Helix formation in preorganized β/γ-peptide foldamers: Hydrogen-bond analogy to the α-helix without α-amino acid residues

Article abstract of DOI:10.1021/ja103233a

We report the first high-resolution structural data for the β/γ-peptide 13-helix (i,i+3 CO...HN H-bonds), a secondary structure that is formed by oligomers with a 1:1 alternation of β- and γ-amino acid residues. Our characterization includes both crystallophaphic and 2D NMR data. Previous studies suggested that β/γ-peptides constructed from conformationally flexible residues adopt a different helical secondary structure in solution. Our design features preorganized β- and γ-residues, which strongly promote 13-helical folding by the 1:1 β/γ backbone.

Full text of DOI:10.1021/ja103233a

Published on Web 05/24/2010
Helix Formation in Preorganized ꢀ/γ-Peptide Foldamers: Hydrogen-Bond
Analogy to the r-Helix without r-Amino Acid Residues
Li Guo, Aaron M. Almeida, Weicheng Zhang, Andrew G. Reidenbach, Soo Hyuk Choi, Ilia A. Guzei,
and Samuel H. Gellman*
Department of Chemistry, UniVersity of Wisconsin, Madison, Wisconsin 53706
Received April 16, 2010; E-mail: gellman@chem.wisc.edu
Identification of new types of foldamers with strong and discrete
secondary structural propensities is a subject of ongoing research.1
These studies enhance our understanding of the relationship between
local conformational preferences and molecular shape. In addition,
new folding patterns can be valuable for specific applications.2,3
Foldamers that contain more than one type of subunit, i.e., oligomers
that have heterogeneous backbones, have been a subject of extensive
recent interest.1e Most examples involve a combination of R-amino
acid residues with other types of subunits, including those derived
from ꢀ-4 or γ-amino acids5 or other building blocks.6 Heterogeneous
backbones that do not include R-amino acid residues have received
relatively limited attention,5e,7 perhaps because R-amino acids are
far more available than are other building blocks. Backbones with
alternating ꢀ- and γ-amino acid residues (ꢀ/γ-peptides) are of
particular interest because a ꢀ/γ-dipeptide has the same number of
atoms between the N- and C-termini as an R-tripeptide.5b An
Figure 1. Structures of ꢀ/γ-peptides 3, 4, 5 (arrows indicate H-bonds in
extended ꢀ/γ-peptide can in principle form a helix containing 13-
membered ring backbone H-bonds (CdO(i)--HsN(i+3)) that are
analogous to the 13-membered ring backbone H-bonds characteristic
of the R-helix (CdO(i)--HsN(i+4)). However, Sharma, Kunwar
et al.5e have recently reported that flexible ꢀ/γ-peptides adopt a
different type of helical conformation in solution. Here we show
that ꢀ/γ-peptides containing appropriately preorganized subunits
do indeed adopt the 13-helix in solution and the solid state.
The ꢀ/γ-peptide 13-helix is predicted by Hofmann et al.5d to
have g+,g+ or g-,g- local conformations about the CR-Cꢀ (ꢁ) and
Cꢀ-Cγ (θ) bonds in the γ-residues and a CR-Cꢀ torsion angle of
∼90° in the ꢀ-residues. Based on these predictions and available
data for the conformational propensities of constrained ꢀ- and
γ-residues in other contexts, we concluded that combining (R,R,R)
γ-residue 1 (Figure 1), which has recently become available,5i,8
with (R,R)-trans-2-aminocyclopentanecarboxylic acid (ACPC, 2)
should favor formation of the left-handed ꢀ/γ-peptide 13-helix (the
right-handed helix should be favored by residues with S configura-
tions). This hypothesis was tested by preparation and analysis of
tetramer 3, pentamer 4, and hexamer 5 (Figure 1).
the crystal structures of 3 and 4).
Figure 2. Crystal structures of 3 (left) and 4 (right): (top) views
perpendicular to helical axis; (bottom) views along the helical axis.
of the possible CdO(i)--HsN(i+3) H-bonds are formed (Figure
2). Table 1 compares backbone torsion angles for the ꢀ- and
γ-residues in pentamer 4 with analogous values from the compu-
tational work of Hofmann et al.5d and from the NMR analysis of
flexible ꢀ/γ-peptides in organic solvent by Sharma, Kunwar et al.5e
The preorganized γ-residues in 4 display g+,g+ local conformations
about the CR-Cꢀ (ꢁ) and Cꢀ-Cγ (θ) bonds and ψ and φ near -120°,
with a somewhat wider distribution for the latter torsion angle.
These values are consistent with the predictions for the 13-helical
conformation from Hofmann et al.5d In contrast, the helical
conformations deduced via NMR for flexible ꢀ/γ-peptides feature
opposite signs for the ꢁ and θ torsion angles (g-,g+) and opposite
signs for the ψ and φ torsion angles. The helical conformation
deduced for these flexible ꢀ/γ-peptides has a distinctive H-bonding
The crystal structure of ꢀ/γ-peptide 3 contains two molecules
in the asymmetric unit; the two conformations are very similar
(Figure 2). Each independent molecule forms one 13-atom H-
bonded ring, involving the NH group of the second ACPC residue
and the carbonyl of the N-terminal Boc group. The other possible
13-atom ring H-bond does not form in either case [N--O distance
∼4.9 Å]; instead, each molecule contains an 8-atom ring H-bond
involving the carbonyl of the first γ-residue and the NH group of
the second γ-residue. Despite this deviation from the 13-helical
H-bonding pattern, the backbone torsion angles for the ꢀ- and
γ-residues in 3 generally fall in ranges predicted by Hofmann et
al.5d for the ꢀ/γ-peptide 13-helix.9
Pentamer 4, containing ꢀ- and γ-residues with S configurations,
adopts the right-handed 13-helix in the crystalline state. All three
9
7868 J. AM. CHEM. SOC. 2010, 132, 7868–7869
10.1021/ja103233a  2010 American Chemical Society

C O M M U N I C A T I O N S
Table 1. Backbone Torsion Angles (deg)a of Helical ꢀ/γ-Peptides
Acknowledgment. This research was supported by the NSF
(CHE-0848847). NMR spectrometers were purchased with partial
support from the NIH and NSF.
Peptides
residues
φ
θ
ꢁ
ψ
ꢀ/γ pentamer 4
ꢀ1
γ2
ꢀ3
γ4
ꢀ5
ꢀ
-107.7
-134.7
-133.6
-147.3
-167.9
93.3
60.1
113.5
57.9
-128.3
59.8 -121.0
-85.7
46.5 -129.8
-155.0
Supporting Information Available: Experimental procedures and
compound characterizations. This material is available free of charge
via the Internet at http://pubs.acs.org.
141.4
computational
89.1 -94.1
121.9
132.0
0
studyb 5d
γ
124.9 -60.4 -62.2
120
120
,
References
(1) (a) Gellman, S. H. Acc. Chem. Res. 1998, 31, 173. (b) Seebach, D.; Beck,
A. K.; Bierbaum, D. J. Chem. BiodiVerstiy 2004, 1, 1111. (c) Hecht, S.,
Huc, I., Eds. Foldamers: Structure, Properties and Applications; Wiley-
VCH Weinheim: Germany, 2007. (d) Goodman, C. M.; Choi, S.; Shandler,
S.; DeGrado, W. F. Nat. Chem. Biol. 2007, 3, 252. (e) Horne, W. S.;
Gellman, S. H. Acc. Chem. Res. 2009, 41, 1399.
flexible ꢀ/γ tetramer
ꢀ
γ
60
-60
(NMR)5e
60
-120
a Nomenclature for the backbone torsion angles in ꢀ/γ-peptides is
described in Figure 1. b Average backbone torsion angles.
(2) Recent examples of biologically active foldamers: (a) Claudon, P.; Violette,
A.; Lamour, K.; Decossas, M.; Fournel, S.; Heurtault, B.; Godet, J.; Mely,
Y.; Jamart-Gregoire, B.; Averlant-Petit, M.-C.; Briand, J.-P.; Duportail,
G.; Monteil, H.; Guichard, G. Angew. Chem., Int. Ed. 2010, 49, 333. (b)
Horne, W. S.; Johnson, L. M.; Ketas, T. J.; Klasse, P. J.; Lu, M.; Moore,
J. P.; Gellman, S. H. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 14751. (c)
Jochim, A. L.; Miller, S. E.; Angelo, N. G.; Arora, P. S. Bioorg. Med.
Chem. Lett. 2009, 19, 6023. (d) Choi, S.; Isaacs, A.; Clements, D.; Liu,
D. H.; Kim, H.; Scott, R. W.; Winkler, J. D.; DeGrado, W. F. Proc. Natl.
Acad. Sci. U.S.A. 2009, 106, 6968. (e) Bautista, A. D.; Stephens, O. M.;
Wang, L. G.; Domaoal, R. A.; Anderson, K. S.; Schepartz, A. Bioorg. Med.
Chem. Lett. 2009, 19, 3736. (f) Brown, N. J.; Wu, C. W.; Seurynck-Servoss,
S. L.; Barron, A. E. Biochemistry 2008, 47, 1808. (g) For earlier examples,
see ref 1d.
Figure 3. Characteristic NOE patterns observed for the 1:1 ꢀ/γ-peptide
hexamer 5 in pyridine-d5.
(3) Sadowsky, J. D.; Fairlie, W. D.; Hadley, E. B.; Lee, H. S.; Umezawa, N.;
Nikolovska-Coleska, Z.; Wang, S. M.; Huang, D. C. S.; Tomita, Y.;
Gellman, S. H. J. Am. Chem. Soc. 2007, 129, 139.
pattern with two types of interaction: CdOγ(i)--HsNꢀ(i-1) and
CdOꢀ(i)--HsNγ(i+3).
(4) (a) De Pol, S.; Zorn, C.; Klein, C. D.; Zerbe, O.; Reiser, O. Angew. Chem.,
Int. Ed. 2004, 43, 511. (b) Hayen, A.; Schmitt, M. A.; Ngassa, F. N.;
Thomasson, K. A.; Gellman, S. H. Angew. Chem., Int. Ed. 2004, 43, 505.
(c) Sharma, G. V. M.; Nagendar, P.; Jayaprakash, P.; Krishna, P. R.;
Ramakrishna, K. V. S.; Kunwar, A. C. Angew. Chem., Int. Ed. 2005, 44,
5878. (d) Mandity, I. M.; Weber, E.; Martinek, T. A.; Olajos, G.; Toth,
G. K.; Vass, E.; Fulop, F. Angew. Chem., Int. Ed. 2009, 48, 2171. (e) For
a heterogeneous backbone review, see ref 1e.
(5) (a) Hagihara, M.; Anthony, N. J.; Stout, T. J.; Clardy, J.; Schreiber, S. L.
J. Am. Chem. Soc. 1992, 114, 6568. (b) Karle, I. L.; Pramanik, A.; Banerjee,
A.; Bhattacharjya, S.; Balaram, P. J. Am. Chem. Soc. 1997, 119, 9087. (c)
Ananda, K.; Vasudev, P. G.; Sengupta, A.; Raja, K. M. P.; Shamala, N.;
Balaram, P. J. Am. Chem. Soc. 2005, 127, 16668. (d) Baldauf, C.; Gunther,
R.; Hofmann, H. J. J. Org. Chem. 2006, 71, 1200. (e) Sharma, G. V. M.;
Jadhav, V. B.; Ramakrishna, K. V. S.; Narsimulu, K.; Subash, V.; Kunwar,
A. C. J. Am. Chem. Soc. 2006, 128, 14657. (f) Baruah, P. K.; Sreedevi,
N. K.; Gonnade, R.; Ravindranathan, S.; Damodaran, K.; Hofmann, H. J.;
Sanjayan, G. J. J. Org. Chem. 2007, 72, 636. (g) Vasudev, P. G.; Ananda,
K.; Chatterjee, S.; Aravinda, S.; Shamala, N.; Balaram, P. J. Am. Chem.
Soc. 2007, 129, 4039. (h) Chatterjee, S.; Vasudev, P. G.; Raghothama, S.;
Ramakrishnan, C.; Shamala, N.; Balaram, P. J. Am. Chem. Soc. 2009, 131,
5956. (i) Guo, L.; Chi, Y.; Almeida, A. M.; Guzei, I. A.; Parker, B. K.;
Gellman, S. H. J. Am. Chem. Soc. 2009, 131, 16018. (j) Chakraborty, T. K.;
Rao, K. S.; Kiran, M. U.; Jagadeesh, B. Tetrahedron Lett. 2009, 50, 4350.
(k) Araghi, R. R.; Jackel, C.; Cofen, H.; Salwiczek, M.; Vokel, A.; Wagner,
S. C.; Wieczorek, S.; Baldauf, C.; Koksch, B. ChemBioChem 2010, 11,
335.
(6) (a) Yang, D.; Li, W.; Qu, J.; Luo, S. W.; Wu, Y. D. J. Am. Chem. Soc.
2003, 125, 13018. (b) Chowdhury, S.; Schatte, G.; Kraatz, H. B. Angew.
Chem., Int. Ed. 2006, 45, 6882. (c) Olsen, C. A.; Bonke, G.; Vedel, L.;
Adsersen, A.; Witt, M.; Franzhk, H.; Jaroszewski, J. W. Org. Lett. 2007,
9, 1549. (d) Zhao, Y.; Zhong, Z. Q.; Ryu, E. H. J. Am. Chem. Soc. 2007,
129, 218. (e) Angelici, G.; Luppi, G.; Kaptein, B.; Broxterman, Q. B.;
Hofmann, H. J.; Tomasini, C. Eur. J. Org. Chem. 2007, 2713. (f) Sakai,
N.; Mareda, J.; Matile, S. Acc. Chem. Res. 2008, 41, 1354. (g) Sharma,
G. V. M.; Babu, B. S.; Ramakrishna, K. V.; Nagendar, P.; Kunwar, A. C.;
Schramm, P.; Baldauf, C.; Hofmann, H. J. Chem.sEur. J. 2009, 15, 5552.
(h) Sharma, G. V. M.; Babu, B. S.; Chatterjee, D.; Ramakrishna, K. V. S.;
Kunwar, A. C.; Schramm, P.; Hofmann, H. J. J. Org. Chem. 2009, 74,
6703. (i) Hetenyi, A.; Toth, G. K.; Somlai, C.; Vass, E.; Martinek, T. A.;
Fulop, F. Chem.sEur. J. 2009, 15, 10736.
Hexamer 5 did not produce high-quality crystals, but 2D 1H NMR
analysis in pyridine-d5 solution indicated that the 13-helix is
significantly populated under these conditions. Among the unam-
biguous NOEs involving backbone protons, six strong NOEs were
observed between protons from residues that are not adjacent in
the sequence: CꢀH(1)--NH(3), CꢀH(1)--CRH(3), CγH(2)--NH(4),
CꢀH(3)--NH(5), CꢀH(3)--CRH(5), and CγH(4)--NH(6) (Figure 3).
These NOEs are consistent with intramolecular proton-proton
distances in the crystal structure of pentamer 4: CꢀH(1)--NH(3) )
3.5 Å, CꢀH(1)--CRH(3) ) 2.7 Å, CγH(2)--NH(4) ) 2.8 Å, CꢀH(3)--
NH(5) ) 2.3 Å, and CꢀH(3)--CRH(5) ) 2.2 Å. Thus, the three NOE
patterns observed for 5, CꢀH(i)--NH(i+2) and CꢀH(i)--CRH(i+2)
for ꢀ-residues and CγH(i)--NH(i+2) for γ-residues, appear to be
general indicators of ꢀ/γ-peptide 13-helical secondary structure.
The ꢀ/γ-peptide helix we have documented is interesting because
of its relationship to the R-helix formed by pure R-residue
backbones. Both helices contain 13-atom ring H-bonds. Detailed
comparison of the two helices reveals further similarities: both have
a rise-per-turn of 5.4 Å, and the radii are similar (2.5 vs 2.3 Å).9
These parameters suggest that the ꢀ/γ-peptide 13-helix may be a
promising scaffold for functional mimicry of natural R-helices.2b,3
Our results show that appropriately preorganized residues
promote the formation of the 13-helical conformation in short ꢀ/γ-
peptides. This secondary structure was anticipated (along with
alternative helices) in computational studies,5c,d and hints of 13-
helical propensity can be found in the local conformations observed
in crystal structures for isolated ꢀ-γ segments,5b,g but the only
previous analysis of ꢀ/γ-peptide oligomer folding indicated the
formation of a different helical conformation, containing both 11-
and 13-membered ring H-bonds.5e Conformationally constrained
ꢀ-amino acid residues have been shown to induce novel secondary
structures,1a,e,10 and the present studies highlight the prospect that
constrained γ-amino acid residues will be similarly useful in
controlling molecular shape.
(7) (a) Gong, B.; Zeng, H.; Zhu, J.; Yuan, L.; Han, Y.; Cheng, S.; Furukawa,
M.; Parra, R. D.; Kovalevsky, A. Y.; Mills, J. L.; Skrzypczak-Jankun, E.;
Martinovic, S.; Smith, R. D.; Zheng, C.; Szyperski, T.; Zeng, X. C. Proc.
Natl. Acad. Sci. U.S.A. 2002, 99, 11583. (b) Delsuc, N.; Godde, F.;
Kauffmann, B.; Leger, J. M.; Huc, I. J. Am. Chem. Soc. 2007, 129, 11348.
(8) A complementary example: Nodes, W. J.; Nutt, D. R.; Chippindale, A. M.;
Cobb, A. J. A. J. Am. Chem. Soc. 2009, 131, 16016.
(9) See the Supporting Information.
(10) Schmitt, M. A.; Choi, S. H.; Guzei, I. A.; Gellman, S. H. J. Am. Chem.
Soc. 2005, 127, 13130.
JA103233A
9
J. AM. CHEM. SOC. VOL. 132, NO. 23, 2010 7869