The tert-butyl side chain: A powerful means to lock peptoid amide bonds in the cis conformation

Article abstract of DOI:10.1021/ol400820y

The very simple sterically hindered tert-butyl side chain exerts complete control over the peptoid amide geometry which only exists in the cis conformation. It is exemplified in NtBu glycine homo-oligomers and in linear oligopeptoids designed with an alte

Full text of DOI:10.1021/ol400820y

ORGANIC
LETTERS
XXXX
Vol. XX, No. XX
000–000
The tert-Butyl Side Chain: A Powerful
Means to Lock Peptoid Amide Bonds
in the Cis Conformation
O. Roy,†,‡ C. Caumes,†,‡ Y. Esvan,†,‡ C. Didierjean,§ S. Faure,†,‡ and C. Taillefumier*,†,‡
ꢀ
Clermont Universite, Universite Blaise Pascal, Institut de Chimie de Clermont-Ferrand,
BP 10448, F-63000 Clermont-Ferrand, France, CNRS, UMR 6296, ICCF, BP 80026,
ꢀ
ꢁ
F-63171 Aubiere, France, and LCM3B, Equipe Biocristallographie, UMR 7036
CNRS-UHP, Faculte des Sciences et Techniques, Nancy Universite, BP 239, 54506
ꢀ
ꢀ
ꢁ
Vandoeuvre-les-Nancy, France
claude.taillefumier@univ-bpclermont.fr
Received March 26, 2013
ABSTRACT
The very simple sterically hindered tert-butyl side chain exerts complete control over the peptoid amide geometry which only exists in the cis
conformation. It is exemplified in NtBu glycine homo-oligomers and in linear oligopeptoids designed with an alternating cisꢀtrans backbone
amide pattern.
Peptoids (N-substituted glycines) are formally achieved
by shifting the side chains of a peptide from the CR carbons
to the adjacent amide nitrogen atoms.1 The location of side
chains on the amides has a great impact on the conforma-
tional behavior of peptoids. Peptoid backbones which are
deprived of free NH amides have ineluctably reduced
H-bonding capabilities. In addition their N,N-disubsti-
tuted amides are prone to cis/trans isomerization, which
explains to a large extent substantial conformational
heterogeneity of oligopeptoids.2 On the other hand, cis/
trans isomerization should be regarded as a source of
conformational diversity at the peptoid backbone level.
While amide bonds in peptides and proteins are mainly
in the transoid form,3 the polyproline type I (PPI) peptide
helix featuring only cis amides is a typical peptoid second-
ary structure.4,5 Cis/trans amide isomerism is also respon-
sible for the unique threaded loop conformation adopted
by some linear peptoid nonamers.6 Recently, great efforts
(3) (a) Pauling, L.; Corey, R. B.; Branson, H. R. Proc. Natl. Acad.
Sci. U.S.A. 1951, 37, 205. (b) Ramachandran, G. N.; Sasisekharan, V.
Adv. Protein Chem. 1968, 23, 283.
(4) (a) Armand, P.; Kirshenbaum, K.; Falicov, A.; Dunbrack, R. L.,
Jr.; Dill, K. A.; Zuckermann, R. N.; Cohen, F. E. Fold. Des. 1997, 2, 369.
(b) Kirshenbaum, K.; Barron, A. E.; Goldsmith, R. A.; Armand, P.;
Bradley, E. K.; Truong, K. T. V.; Dill, K. A.; Cohen, F. E.; Zuckerman,
R. N. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 4303. (c) Wu, C. W.;
Sanborn, T. J.; Huang, K.; Zuckermann, R. N.; Barron, A. E. J. Am.
Chem. Soc. 2001, 123, 6778. (d) Sanborn, T. J.; Wu, C. W.; Zuckermann,
R. N.; Barron, A. E. Biopolymers 2002, 63, 12. (e) Patch, J. A.; Barron,
A. E. J. Am. Chem. Soc. 2003, 125, 12092. (f) Wu, C. W.; Kirshenbaum,
K.; Sanborn, T. J.; Patch, J. A.; Huang, K.; Dill, K. A.; Zuckermann,
R. N.; Barron, A. E. J. Am. Chem. Soc. 2003, 125, 13525.
†
ꢀ
Universite Blaise Pascal.
‡ CNRS.
§
ꢀ
Nancy Universite.
(1) (a) Simon, R. J.; Kania, R. S.; Zuckermann, R. N.; Huebner,
V. D.; Jewell, D. A.; Banville, S.; Ng, S.; Wang, L.; Rosenberg, S.;
Spellmeyer, D. C.; Tan, R.; Frankel, A. D.; Santi, D. V.; Cohen, F. E.;
Bartlett, P. A. Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 9367.
(b) Zuckermann, R. N. Biopolymers 2011, 96, 545.
(2) Sui, Q.; Borchardt, D.; Rabenstein, D. L. J. Am. Chem. Soc. 2007,
129, 12042.
(5) Stringer, J. R.; Crapster, J. A.; Guzei, I. A.; Blackwell, H. E.
J. Am. Chem. Soc. 2011, 133, 15559.
r
10.1021/ol400820y
XXXX American Chemical Society

have been devoted to controlling peptoid amide bond
geometry in order to minimize backbone conformational
heterogeneity. For example, it was demonstrated that
chain exhibits a Kcis/trans value of 6.3 in acetonitrile,7b
as determined from the same monomeric model, and
triazolium-type side chains have Kcis/trans values around 11.9
n f π*Ar donation from the oxygen of a carbonyl (Oiꢀ1
)
to the antibonding orbital (π*) of the aromatic ring of
an R-branched benzylic-type side chain (residue iþ1)
stabilizes the cis-amide conformation.7,8 The triazolium-
containing side chain is a prominent example of a side
chain which utilizes the n f π*Ar effect to enforce the cis-
geometry, independently of any steric contributions.9 The
1-naphthylethyl side chain (1npe) has also been proposed
in this context and has allowed for the first homogeneous
and robust PPI-type peptoid helices to be prepared.5 From
X-ray analysis of the shorter Ns1npe oligomers it was
however concluded that steric interactions are certainly
the primary cause for conformational restriction in this
family. The role of side chain steric hindrance in promoting
cis amides is actually well-known.7b So, for example,
N-CR-branched side chains are commonly used for pro-
moting PPI-type helices. However, with the exception of
the 1npe side chain, no other sterically hindered side chain
capable of ensuring complete control of R-peptoid amide
geometry has beendescribed todate. The highly bulky tert-
butyl side chain has been shown to produce exclusively
the cis amide conformation in N-substituted aminomethyl
benzamides, termed arylopeptoids,10 but insertion of tert-
butyl groups in R-peptoids had never been reported.11 In
this communication we demonstrate the full cis-directing
effect of the tBu side chain in R-peptoids and also report its
use for the design and construction of peptoids displaying
alternated cis and trans amides in a controlled manner.
The effect of a tBu side chain on cis/trans amide
isomerism was first studied in the monomeric model 1
capped with acetyl and piperidinyl groups (Scheme 1).12
Whatever the solvent used for NMR analysis including
deuterated water, only one rotamer was observed
(Kcis/trans > 19), whose cis geometry was firmly established
by 2D-NOESY experiments. The tBu effect on the back-
bone amide is remarkable. By comparison, the 1npe side
Scheme 1. Preparation of Model 1 and Cis/Trans Ratios
(Kcis/trans) Determined by NMR in Various Solvents (CDCl3,
CD3CN, (CD3)2CO, MeOD, D2O)
Next, we turned our attention to the solution-phase
synthesis of NtBu homo-oligomers by the submonomer
method. The initial conditions for the acylationꢀsubstitu-
tion iterations from N-tert-butyl glycine 3 were as follows:
bromoacetyl bromide in THF/Et3N at 0 °C for the first
step followed by the reaction of bromoacetamide inter-
mediates with tBuNH2 (4 equiv) in THF/Et3N at rt. These
conditions furnished only modest yields in bromoaceta-
mides, around 60%. We then found that replacing bro-
moacetyl bromide by freshly prepared bromoacetic
anhydride produced better yields.13 With the optimized
conditions (Scheme 2), chromatography is needed only
once by iteration, after the acylation; the excess of tBuNH2
used in the substitution is just evaporated off.14 The crude
secondary amines were directly used in the next iteration or
capped with an acetyl group to yield compounds 4ꢀ7.
Although tedious it might be possible to synthesize longer
NtBu glycine oligomers in solution, following our bro-
moacetic anhydride based protocol. A block approach
consisting of coupling short oligomers would, however,
be more straightforward to access longer oligomers. With
this in mind several conditions were tested for coupling
the amine 3 and the monomer acid AcꢀNtBuꢀOH. What-
ever the conditions used (HATU/DIEA, PyBrOP/DIEA,
EDCI/DMAP, and DIC/DMAP), the expected dimer 4
was not observed or produced in a very poor yield, not
exceeding 10%. Accordingly, the very sterically demand-
ing tBu side chain prevents any peptide coupling reaction,
even in solution.
(6) (a) Gorske, B. C.; Blackwell, H. E. J. Am. Chem. Soc. 2006, 128,
14378. (b) Huang, K.; Wu, C. W.; Sanborn, T. J.; Patch, J. A.;
Kirshenbaum, K.; Zuckermann, R. N.; Barron, A. E.; Radhakrishnan,
I. J. Am. Chem. Soc. 2006, 128, 1733. (c) Fowler, S. A.; Luechapanichkul,
R.; Blackwell, H. E. J. Org. Chem. 2009, 74, 1440.
(7) (a) Gorske, B. C.; Bastian, B. L.; Geske, G. D.; Blackwell, H. E.
J. Am. Chem. Soc. 2007, 129, 8928. (b) Gorske, B. C.; Stringer, J. R.;
Bastian, B. L.; Fowler, S. A.; Blackwell, H. E. J. Am. Chem. Soc. 2009,
131, 16555.
(8) The effect of thioamides in peptoids has been addressed recently:
Laursen, J. S.; Engel-Andreasen, J.; Fristrup, P.; Harris, P.; Olsen, C. A.
J. Am. Chem. Soc. 2013, 135, 2835.
(9) Caumes, C.; Roy, O.; Faure, S.; Taillefumier, C. J. Am. Chem.
Soc. 2012, 134, 9553.
1H and 13C NMR analysis of the NtBu series in various
deuterated solvents showed that these peptoids display
conformational homogeneity in solution. For example,
dimer 4 displays a unique set of resonances in CDCl3,
C6D6, CD3CN, CD3OD, (CD3)2CO, and(CD3)2SO, (see SI
(10) (a) Hjelmgaard, T.; Faure, S.; Staerk, D.; Taillefumier, C.;
Nielsen, J. Eur. J. Org. Chem. 2011, 4121. (b) Hjelmgaard, T.; Faure,
S.; De Santis, E.; Staerk, D.; Alexander, B. D.; Edwards, A. A.;
Taillefumier, C.; Nielsen, J. Tetrahedron 2012, 68, 4444.
(13) Bromoacetic anhydride is scarcely used in peptoid synthesis; see:
(a) Saha, U. K.; Roy, R. J. Chem. Soc., Chem. Commun. 1995, 2571.
(b) Hara, T.; Durell, S. R.; Myers, M. C.; Appella, D. H. J. Am. Chem.
Soc. 2006, 128, 1995. (c) Mas-Moruno, C.; Cruz, L. J.; Mora, P.;
Francesch, A.; Messeguer, A.; Perez-Paya, E.; Albericio, F. J. Med.
Chem. 2007, 50, 2443. (d) Jagasia, R.; Holub, J. M.; Bollinger, M.;
Kirshenbaum, K.; Finn, M. G. J. Org. Chem. 2009, 74, 2964.
(14) Our group has developed a highly convenient solution-phase
methodology using volatile amines: Caumes, C.; Hjelmgaard, T.;
Remuson, R.; Faure, S.; Taillefumier, C. Synthesis 2011, 257.
(11) It has been shown in peptides that the cis-isomer population of
the prolyl amide bond is enhanced when a proline residue is replaced by a
sterically hindered 5-tert-butylproline residue: (a) Halab, L.; Lubell,
W. D. J. Am. Chem. Soc. 2002, 124, 2474. (b) Halab, L.; Becker, J. A. J.;
ꢀ
ꢀ
ꢀ
Darula, Z.; Tourwe, D.; Kieffer, B. L.; Simonin, F.; Lubell, W. D.
J. Med. Chem. 2002, 45, 5353.
(12) This model is well suited for predicting the cis/trans ratio
(Kcis/trans) in oligomers: see ref 7b.
B
Org. Lett., Vol. XX, No. XX, XXXX

Table 1. Dihedral Angles of Dimer 4 Crystal Structure
Scheme 2. Optimized Solution-Phase Synthesis of NtBu Glycine
Oligomers
monomer
ω
j
ψ
Ac-(NtBu)
13.3
3.5
77.8
170.3
(NtBu)-COOBn
ꢀ97.4
ꢀ151.8
for details). 2D-NOESY data established a cisꢀcis amide
arrangement for dimer 4, and the cis-amide geometry
could be determined for three amides of four in the case
of tetramer 6. Overlapping of the methylene signals of the
Scheme 3. Solution-Phase Synthesis of (NtBu-NPh) Oligomers
1
backbone in the H NMR spectrum precluded amide
geometry determination of the fourth amide, and for the
same reason, amide geometry of longer oligomers could
not be established. Nevertheless, based on the observation
that the amides of the first members of the NtBu glycine
homo-oligomers exist exclusively in the cis conformation,
together with the observation that all the compounds
provide a unique set of 1H NMR signals, it can be assumed
that all the NtBu peptoids display an all-cis arrangement.
We were pleased to obtain crystals of dimer 4 (by slow
evaporation in Et2O) suitable for X-ray analysis (Table 1).
The crystal structure of dimer 4 confirmed that the two
amides were in the cis geometry. The centrosymmetric unit
cell contains obviously two enantiomeric forms of 4. The
dihedral angle (Table 1) values are very similar to those
observed in the crystal structure of the dimer Ac-(s1npe)2-
CO2tBu5 and in PPI-type peptoid helices.4f Therefore, it
is reasonable to assume that the NtBu homo-oligomers
adopt well-defined helical secondary structures similar to
those observed for peptoids bearing N-CR-branched side
chains. A model of the NtBu glycine peptoid hexamer 7
was constructed from the dihedral angles of the dimer 4
crystal structure and minimized at the B3LYP/6-31G(d)
level. This structure resembles a PPI-type helix and can be
superposed with great accuracy to the crystal structure of
pentamer Nrch54f (see SI for details).
backbone amide patterns. Indeed N-aryl side chains have
proven to be powerful side chains for enforcing trans
amides in peptoids;15 N-aryl amide bonds usually display
a >95% preference for the trans amide geometry in small
peptoid models.15a Repeating cisꢀtrans amide arrange-
ments were conceptually imagined more than half a century
ago by L. Pauling anR. Corey,16 but to date very little work
has yet been undertaken to explore the synthesis
and conformation of oligoamides involving cis and trans
amides in alternation.17 The expected peptoid series was
synthesized using a solution-phase submonomer protocol
Having demonstrated the applicability of the submono-
mer protocol for synthesizing NtBu homo-oligomers
featuring all-cis amide bonds, we next envisioned preparing
(NtBu-NPh) oligomers that display alternating cisꢀtrans
(15) (a) Shah, N. H.; Butterfoss, G. L.; Nguyen, K.; Yoo, B.;
Bonneau, R.; Rabenstein, D. L.; Kirshenbaum, K. J. Am. Chem. Soc.
2008, 130, 16622. (b) Stringer, J. R.; Crapster, J. A.; Guzei, I. A.;
Blackwell, H. E. J. Org. Chem. 2010, 75, 6068. (c) Paul, B.; Butterfoss,
G. L.; Boswell, M. G.; Renfrew, P. D.; Yeung, F. G.; Shah, N. H.; Wolf,
C.; Bonneau, R.; Kirshenbaum, K. J. Am. Chem. Soc. 2011, 133, 10910.
(16) Pauling, L.; Corey, R. B. Proc. Natl. Acad. Sci. U.S.A. 1953, 39,
247.
Org. Lett., Vol. XX, No. XX, XXXX
C

and SI for details), and the observation of a single set
of resonances for all the peptoids of this series evokes a
repeating cisꢀtrans pattern along the backbone of all the
members of the (NtBu-NPh) oligomers.
In conclusion, we have demonstrated that incorporation
of tBu side chains into peptoids locks the amide sites
in the cis conformation. Full suppression of the trans
conformers, whatever the solvent, organic or water and
the oligomer length is without precedent. We have further
shown the applicability of solution-phase submonomer
protocols for synthesizing all-cis NtBu glycine homo-
oligomers and a series of oligopeptoids displaying repeat-
ing cisꢀtrans amide patterns. Solid-phase synthesis of
peptoids containing NtBu side chains is currently investi-
gated in our group, and tBu functionalized side chains
bearing water-solubilizing groups and/or recognition
elements will be developed in due course.18
Figure 1. Conformation of peptoid 14 in solution. Observed
NOEs between backbone and side chains.
from tert-butyl bromoacetate (Scheme 3). Typically the
monomers were created by bromoacetylation (bromo-
acetylbromide in EtOAc at 0 °C in presence of Et3N)
followed by amine displacement with alternatively aniline
and tBuNH2. Reactions times of the substitutions were
approximately the same for both amines (15 h), but heating
(60 °C) was required in the case of substitution by aniline,
due to its deactivated character. All peptoids (9ꢀ13) were
readily synthesized in yields ranging from 58% to 75%
by iteration, with only one SiO2 chromatography every two
steps. Compounds 9, 11, and 13 were further acetylated to
yield peptoids 14ꢀ16.
Acknowledgment. This work was supported by the
French Ministry of Higher Education and Research
(MESR). We gratefully thank P.-A. Brun and M. Maltrait
ꢀ
(undergraduate students, Clermont-Universite) for their
contribution and A. Job and B. Legeret (Clermont-
ꢀ
ꢀ
Universite, ICCF) for HPLC and mass spectrometry
1D NMR analysis indicated that this series of peptoids
involving cis and trans directing side chains in alternation
display conformational homogeneity in solution. Despite
great effort in obtaining suitable crystals for X-ray diffrac-
tion, we were not able to grow crystals of sufficient size.
The cisꢀtrans arrangement was however firmly estab-
lished for dimer 14 from NOESY cross peaks (Figure 1
analysis. The authors thank the ‘service commun de
diffraction X” of the University of Lorraine for XRD
facilities.
Supporting Information Available. Experimental pro-
cedures; NMR and mass spectrometry characterization
1
for compounds 1, 4ꢀ8, and 14ꢀ16; H and 13C spectra
for compounds 1, 4ꢀ7, and 14ꢀ16; NOESY spectra for
compounds 4 and 14; analytical RP-HPLC for com-
pounds 4ꢀ7 and 14ꢀ16; computational-based model
structure of hexamer 7. This material is available free of
charge via the Internet at http://pubs.acs.org.
(17) (a) Crisma, M.; Moretto, A.; Toniolo, C.; Kaczmarek, K.
Macromolecules 2001, 34, 5048. (b) Paul, B.; Butterfoss, G. L.; Boswell,
M. G.; Huang, M. L.; Bonneau, R.; Wolf, C.; Kirshenbaum, K. Org.
Lett. 2012, 14, 926. (c) This work was published during the editing
process of our article: Crapster, J. A.; Guzei, I. A.; Blackwell, H. E.
Angew. Chem. Int. Ed. 2013, DOI: 10.1002/anie.201208630.
(18) Pandey, A. K.; Naduthambi, D.; Thomas, K. M.; Zondlo, N. J.
J. Am. Chem. Soc. 2013, 135, 4333.
The authors declare no competing financial interest.
D
Org. Lett., Vol. XX, No. XX, XXXX