Formation of a stable 14-helix in short oligomers of furanoid cis-β-sugar-amino acid

Article abstract of DOI:10.1021/ja0467667

Oligomers of a new class of sugar amino acids (SAA) using a xylofuranoic acid has been shown to generate a robust 14-helix. The design involved the use of xylofuranose with a cis arrangement between the amine and carboxyl groups to promote the adoption of a 14-helix instead of a mixed 12/10-helix observed in a sugar oligomer using a ribofuranoic acid and β-Ala. The observation of a stable right-handed 14-helix in a cis-SAA is unprecedented. Copyright

Full text of DOI:10.1021/ja0467667

Published on Web 10/05/2004
Formation of a Stable 14-Helix in Short Oligomers of Furanoid
cis-â-Sugar-Amino Acid|
Srivari Chandrasekhar,*,† Marepally Srinivasa Reddy,† Bharatam Jagadeesh,*,‡
Anabathula Prabhakar,‡ Mallem H. V. Ramana Rao,‡ and Bulusu Jagannadh*,§
Indian Institute of Chemical Technology, Hyderabad 500 007, India
Received June 2, 2004; E-mail: srivaric@iict.res.in; bj@iict.res.in; jagan@iict.res.in
Scheme 1
The design and synthesis of new molecular architectures with
predictable, well-defined secondary templates is an important area
of research. â-Peptides have recently emerged as key leads in the
design of such structures because they display an impressive range
of structural diversity, including helices, sheets, and turns.1 The
interest in unnatural biopolymers is attracting increasing attention
due to the new biocompatible materials that can be made from them.
The applications include, among others, self-assembling complexes
and lead candidates in drug discovery programs. Research groups
of Seebach2 and Gellman3 have shown in their pioneering contribu-
tions that the oligomers using different side chains at the â2 or â3
positions offer the opportunity for the rational design of different
types of helical conformations. The conformational space of â-pep-
tides was extensively studied to understand the design principles
of the secondary structures.4
The ongoing research activity in our laboratory focuses on the
conformational control over the helix type and symmetry.5 Gell-
man’s research group3b has shown that by incorporating the CR
and Câ bond into a trans cycloalkane based â-amino acid and by
varying the ring size the helix type can be controlled. Five- and
six-membered rings stabilize the 12- and 14-helix, respectively.
Kessler’s research group6 has shown that a mixed oligomer
containing a furanoid (ribofuranoic acid) trans-sugar amino acids
(SAA) and a â-Ala generated a mixed 12/10-helix. Here, we show
that a choice of xylofuranoic acid over a ribofuranoic acid in a
cis-SAA can induce the formation of a stable 14-helix in a
homooligomer. The molecular mechanics calculations carried out
by us on a ribofuranoic acid and a xylofuranoic acid have shown
that the angle NsCâsCRsC(dO), designated7 as θ, takes a value
either ∼90° (in a 12-helix) or ∼60° (in a 14-helix). The calculations
have encouraged the synthesis and structural characterization of
cis-SAA homooligomers.
The increased molecular ellipticity per residue in the CD spectra
of 5 and 6 confirm the stabilization of and increase in the population
of the 14-helix with the increasing length of the peptide.
It would be instructive to obtain structural insight into the new
amino acid in particular regarding the helix-forming nature of the
homooligomer. Accordingly, we have studied the conformations
of 4-6 by NMR investigations, which were supplemented by
molecular mechanics and restrained molecular dynamics calcula-
tions.
NMR studies were carried out in CDCl3 solution, and the signal
assignments were established by two-dimensional DQF-COSY,
TOCSY, and ROESY experiments. The dispersion of the chemical
shifts of the amide protons indicates the presence of a secondary
structure, which increases from 1.06 to 1.33 ppm with increasing
3
number of residues in 4-6. For all these peptides JCRH-CâH was
observed to be <5 Hz which clearly demonstrated the presence of
predominantly a single conformation around CR-Câ (θ) ≈ 60°
for each residue, a prerequisite for a helix3a. Furthermore, the
calculations of sugar-ring pucker using the refined Karplus equa-
tion13 has resulted in P ≈ 180° and φm ≈ 55° for all the residues.
The φm value also agrees with the requirement of a 14-helix.
The monomers 2a and 2b were synthesized8 from known azido
sugar derivative9 1 (Scheme 1) which were subsequently used to
prepare dimer 3, tetramer 4, hexamer 5, and octamer 6 (Figure 2)
by standard coupling protocol using EDCI and HOBt re-
agents.10,11 In the present scheme the azido group was retained until
the end of oligomer synthesis, and then it was converted to the
NH-Boc.
The circular dichroism (CD) spectroscopy of â-amino acids
provides characteristic signatures of helical conformation of various
peptides. The CD spectra for 4-6 in 200 µM solutions in methanol
presented in Figure 1 suggest the adoption of a distinctive secondary
structure. Tetramer 4 displays a minimum, zero crossing and a
maximum at 198, 209, and 218 nm, respectively, corresponding to
the formation of a right-handed 14-helix.12
† Division of Organic Chemical Sciences.
‡ NMR Group.
§ Molecular Modeling Group.
| IICT Communication No: 040516.
Figure 1. CD spectra of 4-6 normalized for amide chromophores.
9
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10.1021/ja0467667 CCC: $27.50 © 2004 American Chemical Society

C O M M U N I C A T I O N S
Figure 3. NMR structures of the cis-SAA peptides 4-6 as a bundle of the
10 lowest-energy structures calculated from restrained MD simulations: (a)
tetramer 4, side view; (b) hexamer 5, top view from C-terminus; and (c)
octamer 6, side view. For the sake of clarity acetanilide groups in 5 and 6
are not shown.
Figure 2. Schematic view of the hydrogen bonding (dashed arrows) and
NOEs (dark arrows) of NHi- -CâHi+2 and NHi- -CâHi+3 that characterize
the 14-helix.
defined medicinal properties makes these molecules useful in
pharmaceutical applications. Work is in progress in this direction.
3
Large values (8.0-10.8 Hz) of JNH-CâH in 4-6 correspond to
an antiperiplanar arrangement between these protons and also
indicates the presence of a secondary structure in solution. NOESY
data of 4-6 revealed several medium and long-range backbone
NOEs between NHi f CâHi+2 and NHi f CâHi+3 (shown in Figure
2), which are distinctive for the 14-helix. For the tetramer 4, the
two possible NOE signals between NHi f CâHi+2 are well resolved,
while the assignment of NHi f CâHi+3 (i ) 1), NOE signal is
obscured due to resonance overlap. Nevertheless, despite the overlap
of several resonances, the characteristic NOEs that represent a 14-
helix are more pronounced for hexamer 5 and octamer 6. In the
case of 5, all four expected NHi f CâHi+2 NOEs are observed and
two out of three NHi f CâHi+3 NOEs are assigned without
ambiguity. Similarly four out of six NHi f CâHi+2 and three out
of five NHi f CâHi+3 NOEs are clearly distinguished for 6.
Furthermore, formation of 14-membered NHi f COi+3 hydrogen
bonds in all the peptides has been confirmed by individual titration
studies.14 Two, four, and six hydrogen bonds are formed in 4, 5,
and 6, respectively, which are shown schematically in Figure 2.
For all the peptides studied the hydrogen bonds of the 14-helix
begin from the first residue. The exceptional stability and organiza-
tion of the 14-helix observed in tetramer 4 are more pronounced
in the hexamer 5 and octamer 6.
Acknowledgment. M.S.R. is thankful to CSIR, New Delhi; A.P.
and M.H.V.R.R. acknowledge IICT for financial support. This work
is dedicated to the memory of Dr. A. K. Singh.
Supporting Information Available: Synthesis, NMR, and distance
constraints used for the MD calculations. This material is available
free of charge via the Internet at http://pubs.acs.org.
References
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(14) The solvent titration was carried out by sequentially adding up to 33% of
DMSO-d6 to CDCl3 solutions of the peptides.
The restrained MD calculations11 for 4-6 very clearly bring out
the salient features. The distance restraints were obtained from the
ROESY spectra by using the volume integrals and two-spin
approximation. Figure 3 depicts the superimposition of the 10
lowest-energy structures of the peptides 4-6. They are representa-
tive of the ordered structures in solution. The NMR structures of
4-6 show the 14-helix with the pitch of ∼5 Å and three residues
per turn. Fraying is seen at the C-terminus end of 4-6 consistent
3
with the NMR experiment (decrease in the value of JCRH-CâH ).
In summary, this study shows that the furanoid cis-â-sugar amino
acid oligomer adopts in solution a well-defined right-handed 14-
helix. Functionalization of the conformationally rigid oligomers with
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