Multivalent glycocluster design through directed evolution

Article abstract of DOI:10.1002/anie.201105555

Selection with modified aptamers: A method is described for design of glycocluster ligands by directed evolution. Glycan azides are attached to a library of alkyne-containing DNA sequences. DNA sequences which cluster the glycans best for multivalent bind

Full text of DOI:10.1002/anie.201105555

Communications
DOI: 10.1002/anie.201105555
DNA-Scaffolded Glycoclusters
Multivalent Glycocluster Design through Directed Evolution**
Iain S. MacPherson, J. Sebastian Temme, Sevan Habeshian, Krzysztof Felczak,
Krzysztof Pankiewicz, Lizbeth Hedstrom,* and Isaac J. Krauss*
A vast number of biological processes are mediated by
multivalent ligand–receptor interactions, including cell adhe-
sion, host invasion by pathogens, pathogen neutralization by
host, and numerous cell regulatory signaling pathways.[1]
Multivalency is especially important for carbohydrate–recep-
tor interactions: whereas individual glycans[2] may bind with
low affinity to a single binding site, the clustering of glycans
creates a high-avidity interaction with clustered binding sites.
This “carbohydrate cluster effect”[1b] has been demonstrated
experimentally with synthetic multivalent carbohydrate
ligands which bind well to protein targets. These ligands
have included oligo- and polyvalent clusters of glycans on
diverse scaffolds, including small molecules, dendrimers,
polymers, and even viral capsids.
To date, most glycocluster ligands have been designed for
synthetic convenience rather than control of tertiary struc-
ture. However, the biological activity of the natural glyco-
cluster may be influenced by tertiary structure and other
elements which are not usually addressed in synthetic
glycocluster designs, such as: 1) Glycan spacing and orienta-
tion—glycans are normally attached to synthetic scaffolds
through long flexible linkers, and the scaffolds themselves are
often flexible.[3] 2) Glycan internal flexibility—in a natural
glycocluster, neighboring structures may restrict a glycanꢀs
conformational ensemble, but this fingerprint is lost when the
glycan is placed on an artificial scaffold. 3) Non-carbohydrate
recognition elements—some receptors may recognize a
combination of glycans and peptide or lipid elements.[4] Few
structures of glycocluster–receptor complexes have been
solved, providing little data on which to base synthetic
glycocluster designs. Even with unlimited structural data, this
would be an exceedingly complex challenge for rational
design.
Figure 1. Directed evolution of glycosylated DNA scaffolds.
ters. The “best” glycoclusters are selected from the pool by
binding to the target protein. These selection winners are then
replicated to form a second-generation library and the
process is repeated for several rounds until the pool is
sufficiently enriched in high-affinity binders. We have chosen
DNA as our glycocluster scaffolding material because DNA is
easy to synthesize, easy to replicate by PCR, can fold into
diverse sequence-dependent structures, and is amenable to
sequence-specific “glycosylation” by glycan azides using
CuAAC[5] (“click”) attachment to alkyne-modified nucleo-
bases. Iterative selection/amplification of DNA structures
(SELEX) is often performed to obtain DNAs which bind to a
target.[6] Our method, by contrast, would yield DNA scaffolds
whose major function would be to position and support
glycans optimally for target binding. However, these DNAs
might also contain elements which would interact directly
with the target, mimicking any non-carbohydrate components
necessary in the natural ligand.
We decided to test this concept in the design of
glycoclusters which mimic the epitope of 2G12, an antibody
which protects against HIV infection and binds to a cluster of
high-mannose glycans on the HIV envelope protein gp120.[7]
Rationally designed clusters of these glycans have been tested
as vaccines to elicit 2G12-like antibodies, but without
success.[8] Our evolution-based design would be the product
of the procedure outlined in Figure 1, using a high-mannose
glycan as the azide and 2G12 as the target protein. However,
As an alternative to rational design, we have been
interested in directed evolution-based design of glycocluster
ligands. Figure 1 outlines this concept: a library of scaffold
molecules is glycosylated, generating a library of glycoclus-
[*] Dr. I. S. MacPherson, J. S. Temme, S. Habeshian, L. Hedstrom,
Prof. I. J. Krauss
Department of Chemistry
Departments of Biology and Chemistry, Brandeis University
415 South St., Waltham, MA 02454 (USA)
Dr. K. Felczak, Prof. K. Pankiewicz
Center for Drug Design, University of Minnesota
516 Delaware St. SE, MMC 204, Minneapolis, MN 55455 (USA)
[**] I.J.K. gratefully acknowledges Brandeis University and the NIH (R01
AI090745). L.H. gratefully acknowledges the NIH (U01 AI75466-01
and R01 GM054403).
Supporting information for this article is available on the WWW
under http://dx.doi.org/10.1002/anie.201105555.
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to enable PCR amplification of selection winners with such
large modifications on the DNA bases, we have significantly
redesigned the traditional SELEX protocol. Our method,
which we term SELMA[9] (“selection with modified apta-
mers”) is detailed in Scheme 1.
be efficiently amplified by PCR, serving as the genetic
“barcode”.[10] The best binders are then isolated from the
library by capture on solid-phase-bound 2G12, and this small
fraction of the library (e) is amplified by PCR (primers 1 and 2
+ natural dNTPꢀs) affording the (n + 1)th-generation library
without the hairpin portion (f). The (n + 1)th-generation
library is then restored to ssDNA hairpin form (i) by
bidirectional polymerase extension with an overhanging
biotinylated primer and removal of the biotinylated strand
(g–i). A similar selection scheme has been proposed, but not
reduced to practice, for threose nucleic acid (TNA) libra-
ries.[11]
To facilitate rapid testing of our method, we chose to
glycosylate our first library with easily synthesized Man4
tetrasaccharide (Scheme 2), which comprises the majority of
Scheme 2. Synthesis of Man4-azide. [a] Yield based on 0.8 equiv Tf2O
as limiting reagent. PMB=p-methoxybenzyl; Bn=benzyl; Tf=trifluoro-
methanesulfonyl; TTBP=2,4,6-tri-tert-butylpyrimidine; DCM=dichloro-
methane; DDQ=2,3-dichloro-5,6-dicyano-1,4-benzoquinone.
the carbohydrate recognized by 2G12. Crich–Kahne b-
mannosylation[12] attached the core b-mannose 1 to cyclohe-
xyl linker 2. Protection of the sulfonamide NH was essential
to ensure clean monocoupling of 3 with trisaccharide donor
4.[13] Global deprotection of 5,[14] followed by azidation,[15]
reliably afforded 100 mg quantities of the desired Man4-azide
(6).
With Man4-azide in hand, selection was then initiated with
ca. 40 pmol of library (ca. 2 ꢁ 1013 sequences). For the first
cycle of SELMA, the state of the library at each selection
stage was validated by observation in a PAGE gel (Figure 2).
The original ssDNA hairpin library (Scheme 1a) ran as a
poorly staining smear (Figure 2, lane 1). After polymerase
extension in the presence of dATP, dCTP, dGTP and EdUTP,
the resulting duplex hairpin structure (Scheme 1b) ran on the
gel as a narrow band (Figure 2, lane 2) with much less
mobility than simple dsDNAs of similar length, due to the
large molecular radius of the hairpin moiety. After CuAAC
attachment of Man4 glycans, the glyco-dsDNA hairpins
(Scheme 1c) ran as a diffuse band (Figure 2, lane 3) with
still less mobility in the gel.[16] After strand displacement, the
Scheme 1. SELMA (selection with modified aptamers).
The SELMA method (Scheme 1) begins with (a) a
synthetic library of ssDNA hairpins containing a stem-loop,
a (ꢀ)-sense random region (colored hollow bar) and primer
sites 1 and 2. Polymerase extension with alkyne-substituted
EdUTP instead of dTTP creates a dsDNA hairpin library (b),
with alkyne-modified EdU bases only in the (+)-sense strand.
CuAAC chemistry with a glycan azide transforms the alkynyl
bases into “glyco-bases”, affording a glyco-dsDNA library (c).
As before, the base modifications (now carbohydrates) are
present only in the (+)-strand. Generation of the library is
then completed by a strand displacement reaction: annealing
of primer 2 inside the loop and polymerase extension with all-
natural dNTPs creates an all-natural (+)-sense strand which
displaces the glycoDNA strand, creating a library of glyco-
ssDNA–dsDNA hybrids (d). The glyco-ssDNA (+)-sense
strand now folds in a sequence dependent manner and
exhibits a “phenotype”. The covalently linked dsDNA region
contains the same sequence with no nonnatural bases and can
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were cloned. Sequencing of 20 randomly selected clones
yielded 19 full sequences, including 2 pairs of duplicates and
15 unique sequences with no apparent similarity (see
Supporting Information).
Examination of these sequences showed that they con-
tained 7–14 glycosylation (EdU) sites. Three glycoclusters
(clones 4/5, 16/23, 18), each containing 10 glycosylation sites,
were synthesized and their Kd values with 2G12 were
measured in a filter binding assay. Glycoclusters 4/5, 16/23,
and 18 displayed moderate affinity for 2G12, with values of
Kd = 270 ꢁ 40 nm, 220 ꢁ 50 nm, and 330 ꢁ 30 nm, respectively
(Figure 3a).[17] This moderate affinity, combined with the
large number of glycosylation sites, might have suggested that
high valency alone was responsible for the observed binding
to 2G12. However, neither the starting library (of which
> 75% contained 7–15 glycosylations)[18] nor a random
sequence containing 10 glycosylated positions showed detect-
able binding to 2G12. Therefore, the affinity of our selection
winners is sequence-dependent and not simply the result of
high valency.
We then performed several experiments with glycocluster
16/23 to clarify the elements necessary for binding to 2G12
(Figure 3b). When annealed to its complementary DNA
strand, glycocluster 16/23 bound 2G12 significantly less
efficiently, showing that binding is dependent on tertiary
structure. Additionally, no binding was observed in the
absence of glycosylation, strongly suggesting the binding
contacts with 2G12 are mostly or exclusively made through
glycans and not through DNA alone. Gratifyingly, binding
was significantly diminished in the presence of gp120, showing
that gp120 and glycocluster 16/23 compete for the same (or
overlapping) site(s) on 2G12.
Figure 2. PAGE Analysis of Individual SELMA Steps.
glyco-ssDNA–dsDNA hybrid structure of the library (see
Scheme 1d) was confirmed by several observations and
control experiments. First, it ran as a smear in the gel
(Figure 2, lane 5). Additionally, treatment with exonuclease I
(which digests the 3’-terminal ssDNA portion) resulted in the
appearance of a sharp 80 bp band corresponding to the
dsDNA portion (Figure 2, lane 6). By contrast, the glyco-
dsDNA hairpins (Scheme 1c) showed no change upon
exonuclease treatment (Figure 2, lanes 3 vs. 4). Heating the
hybrids to 958C (but not 758C) destabilized the duplex
portion of the hybrid structure, allowing the glycosylated
strand to reinvade and expel the unglycosylated single strand.
This results in a return to the glyco-dsDNA hairpin structure
(Scheme 1c), which is impervious to the exonuclease
(Figure 2, lane 8, same as lanes 3 and 4).
After this confirmation of the desired dsDNA–ssDNA
hybrid structure, we began selection: the library was incu-
bated with 2G12 and the 2G12-bound fraction was captured
with protein A beads. Bound glycoclusters were retrieved
from the beads by thermal denaturation and subjected to
PCR with biotinylated primer 2, giving the 2nd-generation
library in dsDNA format (Scheme 1 f), which ran as the
expected sharp 80 bp band on the PAGE gel (Figure 2,
lane 9). The library was then converted back to its ssDNA
hairpin form (Scheme 1i) in three steps. Removal of primer-2-
derived biotinylated strand with streptavidin beads and
polymerase extension with an overhanging biotinylated
primer afforded 120 bp dsDNA product (Scheme 1h and
Figure 2, lane 10). Finally, removal of the biotinylated strand
from the 120 bp duplex afforded the 2nd-generation library in
ssDNA hairpin format (Scheme 1i). This ssDNA hairpin
could now be extended with dATP, dCTP, dGTP and EdUTP,
to produce the 2nd-generation library in dsDNA hairpin form
(Scheme 1b) which again ran as a sharp band, identical to the
first cycle (Figure 2, lane 11 vs. lane 2).
Next, we carefully dissected the binding determinants of
glycocluster 16/23 through a series of mutagenesis experi-
ments (Figure 3c), starting with truncation at both the 5’ and
3’ ends (entries 1–8). The extreme ends were not essential for
binding to 2G12; however, truncations extending beyond the
first and last glycosylation sites did result in total loss of
binding. We then performed point mutagenesis, replacing
each glycosylated EdU residue with cytosine (entries 9–21).
Seven of these mutations produced little change in the value
of Kd, but mutations in the 2nd, 4th, and 10th glycosylation
positions (entries 11, 13, and 19) caused a drastic loss of
binding (Kd @ 800 nm), suggesting that these glycans directly
contact 2G12. However, glycoclusters containing only these
three glycosylation sites (entries 20 and 21) failed to bind to
2G12, suggesting that the other glycans may be important for
maintaining tertiary structure. We attempted to gain addi-
tional insight into this question by Mfold secondary structure
prediction,[19] but the resulting structures did not provide an
obvious explanation for the importance of the 2nd, 4th, and 10th
glycosylation sites. Mfold calculation is probably of limited
validity in this case, as it does not take into account the Man4-
modification of ten bases.
Now that all SELMA steps had been validated, the entire
cycle was repeated through multiple rounds. Rounds 2, 4, and
6 included a negative selection to remove library members
that bound to protein A beads. Enrichment of 2G12 binders
in the population was assessed by monitoring the number of
PCR cycles required to regenerate the library. Between
rounds 5, 6 and 7, enrichment of the library leveled off, so the
selection was terminated and the resulting PCR products
In conclusion, this work is the first to demonstrate the
feasibility of directed evolution for glycocluster design. We
have shown that an “evolved” Man4 glycocluster binds to
2G12 and can compete with gp120. Future work will involve
structural studies of these glycoclusters, refinement of the
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Figure 3. Selection Results. a) Preliminary 2G12-dependent filter binding data for clones 4/5, 16/23 and 18, the starting library, and arbitrary
sequence containing 10 glycosylation sites. b) Effects of glycosylation, gp120 competition, and single/double strandedness on 2G12-binding by
glycocluster 16/23 determined by filter binding. c) Mutagenesis study: values of Kd and fraction bound (Fmax) for truncated and mutated
glycocluster 16. Entry 1 is the parent sequence. Underlined sequence is the random region. S in gray box denotes Man4-glycosylated EdU. [a] Kd
and Fmax were calculated by fitting Fbound =(Fmax [2G12])/(Kd+[2G12]) to data points. Errors reported are the standard error of the curve fit in all
cases except entry 1, for which the average of errors in entries 1–8 is reported. [b] The values of Kd reported in the text, in entries 1–8 and
entries 9–21 were measured with different batches of 2G12, giving slightly different values of Kd for the parent clone 16 (text vs. entries 1 vs. 9).
The Kd values in entries 10–21 should be compared only with entry 9. [c] Kd was much greater than the maximum 2G12 concentration tested and
Fmax was constrained to 1 to fit curve with finite Kd value.
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[3] Examples of rigid scaffolds include cyclodextrins and calixar-
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Keywords: carbohydrates · cluster effect · directed evolution ·
glycoconjugates · multivalency
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[16] Completion of the CuAAC reaction was assessed by control
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P
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