Design, synthesis, and solution structure of a pyrrolinone-based β-turn peptidomimetic [17]

Full text of DOI:10.1021/ja002964w

J. Am. Chem. Soc. 2000, 122, 11037-11038
11037
that D,L-alternating (i.e., heterochiral) polypyrrolinones might also
preferentially adopt a turn conformation. Indeed, a Monte Carlo
conformational search performed on the simple D,L,D,L-tetrapyr-
rolinone 1 indicated that the low-energy conformations do in fact
adopt a â-turn conformation (Figure 1).
Design, Synthesis, and Solution Structure of a
Pyrrolinone-Based â-Turn Peptidomimetic
Amos B. Smith, III,* Wenyong Wang,
Paul A. Sprengeler, and Ralph Hirschmann*
Department of Chemistry
UniVersity of PennsylVania
Philadelphia, PennsylVania 19104
ReceiVed August 9, 2000
The design and synthesis of privileged nonpeptide scaffolds1
that can adopt the three principal secondary structures analogous
to peptides and proteins constitutes a significant advance in
molecular mimicry. Such scaffolds hold considerable promise for
the development of selective, low-molecular weight nonpeptide
ligands for biomedically important receptors. Ideally, conforma-
tional control of the privileged nonpeptide scaffold would be
effected via simple structural modifications of the individual
monomers. To date, however, most designed scaffolds can adopt
only a single conformation;2 exceptions include the Schreiber
vinylogous amides,3 the Hamilton oligoanthranilamides4 and the
â-peptides of Gellman5 and Seebach.6
Having established the 3,5-linked (nitrogen displaced) homo-
chiral polypyrrolinone motif as an excellent â-sheet/â-strand
peptidomimetic both in the solid state7a,b and in solution,7c
including the design and synthesis of a potent, orally bioavailable
HIV-1 protease inhibitor7d and a competent ligand for the class
II MHC protein HLA-DR1,7e we sought to extend the diversity
of conformational space available to the polypyrrolinone structure
motif. The observation of Ghadiri et al.8,9 that alternating D- and
L-cyclic peptides assemble into nanotubes, in conjunction with
the recollection that D-amino acids stabilize â-turns10 suggested
Figure 1. Tetrapyrrolinone 1 and Monte Carlo conformational search.
However, since previous studies7b have demonstrated that the
use of methyl side-chain substituents is an oversimplification, we
set (-)-9 as our initial target. Additional conformational searches
supported this choice.
The requisite R,R-disubstituted amino esters (i.e., 2, 5, and 8;
Scheme 1) required for the synthesis of the D,L-mixed polypyr-
rolinones exploiting our polypyrrolinone synthetic protocol,7b were
prepared via the enantioretentive alkylation tactic developed by
Kadary11a and Seebach.11b Construction of the D,L-mixed tetrapyr-
rolinone (-)-9 was prepared as illustrated in Scheme 1; the overall
Scheme 1
(1) For a discussion of the term “privileged structure (scaffold)” see: Evans,
B. E.; Rittle, K. E.; Bock, M. G.; DiPardo, R. M.; Freidinger, R. M.; Whitter,
W. L.; Lundell, G. F.; Veber, D. F.; Anderson, P. S.; Chang, R. S. L.; Lotti,
V. J.; Cerino, D. J.; Chen, T. B.; Kling, P. J.; Kunkel, K. A.; Springer, J. P.;
Hirshfield, J. J. Med. Chem. 1988, 31, 2235.
(2) (a) Gude, M.; Piarulli, U.; Potenza, D.; Salom, B.; Gennari, C.
Tetrahedron Lett. 1996, 37, 8589; Gennari, C.; Salom, B.; Potenza, D.;
Williams, A. Angew. Chem., Int. Ed, Engl. 1994, 33, 2067. (b) Nowick, J. S.;
Mahrus, S.; Smith, E. M.; Ziller, J. W. J. Am. Chem. Soc. 1996, 118, 1066.
(c) Lokey, R. S.; Iverson, B. L. Nature 1995, 375, 303. (d) Cho, C. Y.; Moran,
E. J.; Cherry, S. R.; Stephans, J. C.; Fodor, S. P. A.; Adams, C. L.; Sundaram,
A.; Jacobs, J. W.; Schultz, P. G. Science (Washington D. C.) 1993, 261, 1303.
(e) Murray, T. J.; Zimmerman, S. C. J. Am. Chem. Soc. 1992, 114, 4010.
(3) Hagihara, M.; Anthony, N. J.; Stout, T. J.; Clardy, J.; Schreiber, S. L.
J. Am. Chem. Soc. 1992, 114, 6568.
(4) Hamuro, Y.; Geib, S. J.; Hamilton, A. D. J. Am. Chem. Soc. 1996,
118, 7529
(5) (a) Dado, G. P.; Gellman, S. H. J. Am. Chem. Soc. Chem. 1994, 116,
1054; review see: Gellman, S. H. Acc. Chem. Res. 1998, 31, 173.
(6) (a) Seebach, D.; Overhand, M.; Ku¨hnle, F. N. M.; Martinoni, B.; Oberer,
L.; Hommel, U. and Widmer, H. HelV. Chim. Acta 1996, 79, 913. (b) For a
review, see: Seebach, D.; Matthews, J. L. Chem. Commun. 1997, 2015.
(7) (a) Smith, A. B., III; Keenan, T. P.; Holcomb, R. C.; Sprengeler, P.
A.; Guzman, M. C.; Wood, J. L.; Carroll, P. J.; Hirschmann, R. J. Am. Chem.
Soc. 1992, 114, 10672. (b) Smith, A. B., III; Guzman, M. C.; Sprengeler, P.
A.; Keenan, T. P.; Holcomb, R. C.; Wood, J. L.; Carroll, P. J.; Hirschmann,
R. J. Am. Chem. Soc. 1994, 116, 9947. (c) Guzman, M. C. Ph.D. Thesis,
University of Pennsylvania, 1995. (d) Smith, A. B., III; Hirschmann, R.;
Pasternak, A.; Yao, W.; Sprengeler, P. A.; Holloway, M. K.; Kuo, L. C.;
Chen, Z.; Darke, P. L.; Schleif, W. A. J. Med. Chem. 1997, 40, 2440. (e)
Smith, A. B., III; Benowitz, A. B.; Sprengeler, P. A.; Barbosa, J.; Guzman,
M. C.; Hirschmann, R.; Schweiger, E. J.; Bolin, D. R.; Nagy, Z.; Campbell,
R. M.; Cox, D. C.; Olson, G. L. J. Am. Chem. Soc. 1999, 121, 9286.
(8) Ghadiri, M. R.; Kobayashi, K.; Granja, J. R.; Chadha, R. K.; McRee,
D. E. Angew. Chem., Int. Ed. Engl. 1995, 34, 93. See also: Chiang, C. C.;
Karle, I. L. Int. J. Pept. Res. 1982, 20, 133.
yield was 18%. The structure of (-)-9 was confirmed by a series
1
of H, 13C, COSY, TOCSY, and NOESY NMR experiments.
To assign the solution structure of (-)-9, we first performed
1H NMR analysis to determine the lowest concentration at which
(9) Ciufolini and co-workers subsequently reported that R-N-coupling of
piperazic acid of given configuration (D or L) with an R-aminoacyl unit of
opposite configuration (L or D) produces dipeptides that exist in a conformation
conducive to the formation of a peptide turn. Xi, N.; Alemany, L. B.; Ciufolini,
M. A. J. Am. Chem. Soc. 1998, 120, 80.
(10) Nutt, R. F.; Veber, D. F.; Saperstein, R.; Hirschmann, R. Int. J. Pept.
Protein Res. 1983, 21, 66.
(11) (a) Karady, S.; Amato, J. S.; Weinstock, L. M. Tetrahedron Lett. 1984,
25, 4337. (b) Seebach, D.; Fadel, A. HelV. Chim. Acta 1985, 68, 1243.
10.1021/ja002964w CCC: $19.00 © 2000 American Chemical Society
Published on Web 10/24/2000

11038 J. Am. Chem. Soc., Vol. 122, No. 44, 2000
Communications to the Editor
intermolecular hydrogen bonding occurs.12 The chemical shift at
δ 5.41 ppm (Figure 2) corresponds to the N-terminal pyrrolinone
N-H (i.e., hydrogen 4). The large concentration dependence of
this chemical shift clearly indicates exposure to the solvent. In
contrast, the chemical shifts of hydrogens 1, 2, and 3 (i.e., δ 7.05,
7.38, and 7.34 ppm) were invariant over the concentration range
studied ( ∼5 × 10-4 to 0.05 M), indicative of intramolecular
hydrogen bonding. Taken together these results indicate that the
lowest concentration at which intermolecular hydrogen bonding
occurs is ∼10-3 M. FT-IR analysis of compound (-)-9 over a
range of concentrations from 0.001 to 0.05 M revealed both a
non-hydrogen-bonded N-H band at 3440 cm-1, and a hydrogen-
bonded N-H band at 3350 cm-1, in agreement with the 1H NMR
results.12
Figure 4. (a) Lowest-energy conformer of tetrapyrrolinone (-)-9 in
CHCl3; (b) superimposition of all 34 low-energy conformers within 2
kcal/mol; (c) overlay of representative structures of two major clusters;
(d) overlay of the lowest-energy conformers generated from five force
fields.
(CHCl3).15 The lowest-energy conformer of (-)-9 is shown in
Figure 4a. The structure is consistent with the NOE data except
for one violation in the distance between hydrogen 1′ and 8 (5.6
Å versus the 1.8-5.0 Å range), presumably due to the flexibility
of the prenyl side chain. The hydrogen bonding pattern in the
lowest-energy conformer of (-)-9 is consistent with the NMR
and FT-IR dilution studies.16 The overlay of all 34 low-energy
conformers within 2 kcal/mol indicates high conformational
homology (Figure 4b). Among 560 conformers generated in the
5000-step Monte Carlo conformational search, 530 conformers
were grouped into two major clusters using Xcluster analysis,17
with 217 and 303 members respectively at cluster level 545. An
overlay of a representative structure from each cluster revealed
excellent agreement (Figure 4c). Since the accuracy of the
molecular dynamic calculations relies on the ability of the
parameters to mimic the potential energy of the molecule, we
evaluated the suitability of the MM2* force field for (-)-9, by
comparing the derived conformations obtained employing the
other force fields available in MacroModel. Although Amber94
was not suitable for the pyrrolinone functionality, MM3*, MMFF,
Amber*, and OPLS* gave excellent atom-for-atom correlation
for the lowest-energy conformations (Figure 4d).
Figure 2. Concentration dependence of the N-H chemical shifts of
tetrapyrrolione (-)-9 in CDCl3: H1 (4); H2 (×); H3 (O); H4 (0).
To define the secondary structure of tetrapyrrolinone (-)-9,
we performed a series of 2D NOESY NMR studies13 (10-3 M,
CDCl3). The nuclear Overhauser effect (NOE) time-dependence
intensity profile of (-)-9 indicated that for most cross-peaks the
intensities were in the linear range up to 500 ms. A total of 35
NOE cross-peaks were observed with 450 ms as the mixing time.
Among them, 5 long range sequential NOEs (Figure 3) clearly
established that the prenyl side chain was in close contact with
the pyrrolinone ring at the C terminus of the molecule, consistent
with a turn conformation.
In summary, these studies demonstrate the feasibility of
designing a turn structure utilizing D,L-mixed polypyrrolinones.
Efforts to crystallize (-)-9 and to design a somatostatin mimic
exploiting the D,L-mixed polypyrrolinone scaffold are in progress.
Acknowledgment. Financial support was provided by the National
Institute of Allergy and Infectious Diseases through Grant AI-42010.
Figure 3. Long-range NOEs in tetrapyrrolinone (-)-9 using 450 ms as
mixing time.
Supporting Information Available: Spectroscopic, analytical data
for 2, 4-7, 9 and selected experimental procedures, NOESY spectra
(PDF). This material is available free of charge via the Internet at
http://pubs.acs.org.
The solution structure of tetrapyrrolinone (-)-9 was then
generated using the NOE constraints as imputs to a 5000-step
Monte Carlo conformational search employing the MM2*14 force
field in MacroModel, with the GB/SA solvation continuum model
JA002964W
(15) Hasel, W.; Hendrickson, T. F.; Still, W. C. Tetrahedron Comput.
Method 1988, 1, 103.
(12) Liang, G,-B.; Desper, J. M.; Gellman, S. H. J. Am. Chem. Soc. 1993,
115, 925.
(13) Billeter, M. J. Mol. Biol. 1982, 155, 321.
(14) Mohamadi, F.; Richards, N. G. J.; Guida, W. C.; Liskamp, R.; Lipton,
M.; Caufield, C.; Chang, G.; Hendrickson, T.; Still W. C. J. Comput. Chem.
1990, 4, 440; Allinger, N. L. J. Am. Chem. Soc. 1977, 99, 8127.
(16) Three intramolecular hydrogen bonds exist in (-)-9 with distances of
2.45, 2.67, 2.36 Å. Hydrogen bonding angles for N-H‚‚‚‚O are 109°, 100°,
and 94°, respectively. As expected, the N-terminal hydrogen 4 is exposed to
the solvent.
(17) Shenkin, P. S.; McDonald, D. Q. J. Comput. Chem. 1994, 15, 899.