Biomimetic catalysis of diketopiperazine and dipeptide syntheses

Article abstract of DOI:10.1002/anie.200704266

Modular supramolecular catalysts with a coiled-coil peptide scaffold, designed to mimic nonribosomal peptide synthetases, catalyze the formation of diketopiperazines and linear dipeptides for several aminoacyl substrates (see scheme). The nature of the ac

Full text of DOI:10.1002/anie.200704266

Communications
DOI: 10.1002/anie.200704266
Peptidic Catalysts
Biomimetic Catalysis of Diketopiperazine and Dipeptide Syntheses
Zheng-Zheng Huang, Luke J. Leman, and M. Reza Ghadiri*
In recent years significant progress has been made in the
design of synthetic peptide catalysts that carry out isolated
chemical reactions similar to those catalyzed by enzymes,
albeit with significantly lower efficiencies.[1,2] An unmet
challenge in the de novo design of enzymes is to engineer
peptides capable of bringing about more complex, multistep
synthetic processes.[3] One such biosynthetic pathway is that
of diketopiperazine (DKP) formation, which minimally
requires simultaneous binding and activation of two amino-
acyl substrates, aminoacyl transfer to generate a linear
dipeptide intermediate, and cyclization of the dipeptide to
yield the product DKP.[4,5] Herein we report the design and
characterization of supramolecular peptide assemblies that
catalyze DKP and dipeptide syntheses for a variety of
aminoacyl substrates. The peptides covalently capture two
aminoacyl substrates from the solution, hold them in prox-
imity to make the aminoacyl transfer step effectively intra-
molecular, and release product in the form of DKP. We also
establish that the nature of the active-site residues in the short
a-helical homo or heterotetrameric peptide catalysts influen-
ces the relative yields of DKP, linear dipeptide, and hydro-
lyzed substrates, indicating that appropriate active-site engi-
neering might eventually be used to govern product elonga-
tion or termination by hydrolysis or cyclization.
The dedicated biosynthetic pathways employed to syn-
thesize DKP sometimes involve nonribosomal peptide syn-
thetases (NRPSs).[4] These modular multienzyme complexes
catalyze a series of directed, intermodular aminoacyl transfer
Figure 1. Schematic representations of aminoacyl loading and inter-
reactions between adjacent covalently anchored aminoacyl
thiolester substrates (Figure 1a).[6] Our designed catalysts[1]
modular aminoacyl transfer in a) the nonribosomal peptide synthe-
tases (NRPSs); b) the designed coiled-coil catalysts. X1 and X2
aim to functionally mimic NRPSs by relying on peptide self-
assembly to juxtapose two cysteine residues, each used for the
represent active-site residues that are modified. c) Active-site residues
of aminoacyl transfer catalyst 1 modeled onto the crystal structure of a
coiled-coil homotetramer.[9] The peptide sequences are shown on the
right and the active-site residues are underlined.
covalent capture of aminoacyl substrates from solution by
transthiolesterification, at the helical interfaces of a coiled-
coil[7] assembly (Figure 1b,c). The resulting high effective
concentration[8] of aminoacyl donor and acceptor moieties,
and possible electrostatic or general acid–base contributions
provided by the flanking X1 and X2 residues, afford signifi-
cantly enhanced rates for the intermodular aminoacyl trans-
fer.[1] The final step required in DKP synthesis, cyclization of
the dipeptide intermediate, could similarly be accelerated by
contributions from appropriate active-site residues.
We anticipated that the most beneficial active-site resi-
dues for DKP formation might differ from those identified in
our earlier model studies[1] because of the additional mech-
anistic requirements of DKP synthesis. Therefore we initially
investigated stoichiometric aminoacyl transfer reactions
involving preformed l-phenylalanine peptidyl thiolesters of
sequences 1–5, which differ only in the active-site X1 and X2
residues. Encouragingly, in all cases we observed aminoacyl
transfer to form linear dipeptide intermediates bound to the
coiled coil and subsequent cyclization to yield DKP (RP-
HPLC) (Figure 2). The peptide active-site residues signifi-
cantly influenced the rates of both product formation and
substrate hydrolysis (Figure 2, see the Supporting
Information, Figure S1). The observed concentration of free
dipeptide produced was less than 3% in all cases, indicating
that dipeptide cyclization is significantly more efficient than
[*] Dr. Z.-Z. Huang, Dr. L. J. Leman, Prof. Dr. M. R. Ghadiri
Department of Chemistry and
The Skaggs Institute for Chemical Biology
The Scripps Research Institute
10550 North Torrey Pines Road, La Jolla, CA 92037 (USA)
Fax : (+1)858-784-2798
E-mail: ghadiri@scripps.edu
Supporting information for this article is available on the WWW
under http://www.angewandte.org or from the author.
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DKP (Figure 2d). In a background reaction of the 3-
mercaptopropionic acid thiolester of l-Phe (5 mm), less than
1.0 mm DKP was formed after 4 hours under otherwise
identical conditions.
We next examined the generality of the designed amino-
acyl transfer process using homo- and heterotetrameric
assemblies of sequence 2 preloaded with various aminoacyl
thiolester substrates (Table 1). In homotetrameric assemblies
Table 1: Product yields for reactions involving peptide 2 preloaded with
various aminoacyl thiolester substrates at Cys8 or Cys13.[a]
Entry Cys8 TE Cys13 TE [Pep] [mm] t [h] Products[b] (% Yield)
1
2
3
4
5
6
7
Phe
Met
LeuLeu 99
Tyr
Val
d-Phe
Phe
Met
Phe
Met
111
147
4
4
DKP (35), linear (31)
DKP (57)
Figure 2. Product formation versus time for reactions initiated with
preformed bis(l-Phe) thiolesters of sequences 1–6. Reaction condi-
tions: peptide (ca. 100 mm), 50 mm N-(2-hydroxyethyl)-piperazine-N’-2-
ethanesulfonic acid (HEPES; pH 7.0), tris-carboxyethyl phosphine
(TCE; 10 mm) as a reducing agent, acetamidobenzoic acid (Aba;
50 mm) as an internal concentration standard. a) Reaction profile for
peptide 2, showing consumption of the bis-substrate-loaded starting
peptide (&) and formation of coiled-coil-bound linear dipeptide
4
DKP (43)
Tyr
Val
d-Phe
Phe
Met
118
175
125
64
4
4
4
4
DKP (12)
DKP (<1)
DKP (20), linear (10)
Phe-Met DKP (35),
Met-Met DKP (42),
Phe-Phe DKP (8)
DKP (63), linear (18)
64
8
9
Acm
Phe
Acm
Phe
Gly
Acm
His
81
504
60
2
2
~
^
intermediate ( ), diketopiperazine ( ), total aminoacyl transfer prod-
*
ucts (linear dipeptide intermediate plus DKP, ), and l-Phe (substrate
DKP (54), linear (20)
^
hydrolysis, ”). b) DKP formation for sequences 1 ( ), 2 (+), 3 (&),
Acm
316
~
*
4 ( ), 5 ( ), 6 (”). c) Formation of total coiled-coil-bound linear
~
[a] Cys8 TE and Cys13 TE refer to the aminoacyl thiolester loaded at the
respective active-site Cys residues and Acm denotes the acetamido-
methyl protecting group. For entries 7–9, two differentially preloaded
derivatives of peptide 2 were mixed to initiate the reaction. [b] Linear
refers to the linear coiled-coil-bound dipeptide species. Unless otherwise
noted, the yield of this species was less than 10%. For entry 7, the yield of
Phe-Met DKP is based on the total concentration of peptide (128 mm),
whereas the yields of homo-DKP species are based on the concentration
of parent peptides (64 mm). For entries 7–9, yields are based on the
concentration of the limiting substrate peptide.
^
dipeptide intermediates for sequences 1 ( ), 2 (+), 3 (&), 4 ( ), and
*
5 ( ). d) Comparison of DKP (solid symbols) and coiled-coil-bound
linear dipeptide (open symbols) for sequences 1 (X2 =His, triangles)
and 2 (X2 =Asp, circles).
dipeptide hydrolysis. The highest yields of DKP were
observed for sequences 1 and 2 that contain His at the X1
position (Figure 2b);[1] the high yields are likely because the
imidazole group of the His side chain can provide general
acid–base or proton-transfer catalysis. Furthermore, for
sequences 1 and 2 (X1 = His) we observe that only the
aminoacyl substrate loaded at Cys8 is acting as the acyl-
acceptor moiety (Figure 1b, path a) (no dipeptide species are
observed bound at position 13), whereas for sequence 5 (X1 =
Asp) we instead observe that the substrate anchored to Cys13
is acting as the aminoacyl acceptor (Figure 1b, path b). The
results suggest that the X1 and X2 active-site positions could
be exploited to bring about directed aminoacyl transfer
through appropriate active-site engineering. At the X2 active-
site position, incorporation of an Asp residue appeared to
stabilize the coiled-coil-bound aminoacyl thiolester substrates
and dipeptide species relative to sequences with His or Ala at
the X2 position (Figure 2c, see the Supporting Information,
Figure S1). Thus, changing the X2 active-site residue from His
(peptide 1) to Asp (peptide 2) significantly increases the
relative concentration of linear coiled-coil-bound dipeptide to
(Table 1, entries 1–6), product yields were highest for Phe,
Met, and Leu. The supramolecular nature of the coiled-coil
scaffold allowed us to mix equal amounts of two differentially
preloaded derivatives of peptide 2 (Table 1, entry 7), resulting
in the formation of the mixed DKP product in a 35% yield.
Whereas observation of the heteromeric product (Phe-Met
DKP) supports the possibility of heterotetramer formation
and subsequent aminoacyl transfer between the different
anchored substrates, the reaction also generated the homo-
meric DKP species (Phe-Phe and Met-Met), which we
expected because the assembly of both the homo- and the
heterotetrameric coiled coils results in productive complexes
that juxtapose aminoacyl substrates. To circumvent the
formation of product mixtures, we disabled one of the
active-site Cys residues in each peptide using an acetamido-
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Communications
methyl (Acm) protecting group, such that parallel homo-
tetrameric assemblies are prevented from juxtaposing amino-
acyl donor and acceptor moieties, and heterotetrameric
bundles form competent active sites (Table 1, entries 8 and
9, see the Supporting Information, Figure S2). Encouragingly,
when sequences preloaded with Gly (Table 1, entry 8) or His
(Table 1, entry 9) were mixed with an approximately fivefold
excess of a Phe-loaded peptide, we observed efficient amino-
acyl transfer (81% and 74% total yields, respectively). In
both reactions, no homo-DKP was found, supporting the
proposed mechanism of intermodular aminoacyl transfer
brought about by parallel heterotetrameric coiled coils.
Achieving turnover remains one of the most challenging
aspects of biomimetic catalysis. We examined the potential
for catalytic DKP formation in reaction cycles involving
aminoacyl substrate loading from solution, intermodular
aminoacyl transfer, and dipeptide cyclization to generate
DKP while regenerating peptide catalyst 1 (Figure 3a). An l-
Phe substrate was used at a slightly lower pH value of 6.0 to
reduce the rate of background DKP formation. We observed
significantly enhanced DKP formation relative to a back-
ground reaction carried out in the absence of peptide 1;
furthermore, the amount of DKP produced was strongly
dependent on the concentration of 1 (Figure 3b). Derivatives
of sequence 1 that were Acm-protected at either Cys8 or
Cys13effected almost no rate enhancement relative to the
background reaction (Figure 3b), supporting the proposed
intermodular mechanism of aminoacyl transfer between the
Cys8 and Cys13positions. We also examined the generality of
catalytic DKP formation by using several aminoacyl thiol-
ester substrates (Figure 3c). Only very modest turnover
numbers were observed with the l-Phe substrate producing
approximately two equivalents of DKP in 48 hours at all
catalyst concentrations. One possible cause of low turnover in
these reactions can be attributed to the formation of low
(ca. 25%) steady-state levels of coiled-coil-bound thiolesters.
A juxtaposition of two loaded peptide species is required for
DKP formation, but in a statistical association of peptides in
Figure 3. Catalytic DKP formation for reactions initiated with sequence
1 at various concentrations and free aminoacyl thiolester substrates
(5 mm) in solutions containing 50 mm 2-(N-morpholino)ethanesul-
fonic acid (MES; pH 6.0), TCEP (10 mm), and Aba (50 mm). a) Reac-
tion scheme depicting catalytic formation of DKP. b) DKP formation as
a function of time for reactions initiated with the l-Phe mercaptopro-
which only 25% are loaded, only 1= of the helical interfaces
16
would contain the requisite two anchored thiolesters. The low
level of productive interfaces combined with competing
thiolester hydrolysis, could give rise to the poor product
yields. The low turnover observed might therefore represent
an inherent limitation of using randomly assorting noncova-
lently associated molecules as catalyst scaffolds, especially
when proximity is an important component of catalysis.
Attempts to increase the steady-state concentration of loaded
catalyst species by employing substrates with different thiol
leaving groups, or by sequestering the thiol released by
substrate hydrolysis or transthiolesterification, did not sig-
nificantly improve catalyst turnover (data not shown).
Another possible cause of low turnover is that a conforma-
tional requirement (such as an amide trans to cis isomer-
ization of the coiled-coil-bound dipeptide) limits DKP
formation, although this seems unlikely considering the
moderate to good DKP yields in the reactions initiated with
preloaded peptides (Table 1).
*
pionic acid thiolester substrate (5 mm) and peptide 1 at 78 mm ( ),
^
50 mm (&), 25 mm ( ), 0 mm (”), or with the derivative of 1 Acm-
~
protected at Cys8 (82 mm, ) or at Cys13 (86 mm, +). c) Background-
subtracted DKP formation as a function of time for reactions initiated
with peptide 1 (ca. 100 mm) and the 3-mercaptopropionic acid thiol-
~
*
^
esters (5 mm) of Met ( ), Phe (&), Leu( ), and Tyr ( ).
ing higher turnover and better control of product elongation
and termination steps. It remains to be seen if these relatively
simple peptides are capable of providing the subtle chemical
effects required to synthesize longer, more complex peptide
products.
Received: September 16, 2007
Revised: November 11, 2007
Published online: January 22, 2008
The major challenges remaining for the use of simple
coiled-coil assemblies to effectively mimic NRPSs are achiev-
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Keywords: biomimetic synthesis · diketopiperazine ·
organocatalysts · peptides · supramolecular chemistry
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