Pyrrolinone-pyrrolidine oligomers as universal peptidomimetics

Article abstract of DOI:10.1021/ja2033734

Peptidomimetics 1-3 were prepared from amino acid-derived tetramic acids 7 as the key starting materials. Calculations show that preferred conformations of 1 can align their side-chain vectors with amino acids in common secondary structures more effectively than conformations of 3. A good fit was found for a preferred conformation of 2 (an extended derivative of 1) with a sheet/β-turn/sheet motif.

Full text of DOI:10.1021/ja2033734

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PyrrolinoneÀPyrrolidine Oligomers as Universal Peptidomimetics
Arjun Raghuraman,† Eunhwa Ko,† Lisa M. Perez,† Thomas R. Ioerger,‡ and Kevin Burgess*,†
†Department of Chemistry and Laboratory for Molecular Simulation, Texas A&M University, Box 30012, College Station, Texas 77842,
United States
‡Department of Computer Science, Texas A&M University, College Station, Texas 77843-3112, United States
S Supporting Information
b
For the preparation of scaffold 1, an efficient procedure from
ABSTRACT: Peptidomimetics 1À3 were prepared from
Merck was used to decarboxylate trans-4-hydroxyproline to give
more than 50 g of crystalline (R)-3-hydroxypyrrolidine.13 That
amino acid-derived tetramic acids 7 as the key starting
materials. Calculations show that preferred conformations
of 1 can align their side-chain vectors with amino acids in
common secondary structures more effectively than con-
formations of 3. A good fit was found for a preferred
conformation of 2 (an extended derivative of 1) with a
sheet/β-turn/sheet motif.
pyrrolidine was N-protected to give the starting material indi-
cated in Scheme 1. Nucleophilic displacement on a triflate deriva-
tive of this (under conditions optimized to avoid elimination)14
gave amino esters 4. X-ray analysis of 4d HCl indicated that its
3
formation occurred via a single inversion. The crystalline hydro-
chloride salts of 4 were reacted with Bestmann’s ylide15À17 to
give pyrrolinones 5. Hydrogenolysis followed by condensation of
the free pyrrolidine NH groups with 5-substituted 2,4-pyrrolidi-
nediones (tetramic acids) 7 gave the featured trimers 1. The
tetramic acid derivatives 7 are useful starting materials because they
inimalist peptidomimetics, which present amino acid side
M
chains without any structure to directly resemble peptide
backbones, are the focal point of many recent studies inspired by
Smith and Hirschmann1À5 and Hamilton.6À10 We recently
designed sets of scaffolds, of which A is typical, that are analogues
of local pairs of amino acids (including noncontiguous ones) in any
secondary structure (i.e., they are universal peptidomimetics).11,12 That
work featured five peptidomimetic designs that together could be
used to mimic almost all local pairs of amino acid side chains in
six of the most common secondary structure motifs. This paper
describes an alternative scaffold design, 1, having preferred
conformations that overlay well with pairs of amino acid residues
in three different types of helix (310, Rand π), in β-strands, and in
both parallel and antiparallel β-sheets. Furthermore, an exten-
ded form of that same scaffold design, 2, has a preferred confor-
mation that overlays well with three amino acid side chains in a
sheet/β-turn/sheet motif (an antiparallel β-sheet). These two
scaffolds are contrasted with A and a compound in series 3 wherein
side chains are expressed on contiguous rings.
Scheme 1. Syntheses of Trimers 1 and Pentamers 2
Received: April 25, 2011
Published: July 22, 2011
r
2011 American Chemical Society
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can be prepared from N-Boc-protected amino acids via a one-pot
procedure that affords tens of grams without chromatography.18À21
NMR and X-ray analysis of compound 6d indicated that its forma-
tion was not complicated by epimerization. Condensation of dimers
6 with C-deprotected derivatives of trimers 1 gave pentamers 2;
hence, the overall synthesis can be divergentÀconvergent, as shown
in Scheme 1.
helical form (310), three on an R-helix, and three on the most
compressed helical form, the π-helix (with another at an RMSD
of 0.31 Å). Other conformers overlay well on various side-chain
pairs of β-strand and parallel β-sheet residues, while the overall
best match was for a parallel β-sheet. Interestingly, several of the
favored overlays involved noncontiguous five-membered rings in
structures 1 and 2 on contiguous amino acids in the secondary
structures; this reflects the way the featured molecules can coil.
All of the preferred conformations highlighted in Table 1 were
within 3.0 kcal/mol of the minimum conformation identified, so
these structures are thermodynamically accessible.
Table 1 also compares the overlay of scaffold A on the same
elements of secondary structure. It shows that scaffold A covers a
more limited range of “secondary structure space”, as expected since
the CR atoms in this structure are held rigidly at one separation.
A brief comparison was also made for the same elements of secon-
dary structure with the core building blocks of the Hirschmann/
Smith pyrrolinones5 and Hamilton’s terphenyl systems [see the
Supporting Information (SI) for structures]. The Hirschmann/
Smith system overlaid well with parallel and antiparallel β-sheets, a
β-strand, and a 310-helix (RMSD = 0.10À0.29 Å). A biphenyl repre-
senting part of Hamilton’s terphenyls overlaid better with 310- and
π-helices than the R-helix.26 An outline of these studies is given in
the SI, and a more extensive comparison will be reported elsewhere.
It is harder to fit six coordinates than four, so matches of the
mimics involving three side chains must have higher RMSD’s. In
the event, the best match for pentamer 2 was with three residues
of a sheetÀturnÀsheet motif (1.93 kcal/mol above the mini-
mum-energy conformer; RMSD = 0.46 Å; Figure 1). Moreover,
we found one example of a proteinÀprotein interaction (between
monomers in the RAD52 undecamer) where 2aaa matched three
side chains with an RMSD of only 0.14 Å (see the SI).
NMR studies to detect preferred conformations in these types
of molecules are inappropriate because of conformational averaging.
Consequently, two complementary molecular modeling methods
were used. Quenched molecular dynamics (QMD)22À25 probes
thermodynamic accessibilities of conformational states, as described
previously.11 Briefly, this technique generates 600 minimized
structures; ones that are energetically below a user-defined cutoff
from the minimum energy conformer (here 3.0 kcal/mol) are clus-
tered into families based on root-mean-square deviations (RMSD's)
from user-defined atoms (0.5 Å). We have postulated11 that
matching the CRÀCβ bond vectors forms a good basis for measur-
ing the fit to secondary structures, and thus, preferred conforma-
tions of the scaffolds are defined by frameworks with only Me
side chains (i.e., Ala analogues), such as 1aa and 2aaa. For this
reason, preferred conformers of 1aa and 2aaa were clustered
based on CRÀCβ coordinates, and representative members of
each cluster were tested for their fit to CRÀCβ atom positions of
ideal secondary structure motifs.
In our experience, a good fit of structures based on two amino
acid side chains corresponds to an RMSD of 0.3 Å or less. On the
basis of this standard, Table 1 reveals that preferred conformers
of compound 1 fit two different residue pairs on the most elongated
Table 1. Fit of the Most Appropriate Conformers of Mimics
A, 1, and 3 on Secondary Structures (Based on QMD
Analyses)a
Figure 1. Overlay of 2aaa on a sheet/β-turn/sheet motif.
The next milestone in this study was to check that the different
conformers are kinetically accessible. To do this, a density func-
tional theory (DFT) method was used to investigate interconver-
sion between the preferred states of 6a (Figure 2a; also see the SI).
A maximum energy barrier of 5.10 kcal/mol was calculated using
this method (Figure 2b). This indicates that conformers of 6a
1
should rapidly interconvert on the H NMR time scale, and
experimentally this was shown to be the case.
Consideration of Newman projections through the bond
labeled in Figure 2a indicates that this molecule would tend to
rest predominantly in three conformational states. This assertion
a All rmsd values (Å) are for the conformers (within 3.0 kcal/mol of the
minimum-energy conformer) that overlay on the secondary structures
shown (ΔG values are in kcal/mol). See the SI for secondary structure
templates.
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Scheme 2. Synthesis of 3 with Side Chains on Contiguous
Rings
acid side chains; (ii) kinetically and thermodynamically accessible
conformations for induced fit; (iii) only moderate loss of entropy
on docking; and (iv) appropriate CRÀCβ coordinates of an
accessible conformation of the mimic matching those of the
secondary structures. An advantage of defining a parameter such
as (iv) (i.e., matching side-chain CRÀCβ coordinates) is that the
fit can be quantitated in terms of parameters such as RMSD's. This
provides a firm basis for comparing the abilities of peptidomimetics
such as A and 1À3 to mimic secondary structures.
Figure 2. (a) Structures and parameters used for DFT and QMD
analyses. (b) Low-energy conformers and energy barriers for intercon-
version from DFT calculations. (c) Preferred conformers from QMD
calculations. All energies shown are free energies (ΔG°) in kcal/mol.
is supported by the fact that three low-energy conformational states
emerged from both the DFT and QMD calculations (Figure 2b,c).
The free energy differences from the DFT calculations predict
that the relative populations of the three conformers should be in
the ratio 1.00:0.34:0.12.
’ ASSOCIATED CONTENT
S
Supporting Information. Preparations and spectra of com-
b
A synthesis of one compound in series 3 was developed to
demonstrate that both heterocyclic rings in the “main chain” of
these peptidomimetics could be functionalized with amino acids.
That route (Scheme 2) employs a known diastereoselective hydro-
genation27 and is similar to Scheme 1 except that a thioamide was
introduced (9 to 10) and then reduced to the amine (12 to 3).
Extensive conformational analyses were performed for com-
pound 3. The full data set is shown in the SI, but the key point
emerges from Table 1. Specifically, preferred conformers of 3 do
not fit pairs of amino acid side chains in secondary structures as
well as conformers of trimers 1 do. The side chains in 3 on
contiguous residues are constrained in ways that preclude good
overlap on common secondary structure motifs. This is sup-
ported by the modeling studies shown here and X-ray crystal-
lographic analyses of compound 11 (see the SI). Conversely,
trimers 1 have at least one extra significant degree of freedom,
and this allows them to flex into conformations that match
secondary structures well.
pounds 1À12, modeling procedures, overlays on secondary
structures (preferred conformers of 1, 1aa, and 2aaa on second-
ary structure motifs in proteins {RMSD < 0.14 Å}; Hirschmann/
Smith pyrrolinones and Hamilton’s terphenyl systems) and
complete ref 2 (as SI ref 10). This material is available free of
charge via the Internet at http://pubs.acs.org. CCDC 822217À
822219 contain the supplementary crystallographic data, which
can be obtained free of charge from the Cambridge Crystal-
lographic Data Centre via www.ccdc.cam.ac.uk/data_request/cif.
’ AUTHOR INFORMATION
Corresponding Author
burgess@tamu.edu
’ ACKNOWLEDGMENT
We thank the National Institutes of Health (GM087981) and
the Robert A. Welch Foundation (A-1121) for financial support,
Joseph H. Reibenspies for X-ray crystallographic analysis,
Dr. Marc Parisien for modification of the β-sheet builder program,
and Dr. Dmytro Fedoseyenko for helpful discussions.
The accessibility of tetramic acid derivatives 7 from different
amino acids gives the syntheses here some considerable scope. We
recently argued11,12 that there are four structural criteria common to
effective minimalist mimics: (i) facile syntheses with most amino
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’ NOTE ADDED AFTER ASAP PUBLICATION
Scheme 1 and the corresponding information in the Supporting
Information have been corrected and reposted August 10, 2011.
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