DOI: 10.1002/cbic.201200227
Enzyme-Specific Activation versus Leaving Group Ability
Roseri J. A. C. de Beer,[a] Berry Bçgels,[a] Gijs Schaftenaar,[b] Barbara Zarzycka,[b]
Peter J. L. M. Quaedflieg,[c] Floris L. van Delft,[a] Sander B. Nabuurs,[b] and
Floris P. J. T. Rutjes*[a]
Enzyme-specific activation and the substrate mimetics strategy
are effective ways to circumvent the limited substrate recogni-
tion often encountered in protease-catalyzed peptide synthe-
sis. A key structural element in both approaches is the guanidi-
nophenyl (OGp) ester, which enables important interactions for
affinity and recognition by the enzyme—at least, this is usually
the explanation given for its successful application. In this
study we show that leaving group ability is of equal or even
greater importance. To this end we used both experimental
and computational methods: 1) synthesis of close analogues of
OGp, and their evaluation in a dipeptide synthesis assay with
trypsin, 2) molecular docking studies to provide insights into
the binding mode, and 3) ab initio calculations to evaluate
their electronic properties.
Introduction
These days enzymes are commonly used in organic synthesis.[1]
The benefits of enzymatic reactions, including their generally
excellent regio- and enantioselectivity, are widely recognized.
Because of the usually mild reaction conditions, enzymatic
conversions are often regarded as a green alternative to classic
organic reactions. However, the limited substrate scope of
many enzymes remains a big disadvantage.
group ability may be an important factor.[5] In this study, the
contribution of these components was investigated by both
experimental and computational methods. Several analogues
of OGp were designed, synthesized, and docked to trypsin to
provide insight in the binding mode. Subsequently, their effec-
tiveness in dipeptide formation was experimentally deter-
mined, and an attempt was made to increase the activity by
further variation of one of the analogues. An ab initio study
provided insight into the electronic properties of the ana-
logues under investigation.
One of the areas of application of enzymes is peptide syn-
thesis. In this field, proteases are employed to form the pep-
tide bonds (which they would natively hydrolyze) by exploiting
the reversibility of chemical reactions. A prerequisite for this
enzymatic activity, irrespective of whether aqueous media or
organic solvents are used, is that specific amino acids are rec-
ognized.[2] This problem of recognition can be circumvented
by applying the “substrate mimetics” strategy as previously de-
scribed for trypsin and other proteases.[3] The guanidinophenyl
(OGp) ester, which in essence resembles the naturally recog-
nized side chain of arginine, is claimed to serve as a recognition
moiety for trypsin, thereby making recognition independent of
the side chain of the amino acid and thus broadening sub-
strate scope. This approach is typically applied under aqueous
conditions; but because OGp also functions as a leaving
group, the commonly occurring secondary hydrolysis is pre-
vented, as the product formed becomes unrecognizable for
the enzyme.
Results and Discussion
Prediction of the binding mode of OGp analogues to trypsin
To distinguish between the effects of affinity for the enzyme
and leaving group ability, we evaluated a set of close ana-
logues of OGp that differed slightly in both properties. We
opted for trypsin as the model system, because this enzyme is
highly specific for arginine, in contrast to papain, which exhib-
its broad substrate specificity, with only a slight preference for
arginine. Moreover, the catalytic mechanism of the serine pro-
[a] R. J. A. C. de Beer, B. Bçgels, Dr. F. L. van Delft, Prof. F. P. J. T. Rutjes
Institute for Molecules and Materials, Radboud University Nijmegen
Heyendaalseweg 135, 6525 AJ Nijmegen (The Netherlands)
A similar solution to limited substrate acceptance was found
for papain, that is, to overcome enzyme-specific activation.[4]
Based on docking studies, the OGp group is predicted to bind
to papain in a different orientation than the natural substrate,
arginine. By taking advantage of this alternative recognition,
papain is able to catalyze dipeptide formation without being
restricted to specific amino acid residues. We noticed these
versatile applications of the OGp moiety and wondered what
was the reason for these remarkable properties. Additional re-
search, in which OGp was replaced with simpler esters, indicat-
ed that besides enzyme recognition and affinity, the leaving
[b] Dr. G. Schaftenaar, B. Zarzycka, Dr. S. B. Nabuurs
Computational Drug Discovery
Center for Molecular and Biomolecular Informatics
Radboud University Nijmegen Medical Centre
P.O. Box 9101, 6500 HB Nijmegen (The Netherlands)
[c] Dr. P. J. L. M. Quaedflieg
DSM Innovative Synthesis BV
P.O. Box 18, 6160 MD Geleen (The Netherlands)
Supporting information for this article is available on the WWW under
http://dx.doi.org/10.1002/cbic.201200227.
ChemBioChem 0000, 00, 1 – 7
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