4-Naphthylmethyl Proline Forms a Channel Structure

Article abstract of DOI:10.1002/hlca.201900052

Proline and proline derivatives are useful tools to control the structural properties of peptides and proteins, and thereby modulate numerous processes. Here, we show that proline derivatives can have unique structural properties in the solid state by presenting the crystal structure of zwitterionic (2S,4S)/(2S,4R)-4-[(naphthalen-2-yl)methyl]proline (H-Nap-OH). This amphiphilic proline derivative forms a columnar structure around large hydrophilic and small hydrophobic channels with diameters of 9 ? and 4 ?, respectively. We show that this architecture, which is unprecedented for amino acids, results from the combination of a hydrogen bond network between the ammonium and carboxylate moieties and π–π as well as CH–π interactions between the aromatic moieties.

Full text of DOI:10.1002/hlca.201900052

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Accepted Article
Title: 4-Naphthylmethyl Proline Forms a Channel Structure
Authors: Helma Wennemers, Carlotta Foletti, Nils Trapp, Simon Loosli,
and Bartosz Lewandowski
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10.1002/hlca.201900052
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4-Naphthylmethyl Proline Forms a Channel Structure
Carlotta Foletti, Nils Trapp, Simon Loosli, Bartosz Lewandowski and Helma Wennemers*
Laboratorium für Organische Chemie, D-CHAB, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich
helma.wennemers@org.chem.ethz.ch
Dedicted to our friend and colleague Prof. Dr. François Diederich
Proline and proline derivatives are useful tools to control the structural properties of peptides and proteins, and thereby modulate numerous processes.
Here, we show that proline derivatives can have unique structural properties in the solid state and present the crystal structure of zwitterionic (2S,4S/R)-
4-(methyl-2-naphthyl)proline (H-Nap-OH). This amphiphilic proline derivative forms a columnar structure around large hydrophilic and small
hydrophobic channels with diameters of 9 Å and 4 Å, respectively. We show that this architecture, which is unprecedented for amino acids, results from
the combination of a hydrogen bond network between the ammonium and carboxylate moieties and π-π as well as CH-π interactions between the
aromatic moieties.
Keywords: Proline, amino acid, crystal structure, channel structure
Specifically, peptides consisting of cationic residues and (2S,4R)-4-
Introduction
(methyl-2-naphthyl)proline exhibit excellent binding affinity and
Proline, the only proteinogenic amino acid with a cyclic backbone, is used
selectivity towards c-di-GMP. These studies led us to establish a general
both by Nature and scientists to control the conformation of peptides
synthetic route that provides access to proline derivatives bearing a
and proteins.[1-5] However, proline’s unique structural features manifest
themselves not only when incorporated into polypeptide chains. In fact,
the architecture of monomeric proline crystal structures differs from
those of all other amino acids.[6, 7] The amino group of zwitterionic proline
provides, in comparison to the other proteinogenic amino acids, at most
two H-bond donors and the pyrrolidine ring restricts the Θ and Ψ angles,
effectively limiting the accessible conformational space of proline. As a
result, proline adopts distinctly different structures compared to other
hydrophobic amino acids. Zwitterionic leucine, tryptophan, and
phenylalanine form double sheet assemblies with a hydrophobic layer
composed of the alkyl or aryl moieties and a hydrophilic layer with an
extended H-bond network.[8] In contrast, zwitterionic proline crystallizes
variety of different methyl-aryl moieties at Cγ.[19] In addition, we became
interested in the structural features of such proline derivatives in the solid
state. We hypothesized that the aromatic moiety tethered to the proline
backbone would lead to unique structures that are driven by
a
combination of electrostatic and hydrophobic interactions. Herein we
show that zwitterionic (2S,4R)/(2S,4S)-4-(methyl-2-naphthyl)proline (1, H-
Nap-OH) crystallizes into a unique columnar structure that contains large
(Ø = 9 Å) and small (Ø = 4 Å) channels.
γ
*
O
N
7]
in single sheets or one-dimensional tapes.[6, However, (4R)-4-phenyl
H
H
O
1
proline, a proline derivative bearing a phenyl moiety at Cγ, crystallized
Scheme 1. (2S,4S)/(2S,4R) H-4-(methyl-2-naphthyl)proline-OH (H-Nap-OH, 1).
into double-sheets,[9]
a molecular organization reminiscent to that
observed for amino acids with large hydrophobic side chains. A similar
switch of the assembly geometry was observed for azetidine[10] and (3S)-
3-phenyl azetidine[11] – the phenyl groups form a distinct hydrophobic
Results and Discussion
We obtained single crystals of a diastereoisomeric mixture (~3:2) of
(2S,4S)-
and
(2S,4R)-configured
4-(methyl-2-naphthyl)proline
layer enforcing
a double-sheet assembly as opposed to the tape
(1, H-Nap-OH) suitable for X-ray structure analysis from precipitation of 1
in acidic aqueous solution (6 M HCl in dioxane:H2O 1:1). H-Nap-OH
crystallized as a zwitterion1 in a hexagonal structure (space group P63)
with a large channel along the 6-fold rotational axis (C6) and a small
channel along a C3-axis (Figure 1a).2
geometry of the non-decorated cyclic amino acid. These examples
exemplify how substituents on cyclic amino acids can alter their self-
assembly properties.
Our research group has been using the unique structural and
functional properties of proline and proline derivatives bearing
substituents at Cγ for applications in chemical biology, supramolecular
chemistry and asymmetric catalysis.[5,12–17] Recently, we became
interested in peptides containing methyl-aryl substituents at Cγ for their
value as selective binders of the bacterial second messenger c-di-GMP.[18]
1 The two C–O bonds of the CO2-moiety have essentially the same length (1.24 Å and
1.25 Å)
2 CCDC 1846337
1
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10.1002/hlca.201900052
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a)ꢀ Top view of H-Nap-OH crystal structure:
c) Side view of large channel:
z!
z!
x!
C6
y!
y!
C3
Hexameric ring unit of large channel
Ø = 9.09(1) Å
!
y!
h = 2.83(1) Å
x!
d) Top and side view of small channel
3.63(1) Å
b) Diastereoisomers of H-Nap-OH:
(2S,4R)-isomer
Cγ-endo
3.60(1) Å
3.70(1) Å
z!
z!
α = 61.3(1)°
α
Ø = 4.05(1) Å
=
(2S,4S)-isomer
Cγ-exo
z!
y!
y!
x!
Figure 1. Crystal structure of H-Nap-OH (1). a) Packing of H-Nap-OH and depiction of rotation axes. b) Overlay of H-Nap-OH isomers with pyrrolidine ring puckers. c) Side view
of large channel and schematic representation of the hexameric ring subunit. d) Top and side view of small channel indicating the tilt of the naphthyl groups with respect to
the z-axis. The coordinate system was chosen such that the z-axis is aligned with the crystallographic c-axis.
proximity to each other (3.70 Å) as well as to the CH-groups at C(β) and
The channels are filled with disordered water molecules (not shown in
figures for clarity). Disorder also occurs at the pyrrolidine rings as the
(2S,4S)- and (2S,4R)-diastereoisomers adopt C(γ)-exo and C(γ)-endo
puckers, respectively, (Figure 1b).
C(γ) of the proline rings (3.60 Å and 3.63 Å), distances indicative of weak
π-π and CH-π interactions.[20] The naphthyl groups are not parallel to the
z-axis but tilted at an angle α = 61.3°. This tilting allows for edge-to-face
interactions between the naphthyl groups at the borders of neighboring
channels along the z-axis, d(C…C) = 3.36 Å, and results in an angle of
β = 57.3° between the planes defined by the naphthyl rings (Figure 2b).
Thus, an extended H-bonding network between the hydrophilic
carboxylate and ammonium groups lines the inside of the large channels
and hydrophobic naphthyl groups in distances typical for π-π interactions
line the outside (Figure 1a and Figure 2).
The large channel has
a ,
diameter of 9.09 Å (Ø = d(Ni…Ni+3
projection onto XY plane) and is formed by six molecules of 1 (Figure 1c).
Within the hexameric ring every other molecule is shifted along the z-axis
-
by 2.83 Å. As a result, the CO2 -groups of the molecules in one plane are in
close proximity (2.72 Å and 2.84 Å) to the NH2+-groups of the molecules in
the plane above and below (Figure 1c and 2a, green and blue layers). This
leads to an extended H-bonding network between the ammonium group
of a molecule in one plane (green) with the carboxylate group of the
molecules (blue) in planes above and below (Figure 2a). While the
hydrophilic moieties of
1 line the rim of the large channel, the
hydrophobic naphthyl moieties point away from these hexagonal
channels. This orientation gives rise to smaller channels (Ø = 4.05 Å) that
are flanked by the naphthyl groups of three molecules within the same
plane (Figure 1d).3 The naphthyl moieties of adjacent molecules are in
3 The radius of the small channel was defined by the distance between the closest
hydrogen atom of the naphthyl ring to the C3 rotation axis.
2
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10.1002/hlca.201900052
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arises from the combination of amphiphilicity and rigidity of this unique
proline derivative paired with sufficient conformational flexibility. We
envision that these insights are useful for the design of other channel
structures.
a) H-bonding along the inside ofthe large channel:
2.835(1) Å
2.715(1) Å
Experimental Section
General Aspects
Reactions were monitored by thin layer chromatography on Merck Silica
Gel F254 TLC glass plates and visualized by ultraviolet light (UV). NMR
spectra were recorded on a Bruker DPX 400 spectrometer. Chemical shifts
are reported in ppm using the residual solvent peak as a reference. An IR
spectrum of the neat compound was recorded using an Agilent
Technologies Cary 630 FTIR. Only selected peaks are reported. The
melting temperature was measured on a Büchi melting point M-560. X-
ray diffraction experiments were performed on a Bruker Kappa Apex-II
Duo diffractometer.
z
y
b) Edge-to-face interactions along z-axis:
β = 57.32(1)°
3.360(1) Å
Synthesis of H-Nap-OH (1)
=
Boc-(2S,4S/R)Nap-OtBu (0.55 g, 1.32 mmol) was dissolved in 6 M HCl in
1,4-dioxane (10 mL) and stirred for 3 h at room temperature. Crystals
suitable for single crystal X-ray diffraction were obtained from this
mixture. Since the starting material was a 3:2 mixture of the major (4S)-
and the minor (4R)-configured diastereoisomer, also 1 in a mixture of
diastereoisomers in a ratio of ~3:2. Analytical data: FT-IR (neat): 2918 (br,
C–H aromatic and C–H aliphatic), 1734 (C=O), 1599 (N–H), 1390 (O–H),
1253 (C–H aliphatic), 825 (C–H, aromatic). 1H-NMR (500 MHz, D2O, 60 °C):
δ 8.36 – 8.22 (m, 3H), 8.17 – 8.11 (m, 1H), 7.98 – 7.88 (m, 2H), 7.85 – 7.79
(m, 1H), 4.72 – 4.64 (m, 1H), 3.95 (dd J = 11.7, 7.2 Hz, 0.36H, (4R)),
3.88 (dd J = 11.7, 7.3 Hz, 0.64H, (4S)), 3.60 – 3.49 (m, 1H), 3.38 – 3.28 (m,
2H), 3.27 – 3.11 (m, 1H), 2.96 – 2.22 (m, 2H). (Note, Ha of the (4R)-
configured diastereoisomer is located below the solvent peak.) 13C NMR
(126 MHz, D2O, 60°C): δ 137.7, 137.6, 133.7, 132.3, 128.6, 128.0, 127.9,
127.8, 127.3, 126.9, 126.3, 60.9, 60.5, 50.8, 50.8, 40.1, 38.7, 37.8, 37.7, 34.6,
34.4. HR-ESI-MS (pos.): 256.1331 ([M + H]+, C16H18NO2+; calc. 256.1332).
Melting temperature: 154–156 °C.
z
y
y
x
Figure 2. Intermolecular a) H-bonding and b) edge-to-face interactions in the
crystal structure of H-Nap-OH.
The crystal structure of H-Nap-OH differs significantly from that of proline
and other zwitterionic hydrophobic amino acids.[6–8] Contrary to the
double-sheet assemblies seen for hydrophobic amino acids and phenyl-
decorated proline, a channel structure results from the tethering of the
methyl-naphthyl group to the proline backbone. This unique structure
likely arises from the amphiphilicity of zwitterionic H-Nap-OH, its
geometrically-constrained ammonium and carboxylate groups combined
with the conformational flexibility of the pyrrolidine ring and the methyl-
naphthyl moiety that allows to accommodate the naphthyl group in a
hydrophobic environment. Channel structures are generally rare for
organic compounds and the few examples that have been observed in
the solid state with cyclic and linear peptides are typically hydrophobic in
nature and have significantly smaller diameters.[21–26] To the best of our
knowledge, the solid-state structure of H-Nap-OH is the first example of
an amino acid that forms a large channel with a hydrophilic interior.
Supplementary Material
Supporting information for this article is available on the WWW under
http://dx.doi.org/10.1002/MS-number.
Acknowledgements
We thank the ETH Zürich and the Swiss National Science Foundation
(Grant 200020_169423) for financial support. The authors thank Michael
Solar (ETH Zürich) for recording the crystallographic data and Dr. Bartosz
Lewandowski for help in recording the analytical data.
Conclusions
In conclusion, we have shown that the amphiphilic proline derivative
H-Nap-OH crystallizes into a channel structure with a large hydrophilic
and a small hydrophobic channel with diameters of 9 Å and 4 Å,
respectively. This architecture, which is unprecedented for amino acids,
3
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chemical and biological recognition: energetics and structures‘,
Angew. Chem. Int. Ed., 2011, 50, 4808-4842.
[21] S. Wu, J. P. Declercq, B. Tinant, M. Vanmeerssche, ‘Crystal-Structure
and Conformation of Short Linear Peptides: PartVIII: L-Leucyl-L-
Tryptophanyl-L-Leucine Hydrochloride Dihydrate’, B. Soc. Chim.
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[22] D. V. Soldatov, I. L. Moudrakovski, J. A. Ripmeester, ‘Dipeptides as
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Author Contribution Statement
CF obtained the single crystals and NT solved the crystal structure. SL
recorded the other analytical data. CF, NT, and HW contributed to the
analysis of the crystal structure and the writing of the manuscript.
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Entry for the Table of Contents
((Insert TOC Graphic here; max. width: 17.5 cm; max. height: 7.0 cm))
hydrophilic
channel
9Å
*
O
N
H
H
O
Twitter
The first reported amino acid-based large hydrophilic channels – assemblies in the solid state of the unique (2S,4S/R)-4-(methyl-2-
naphthyl)proline, H-Nap-OH.
5
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