Chemistry Reference
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on-bead binding assay with vitamin B
12
. The effects appeared to be kinetic in
nature. Indeed, the cationic analog
(AcLysSer)
8
(DapLysAla)
4
(LysAmbTyr)
2-
DapCysLeuNH
2
where the 12 glutamate residues have been replaced by cationic
lysines did not show measurable binding to vitamin B
12
due to an extremely slow
binding equilibrium, and the neutral glutamine analog
B1K
(AcGlnSer)
8
(DapGln-
Ala)
4
(DapAmbTyr)
2
DapCysAspNH
2
showed stronger and slower binding compared
to
N3
[24c].
In the third case, a similar control of metal coordination by charged residues was
encountered in peptide dendrimers bearing a bipyridine ligand at their core [25]. In
this system, multiple negative charges in the outer dendrimer branches of den-
drimer
B1
5
0
-amino-2,2
0
-
E1
(AcGluThr)
4
(DapGluVal)
2
DapBip
b
AlaAspNH
2
(Bip
¼
bipyridine-5-carboxylic acid) (7 negative charges) and
(AcLysAla)
4
(DapGlu-
Pro)
2
DapGlyBipGlyLeuNH
2
(2 negative and 4 positive charges) lead to the
formation of stable ternary complexes with Fe(II) Fe(
G1
10
14
M
3
)
E1
)
3
(K
a
¼
3.1
10
15
M
3
). However, no complexation took place when
multiple positive charges and no negative charges were present in the outer
branches as in dendrimer
and Fe(
G1
)
3
(K
a
¼
1.1
(AcArgLys)
4
(DapHisVal)
2
DapBipAmbTyrNH
2
(8
positive charges), an effect which is probably also caused by kinetic inhibition of
metal coordination.
E2
15.3.3 Optimization by Amino Acid Substitution
A broad variety of Fmoc-protected amino acids, including proteinogenic and non-
natural amino acids in both enantiomeric forms, are commercially available and
can be used to vary the structure of any peptide dendrimer. This allows the
straightforward design and synthesis of dendrimer combinatorial libraries and
the preparation of analogs. In the absence of significant technical hurdles in the
process, in particular by the use of the TAGSFREE design algorithm to facilitate
analysis (see above) [20], iterative cycles of library design, synthesis, and func-
tional selection offer a viable approach to discover and optimize peptide dendri-
mers for any given function. Dendrimer optimization by this process is related to
the Darwinian evolution by mutagenesis and selection, which leads to functional
proteins in nature.
Activity optimization by analog synthesis can be exemplified by the multivalent
esterase dendrimers derived from the (HisSer)
2
Dap dendron (Figure 15.4) [27]. A
series of 32 analogs of the third-generation peptide dendrimer
(AcHisSer)
8
(DapHisSer)
4
(DapHisSer)
2
DapHisSerNH
2
incorporating designed structural
changes such as selected shuffling of amino acids between positions and addition
or deletion of key residues uncovered structure-activity relationships that were not
apparent from the initial study of dendritic effects in catalysis [28]. In particular,
while the number of histidine residues primarily controlled substrate binding (K
M
),
the catalytic rate constant k
cat
depend on the particular arrangement of histidine in the
peptide dendrimer, and the nature of the other amino acids. The SAR study identified
dendrimer
G3
A3C
(AcHisThr)
8
(DapHisThr)
4
(DapHisThr)
2
DapHisThrNH
2
as the most
active dendrimer. In this dendrimer, the serine residues have been exchanged
