.
Taken together, these results suggest that the lowest
concentration at which intermolecular hydrogen bonding
occurs is ca. 10-3 M.
In summary, the design, synthesis, and structural analysis
of an alternating D,L-hexapyrrolinone (-)-4 has been achieved.
Structural analysis, involving solution NMR studies and
X-ray crystallography, reveals that (-)-4 adopts a turn
conformation both in solution and in the solid state, with
aggregation occurring in solution and nanotube-like structures
in the solid state. Further extension of the D,L-alternating
pyrrolinone motif holds the promise of additional novel
chemical and structural properties (e.g., helices). Studies to
this end continue in our Laboratory.
define the lowest concentration at which intermolecular
interactions occur (Figure 4). A significant change in the
proton resonance at δ 5.50 ppm (1 × 10-4 M), highly
indicative of solvent exposure, was observed with increasing
concentration (ca. 1 × 10-4 M to 3 × 10-2 M). We therefore
assigned this resonance to the N-terminal pyrrolinone
N-H(6), the only pyrrolinone N-H that cannot form an
intramolecular hydrogen bond with the carbonyl oxygen of
an adjacent pyrrolinone. The internal pyrrolinone N-Hs
Acknowledgment. Support was provided by the NIH
through Grant AI-42010. Additional support was provided
by Graduate Fellowships from Bristol-Myers Squibb and the
University of Pennsylvania to A.K.C. We thank Dr. G. Furst
at University of Pennsylvania for assistance obtaining and
analyzing the 2D NMR spectra. We also thank Samuel H.
Gellman, the Ralph Hirschmann Professor of Chemistry at
the University of Wisconsin, for insightful discussion.
Supporting Information Available: Experimental pro-
cedures and spectroscopic data for all new compounds. This
material is available free of charge via the Internet at
http://pubs.acs.org.
Figure 4. Concentration dependence of the N-H chemical shifts
in CDCl3 for the D,L-mixed hexapyrrolinone (-)-4. N-Terminal
N-H(6) (O). Internal N-Hs (NH(1-5) (∆)029)).
OL101007N
(22) For crystallographic data of hexapyrrolinone (-)-4, see Supporting
Information.
Org. Lett., Vol. 12, No. 13, 2010
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