Omegatides: Constrained analogs of peptide primary sequence

Article abstract of DOI:10.1039/c2ob06692k

A study was conducted to demonstrate a design for contiguous constrained amino acid surrogates, called omegatides, that had side chains to reflect the primary sequence di- and tri-peptides. A solution phase strategy for the preparation of omegatides was developed, which started with 5-substituted 2,4-pyrrolidinediones (tetramic acids) A that were prepared from amino acids on multigram scales via a one-pot procedure without chromatography. Procedures were developed to add an amino acid to analogous compounds and to reduce the resulting vinylogous ureas. Two methods were used to assess the conformational biases and constraints on these systems. The first was quenched molecular dynamics (QMD) to probe thermodynamic accessibility of conformational states. The molecule was energy minimized and subjected to a molecular dynamics run at high temperature for a short time in this technique and conformational states were recorded every 1 ps and minimized via molecular mechanics.

Full text of DOI:10.1039/c2ob06692k

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Omegatides: constrained analogs of peptide primary sequence†
Dmytro Fedoseyenko, Arjun Raghuraman, Eunhwa Ko and Kevin Burgess*
Received 5th October 2011, Accepted 21st November 2011
DOI: 10.1039/c2ob06692k
Certain motifs of two or three contiguous amino acids are
associated with important and varied pharmacological activities.1
Consequently, methods to make conformationally constrained
compounds that closely reflect the primary sequence and structures
of di- and tri-peptides are important. Of these, retroinverso-
mimics,2 peptoids,3,4 oligomers of b-amino acids,5,6 and ester-
based analogs,7 tend to be more flexible than parent systems.
Oligomers of N-methyl-,8,9 or a-methyl-,10,11 and cyclopropyl-
skipped tetramic acids.20 These are oligomers based on tetramic
acids building blocks wherein the U and y angles are locked, and
rotation about the w-bond is less constrained. This is opposite to
the situation for peptides where the w-vector is more constrained
than U and y.
A solution phase strategy for the preparation of omegatides
was developed (Scheme 1). It starts with 5-substituted 2,4-
pyrrolidinediones (tetramic acids) A that can be prepared from
amino acids on multigram scales via a one-pot procedure with-
out chromatography.21–24 Tønder developed procedures to add
an amino acid to analogous compounds (different side-chains
to the ones shown), and to reduce the resulting vinylogous
ureas;25,26 those procedures were applied here to give our starting
materials 1 and 2. Scheme 1 shows the steps leading up to
these materials so that this graphic represents the true length
of the synthesis. Compounds 2 are nucleophilic amines which
can be cyclized to 3 using (triphenylphosphoranylidene)ketene.27
Significant water solubilities were observed for compounds 3 and
the “C-deprotected” forms 4; this facilitated their isolation from
triphenylmethylphosphonium trifluoroacetate in this synthesis
(we found that excess ketene is hydrolyzed in the presence of
water to this salt). Transformation of 4 into the trimers 7, via
the intermediates 5 and 6, involves reiteration of steps already
described. None of the anti-diastereomer was detected (1H NMR)
in the hydrogenation of 5 or of 1.
12,13
amino acids are more rigid, but they contain acyclic amide
bonds. Smith/Hirschmann devised routes to oligomers of g-
pyrrolidones,14–17 but their syntheses are labor intensive (e.g.
15 steps, 11% yield, involve separation of diastereomers by
chromatography etc.) even for simple alkyl-side chains.15–17 Con-
sequently, even though about 30 years have passed since genesis
of the term “peptide-mimic” or “peptidomimetic”,18 there is a
need for facile methods to construct oligomers of contiguous
constrained amino acid surrogates. Arora et al. recently published
an example of this based on oligooxopiperazines;19 here we wish
to add another.
This manuscript is about a design for contiguous constrained
amino acid surrogates that have side chains to reflect the primary
sequence di- and tri-peptides; we call this design “omegatides”
(Fig. 1). It follows from our previous work on analogs containing
Two methods were used to assess the conformational biases and
constraints on these systems. The first was quenched molecular
dynamics (QMD)28–31 to probe thermodynamic accessibility of
conformational states. In this technique the molecule is energy
minimized then subjected to a molecular dynamics run at high
temperature (1000 K) for a short time (600 ps), conformational
states are recorded every 1 ps, then these are minimized via
molecular mechanics. The lowest energy structures below a user-
defined cut-off are selected then clustered into families based on
root mean squared deviation (RMSD) from user-defined atoms.
Once these states have been identified, density functional theory
(DFT) was used to investigate kinetic barriers to interconversion
(see the ESI†).
Fig. 1 Peptides, tetramic acids, previous work (skipped tetramic acid
analogs), and omegatides.
Application of the QMD technique to 4a showed an overwhelm-
ing preference for it to exist in two preferred conformations {594
of the 600 structures sampled existed as these two conformers
Department of Chemistry, Texas A&M University, Box 30012, College
Station, TX 77842, USA. E-mail: burgess@tamu.edu
† Electronic supplementary information (ESI) available: Experimental
procedures and characterization data for the new compounds reported.
CCDC reference numbers 854831–854833. For ESI and crystallographic
data in CIF or other electronic format see DOI: 10.1039/c2ob06692k
˚
to within an RMSD of 0.5 A}. Within those two families, the
lowest energy structure was found in the most populated family
(474 structures). Members of this family present the two methyl
side chains on the same side of the molecule, so we refer to this
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Fig. 2 Favored conformers and barrier to their interconversion for 4a
(energies in kcal mol-1).
25 ◦C. No dihedral angle in omegatides exactly corresponds to w
in peptides, but the CHCH–NCH angle is closely related. This has
a value of -110◦ in syn-4a, while for anti-4a it was 101◦ (using the
data from DFT).
Different envelope conformations of the five-membered rings
mean that the f,y-angles in omegatides can vary slightly, but
only within quite narrow ranges. Fig. 3 shows a Ramachandran
plot for the 600 conformers selected in the QMD experiment for
Scheme 1 Syntheses of omegatides 3, 4, and 7aa.
as syn-4a. X-Ray crystallographic analysis of 3c (a close analog
of 4a) revealed that the syn conformation is preferred in the solid
state. We call the other preferred family anti-4a because the side
chains are approximately on opposite faces (Fig. 2).
DFT calculations on 4a indicated the energy difference between
the syn (preferred) and anti conformers was only 0.42 kcal mol-1
and the energy barrier that must be surmounted to interconvert
them was only 9.58 kcal mol-1. Thus theory predicts that these two
conformers should be rapidly interconverting on the NMR time-
scale; this was consistent with the 1H NMR of these materials in
several solvents for which only one set of signals is observed at
Fig. 3 Ramachandran plot for diastereomers of 4a. Red (LL), blue (DD),
pink (LD), green highlighted with black arrow (DL).
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compound 4a. This dot plot shows the f,y-angles sampled for the
L,L- (and, incidentally, the D,L-)-isomer correspond to dihedrals
found in b-sheet secondary structures; it also shows the degree of
variance of f,y-angles is much less than in peptides.
A single crystal study of the triomegatide 7 revealed f and y
dihedrals in the solid state, which are similar to those predicted by
DFT calculations. In the solid state, 7 crystallized in an anti,anti-
conformation using the nomenclature defined in Fig. 4.
Fig. 4 Analysis of X-ray crystal structure for 7.
Fig. 5 Overlay of a preferred conformation of 8 on an ideal b-strand.
Both diagrams are the same, except the strand is shown in pink on the
right, and 8b is an epimer of 8a. The conformer overlaid is 1.29 kcal mol-1
above the lowest energy structure obtained in the QMD experiment for 8a
and 0.67 kcal mol-1 for 8b.
Recently, we hypothesized that overlap of Ca–Cb bond vectors
is pivotal for comparing structures of peptidomimetics with ideal
secondary structures.32,33 We did not design omegatides to be
secondary structure mimics, but were curious about how they
might match. Systematic overlay of the preferred conformations
elements.20 Omegatides based on contiguous tetramic acid-derived
residues, as described here, are different insofar as they provide
rigid analogs of very particular conformations of di- and tri-
peptides.34
t
of 8 (a close analog of 7, but lacking the Bu group) on to both
contiguous and non-contiguous side chains of preferred secondary
structures revealed a preferred match corresponding to overlay
of a syn,anti-8a conformer on three side chains of a b-strand
Further research is necessary to refine the synthetic procedures
to prepare omegatides. In particular, the ketene cyclization of
materials 6 where the R1 side-chains are larger than methyl
seems to be sensitive to steric effects, and preparation of analogs
with other functionalized side-chains must be addressed. These
investigations are potentially worthwhile because the featured
compounds should be both proteolytically stable, and more
bioavailable than peptides. Further, it is encouraging for ap-
plications in medicinal chemistry that compounds like 3 and
4 have some water solubilities. Most importantly, omegatides
can only exist in a limited range of conformations, so rational
syntheses of second generation analogs based on these preferred
states in bioactive hit compounds is feasible; peptides and
peptoids are far less amenable to this because there are more
possible bioactive conformations for hit compounds having these
structures.
˚
motif (Fig. 5a). The RMSD for this match was 0.72 A which,
in our experience for a system based on three side-chains, is only
a moderate fit. However, modeling showed the L,D,L-form of 8b
˚
overlays with an RMSD of 0.43 A (Fig. 5b).
Structural constraints do not allow proline to be incorporated
as an internal residue into omegatides, but it could be added at
the N- and C-termini. To illustrate the latter possibility and an
easy way to mimic a C-terminal serine, prolinol was added to the
precursor 4b to give the Ala-Gly-Ser mimic 9.
This work illustrates first stage preparations of peptidomimetics
formed from contiguous restrained amino acid surrogates. It
complements other studies in this laboratory on peptidomimetics
from alternating tetramic acid-based lactams and pyrrolidones
where the limited but extended conformational flexibility of these
systems enables mimicry of several common secondary structure
Acknowledgements
Financial support for this project was provided by the National
Institutes of Health (MH070040, GM076261), and the Robert A.
Welch Foundation (A-1121). TAMU/LBMS-Applications Lab-
oratory provided mass spectrometric support. The NMR
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instrumentation at Texas A&M University was supported by a
grant from the National Science Foundation (DBI-9970232) and
the Texas A&M University System.
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18 P. S. Farmer, in Drug Design, ed. E. J. Ariens, Academic Press, San
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