Protein-protein interface mimicry by an oxazoline piperidine-2,4-dione

Article abstract of DOI:10.1021/ol5036547

Representative minimalist mimics 1 were prepared from amino acids. Scaffold 1 was not designed to mimic any particular secondary structure, but simulated accessible conformations of this material were compared with common ideal secondary structures and with >125000 different protein-protein interaction (PPI) interfaces. This data mining exercise indicates that scaffolds 1 can mimic features of sheet-turn-sheets, somewhat fewer helical motifs, and numerous PPI interface regions that do not resemble any particular secondary structure.

Full text of DOI:10.1021/ol5036547

Letter
pubs.acs.org/OrgLett
Protein−Protein Interface Mimicry by an Oxazoline Piperidine-2,4-
dione
†
,‡
‡
‡
,‡
Xun Li, Jaru Taechalertpaisarn, Dongyue Xin, and Kevin Burgess*
†Key Laboratory of Chemistry and Biology of Natural Product of Ministry of Education, School of Pharmaceutical Sciences,
Shandong University, WenHuaXi Road No 44, Ji’nan 250012, P. R. China
‡
Chemistry Department, Texas A & M University, P.O. Box 30012, College Station, Texas 77842, United States
*
S Supporting Information
ABSTRACT: Representative minimalist mimics 1 were pre-
pared from amino acids. Scaffold 1 was not designed to mimic
any particular secondary structure, but simulated accessible
conformations of this material were compared with common
ideal secondary structures and with >125000 different protein−
protein interaction (PPI) interfaces. This data mining exercise
indicates that scaffolds 1 can mimic features of sheet-turn-sheets,
somewhat fewer helical motifs, and numerous PPI interface regions that do not resemble any particular secondary structure.
arly minimalist mimics of secondary structures inspired by
Hamilton’s terphenyls featured planar aromatic units that
incorporate many genetically encoded amino acid side chains,
to elucidate the bias of this scaffold toward all the common
ideal secondary structures and to show illustrative cases where
EKO predicts an excellent match of accessible conformers of 1
on PPI interface regions.
1
E
display side chains in appropriate orientations. More recently,
this field has turned toward chiral and heterocyclic designs that
exist in coiled conformations and/or tend to have superior
2
water solubilities. It is convenient if mimics of this kind can be
Scheme 1 shows how the oxazoline fragments were prepared
from Fmoc-protected or Cbz-protected amino acids and amino
alcohols. Throughout this paper, compounds are numbered
according to the scaffold (or scaffold intermediate), and lower
produced from amino acid starting materials; otherwise, it is
difficult to incorporate all the different side chains. The recently
reported oligooxopiperazines, for example, are derived from
3
amino acids.
1
3
case one-letter codes are used to relate the side chains R −R to
Even though effective minimalist mimics are more rigid than
t
the closest amino acids [e.g., d′ for the −CH CO Bu of Asp
4
2
2
peptides, most populate multiple solution conformers that
(
d) and k′ for the −(CH ) NHCbz of Lys (k)]. After a routine
5
2 4
display side chains in different orientations. We developed two
6
coupling to obtain molecules 2, the primary alcohol was
mesylated and then treated with base to initiate oxazoline
formation. Some Fmoc-protected compounds related to 3 have
strategies, EKO and EKOS (exploring key orientations on
7
secondary structures), to ascertain how conformations of
minimalist mimics resemble protein−protein interface regions
and ideal secondary structures, respectively. Application of
EKO exposes the enormous diversity of PPI interfaces: even a
small fraction of these could not be accurately represented by
all the secondary structure mimics reported in the literaure to
date. Consequently, there is a need to develop and understand
new chemotypes for the key issue of interface mimicry.
8
been reported prior to this work, but most of the systems with
the side chains indicated in Scheme 1 have not been prepared
before. The cyclization conditions in Scheme 1 were arrived at
after some optimization; they are a modification of those used
8a
in Sigman’s aminooxazoline syntheses. Many other conditions
that did not use DMAP or relied upon activation via PPh /CCl
3
4
This paper introduces chiral, nonaromatic, interface mimics 1
composed of piperidine-2,4-dione and oxazoline fragments
linked by −NHCHR− units (Figure 1). The objectives of this
study were to develop a synthesis of molecules 1 that could
gave poor product yields. Removal of the FMOC protecting
group from the protected amines 3 gave the aminooxazolines 4.
A similar procedure was used, but with N-Cbz protected Phe,
to access the ff chiron.
Having obtained a set of aminooxazolines, we developed two
9
methods (A and B in Scheme 2) to add these to the
1
0,13,14
piperidine-2,4-dione derivatives 5;
product was obtained
using either approach, but the yields differed on a case-by-case
basis. Overall, the synthetic route is divergent−convergent
because any ketone 5 can be condensed with any amine 4.
Figure 1. Scaffold 1 is a minimalist mimic of secondary structures with
favorable predicted properties for cell and oral bioavailability.
Received: December 18, 2014
Published: January 27, 2015
©
2015 American Chemical Society
632
DOI: 10.1021/ol5036547
Org. Lett. 2015, 17, 632−635

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Letter
Scheme 1. Fmoc Approach Was Used To Obtain Most
Chirons 4, but Cbz Was Used To Access the ff Chiron
Figure 2. RMSD (Å) for the simulated conformers in the ensemble
that best overlay the indicated ideal secondary structures, relative to
the average values for the best conformers overlaid on each of the
seven motifs, are shown.
Scheme 2. Syntheses of the Target Compounds 1
since it can adopt a conformation that matches an ideal α-helix
with a RMSD of only 0.26 Å.
7
Achiral minimalist mimics like terphenyls have only one
isomer to compare with ideal secondary structures. Con-
formations of chiral minimalist mimics, however, are stereo-
chemically dependent, and we offer two observations related to
this. First, stereochemical changes can significantly alter the
conformational bias of many minimalist mimics such that one
isomer can match extended conformations whereas another is
more closely overlaid on helical motifs; comparison of LLL-1aaa
with LDL-1aaa illustrates this. Thus, even though the LLL-isomer
is disposed to α-helical conformations (blue bar) and can
match sheet-turn-sheet motifs almost as well (red bar in Figure
2
a), the LDL-form is biased toward extended motifs and not
helical ones (Figure 2b). The second observation is that
correlations of mimic stereochemistries and conformational
biases are beyond what the human mind can perceive;
systematic data mining (the EKOS strategy) is essential for this.
Most of the compounds 1 prepared here were not solids,
though in one case, LLL-1fii, we were able to collect crystals and
obtain an X-ray structure. That molecule crystallized in two
similar conformations (differing by RMSD 0.28 Å, based on the
6 Cα and Cβ coordinates, see the Supporting Information), but
which nevertheless project the side chains in slightly different
orientations. We recently outlined another technique based on
exploring key orientations that can be used to relate X-ray
EKOS was used to relate the ensemble of simulated
accessible conformers of 1aaa to ideal secondary structures.
This process was carried out for all stereoisomers of 1aaa; full
data are shown in the Supporting Information, and two select
examples are given here. First, conformers of LLL-1aaa matched
better on an ideal α-helix than on any of the other secondary
structures (Figure 2a; for a full explanation of these plots see ref
10). In our experience, it is much harder to design good helical
mimics than ones that overlay other motifs. Our application of
3
EKOS on oligooxopiperazines (all stereoisomers, unpublished
10
data) indicate they have accessible conformations that overlay
well on an ideal α-helix with a RMSD of 0.44 Å (based on the 6
Cα and Cβ coordinates), and that is better than nearly all of the
other mimics of ideal α-helical conformations in the literature.
However, LLL-1aaa appears to be a superior α-helical mimic
structures to simulated solution conformations: EKOX.
Application of EKOX to LLL-1fii in the crystal reveals that
one conformer fits well on one strand of a sheet−turn−sheet
motif (Figure 3a), consistent with the predictions in Figure 2a
(red bars, respectively); this is interesting because minimalist
7
6
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Figure 3. One conformer in the crystal structure of LLL-1fii optimally
overlays with a sheet-turn-sheet motif (a), while neither overlaid
particularly well on an ideal α-helix (b shows the best match).
Figure 5. Statistical distribution of the best 257 overlays of preferred
conformers of LLL-1aaa (generated using EKO; all RMSD < 0.31 Å).
strand mimics are rare. However, neither of the conformers in
the crystal structure overlaid particularly well on an α-helix; the
best one is shown in Figure 3b.
Some parameters of scaffolds 1 relevant to their use as
cellular probes were also considered. Molecule 1aaa has a low
molecular mass and no amide bonds; these characteristics are
When accessible conformers of LLL-1aaa were simulated and
data mined on over 125,000 PPIs in the PDB, 257 “hits” were
found. The applied definition of a hit was that the three methyl
side-chain coordinates of the mimic overlaid with three
interface side chains with an RMSD of 0.3 Å or better. The
best overlay occurred on an interface sheet−turn−sheet motif
as shown in Figure 4 (RMSD 0.12 Å). The other 256 hits are
tabulated in the Supporting Information.
11
favorable for cellular- and oral-permeability. QikProp was
used to predict some other key parameters of 1aaa (Figure 1).
Simulated permeability of 1aaa through Caco cells is excellent
(i.e., >500 nm/s), and the estimated log octanol/water partition
coefficient, 1.54, is near the midpoint of the optimal range
12
(−2.0 to +6.5). Moreover, there are no rule of five violations
for this structure. Obviously, these properties will be modulated
when side chains other than methyl are involved, but the
scaffold provides a good framework for probe development.
Overall, we conclude that compounds based on LLL-1aaa can
be excellent helical mimics, but they may adopt a range of
conformations that overlay well on other secondary structures,
notably sheet−turn−sheet motifs. Like many other minimalist
mimics, however, molecules 1 can overlay on diverse interface
regions, most of which are not directly related to secondary
structures.
ASSOCIATED CONTENT
Supporting Information
■
*
S
Experimental procedures and characterization data for the new
compounds, procedure for mathching on ideal secondary
structures, X-ray data, and best hits from EKO mining for the
featured chemotypes. This material is available free of charge
via the Internet at http://pubs.acs.org.
Figure 4. Accessible simulated conformer of LLL-1aaa overlays with
excellent correspondence on the interface region of inosine 5′-
monophosphate dehydrogenase (pdbid = 4ff0, RMSD = 0.12 Å).
Despite Figure 2a, it would be incorrect to assume that
simulated accessible conformers of LLL-1aaa overlay well on
only sheet−turn−sheet and helical motifs at interfaces. The
statistical distribution of overlays in each of the featured ideal
secondary structures is depicted in Figure 5. Consistent with
the findings from EKOS based on ideal secondary structures
AUTHOR INFORMATION
Corresponding Author
■
*
E-mail: burgess@tamu.edu.
Notes
The authors declare no competing financial interest.
(
Figure 2a), α-helical and sheet-turn-sheet motifs are the most
ACKNOWLEDGMENTS
common matches for LLL-1aaa at interfaces. However, Figure 5
shows over 50% of the overlays occur on nearly consecutive
amino acids (“single segments” in Figure 5) that are not part of
any ideal secondary structure. Moreover, the next most
common type of overlay was on amino acid sequences from
different parts of the chain, and which also do not resemble any
ideal secondary structure (ie “multiple segments”). Conse-
quently, most of the potential for LLL-1aaa in interface mimicry
appears not to be correlated with any particular secondary
structure.
■
Financial support for this project was provided by the National
Institutes of Health (GM087981), the Robert A. Welch
Foundation (A-1121), and the High Impact Research (HIR
(UM.C/625/1/HIR/MOHE/MED/17 & UM.C/625/1/HIR/
MOHE/MED/33) from the Ministry of Higher Education,
Malaysia. TAMU/LBMS-Applications Laboratory provided
mass spectrometric support. The NMR instrumentation at
Texas A&M University was supported by a grant from the
National Science Foundation (DBI-9970232) and the Texas
6
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Letter
A&M University System. We thank Dr. J. Reibenspies at
TAMU for the crystallographic analysis.
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DOI: 10.1021/ol5036547
Org. Lett. 2015, 17, 632−635