Cyclols Revisited: Facile Synthesis of Medium-Sized Cyclic Peptides

Article abstract of DOI:10.1002/chem.201703616

Medium-sized rings, particularly the corresponding cyclic peptides, are challenging synthetic targets. In the present study, we report an approach to medium-sized cyclic peptides through targeted formation and collapse of cyclol intermediates. This methodology operates on β-amino imides derived from 2,5-diketopiperazines and offers a straightforward transition from frequently examined scaffolds in drug discovery to a rarely visited class of medium-sized rings.

Full text of DOI:10.1002/chem.201703616

A Journal of
Accepted Article
Title: Cyclols Revisited: Facile Synthesis of Medium-Sized Cyclic
Peptides
Authors: Rodrigo Mendoza-Sanchez, Victoria B. Corless, Q. Nhu. N.
Nguyen, Milan Bergeron-Brlek, John Frost, Shinya Adachi,
Dean J. Tantillo, and Andrei K. Yudin
This manuscript has been accepted after peer review and appears as an
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of the final Version of Record (VoR). This work is currently citable by
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To be cited as: Chem. Eur. J. 10.1002/chem.201703616
Link to VoR: http://dx.doi.org/10.1002/chem.201703616
Supported by

10.1002/chem.201703616
Chemistry - A European Journal
COMMUNICATION
Cyclols Revisited: Facile Synthesis of Medium-Sized Cyclic
Peptides
Rodrigo Mendoza-Sanchez‡[a], Victoria B. Corless‡[a], Q. Nhu N. Nguyen[b], Milan Bergeron-Brlek[a],
John Frost[a], Shinya Adachi[a], Dean J. Tantillo*[b], Andrei K. Yudin*[a]
Abstract: Medium-sized rings, particularly the corresponding cyclic
peptides, are challenging synthetic targets. In the present study, we
report an approach to medium-sized cyclic peptides through targeted
formation and collapse of cyclol intermediates. This methodology
operates on β-amino imides derived from 2,5-diketopiperazines and
offers a straightforward transition from frequently examined scaffolds
in drug discovery to a rarely visited class of medium-sized rings.
robust methodologies to access medium-sized ring cyclic
peptides.
Herein, we report an efficient protocol for the synthesis of
challenging medium-sized cyclic peptides from β-amino
imides.[34–39] The enabling feature of this study is control over the
collapse of the cyclol intermediate B through which a ring
expansion pathway takes place (Scheme 1).[40–47]
O
R
N
In 1936, Dorothy Wrinch proposed the first structural
model for protein folding.[1–3] Repeating polypeptide motifs could
hypothetically be folded into rigid protein scaffolds through what
O
A
O
i) PG removal
ii) ring expansion
PG
N
N
R
8-12 membered rings
N
H
O
was termed
a cyclol. The proposal, while intriguing, was
eventually discredited by Linus Pauling, who pointed out the
implausible thermodynamics of this idea.[4] Nonetheless,
examples of substantially smaller cyclol-containing molecules
were eventually uncovered.[5–10] Despite their thermodynamic
instability, cyclols have been implicated in key biological
processes such as chromophore maturation in green fluorescent
protein (GFP).[11][12] In this paper, we consider factors that
influence cyclol stability in settings that are likely to display
transannular interactions between amides. In combination with
C
R
N
HO
N
O
B
Scheme 1. Ring expansion via cyclol intermediate to access synthetically
challenging medium-sized rings and cyclic tripeptides.
computational
analysis,
our
study
highlights
"cyclol
management" as an enabling avenue to access synthetically
challenging medium-sized rings.
Medium-sized rings are prevalent in many natural products
and possess a range of biological activities.[13–18] They represent
the “middle ground” between macrocycles and small molecules.
However, despite their abundance and diverse functions,
medium-sized rings are not commonly examined in drug
discovery programs or found in the structures of pharmaceutical
agents.[19] This absence can be attributed to unique challenges
associated with the cyclization of medium-sized linear
precursors which include unfavorable transannular interactions
and entropic factors.[20–25] Ring expansion methodologies have
been shown to circumvent some of the issues inherent in
traditional cyclizations and have led to otherwise challenging
substrates.[26–32] An important subclass of medium-sized rings
are cyclic peptides, the synthesis of which is particularly difficult
due to the preference of the amide linkage to exist in its trans-
form.[33] As such, there is a need to develop straightforward and
Scheme 2. Synthesis of medium-sized rings using from amino imides derived
from lactams.
[a] Rodrigo Mendoza-Sanchez, Victoria B. Corless, Milan Bergeron-Brlek,
John Frost, Shinya Adachi and Andrei K. Yudin
Davenport Research Laboratories, Department of Chemistry,
University of Toronto
As proof of concept, we began by assessing the likelihood
of forming the desired medium-sized rings using Boc-protected
β-amino imide 1c as a model substrate. While numerous
methodologies for the synthesis of acyclic imides have been
reported in the literature, we sought a protocol that was
compatible with our Boc-protected β-amino acid fragments
(Scheme 2). We therefore opted to use the direct acylation of
amides using pentafluorophenol active esters as coupling
partners[48–50] and obtained β-amino imides 1a-f in moderate to
good yields (See Supporting Information).
80 St. George St. Toronto, ON, M5S 3H6, Canada
E-mail: ayudin@chem.utoronto.ca
[b]
Q. N. Nguyen, Dean J. Tantillo
Department of Chemistry, University of California Davis
1 Shields Avenue, Davis, CA, USA
E-mail: djtantillo@ucdavis.edu
‡These authors contributed equally.
Supporting information for this article is given via a link at the end of
the document
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10.1002/chem.201703616
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Computational analysis (See Supporting Information) of
the ring expansion of 1c predicted that the resulting ring
expanded form 2c would be favored through the collapse of the
cyclol intermediate as outlined in Scheme 1B. Removal of the
Boc protecting group was carried out by stirring 1c in TFA for
one hour. Neutralization of the isolated TFA salt was achieved
using 5.0 equivalents of DIPEA and yielded the desired 10-
membered ring 2c after 28 h stirring at room temperature. Upon
heating to 50 ºC, we observed complete conversion to 2c in
under 4h with no adverse effect on isolated yield.
to generate 6e-h, which produced the desired ring expanded
products 7e-h in comparable yields to the proline derived amino
imides with the exception of 7g, which was obtained in moderate
yield. Reaction times ranged from 12 to 36 hours.
The generality of the ring expansion was investigated
using several β-amino imides derived from simple lactams.
Gratifyingly, an array of 8–12 membered rings were obtained in
moderate to good isolated yields (Scheme 2). Compounds 2a-d
were obtained using our optimized conditions. However, for
compounds 2e-f, allowing the reactions to proceed at room
temperature resulted in clean and complete conversion to the
desired medium-sized rings in just under 2h. Neither the ring
size nor the aromatic substituents adversely affected the
reaction outcome, which showed promise in extending this
methodology to more complex systems. Having secured a
reliable route to medium-sized rings from simple lactams, we
investigated the possibility of using an α-amino imide
fragment.[51–53] Using glycine-derived α-amino imide 3 as our
model substrate we calculated the probability of forming a 9-
membered ring however, computational analysis predicted that
the cyclol form of this system would be thermodynamically
favored over the ring expanded product (see Supporting
Information). Synthesis of the α-amino imide 3 and removal of
the Boc-protected amine proceeded smoothly, but after
subjecting the unprotected amine to the standard ring expansion
conditions we isolated the oxidized cyclol 4 as a single product
(Scheme 3).
Figure 1. R = p-NO2-Bn. Lowest energy conformers for the unprotected β-
amino imide of 6a, the corresponding cyclol and 10-membered ring expansion
product 7a. Free energies (gas phase) shown in kcal mol-1 were computed
using density functional theory at M06-2X/6-31G(d) (See Supporting
Information). All energies are normalized relative to trans-amide 7a.
Scheme 3. Formation of oxidized cyclol 4 from glycine-derived amino imide 3.
Next, we applied our ring expansion methodology to the
synthesis of cyclic tripeptides from 2,5-diketopiperazines, which
are common by-products of peptide coupling reactions.[54]
Computational analysis using the unprotected imide of 6a
indicated favorable formation of the 10-membered cyclic
tripeptide (Figure 1). We therefore synthesized imides 6a-j
derived from functionalized 2,5-diketopiperazines (see
Supporting Information) and applied our optimized ring
expansion conditions. The reactions proceeded with clean
conversion to the desired cyclic tripeptides 7a-j (Scheme 4).
Initial experiments involved amino imides 6a-c, which
contain various combinations of D- and L-proline and alanine.
Gratifyingly, the stereochemistry of the amino acids did not
hinder the outcome of the ring expansions. A number of
phenylalanine containing amino imides were then synthesized.
Starting from N-methyl phenylalanine, the ring expanded product
7d was obtained in good yield. N-allyl-phenylalanine was used
Figure 2. Solid state structure of 7a (left) and 7h (right) as determined by
single-crystal X-ray diffraction. 7a was recrystallized from acetonitrile in water
and 7h from deuterated methanol.
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10.1002/chem.201703616
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COMMUNICATION
O
addressed some long-standing challenges in this area such as
high entopic barriers, unwanted oligomerization, poor yields, and
limited substrate accessibility. By avoiding the well-known pitfalls
of cyclization reactions, our study opens doors for the evaluation
of medium sized cyclic peptides in library production for the
purposes of drug discovery.
R
O
O
*
N
N
1) TFA
2) DIPEA
O
N
*
NBoc
R
*
N
*
50ºC
Me
N
H
MeCN
O
O
6a-j
R= p-NO2-Bn
7a-j
R= p-NO2-Bn
O
O
O
R
N
R
R
N
N
N
N
N
O
O
O
Acknowledgements
Me
N
H
Me
N
H
Me
N
H
O
O
O
We would like to thank Dr. Darcy Burns and the NMR staff at the
University of Toronto for their assistance and Dr. Alan J. Lough
for acquiring and solving X-ray crystal structures. V.B.C thanks
the Ontario Graduate Scholarship for funding. R.M.S thanks
NSERC CREATE grant for funding. M. B.-B. thanks FRQNT for
funding. D.J.T. and Q.N.N. acknowledge computational support
from the NSF XSEDE program.
7a, 93%
O
7b, 92%
7c, 89%
Ph
Ph
Ph
Me
O
O
R
R
R
N
N
N
N
N
N
O
O
O
N
H
Me
N
H
Me
N
H
O
O
O
7d, 82%
7e, 78%
Ph
7f, 91%
Ph
N
O
O
O
Keywords: cyclol • medium-sized ring • cyclic peptide • ring
expansion • b-amino imide
R
PMB
N
N
N
N
N
O
O
O
MeOOC
N
H
Me
N
H
N
H
O
O
O
OBn
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Scheme 4: Synthesis of cyclic tripeptides through the ring expansion of 2,5-
diketopiperazines.
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Chemistry - A European Journal
COMMUNICATION
COMMUNICATION
Rodrigo Mendoza-Sanchez‡, Victoria B.
Corless‡, Q. Nhu Nguyen, Milan
Bergeron-Brlek, John Frost, Shinya
Adachi, Dean J. Tantillo*, Andrei K.
Yudin*
Page No. – Page No.
Cyclols Revisited: Facile Synthesis of
Medium-Sized Cyclic Peptides
[a] Rodrigo Mendoza-Sanchez, Victoria B. Corless, Milan Bergeron-Brlek, John Frost, Shinya Adachi and Andrei K. Yudin
Davenport Research Laboratories, Department of Chemistry, University of Toronto
80 St. George St. Toronto, ON, M5S 3H6, Canada
E-mail: ayudin@chem.utoronto.ca
[b]
Q. N. Nguyen, Dean J. Tantillo
Department of Chemistry, University of California Davis
1 Shields Avenue, Davis, CA, USA
E-mail: djtantillo@ucdavis.edu
‡These authors contributed equally.
Supporting information for this article is given via a link at the end of the document
This article is protected by copyright. All rights reserved.