Chemoenzymatic Synthesis of Thiazolyl Peptide Natural Products Featuring an Enzyme-Catalyzed Formal [4 + 2] Cycloaddition

Article abstract of DOI:10.1021/jacs.5b00940

Thiocillins from Bacillus cereus ATCC 14579 are members of the well-known thiazolyl peptide class of natural product antibiotics, the biosynthesis of which has recently been shown to proceed via post-translational modification of ribosomally encoded precursor peptides. It has long been hypothesized that the final step of thiazolyl peptide biosynthesis involves a formal [4 + 2] cycloaddition between two dehydroalanines, a unique transformation that had eluded enzymatic characterization. Here we demonstrate that TclM, a single enzyme from the thiocillin biosynthetic pathway, catalyzes this transformation. To facilitate characterization of this new class of enzyme, we have developed a combined chemical and biological route to the complex peptide substrate, relying on chemical synthesis of a modified C-terminal fragment and coupling to a 38-residue leader peptide by means of native chemical ligation (NCL). This strategy, combined with active enzyme, provides a new chemoenzymatic route to this promising class of antibiotics.

Full text of DOI:10.1021/jacs.5b00940

Communication
pubs.acs.org/JACS
Chemoenzymatic Synthesis of Thiazolyl Peptide Natural Products
Featuring an Enzyme-Catalyzed Formal [4 + 2] Cycloaddition
†
†
‡
§
‡
Walter J. Wever, Jonathan W. Bogart, Joshua A. Baccile, Andrew N. Chan, Frank C. Schroeder,
,†
and Albert A. Bowers*
†Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill,
Chapel Hill, North Carolina 27599, United States
‡
Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853,
United States
§
Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
*
S Supporting Information
ABSTRACT: Thiocillins from Bacillus cereus ATCC
4579 are members of the well-known thiazolyl peptide
1
class of natural product antibiotics, the biosynthesis of
which has recently been shown to proceed via post-
translational modification of ribosomally encoded pre-
cursor peptides. It has long been hypothesized that the
final step of thiazolyl peptide biosynthesis involves a
formal [4 + 2] cycloaddition between two dehydroala-
nines, a unique transformation that had eluded enzymatic
characterization. Here we demonstrate that TclM, a single
enzyme from the thiocillin biosynthetic pathway, catalyzes
this transformation. To facilitate characterization of this
new class of enzyme, we have developed a combined
chemical and biological route to the complex peptide
substrate, relying on chemical synthesis of a modified C-
terminal fragment and coupling to a 38-residue leader
peptide by means of native chemical ligation (NCL). This
strategy, combined with active enzyme, provides a new
chemoenzymatic route to this promising class of anti-
biotics.
hiazolyl peptides are a growing class of highly modified,
Figure 1. (a) Biosynthesis of thiocillins from a modified peptide. LP =
leader peptide. (b) Thiocillin gene cluster from Bacillus cereus ATCC
T
peptide-derived natural products with potent activity
against antibiotic resistant bacteria, including methicillin-
resistant Staphylococcus aureus and vancomycin-resistant Enter-
1
4579. Open reading frames encoding key post-translational enzymes
are shown. (c) Sequence of the 52-residue precursor featuring a 38-
residue leader sequence (gray) and a 14-residue core peptide (black).
1
,2
ococci. Despite their potential therapeutic value, thiazolyl
peptides have gone largely underdeveloped because of their
generally poor solubility and bioavailability. Moreover, efforts
to improve on these limiting properties by means of synthesis
or chemical modification are hindered by the complex
macrocyclic architecture of the compound class: thiazolyl
peptides feature multiple azoline heterocycles alternating with
modified peptide side chains and cyclized on a trisubstituted
pyridine (or piperidine) core (Figure 1).
8
clinical trials for treatment of Clostridium difficile. Nevertheless,
the key central macrocycle, constituting the majority of the
drug pharmacophore, remains largely intractable to semisyn-
thesis, limiting LFF571 solubility and efficacy to infections of
the upper gastrointestinal tract.
Thiazolyl peptides are ribosomally synthesized and post9-
translationally modified peptide natural products (RiPPs).
They are biosynthesized from a precursor peptide containing an
N-terminal leader and a C-terminal core peptide motif.
Knockout studies in Bacillus cereus ATCC 14579 have
Although a number of total syntheses have tackled the task of
modified thiazolyl peptides, to date the most substantive
improvements have come by means of semisynthetic
3
−7
strategies.
Researchers at Novartis installed new solubilizing
functionalities at the C-terminus of Streptomycete-derived
Received: January 27, 2015
GE2270A, yielding LFF571, a derivative currently in phase-II
©
XXXX American Chemical Society
A
DOI: 10.1021/jacs.5b00940
J. Am. Chem. Soc. XXXX, XXX, XXX−XXX

Journal of the American Chemical Society
Communication
Figure 2. (a) Synthesis of the TclM substrate by thiophenol-catalyzed native chemical ligation and sulfhydryl elimination with dibromoadipamide.
b, c) QTOF-MS data of (b) NCL product 15 and (c) elimination product 16.
(
demonstrated the importance of the putative enzyme TclM in
late-stage biosynthetic cyclization of this group of thiazolyl
fragment would allow coupling to an intein-derived thioester of
the leader peptide via native chemical ligation (NCL). Upon
coupling, cysteine side chains could be converted to Dhas by a
1
0−12
peptides.
TclM presents a potentially unique enzymatic
20
activity: the long-hypothesized formal [4 + 2] cycloaddition
between two dehydroalanines (Dhas) to generate the
bisalkylation/elimination protocol.
We chose to prepare a simplified C-terminal fragment
containing all six thiazoles of the natural thiocillin but with
alanines used in place of threonines 4 and 6 and valine 8 and an
ethyl ester in place of the two modified threonines at the C-
terminus. Previous efforts had indicated that TclM would be
permissive to alanine substitution at these sites, although these
13−15
substituted pyridine core of the thiocillins.
This putative
“
hetero-Diels−Alderase” activity is unique from both enzymatic
and purely synthetic standpoints. In terms of enzymology, very
few such “Diels−Alderases” are known, let alone members
effecting a heteroannulative version of the chemistry. Enzymes
16
12
that have been characterized as potential “Diels−Alderases”1
analogues would likely not be antibiotically active. This
7
often enhance spontaneous chemical cyclizations (e.g., SpnF
hexathiazole precursor could be built by adapted protocols
from previous total syntheses by Bagley, Ciufolini, and
1
8
and VstJ ), yet the proposed transformation of TclM is
demonstrably nonspontaneous: Moody and co-workers have
induced this chemistry on simple substrates by severe
3
−5,7,21
Nicolaou (see the Supporting Information (SI)).
Although we anticipate that this route will be readily amenable
to the solid phase, we employed a block solution-phase
synthesis. The desired product was obtained in good yield over
seven steps (longest linear sequence from the building blocks;
see the SI) and could then be deprotected to give compound
12.
19
microwave irradiation. From a synthetic standpoint, TclM
could provide a mild, late-stage route to the thiazolyl peptide
core and allow access to new soluble derivatives. Herein we
develop a combined chemical and biological strategy to access a
leader-peptide-conjugated, doubly dehydrated substrate for
TclM and demonstrate in vitro the ability of TclM to catalyze
a formal [4 + 2] cycloaddition to form the mature pyridine ring.
Previous experiments in our lab suggested that the leader
peptide is necessary for TclM modification of the putative
substrate, but solid-phase peptide synthesis (SPPS) of a full 52-
residue substrate with thiazolyl and dehydroamino acid residues
seemed daunting, even with current SPPS technology. SPPS of
the full substrate would also necessitate complete resynthesis of
C-terminal variants for structure−activity probing of TclM. We
therefore devised a strategy involving separate preparations of
the C-terminal-modified component and the N-terminal leader
peptide (Figure 2a). The fully modified C-terminal fragment
could be prepared by total chemical synthesis, with cysteine
side chains as surrogates for the required dehydroalanine
residues. The use of cysteine at the N-terminus of the modified
The 38-residue leader peptide was cloned into vector
pETXSH (P. Loll lab) containing a C-terminally His -tagged
6
22
Mycobacterium xenopi intein. This could be expressed and
purified by Ni affinity chromatography and cleaved to afford the
2-mercaptoethanesulfonate (Mesna) thioester. Subtractive
purification gave the pure thioester, which was buffer-
exchanged and coupled to an excess of hexathiazole 12.
Elimination to give compound 16 could be carried out under
20
conditions published by Davis and co-workers. The structure
of the final precursor was confirmed by LC/MS (Figure 2c)
and rigorously characterized by MS/MS fragmentation (see the
SI).
To evaluate the ability of TclM to effect the formal [4 + 2]
cycloaddition of the two Dhas, the tclM gene was amplified
from genomic DNA isolated from B. cereus ATCC 14579 and
B
DOI: 10.1021/jacs.5b00940
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Journal of the American Chemical Society
Communication
Figure 3. (a) SDS-PAGE of purified recombinant TclM. (b) Overlaid extracted ion chromatograms of TclM substrate and TclM assay after 20 h of
incubation. The labeled peak indicates the newly formed thiazolyl peptide. (c) MS/MS spectrum of the isolated artificial thiazolyl peptide prepared
1
by the chemoenzymatic method. Ions are labeled according to convention for the cyclic peptide. (d) Aromatic region of the H NMR spectrum
showing new pyridine protons.
subcloned for translation as the N-terminal His MBP-tagged
6
fusion protein. Soluble protein was obtained in over 90% purity
after Ni-NTA affinity and size-exclusion chromatography
followed by tobacco etch virus (TEV) cleavage of the tag
(
Figure 3a and the SI). Although TclM does not have any
obvious predicted cofactor binding pocket, we note that the
purified protein did not appear to have any unusual absorbance
in the visible-light range. Assays for the putative cycloaddition
were conducted in a HEPES buffer at pH 7.2 and room
temperature. Time points were taken at 4 h intervals and
analyzed by high-resolution QTOF LC/MS and UV−vis
(
Figure 3b and the SI). Over course of the reaction, a new
peak grew in at 350 nm, consistent with the known, distinctive
absorbance of the trisubstituted pyridine core in the thiazolyl
peptides.
At 20 h, all of the starting material 16 was consumed in the
presence of TclM, and the new peak at 350 nm ceased to
increase. The observed peak at m/z 962.1171 matches within
Figure 4. Proposed mechanism of formal [4 + 2] cycloaddition
catalyzed by TclM. The reaction may proceed in concerted fashion
from the imidic acid, as illustrated, or else stepwise (not shown) to
yield putative intermediate I. This undergoes further elimination/
aromatization to the trithiazolylpyridine core of the thiocillins
(structure III, R1, R2 = thiazole).
+
instrumental error the value for [M + H ] of expected product
1
7 (m/z 962.1118) and exhibits the distinctive MS/MS
11
fragmentation pattern of thiazolyl peptides (see the SI). We
further scaled up the enzymatic reaction and were able to
isolate milligram quantities of product under unoptimized
conditions to facilitate complete characterization via two-
dimensional NMR spectroscopy. For example, signals repre-
senting the newly formed pyridine protons can be clearly seen
in the aromatic region, confirming the formation of the
trithiazolylpyridine core (Figure 3d and the SI). This
compound was absent from all controls, including those with
heat-denatured enzyme or prolonged (multiple days) solution
without enzyme.
peaks that could represent any putative intermediates but found
none of the anticipated masses, suggesting that either these
intermediates are short-lived or else TclM itself catalyzes the
aromatization.
This work provides direct evidence of the key role of TclM in
the formal [4 + 2] cycloaddition to form the trithiazolylpyridine
core of the thiocillins and most thiazolyl peptides. Our work
further represents the first functional characterization of a
member of this new class of enzymes. TclM and its homologues
are remarkable in that they show little or no homology to
members of other known enzyme classes. Even between
members of the family, homology is low (14/31% identity/
A potential mechanism for the TclM reaction is illustrated in
Figure 4. As drawn, the reaction involves concerted cyclization
via a stabilized tautomer of the amide carbonyl (imidic acid
tautomer). Alternatively, the mechanism could proceed in a
stepwise manner, allowing nucleophilic attack from a stabilized
α-carbanion of the formal 2π component into an imidocarbonyl
intermediate. Regardless of the mechanism, stepwise or
concerted, to arrive at the final product, the putative cyclic
intermediate would have to undergo aromatization by
elimination of water and/or the leader peptide carboxamide;
both steps may be spontaneous. We searched LC/MS traces for
10
similarity to the nearest homologue, TsrE). Remarkably,
TclM is capable of carrying out the formal addition by itself,
without accessory proteins or cofactors.
In conclusion, we have demonstrated that TclM catalyzes the
formation of the trisubstituted pyridine core of an artificial
thiazolyl peptide from a leader-peptide-bound substrate.
Mechanistically, the reaction can be drawn as a formal [4 +
2] cycloaddition between two Dhas with subsequent
C
DOI: 10.1021/jacs.5b00940
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Journal of the American Chemical Society
Communication
aromatization, but the exact mechanism, whether stepwise or
concerted, is still undetermined. Substrate specificity and
enzyme efficiency as well as a detailed mechanistic under-
standing of this new class of enzymes are subjects of ongoing
efforts in our lab. We have also demonstrated a chemo-
enzymatic route to this attractive class of natural products; we
anticipate that this route will allow the preparation of new and
improved analogues that are not accessible by synthetic or
semisynthetic methods.
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́
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ASSOCIATED CONTENT
Supporting Information
■
(
*
S
C. K.; Zentner, I. J. I.; Townsend, T. M. T.; Bhuiya, M. W. M.;
Cocklin, S. S.; Loll, P. J. P. J. Am. Chem. Soc. 2012, 134, 4637.
Experimental details, synthetic schemes, and figures. This
material is available free of charge via the Internet at http://
pubs.acs.org.
AUTHOR INFORMATION
Corresponding Author
abower2@email.unc.edu
■
*
Notes
The authors declare no competing financial interest.
ACKNOWLEDGMENTS
■
The authors thank Scott Allen, Stephen Frye, Harold Kohn, Bo
Li, Chris Neumann, and Chris Walsh for informative
discussions and careful reading of the manuscript. A.A.B. is a
Beckman Young Investigator and acknowledges support by the
Arnold and Mabel Beckman Foundation. Additional support
was provided by NIH Grants R01GM112739 (F.C.S.) and
T32GM008500 (J.A.B.).
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DOI: 10.1021/jacs.5b00940
J. Am. Chem. Soc. XXXX, XXX, XXX−XXX