Cyclopentapeptides as Flexible Conformational Templates
J. Am. Chem. Soc., Vol. 122, No. 14, 2000 3263
been performed mostly by the Karle group (e.g., refs 8-12),
by the Italian groups (e.g., refs 13-15), and by the Gierasch
conformer(s). On the other hand, each value of the conforma-
tional parameter measured by NMR spectroscopy (like the
vicinal coupling constants, NOE’s, etc.) represents an average
over an unknown number of conformers with significant
statistical weights. An attempt to fit all measured parameters
into a single 3D structure imposing the corresponding restrictions
can be justified only in the very unlikely case that one conformer
exists in solution with a highly predominant statistical weight.
Many researchers tackle this problem of conformational averag-
ing either by relaxing the NMR-derived limitations imposed on
the single conformer (see, e.g., ref 23) or by generating a random
family of conformers that satisfy the NMR limitations as a whole
1
6,17
group.
The X-ray structures are now available for several
1
4,18
CPP’s, including those containing unusual amino acids.
As
to NMR studies, two groups of researchers should be mentioned
as, perhaps, the more productive ones. They are the Gierasch
group, which accumulated a large amount of information
concerning CPP’s with one or two proline residues (see ref 19
for a review), and the Kessler group, which studied mostly
CPP’s containing D-amino acid residues (see, e.g., a paper on
20
the RGD-related CPP’s and references therein ).
In fact, employment of CPP’s as receptor probes with known
(see, e.g., refs 29 and 30). In both cases, the suggested 3D
3D structures was initiated by the Kessler group in the early
structures are refined by some procedures involving energy
calculations, such as molecular dynamics simulations. As a
result, the molecule is forced into the nearest energetic minimum
(minima) which is (are) not necessarily of low relative confor-
mational energy. A vivid example is provided by a recent study
by Zanotti et al. showing that the same cyclopentapeptide [cyclo-
(Phe-Phe-Aib-Leu-Pro)] possesses different conformations in
the crystal state and in various apolar solutions, none of which
nineties (e.g., refs 21-23). On the basis of extensive NMR
measurements, they proposed a “conformational template” of
the (aBCDE) type (the lower case denotes D-amino acids) that
possessed a single conformation characterized by a âII′-turn
centered at the aB fragment, and a γ-turn at the D residue (see
24
one of the first papers ). Moving the position of the D-amino
acid residue along the sequence, it would be possible to obtain
new conformational templates of the same type, and to use the
data of their biological testing for elucidation of a peptide
pharmacophore. The Kessler group applied the above approach
to RGD peptides (see the following papers and references
1
5
conformations are of the âII′γ type.
On the other hand, all low-energy conformers for a peptide
backbone of a short peptide can be elucidated by independent
energy calculations, and then may be evaluated as possible
solution conformations. At the same time, the calculated sets
of low-energy conformers can always be validated by NMR
and/or X-ray spectroscopy. Moreover, the combined use of the
independent NMR measurements and energy calculations allows
an estimation of the statistical weights for the actual conformers
observed in solution. This approach was developed by us
2
5,26
therein
), and have designed several types of corresponding
peptidomimetics.2
7,28
However, this approach suffers from a serious drawback. The
problem is that most short peptides, even cyclic ones, exist in
solution as a mixture of different interconverting conformers.
As a consequence, there are unavoidable difficulties in employ-
ing only experimental techniques for determining 3D structures
of CPP’s. X-ray studies produce knowledge of a very few 3D
structures stabilized during the process of crystallization by
intermolecular interactions in the crystal lattice; these 3D
structures do not necessarily correspond to the “receptor-bound”
31
earlier, and has been successfully applied in the cases of spin-
3
2,33
34
35
labeled angiotensin,
DPDPE.
enkephalin, dermenkephalin, and
3
6
Accordingly, the main goal of this study is to outline the
advantages of applying independent energy calculations to CPP’s
as possible receptor probes in comparison to other approaches
(8) Gierasch, L. M.; Karle, I.; Rockwell, A. L.; Yenal, K. J. Am. Chem.
Soc. 1985, 107, 3321-3327.
2
1-23
based on NMR measurements only.
Comparison of results
(9) Karle, I. L. J. Am. Chem. Soc. 1978, 100, 1286-1289.
(10) Karle, I. L. J. Am. Chem. Soc. 1979, 101, 181-184.
(11) Karle, I. L. In The Peptides, Analysis, Synthesis, Biology; Gross,
1
2
3
obtained on 3D structures for a simple cyclo(D-Pro -Ala -Ala -
Ala -Ala ) peptide by the two approaches clearly shows
4
5
E., Meienhofer, J., Eds.; Academic Press: New York, 1981; Vol. 4, pp
inconsistency of the âII′γ model. Our results provide the more
1
-54.
1
2
3
4
5
(
(
(
12) Karle, I. L. Int. J. Pept. Protein Res. 1986, 28, 420-427.
realistic view on flexibility of cyclo(D-Pro -Ala -Ala -Ala -Ala );
13) Toniolo, C. CRC Crit. ReV. Biochem. 1980, 9, 1-44.
14) Lombardi, A.; Saviano, M.; Nastri, F.; Maglio, O.; Mazzeo, M.;
this view is substantiated also by synthesis, energy calculations,
1
2
3
4
5
and NMR studies of cyclo(D-Pro -Ala -Ala -Aib -Ala ). Finally,
we analyze inevitable discrepancies in elucidation of peptide
pharmacophores using NMR measurements only as proposed
Pedone, C.; Isernia, C. V. P. Biopolymers 1996, 38, 683-691.
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M. Biopolymers 1990, 29, 263-287.
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L.; Jonczyk, A. HelV. Chim. Acta 1997, 80, 1280-1300.
21) Kessler, H.; Gurrath, M.; Muller, G.; Aumailley, M.; Timpl, R. In
(
(
25
for the RGD peptides; these discrepancies do not exist when
independent energy calculations are applied.
(
(
(27) Haubner, R.; Schmitt, W.; Holzemann, G.; Goodman, S. L.; Jonczyk,
A.; Kessler, H. J. Am. Chem. Soc. 1996, 118, 7881-7891.
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(
(
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(
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(
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(
(