Ribosomal synthesis of dehydroalanine-containing peptides

Article abstract of DOI:10.1021/ja060966w

Dehydroalanine is a nonproteinogenic amino acid, but it is a component of a wide variety of natural products with therapeutic activities. Indeed, this α,β-unsaturated residue is a highly versatile building block due to its rigidifying effect on peptide backbones and its electrophilicity which allows site-specific thiol ligations of peptides with small molecules or proteins. To harness such versatility in genetically encoded, combinatorial peptide libraries, we report a simple and robust method for the ribosomal synthesis of dehydroalanine-containing peptides. Selenalysine, a selenium-containing lysine analogue, was recruited as a masked dehydroalanine equivalent. This residue is efficiently incorporated by a reconstituted Escherichia coli translation system at high fidelity and efficiency despite the presence of low levels of lysine. Mild oxidative conditions were used to convert selenalysine into dehydroalanine post-translationally. Using this method, we demonstrate the preparation of polyunsaturated and highly decorated peptides. This report is an important step toward the preparation and selection of large libraries of protein-reactive compounds with potential use as novel drugs or as analytical tools. Copyright

Full text of DOI:10.1021/ja060966w

Published on Web 05/13/2006
Ribosomal Synthesis of Dehydroalanine-Containing Peptides
Florian P. Seebeck and Jack W. Szostak*
Howard Hughes Medical Institute and Center for Computational and IntegratiVe Biology, Simches Research Center,
Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114
Received February 9, 2006; E-mail: szostak@molbio.mgh.harvard.edu
The nonribosomal peptides (NRP) feature an enormous chemical
diversity and have given rise to a multitude of therapeutics.1
However, their microbial synthesis by large multifunctional syn-
thetases complicates the construction and sampling of large libraries
of novel NRPs.2 In contrast, peptides synthesized by ribosomal
translation are amenable to ultrahigh throughput screening schemes,
such as mRNA display,3 a combinatorial method that allows the
sampling of more than 1013 individual molecules.4 In the past,
however, these peptide libraries had to be constructed from the 20
canonical L-amino acidssa rather uniform set of building blocks
compared to the variety of L-, D-, â-, and N-methyl and R,â-
unsaturated amino acids from which NRPs are tailored. In an effort
to reduce this limitation, we and others have shown that the in vitro
translation of nonbiological polymers from unnatural L-amino acids
is indeed possible with a reconstituted Escherichia coli translation
system (PURE-system).5-7 However, the ribosomal production of
polymers with additional alternative backbone residues remains a
challenging,8-10 yet indispensable step toward the production of
NRP-like structures in an mRNA-templated fashion.
One backbone alteration found in many natural products, such
as lantibiotics,11 microcystin,12 and thiopeptide antibiotics,13 stems
from the incorporation of dehydroalanine (∆Ala, Scheme 1). R,â-
Unsaturated amino acids exhibit rigidifying effects on the peptide
backbone, which stabilizes secondary structures and increases the
proteolytic stability of the parent molecule.14 Due to its moderate
electrophilicity, ∆Ala may also serve as a warhead in protein-
reactive compounds15 and has proven to be a valuable intermediate
for the preparation of cyclized, glycosylated, or prenylated peptides
through intra- or intermolecular Michael addition.16
To harness this versatility for the in vitro selection of peptides,
we devised a method for constructing dehydropeptides through
mRNA-templated, ribosomal peptide synthesis. Van der Donk et
al. reported the use of Se-phenylselenocysteine (SecPh) as a building
block for solid-phase peptide synthesis that can be converted to
∆Ala via oxidative elimination.17 The chemical conditions for this
process are compatible with biomacromolecules; however, SecPh
is not a reported substrate for any of the E. coli aminoacyl tRNA
synthetases and thus cannot be used for all-enzymatic peptide
synthesis. To circumvent this problem, we investigated the pos-
sibility that selenalysine18 (KSe, Scheme 1) might be an efficient
substrate for lysine aminoacyl tRNA synthetase and thus be
incorporated into peptides as directed by lysine codons on translated
mRNAs. We further surmised that such selenopeptides might
undergo oxidative elimination to expose ∆Ala in a post-translational
manner (Scheme 1).
Figure 1. Selenalysine incorporation assay. Left: The efficiency of peptide
1 production was determined by scintillation counting of specific 35S-Met
activity. The bars represent the average of three independent measurements,
and the averaged value for the lysine-containing reactions (35 ( 3 pmol)
was set to 100%. Control translation reactions without supplemented lysine
(no lysine) show a significant background due to the presence of
contaminating lysine in the translation mixture. Right: MALDI-TOF
analysis of the peptide 2 after translation (A, mcalc ) 1883.6 Da), oxidative
elimination (B, mcalc ) 1524.6 Da), and Michael addition of L-cysteine (C,
mcalc ) 1887.7 Da). Signals consistent with the production of peptides
containing one (a) or two (b) lysines are indicated. To improve detectability
by MALDI-TOF, peptides 1 and 2 were produced as the free N-terminal
amine by omission of the formyl donor (10-formyl-5,6,7,8-tetrahydrofolic
acid) necessary for formylation of methionyl tRNA.
agarose beads and 35S-Met scintillation counting (Figure 1, left).
Reactions supplemented with 0.2 mM lysine typically yielded 30-
40 pmol of peptide. Reactions where lysine was replaced by 0.16
mM KSe produced similar amounts of product, which was subse-
quently identified as the desired selenopeptide by MALDI-TOF
MS (mobs ) 1494.8 Da vs mcalc ) 1494.6 Da). As judged by this
analysis, the KSe-containing reaction did not incorporate lysine. This
is notable since endogenous traces of lysine in the translation
mixture allow considerable synthesis of the lysine-containing
peptide (mobs ) 1428.6 Da vs mcalc ) 1428.7 Da) (Figure 1, left).
As a more rigorous test of the efficiency and fidelity of lysine
replacement by KSe, we prepared an mRNA containing three
consecutive lysine codons. This template was also efficiently
translated into selenopeptide (30 pmol/50 µL) with an observed
mass of mobs ) 1883.2 Da (mcalc ) 1883.6 Da), indicating that
Scheme 1
To test these ideas, we assembled a reconstituted translation
system from E. coli6 as previously described and tested the
19,20
efficiency of KSe
incorporation in place of lysine into a short
peptide (Figure 1, peptide 1). Fifty microliter translation reactions
containing the corresponding mRNA were incubated for 1 h at 37
°C. Product peptide yields were determined by purification on NTA-
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J. AM. CHEM. SOC. 2006, 128, 7150-7151
10.1021/ja060966w CCC: $33.50 © 2006 American Chemical Society

C O M M U N I C A T I O N S
Treatment of the same peptide with 200 mM H2O2 led to a mixture
of non-, mono-, and disulfoxidized species. Reduction of the oxidant
concentration, however, led to satisfactory homogeneity. For the
same reason, we chose to substitute methionine with norleucine
(MNor), an efficient analogue with an oxidation-resistant side chain.25
In summary, we have demonstrated the production of genetically
encoded dehydropeptides. Our approach employs unmodified
components from the translation machinery of E. coli and mild but
robust conditions to install multiple electrophilic functions in linear
or cyclic peptides. The simplicity of this methodology should allow
wide applicability, making highly decorated peptides available
independently of solid-phase peptide synthesis. Furthermore, having
introduced ∆Ala to the toolbox of mRNA-templated peptide
synthesis, we may now embark on ultrahigh throughput selections
for specific protein-reactive or catalytically active compounds.
Figure 2. Incorporation of ∆Ala into a cyclic scaffold. Two concomitant
SN2 reactions between two peptide-borne thiols (A, mcalc ) 1923.7 Da) and
one equivalent of R,R′-dibromo-m-xylene lead to peptide cyclization.
Possible side products, such as the linear adduct of two equivalents of xylene
and one peptide, are not observed (B, mcalc ) 1900.8 Da). A minor signal
16 Da higher than the expected mass indicates partial sulfoxidation of the
newly formed thioethers by the conditions used for ∆Ala formation.
Acknowledgment. We thank Drs. M. C. T. Hartman, K.
Josephson, and B. Seelig for their insightful advice. J.W.S. is an
Investigator of the Howard Hughes Medical Institute, and F.P.S.
is supported by the National Institutes of Health (GM 074505-02).
Supporting Information Available: Experimental details. This
material is available free of charge via the Internet at http://pubs.acs.org.
incorporation of KSe does not significantly inhibit the translational
machinery and that lysine incorporation is effectively outcompeted
(Figure 1A).
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Translated and purified selenopeptide (Figure 1, peptide 2) was
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with 200 mM H2O2 at pH 5-6 on ice for 1 h.17 The mass difference
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by sulfoxidation of the N-terminal methionine (+16) (Figure 1B).
The formation of three electrophilic functions was further confirmed
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peptide with 100 mM L-cysteine (Figure 1C). Indeed, a large variety
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A model peptide (Figure 2, peptide 3) was produced by in vitro
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buffer, pH 8.0 for 1 h at room temperature. The peptides were then
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for 1 h and then analyzed by MALDI-TOF (Figure 2B). The
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