Novel helical foldamers: Organized heterogeneous backbone folding in 1:1 α/nucleoside-derived-β-amino acid sequences

Article abstract of DOI:10.1039/c0cc01724h

Secondary structural conformation of hybrid oligo-peptides comprised of 1:1 alternating Nucleoside Derived β-Amino acid (NDA) and l-amino acid residues has been reported. The studies reveal that the NDA residues organize the heterogeneous backbone featuri

Full text of DOI:10.1039/c0cc01724h

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Novel helical foldamers: organized heterogeneous backbone folding
in 1 : 1 a/nucleoside-derived-b-amino acid sequenceswz
Srivari Chandrasekhar,*a Nayani Kiranmai,a Marelli Udaya Kiran,b Ambure Sharada Devi,bc
Gangireddy Pavan Kumar Reddy,a Mohammed Idrisc and Bharatam Jagadeesh*b
Received 3rd June 2010, Accepted 29th July 2010
DOI: 10.1039/c0cc01724h
Secondary structural conformation of hybrid oligo-peptides
comprised of 1 : 1 alternating Nucleoside Derived b-Amino acid
(NDA) and L-amino acid residues has been reported. The studies
reveal that the NDA residues organize the heterogeneous backbone
featuring the surface properties of both nucleic acids and peptides,
to adopt a novel 11/8-helical fold.
been explored. Herein we report the formation of 11/8 helical
folding in short oligomers 2–5 (trimer to hexamer) comprised
of 1 : 1 alternating NDA and L-amino acid monomers.
Essentially in these heterogeneous backbone structures, the
4-atom achiral phosphodiester linker in a nucleic acid chain is
replaced by a 5-atom linker consisting of a chiral amino acid,
flanked by two peptide bonds.
Hybrid peptides1,2 comprised of natural a and unnatural cyclic
b-amino acids, particularly in 1 : 1, 1 : 2 and 2 : 1 ratios have
emerged as new generation foldamers.3–7 Based on the choice
of b-amino acid monomer and a/b ratio, the relative positions
or orientations of the a-amino acid side-chains can be
controlled so as to access higher order folds8,9 and specific
molecular recognitions, inluding protein inhibition.10–13 These
reports have highlighted the scope for developing new
a/b-hybrid templates and the importance of obtaining
information about their conformational preferences. The
present work focuses in this direction.
The compounds 2–5 (Fig. 1) have been synthesized from
NDA (1) and L-amino acids (Ala, Phe and Val) by using
standard coupling protocols and have been characterized by
using extensive NMR studies, restrained MD simulations and
1
DFT calculations.z H chemical shift assignment has been
carried out by using DQF-COSY, TOCSY and ROESY
experimental data. NH proton chemical shifts are found to
be nearly invariant with the increase of sample concentration
varied up to 10 mM,z suggesting the absence of inter-
molecular aggregation. Sample concetration of B5 mM has
been used for NMR studies of compounds 2–5. Trimer 2 has
been analyzed in pure CDCl3 solvent at 300 K. Complete
exchange of thymidine base NHs and Boc-NH with residual
water present in CDCl3 has suggested that they are freely
accessible by the solvent and not participating in any hydrogen
bonding. The dispersion and down field shifts of the 2NH
and 3NH is consistent with their involvement in hydrogen
Diederichsen’s research group has shown residue based
conformational control in hetero-oligomers comprised of
cyclic-trans-b-ACHC (14-helix promoting motif) and linear
b3-amino acids with nucleobase side-chains. These oligomers
preferentially adopt 14-helix14 and form self-assembled complexes
through inter-helical complementary base-pairing.15 Recently,
our group16 and Threlfall et al.17 have independently reported
Nucleoside Derived b-Amino acid (NDA), 1, which is a novel
cyclic-trans-b-amino acid with nucleobase as a side-chain. In
a logical extension, developing hybrid peptide oligomers
based on a a/NDA combination, where NDA provides the
conformational control, would enhance the realm of
the function oriented molecules as they carry the surface
properties of natural peptides as well as nucleic acids. Gogoi
and co-workers have shown that the 1 : 1 a/NDA peptides
exhibit binding affinity for DNA/RNA strands.18 However, it
is important to know the conformational preferences
and spatial organization of this novel class of molecules for
subsequent design and development, which hitherto have not
3
bonding. JH1,H2 coupling constants of 0–2 Hz for NDA
residues in 2 indicate dihedral angles y of B901–1101. Detailed
analysis of ROESY spectra of 2 has shown a long range
iNHn–(iꢀ2)H2n (i = 3) ROE cross-peak, which is characteristic
of a turn that favours a 11-membered hydrogen bonding
i
between NHn–(iꢀ3)COa (Fig. 2a).z The subscripts ‘n’ and ‘a’
represent NDA and L-amino acid/Boc residues, respectively,
and the superscript ‘i’ represents the residue number.
This folding is further strongly supported by unambiguous
iNHn–(iꢀ2)H1n, iH1n–(iꢀ2)H2n and iH4n–(iꢀ2)H2n (i = 3) ROEs
(for detailed ROESY spectra, please see ESIz). Only one such
11-membered H-bonding is possible in
2
involving
3NH–(Boc)CO. The DMSO-titration studiesz have suggested
that in addition to the 3NH, the 2NH also participates in
a Organic Division-I, Indian Institute of Chemical Technology
(CSIR), Uppal Road, Tarnaka, Hyderabad-500 607 (AP), India.
E-mail: srivaric@iict.res.in
b Centre for Nuclear Magnetic Resonance, Indian Institute of
Chemical Technology (CSIR), Uppal Road, Tarnaka,
Hyderabad-500 607 (AP), India. E-mail: bj@iict.res.in
c Centre for Cellular and Molecular Biology (CSIR), Uppal Road,
Tarnaka, Hyderabad-500 607 (AP), India
w The work has been dedicated to Dr J. S. Yadav on his 60th birthday.
z Electronic supplementary information (ESI) available: Synthesis,
NMR Experimental, MD and DFT data. See DOI: 10.1039/
c0cc01724h
Fig. 1 A schematic representation of Nucleoside Derived Amino
acid, NDA and the hetero-oligomers synthesized from NDA and
L-amino acids.
c
6962 Chem. Commun., 2010, 46, 6962–6964
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Fig. 3 Minimum energy structures obtained from DFT calculations
on (a) trimer 2 and (b) tetramer 3 show the possible 11/8 hydrogen
bonded turns. The 11-member and 8-member hydrogen bonds are
shown in dotted blue and orange lines, respectively.
additional 8-membered H-bonding with iNHa, leading
to [iNHn–(iꢀ3)COa]/[iNHa–(iꢀ2)COa] 11/8 H-bonds in
equilibrium. In 4, the later two ROEs are found for 4NH
also, which, however, support only a 4NH–2CO 8-membered
H-bonded turn as the chain length of the tetramer limits any
further possibility of a 11-membered H-bond for 2CO. The
iH4n–(iꢀ2)H2n and iH1n–(iꢀ2)H2n ROEs observed for the
oligomers 2–4 further portray the overlying arrangement of
consecutive NDA residues. No ROEs are observed that
i
support the geometrical positioning of NHa’s near (iꢀ3)COb
to favor only a single 11-helix in these oligomers. As suggested
by the DMSO titration studies of 3 and 4,z the relatively lower
strength of the 8-membered H-bonds in the 11/8 helical fold
may be attributed to the possible non-linearity of the
H-bonds.z Similar observations are noted for bifurcated
H-bonds in other peptides.19
To ascertain the folding propensities and hydrogen bond
modes in these hybrid peptides, we have carried out DFT
calculations for trimer 2 and tetramer 3, at B3LYP/6-31G*
level by using Gaussian 09.20 The minimum energies of the
system were obtained by harmonic frequency calculations. The
optimization initially was carried out in vacuum and then
optimized in solvent by using PCM (Polarizable Continuum
Model). The lowest energy structures (Fig. 3) have shown
Fig. 2 Schematic representations of observed ROEs (black solid
arrows) that characterize the turns with 11/8 hydrogen bonding for
2 (a), 3 (b), 4 (c) and 5 (d). The 11-member and 8-member hydrogen
bonds are shown in dotted blue and orange lines, respectively.
hydrogen bonding of moderate strength, which is likely an
8-membered hydrogen bonding with the same (Boc)CO. As
shown later, the ROE and 3JH restrained MD simulationsz
have also supported the formation of 11/8-helical fold,
possibly with a rapid inter-conversion of 11 and 8-membered
hydrogen bonding on the time-scales of NMR.
a
helical turn with 11/8 hydrogen bonding involving
iNHn–(iꢀ3)COa and iNHa–(iꢀ2)COa, respectively. The structures
did not violate the observed ROEs and are consistent with the
solution state NMR structures.
Two different tetramers: 3 and 4, with L-amino acid (Phe)
and NDA at N-terminus, respectively, were characterized
further. NMR spectroscopic studies of 3 and 4 have been
carried out in CDCl3 and a mixture CDCl3 (500 mL)/DMSO
(10 mL), respectively. The 2NH resonance in 3 is very broad
and is not useful for accurate estimates of ROEs. Nevertheless,
The hexamer 5, due to its polar nature, is insoluble in CDCl3
and the NMR spectroscopic studies had to be carried out in a
mixture of CDCl3 (500 mL) and DMSO (90 mL). The 1H
resonances are relatively less resolved, however, adequate
spatial information is obtained that can be attributed to a
specific folding. The peptide 5 has exhibited similar ROE
patternz (Fig. 2d) as observed for the oligomers 2–4:
iNHn–(iꢀ2)H2n (two out of the two possible ROEs),
3
and
4
have exhibited characteristic iNHn–(iꢀ2)H2n,
iNHn–(iꢀ2)H1n and H4n–(iꢀ2)H2n long range ROE patternsz
(from fourth NDA residue to the second NDA residue and
from third NDA residue to the first NDA residue, respectively,
Fig. 2b and c) similar to that observed in trimer 2. These
findings are consistent with the formation of 11-membered
iNHn–(iꢀ3)COa hydrogen bonded turns involving 4NH and
(Phe)CO in 3; and 3NH and (Boc)CO in 4. Furthermore, the
iNHa–(i+1)NHn, iNHa–(iꢀ1)H1n and iNHa–(iꢀ1)H2n ROEs
observed for the 3NH (Ala) in 3 and 2NH (Ala) in 4
i
i
iH4n–(iꢀ2)H2n (one out of two), NHa–(i+1)NHn (two out of
two), and iNHa–(iꢀ1)H2n (two out of two) that strongly
support the propagation of 11/8-helix in this higher oligomer
as well. The ROEs that support other helical conformations
are not observed. It is interesting to note that the conforma-
tional preference in these oligomers is unique and differs from
that of other known 1 : 1 a/b hybrid peptides (11 and
14/15-helical folds),4a,5 which are based on cyclo alkane or
furanoid sugar b-amino acids.
i
(Fig. 2b and c)z support a closer proximity between NHa
and (iꢀ2)COa, which implicates this carbonyl oxygen in an
c
This journal is The Royal Society of Chemistry 2010
Chem. Commun., 2010, 46, 6962–6964 6963

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NK, MUK and GPKR thank CSIR, New Delhi for
research fellowship.
Notes and references
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Fig. 4 Superimposed minimum energy structures from MD studies
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3
Phe as 1.8 A reference) and dihedral angles derived from JH
coupling constants, as the restraints. The minimum energy
structures obtained from the simulations have shown a good
convergence to 11/8 helical folds (Fig. 4), with a non-linear
(901–1301) and relatively longer H-bond distance (2.5–2.8 A)
for 8-membered H-bond.z However, the H-bond distances
are observed to be B2.4 A for 11-membered and isolated
C-terminal 8-membered H-bonds. The representative dihedral
angles for NDA residues are (f, y, c) = (ꢀ801, +1201, ꢀ901)
and for L-amino acids (f, c) = (ꢀ651, ꢀ501).
In summary, the present study reveals that the heterogeneous
backbone structures comprised of 1 : 1 NDA and L-amino acids
preferentially adopt a right-handed helical fold with rapidly
interconverting periodic 11/8-hydrogen bonded rings. The
study signifies that the NDA organized spatial arrangement
of the heterogeneous backbone and side-chains differs from that
of other a/b peptides. These studies offer input for subsequent
design and control of the backbone folding with functional
traits of both the biomolecules: proteins and nucleic acids.
Further studies are in progress in this direction.
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6964 Chem. Commun., 2010, 46, 6962–6964
This journal is The Royal Society of Chemistry 2010