Foldamer-templated catalysis of macrocycle formation

Article abstract of DOI:10.1126/science.aax7344

Macrocycles, compounds containing a ring of 12 or more atoms, find use in human medicine, fragrances, and biological ion sensing. The efficient preparation of macrocycles is a fundamental challenge in synthetic organic chemistry because the high entropic

Full text of DOI:10.1126/science.aax7344

RESEARCH
residues in 1, enhances helix stability (22). A
related a/b peptide containing two pyrrolidine-
based residues catalyzes intermolecular crossed
aldol condensations involving formaldehyde as
the electrophile (24). Optimal catalysis required
i,i+3 spacing of the pyrrolidine residues, which
causes alignment of these two catalytic units
upon helical folding. a/b-Peptide 1 is distinct
from the earlier example in that one of the
catalytic units is a primary amine, a difference
that proved to be consequential.
The current study began with an unexpected
observation. We asked whether a/b-peptide 1
would promote cyclization of C9 dialdehyde A
to form cyclooctene-1-aldehyde (Fig. 1B). The
reaction conditions, based on precedents from
Pihko et al. and our previous studies (24, 25),
included propionic acid and triethylamine as
additives and aqueous isopropanol as solvent.
The cyclooctene derivative, however, was not
observed when 10 mM A was allowed to re-
act in the presence of 10 mole % (mol %) 1, al-
though A appeared to be fully consumed within
24 hours. Instead, the foldamer catalyzed for-
mation of a product mixture in which the prin-
cipal components were cyclodimers. We isolated
the major cyclodimer and identified it by two-
dimensional (2D) nuclear magnetic resonance
(NMR) spectroscopy to be the 16-membered
ring E,E diene B. Liquid chromatography–
mass spectrometry (LC-MS) revealed initial
formation of intermolecular aldol adduct C,
but the amount of this intermediate remained
low throughout the reaction, suggesting rap-
id cyclization. By contrast, a 1:1 mixture of
pyrrolidine and n-butylamine (10 mol % each)
ORGANIC CHEMISTRY
Foldamer-templated catalysis of
macrocycle formation
Zebediah C. Girvin, Mary Katherine Andrews, Xinyu Liu, Samuel H. Gellman*
Macrocycles, compounds containing a ring of 12 or more atoms, find use in human medicine,
fragrances, and biological ion sensing. The efficient preparation of macrocycles is a fundamental
challenge in synthetic organic chemistry because the high entropic cost of large-ring closure allows
undesired intermolecular reactions to compete. Here, we present a bioinspired strategy for macrocycle
formation through carbon–carbon bond formation. The process relies on a catalytic oligomer
containing a- and b-amino acid residues to template the ring-closing process. The a/b-peptide
foldamer adopts a helical conformation that displays a catalytic primary amine–secondary amine
diad in a specific three-dimensional arrangement. This catalyst promotes aldol reactions that
form rings containing 14 to 22 atoms. Utility is demonstrated in the synthesis of the natural
product robustol.
acrocyclic compounds, containing a
ring of 12 or more atoms, play impor-
tant roles in biology and medicine
(1–3). Engineered macrocycles have
engendered new technologies (4) and
functionalization of complex substrates (19).
Our work complements the development of
small molecules that serve as bifunctional
catalysts, such as the recent mimicry of glyco-
transferase enzymes with cyclic bis-thioureas
(20) and the recent stereoselective formation
of nucleoside phosphoramidates with bis-
imidazoles (21). Neither of these cases, how-
ever, involved macrocycle formation.
Oligomer 1 (Fig. 1B) contains both a- and
b-amino acid residues and features an abb
backbone repeat pattern, which favors a heli-
cal conformation that has approximately three
residues per turn (22, 23). Use of b residues
with a five-membered ring constraint, such
as the cyclopentane- and pyrrolidine-based
M
new therapeutic strategies (5). Efficient syn-
thesis of macrocycles is challenging because
the entropic penalty associated with ring clo-
sure allows competition from intermolecular
side-reactions, reducing yields of the desired
products (6–10). Preorganization of linear pre-
cursors through multipoint coordination of a
metal cation, an anion, or a neutral partner
can facilitate synthesis of specific macrocycle
classes (Fig. 1A), but this strategy depends on
noncovalent interaction sites in the linear pre-
cursor (9–12). Intramolecular alkene metathe-
sis can be very effective for formation of large
rings (9, 13–15). This process features catalytic
metal-based activation of terminal alkenes in a
linear precursor, but additional coordination
between internal functionality and the metal
center is necessary (9, 13–16). Biosynthetic ma-
chinery overcomes the entropic cost of macro-
cycle formation by holding linear precursors
in appropriate conformations, catalyzing the
ring-closure reaction, and inhibiting compet-
ing intermolecular processes (17, 18). We took
inspiration from biological catalysts to develop
a macrocyclization catalyst in which a well-
folded oligomer activates both ends of a linear
precursor and orients the termini for reaction,
thereby serving as a template for ring closure
through carbon–carbon bond formation.
A Macrocyclization strategies
Foldamer vs. small molecule catalysis
B
Our approach uses a foldamer designed to
facilitate macrocyclization through aldol con-
densation by proper orientation of two cata-
lytic groups. We build on pioneering work by
Miller et al., who employed related design
principles to achieve site-specific catalytic
Department of Chemistry, University of Wisconsin–Madison,
Madison, WI, USA.
*Corresponding author. Email: gellman@chem.wisc.edu
Fig. 1. Macrocyclization strategies. (A) Prior approaches and foldamer approach to macrocyclization.
(B) Divergent reactivity: Foldamer versus small-molecule catalysis. eq., equivalent(s).
Girvin et al., Science 366, 1528–1531 (2019)
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RESEARCH
| REPORT
catalyzed slow formation of the linear dimer
C, with only trace levels of cyclodimer de-
tected after 24 hours. We hypothesized that
the foldamer acts by a bifunctional mecha-
nism, serving as a template to overcome the
entropic cost of large-ring closure.
Scope: Ring size
A
To gain further insight on the capabilities of
foldamer 1, we prepared symmetrical dialde-
hydes D1 to D4 (Fig. 2A), each containing a
central methoxyphenyl ring that allowed us
to monitor starting material, products, and
transient intermediates through ultraviolet
absorbance. Initial studies focused on D3,
which can form a 16-membered ring enal,
matching the ring size of cyclodimer B. When
we reacted D3 with 1, we observed nearly
full conversion to macrocyclic E-enal E3 (full
characterization in supplementary material).
By contrast, the control reaction with pyrrol-
idine and n-butylamine produced only a trace
amount of E3 after 24 hours (fig. S10).
Structure-reactivity relationship
B
a/b-Peptide 1 proved to be versatile in terms
of product ring size (Fig. 2A). We observed
efficient conversion of D4 to 18-membered
ring E-enal E4 and of D2 to 14-membered
ring E-enal E2. The foldamer-catalyzed reac-
tion of D1 took longer to reach completion
and led to a mixture of E-enal E1 and cyclo-
dimers. Precedents suggest that this outcome
arises because of strain that develops upon
12-membered ring formation (7, 8). However,
efficient and stereospecific synthesis of the
14-, 16-, and 18-membered ring enals suggests
that catalyst 1 is broadly competent for for-
mation of larger rings.
Comparing formation of enal E3 with
a/b-peptide 1 and a set of related oligomers
reveals that catalytic efficacy is very sensitive
to specific features of foldamer structure
(Fig. 2B). As noted above, a control mixture
of pyrrolidine and n-butylamine was much
less effective than a/b-peptide 1 at promoting
macrocycle formation. Similarly low reactivity
was observed for a pair of monofunctional a/b
peptides (2 + 3) that provide the secondary
and primary amine groups as b-residue side
chains in separate molecules. These results
are consistent with a bifunctional mechanism
involving activation of the two aldehyde groups
in a substrate on a single catalyst molecule. A
bifunctional mechanism is further supported
by the observation that macrocyclization to
form E3 displayed first-order dependence
on a/b-peptide 1 (figs. S13 and S14). 2D NMR
studies of 1, conducted in either d7-isopropanol
or d3-methanol, revealed numerous nuclear
Overhauser effects consistent with the ex-
pected helical conformation (figs. S31 and S34)
and the alignment of the primary and sec-
ondary amine side chains, which is essential
for bifunctional catalysis.
Fig. 2. Scope and structure-reactivity relationship. (A) Foldamer-catalyzed macrocyclization: Ring size
variation. Isolated yields are reported for foldamer-catalyzed reactions; however, yields for the pyrrolidine–n-
butylamine catalyst pair (“small molecule”) are estimated on the basis of LC-MS data. Ts, p-toluenesulfonyl.
(B) Identification of features critical for foldamer catalysis of macrocyclization. Details are included in the
supplementary materials (figs. S8 to S12).
obtained with a/b-peptides 4 to 6, which are
sequence isomers of 1. When the b residues
bearing the reactive amine groups were ad-
jacent in primary sequence (i,i+1 spacing; 4),
macrocyclization was barely detectable. The
isomers with i,i+2 and i,i+4 spacing, 5 and 6,
were poor catalysts as well. Because the heli-
cal conformation favored by the abb backbone
has three residues per turn (22), differences
among 1 and sequence isomers 4 to 6 support
the conclusion that optimal catalysis requires
alignment of the primary and secondary amine
groups along the helix axis. When the b resi-
dues that provide the reactive groups were
properly spaced (i,i+3) but the linker between
the primary amino group and the backbone was
lengthened, as in 7, catalytic activity suffered.
Thus, even if the primary and secondary amines
are aligned along the helix axis, increased flex-
ibility of the segment between the two amino
groups appears to be deleterious. a/b-Peptide 8
is the diastereomer of 1 that differs only in
the configuration at the backbone carbon
bearing the primary amine side chain, a
change expected to diminish helix stability
(26). We observed only a low yield of enal
E3 with 8, consistent with high sensitivity
of the reaction to the spatial positioning of
the amino groups provided by the foldamer
scaffold. Overall, this set of comparisons shows
that catalytic activity depends on the ability of
the a/b-peptide backbone to achieve a specific
arrangement of the primary amine–secondary
amine diad.
The chemical nature of the amine groups
is critical for intramolecular aldol conden-
sation (figs. S35 to S46). a/b-Peptide 9 pre-
sents a diad of primary amino groups with
the optimal sequence spacing, but the yield of
16-membered ring enal E3 was substantially
lower for this catalyst relative to a/b-peptide 1.
a/b-Peptide 10 presents a secondary amine
The spacing between reactive side chains
along the foldamer backbone is crucial for
catalytic efficacy, as shown by the low yields
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RESEARCH
| REPORT
ing total synthesis of the natural product robustol
(30), which contains a 22-membered ring (Fig.
3B). This compound is related to the turriane
family of natural products, several of which have
been prepared by application of macrocycle-
closing alkene or alkyne metathesis (31). Our
route to an appropriate dialdehyde substrate
began with two nickel-catalyzed reductive cross-
coupling reactions, pioneered by Weix et al. (32),
to prepare boronate ester R1 and phenol R3.
Copper-catalyzed Chan-Lam-Evans coupling of
these two compounds generated diester R4
(33, 34), and redox manipulations provided di-
aldehyde R5. The foldamer-catalyzed reaction
efficiently generated the desired 22-membered
ring skeleton as a mixture of isomers (R6).
Heating with Wilkinson’s catalyst induced de-
carbonylation (35), and the resulting alkene
mixture was hydrogenated to produce R7. The
methyl groups were removed by treatment
with excess BBr3 to yield a single product with
an 1H NMR spectrum matching that of natural
robustol (30).
Macrocyclic core of nostocyclyne A
A
Total synthesis of robustol
B
Our results suggest that a broad range of
macrocycles will be accessible through intra-
molecular aldol condensations catalyzed by
foldamer 1, with limitations arising when ring
closure causes significant internal strain (7, 8).
Because polar groups (amine, carboxylic acid,
hydroxyl) are abundant in the reaction me-
dium, aldol macrocyclizations catalyzed by
a/b-peptide 1 will likely display considerable
functional group tolerance. Macrocyclic com-
pounds are of interest for pharmaceutical
development, as exemplified by the hepatitis C
drug vaniprevir (36), and our method should
enable synthesis of diverse structures to sup-
port discovery of therapeutic agents.
Fig. 3. Applications of foldamer catalysis in total synthesis. (A) Foldamer-catalyzed formation of the
macrocyclic core of nostocyclyne A. Identity of product F2 was established by means of the crystal structure
of the tosylhydrazone derivative. rr, regioisomer ratio. (B) Total synthesis of robustol. The key step,
foldamer-catalyzed closure of the 22-membered ring, is highlighted. Full reaction protocols and product
characterization are in the supplementary materials.
Our use of a foldamer scaffold to achieve
optimal arrangement of the primary amine–
secondary amine diad was inspired by the role
of protein scaffolds in positioning catalytic
groups in enzyme active sites (37). The preva-
lence of b-amino acid residues in our foldamer
backbone allows us to use residue-based strat-
egies for conformational preorganization (23),
an opportunity that is not available for catalyst
designs based entirely on a-amino acid resi-
dues. Well-characterized foldamer scaffolds
allow systematic variation of the arrangement
of a reactive group set, such as the primary
amine–secondary amine diad in 1, which is
useful for catalyst optimization (24). Small-
molecule scaffolds for bifunctional catalysis
(38–40) may be less amenable to exploration
of alternative geometries for a given func-
tional group diad relative to foldamer-based
skeletons because small molecules lack the
modularity of foldamers. We speculate that
the abb backbone of 1, and related backbones
containing preorganized b- and/or g-amino
acid residues, will provide scaffolds that can
be harnessed to enable bifunctional or polyfunc-
tional catalysis of other useful reactions.
diad, and in this case, the macrocyclic product
was barely detectable. The variations in catalytic
efficacy among 1, 9, and 10 may arise because
primary amines favor imine adducts with
aldehydes (27), whereas secondary amines
favor enamine adducts (28). Macrocycle for-
mation presumably requires the generation
of an electrophilic iminium and nucleophilic
enamine on a single catalyst scaffold, a com-
bination that is favored by the reactive diad
of 1. Previously, we found that a/b-peptide 10
was an excellent catalyst for intermolecular
crossed aldol reactions (24). The distinct cat-
alytic profiles of a/b-peptides 1 and 10 show
that once a favorable foldamer scaffold is iden-
tified, reaction selectivity can be achieved by
modifying the catalytic groups.
The modest macrocycle yield obtained with
11 shows that swapping the primary and
secondary amine group positions in the a/b-
peptide backbone causes erosion of catalytic
efficacy. This observation highlights the ability
to explore diverse spatial arrangements of re-
active groups that is provided by a foldamer
scaffold, which is inherently modular. Tri-
peptide 12 features i,i+2 spacing but is too
small to adopt a stable helical conformation.
This tripeptide was slightly more effective than
the longer a/b-peptide with i,i+2 spacing (5),
which raises the possibility that a stable folded
conformation can cause a modest diminution
of intrinsic amine reactivity, perhaps because
of steric hindrance.
The efficient foldamer-catalyzed macro-
cyclization introduced here may be useful for
the synthesis of large-ring natural products,
analogs of these natural products, and mac-
rocycles of potential therapeutic utility. We
could produce the 18-membered ring core of
nostocyclyne A (Fig. 3A) (29) from dialdehyde
F with 10 mol % 1. Because the substrate is
unsymmetrical, two macrocyclic E-enals are
possible. Both were formed in 75% total yield,
with a 2.8:1 ratio. The identity of the major
isomer was established by a crystal structure
of the tosylhydrazone derivative.
We further demonstrated the utility of
foldamer-catalyzed macrocyclization by achiev-
Girvin et al., Science 366, 1528–1531 (2019)
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We thank I. Guzei for x-ray structure determination and A. Maza
for assistance with high pressure hydrogenation. Funding: This
research was supported in part by the U.S. National Science
Foundation (CHE-1904940). Author contributions: Z.C.G. and
S.H.G. conceived the study. Z.C.G, M.K.A., X.L., and S.H.G. designed
experiments. Z.C.G., M.K.A., and X.L. performed experiments. All
authors contributed to data analysis. S.H.G. supervised research and
acquired funding. Z.C.G. and S.H.G. wrote the original draft, which
was reviewed and edited with input from all authors. Competing
interests: The a/b-peptide catalysts described here are covered by
U.S. patent 7,858,737 B2, on which S.H.G. is a coinventor. This
patent covers a/b-peptides containing cyclic b residues. S.H.G. is a
cofounder of and has a secondary affiliation with Longevity Biotech,
which is pursuing therapeutic applications of a/b-peptides. Data
and materials availability: Crystallographic parameters are
available from the Cambridge Crystallographic Data Centre under
references CCDC 1910263 (hydrazone of E3) and CCDC 1910264
(hydrazone of F2). All other data are available in the main text or
supplementary materials. A University of Wisconsin materials transfer
agreement applies to materials acquired directly from the authors.
SUPPLEMENTARY MATERIALS
science.sciencemag.org/content/366/6472/1528/suppl/DC1
Materials and Methods
Figs. S1 to S46
Tables S1 to S21
Spectral Data
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17 April 2019; resubmitted 13 September 2019
Accepted 4 November 2019
10.1126/science.aax7344
Girvin et al., Science 366, 1528–1531 (2019)
20 December 2019
4 of 4

Foldamer-templated catalysis of macrocycle formation
Zebediah C. Girvin, Mary Katherine Andrews, Xinyu Liu and Samuel H. Gellman
Science 366 (6472), 1528-1531.
DOI: 10.1126/science.aax7344
Macrocycles made easy
Macrocycles, which are molecules with large rings of 12 or more atoms, are challenging to produce by
intramolecular cyclization because floppy ends tend to join up with another molecule rather than fold back on themselves.
Girvin et al. identified a foldamer−−a short, structured peptide−−that can cyclize floppy, dialdehyde substrates through a
templated aldol condensation (see the Perspective by Gutiérrez Collar and Gulder). Variation of the residues within the
foldamer suggests that its helical structure helps position amine functional groups crucial for catalysis. The authors
prepared molecules with a wide range of ring sizes and developed a synthesis for robustol, a macrocycle natural product
with a 22-member ring.
Science, this issue p. 1528; see also p. 1459
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