IBodies: Modular synthetic antibody mimetics based on hydrophilic polymers decorated with functional moieties

Article abstract of DOI:10.1002/anie.201508642

Antibodies are indispensable tools for biomedicine and anticancer therapy. Nevertheless, their use is compromised by high production costs, limited stability, and difficulty of chemical modification. The design and preparation of synthetic polymer conjugates capable of replacing antibodies in biomedical applications such as ELISA, flow cytometry, immunocytochemistry, and immunoprecipitation is reported. The conjugates, named "iBodies", consist of an HPMA copolymer decorated with low-molecular-weight compounds that function as targeting ligands, affinity anchors, and imaging probes. We prepared specific conjugates targeting several proteins with known ligands and used these iBodies for enzyme inhibition, protein isolation, immobilization, quantification, and live-cell imaging. Our data indicate that this highly modular and versatile polymer system can be used to produce inexpensive and stable antibody substitutes directed toward virtually any protein of interest with a known ligand.

Full text of DOI:10.1002/anie.201508642

Angewandte
Communications
Chemie
International Edition: DOI: 10.1002/anie.201508642
German Edition: DOI: 10.1002/ange.201508642
Antibody Mimetics
iBodies: Modular Synthetic Antibody Mimetics Based on Hydrophilic
Polymers Decorated with Functional Moieties
+
+
ˇ
ˇ
ˇ
Pavel Sµcha , Tomµs Knedlík , Jirí Schimer, Jan Tykvart, Jan Parolek, Vµclav Navrµtil,
ˇ
ˇ
ˇ
ˇ
Petra Dvorµkovµ, Frantisek Sedlµk, Karel Ulbrich, Jirí Strohalm, Pavel Majer, Vladimír Subr,*
and Jan Konvalinka*
Abstract: Antibodies are indispensable tools for biomedicine
and anticancer therapy. Nevertheless, their use is compromised
by high production costs, limited stability, and difficulty of
chemical modification. The design and preparation of synthetic
polymer conjugates capable of replacing antibodies in bio-
medical applications such as ELISA, flow cytometry, immu-
nocytochemistry, and immunoprecipitation is reported. The
conjugates, named “iBodies”, consist of an HPMA copolymer
decorated with low-molecular-weight compounds that function
as targeting ligands, affinity anchors, and imaging probes. We
prepared specific conjugates targeting several proteins with
known ligands and used these iBodies for enzyme inhibition,
protein isolation, immobilization, quantification, and live-cell
imaging. Our data indicate that this highly modular and
versatile polymer system can be used to produce inexpensive
and stable antibody substitutes directed toward virtually any
protein of interest with a known ligand.
these limitations, researchers have developed alternative
molecular recognition tools capable of replacing antibodies
in biomedical research applications (antibody mimetics).
These include affibodies,[1] designed ankyrin repeat proteins
(DARPins),[2] and aptamers.[3] Recently, chemically synthe-
sized small molecules that fulfill some functions of antibodies
have been described.[4] Polymers capable of molecular
recognition of other molecules were described several
decades ago. These molecularly imprinted polymers (MIPs)
are based on structure complementarity with the target
molecules and are used as molecular biosensors and binders.[5]
We set out to develop novel antibody mimetics based on
N-(2-hydroxypropyl)methacrylamide (HPMA) copolymer
conjugates decorated with three different low-molecular-
weight ligands. We chose water-soluble and biocompatible
HPMA copolymers since they have been used for the
development of drug delivery vectors, imaging agents, and
polymer drugs.[6] The HPMA copolymers are multivalent
synthetic macromolecules that carry a number of reactive
groups that enable covalent attachment of various ligands
such as fluorescent probes, therapeutics, proteins, and oligo-
nucleotides.[7]
T
he discovery of antibodies specifically targeting biologically
relevant molecules revolutionized the life sciences. Never-
theless, the use of antibodies has several disadvantages, such
as limited stability, difficulty of chemical modification, and
difficulty targeting proteins in mouse models. To address
Specific recognition, immobilization, and imaging of
a protein of interest require a specific targeting ligand (e.g.,
an inhibitor), an affinity anchor, and an imaging probe
attached to the polymer backbone (Figure 1a). As an affinity
tag, we chose biotin because it can be readily used for high-
affinity immobilization on a variety of commercially available
resins (Figure 1b). As an imaging probe, we chose the
fluorophore ATTO488 (Figure 1c). The choice of targeting
ligand depends on the protein of interest; we developed and
tested these antibody mimetics with glutamate carboxypepti-
dase II, HIV-1 protease, pepsin, and His-tagged proteins
(Figure 1d–g). To reflect functional similarity to antibodies
and the use of inhibitors as targeting ligands, we propose the
name iBodies for these polymer conjugates. All prepared
iBodies were characterized in terms of chemical identity and
the content of individual ligands, and their characteristics are
summarized in Table 1 and Table S2 in the Supporting
Information. We assume statistical distribution of the at-
tached moieties, since each ligand terminates with the same
sterically unhindered reactive moiety (-CH2CH2NH2). The
synthesis and characteristics of the conjugates are described
in detail in the Supporting Information.
[+]
[*] Dr. P. Sµcha, T. Knedlík,[+] Dr. J. Schimer, Dr. J. Tykvart, J. Parolek,
ˇ
ˇ
V. Navrµtil, P. Dvorµkovµ, Dr. F. Sedlµk, Dr. P. Majer, Dr. J. Konvalinka
Institute of Organic Chemistry and Biochemistry
Academy of Science of the Czech Republic
Flemingovo n. 2, 16610 Prague 6 (Czech Republic)
E-mail: konval@uochb.cas.cz
ˇ
Prof. K. Ulbrich, Dr. J. Strohalm, Dr. V. Subr
Institute of Macromolecular Chemistry
Academy of Science of the Czech Republic
HeyrovskØho n. 2, 16206 Prague 6 (Czech Republic)
E-mail: subr@imc.cas.cz
[+]
Dr. P. Sµcha, T. Knedlík,[+] Dr. J. Schimer, Dr. J. Tykvart, J. Parolek,
ˇ
V. Navrµtil, Dr. J. Konvalinka
Department of Biochemistry, Faculty of Science, Charles University
Hlavova 8, 12843 Prague 2 (Czech Republic)
Dr. F. Sedlµk
First Faculty of Medicine, Charles University
Katerinskµ 32, 12108 Prague 2 (Czech Republic)
[+] These authors contributed equally to this work.
ˇ
Supporting information for this article is available on the WWW
under http://dx.doi.org/10.1002/anie.201508642.
ꢀ 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co.
KGaA. This is an open access article under the terms of the Creative
Commons Attribution Non-Commercial License, which permits use,
distribution and reproduction in any medium, provided the original
work is properly cited and is not used for commercial purposes.
For developing the technique, we chose human glutamate
carboxypeptidase II (GCPII; also known as prostate-specific
membrane antigen or PSMA). GCPII is a transmembrane
metallopeptidase that is strongly expressed in the brain and
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corresponding conjugate lacking the GCPII inhibitor
(iBody 5; Figure S2).
The utility of iBody 1 for the inhibition, binding, and
visualization of GCPII was tested with a variety of common
biochemical methods in which antibodies are normally used:
immunoprecipitation and affinity pull-downs, flow cytometry,
immunocytochemistry, and ELISA.
First, we tested whether iBody 1 inhibits the enzymatic
activity of GCPII and determined Ki values for compound 1
and iBody 1 (Figure 2a). Interestingly, attachment of several
molecules of compound 1 to the HPMA copolymer led to
a significant drop in the Ki value [Ki(compound 1) = 2.0 nm vs.
Ki(iBody 1) = 4.3 pm]. This nearly three-order-of-magnitude
decrease in Ki can be explained by the synergic effect of
several inhibitor molecules on the polymer scaffold and
increased local inhibitor concentration (19 inhibitor mole-
cules per polymer chain).
The binding of iBody 1 to GCPII was further evaluated by
surface plasmon resonance (SPR), which revealed an
extremely high association rate and a low dissociation rate
(Figure 2b). The dissociation constant (KD < 20 pm) is com-
parable to that of the tightest-binding anti-GCPII antibodies
available.
To analyze the utility of iBody 1 for visualizing GCPII-
expressing cells, we incubated LNCaP cells (a cell line that
endogenously expresses GCPII) and PC3 cells (which do not
express GCPII) with iBody 1. As controls, we used iBody 5
(which lacks a GCPII inhibitor) and a fluorescently labeled
anti-GCPII monoclonal antibody 2G7[10] (mAb 2G7-
ATTO488). iBody 1 and the anti-GCPII mAb bound specif-
ically to LNCaP cells and not to PC3 cells, while iBody 5 did
not bind to either LNCaP or PC3 cells. iBody 1 and the mAb
were taken up into the cells through internalization of
membrane-embedded GCPII as expected.[11] Additionally,
binding of iBody 1 to LNCaP cells was blocked by 2-
(phosphonomethyl)pentanedioic acid (2-PMPA), a specific
GCPII inhibitor (Figure 2c).
To analyze the potential use of iBodies in flow cytometry,
LNCaP and PC3 cells were first incubated with iBody 1,
iBody 5, or 2G7-ATTO488[10] and then analyzed by flow
cytometry. The results indicate that both iBody 1 and the anti-
GCPII mAb specifically recognize GCPII-expressing cells
(LNCaP) and enable their separation from GCPII-negative
cells (PC3). Moreover, iBody 1 and iBody 5 exhibited very
low non-specific binding to PC3 cells, which was approx-
imately 5-fold lower than that of mAb 2G7-ATTO488
(Figure 2d).
Furthermore, we used iBody 1 to isolate GCPII from cell
lysates. iBodies 1 and 5 were immobilized on Streptavidin
Sepharose resin, and GCPII was pulled down from LNCaP
cell lysate (Figure 2e). An anti-GCPII mAb (J591[12]) bound
to Protein G Sepharose was used as a positive control. As
shown by subsequent western blot analysis, the amount of
GCPII immunoprecipitated when using iBody 1 was compa-
rable to that obtained with mAb J591. These findings suggest
that iBodies could also be useful for the isolation of target
proteins from complex biological materials such as tissue
lysates or blood samples.
Figure 1. Structures of the iBodies and their functional modules.
a) HPMA copolymer decorated with functional molecules. b) The
affinity anchor biotin. c) ATTO488 fluorophore. d) GCPII inhibitor.
e) HIV-1 protease inhibitor. f) A class-specific inhibitor of aspartic
proteases. g) A nitrilotriacetic acid (NTA)-based ligand for binding the
His-tag.
Table 1: The composition and basic characteristics of the iBodies.
Conjugate Target
No. of
No. of
No. of Ki [nm]
(Mn)
inhibitor ATTO488 biotin
moieties units
units
51
iBody 1
GCPII
HIV-1
19
6
7
–
–
7
6
–
0.0043Æ0.0005
(148800)[a]
iBody 2
7
7.9Æ0.5
(40600)[a] protease
iBody 3
(42100)[a] proteases
iBody 4 His-tag
(135800)[a] sequence
Aspartic
7
9
18.9Æ0.2[b]
12
–
46
41
8
3.5Æ0.1[c]
iBody 5
–
–
–
(108100)[a]
iBody 6
–
–
(37800)[a]
[a] Mn =number-average molecular weight. For full molecular character-
istics of the conjugates, see Table S2–S4 and Figure S8 in Supporting
Information. [b] Ki value was determined for wild-type HIV-1 protease.
[c] For iBody 4, a dissociation constant KD is shown instead of an
inhibition constant Ki.
prostate; its expression is markedly increased in prostate
carcinoma.[8]
The polymer conjugate targeting GCPII (iBody 1, Fig-
ure S1 in the Supporting Information) contains a tight-bind-
ing GCPII inhibitor as a targeting ligand. To avoid steric
hindrance between GCPII and the polymer molecules, the
previously described inhibitor (called compound 22a,[9]
Table S1) was modified with a PEG5 linker to yield com-
pound 1 (Figure 1d). As a negative control, we prepared the
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Figure 2. Application of iBody 1, which targets glutamate carboxypeptidase II (GCPII). a) The inhibition potency of iBody 1 in terms of GCPII
hydrolytic activity. b) SPR analysis of iBody 1 binding to immobilized GCPII (KD <20 pm). c) Confocal microscopy of cells positive (LNCaP) and
negative (PC3) for GCPII expression. Cells were stained with iBody 1; to compare iBody staining with antibody staining, the anti-GCPII monoclonal
antibody (mAb) 2G7[10] labeled with ATTO488 (2G7-ATTO488) was used. Binding of iBody 1 to LNCaP cells can be blocked by using 2-PMPA,
a specific GCPII inhibitor. d) Flow cytometry analysis of LNCaP and PC3 cells incubated with iBody 1, iBody 5 (which lacks the targeting module),
or 2G7-ATTO488. e) Western blot analysis of affinity isolation of GCPII from LNCaP cell lysate using iBody 1 or the anti-GCPII mAb J591. iBody 5,
blank Streptavidin Agarose (NC (SA)), and blank Protein G Sepharose (NC (PGS)) were used as negative controls. rhGCPII is a recombinant
extracellular GCPII. Load=LNCaP cell lysate. f) Sandwich ELISA with the anti-GCPII capture mAb 2G7 and either the biotinylated anti-GCPII mAb
J591 or iBody 1 used as the detecting agent.
Finally, we used iBodies for the quantitative detection of
GCPII. We employed a sandwich ELISA in which the
detecting anti-GCPII mAb was replaced with iBody 1. The
detection limit was as low as 0.5 pg GCPII; furthermore, the
signal was linear over a nearly three-order-of-magnitude
concentration range (Figure 2 f).
To demonstrate versatility of iBodies, we also developed
iBodies targeting the aspartic proteases HIV-1 and pepsin.
HIV-1 protease plays a crucial role in viral replication[13] and
a number of specific inhibitors are available. As aspartic
proteases, both HIV-1 protease and pepsin are also efficiently
inhibited by the peptidic inhibitor pepstatin A.[14]
The polymer conjugate targeted towards HIV-1 protease
(iBody 2; Figure S3) contains compound 2, a specific HIV-1
protease inhibitor derived from the commercially available
inhibitor ritonavir (Figure 1e), as a targeting ligand. The
analogous iBody 3 (Figure S4) contains compound 3 (Fig-
ure 1 f), a derivative of the class-specific aspartic protease
inhibitor pepstatin A, as a targeting ligand. As a negative
control, we prepared the corresponding conjugate lacking an
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inhibitor (iBody 6; Figure S5). We successfully used iBody 2
and iBody 3 to pull down HIV-1 protease from an LNCaP cell
lysate spiked with HIV-1 protease (Figure S7a).
Besides HIV-1 protease, another aspartic protease,
pepsin, was also successfully pulled down from LNCaP
lysate (spiked with pepsin) by using iBody 3 (Figure S7b),
thus showing the general applicability of this iBody. In both
experiments, iBody 6 (which contains only biotin and no
inhibitor) was used as a negative control. This iBody was
unable to pull down either HIV-1 protease or pepsin from an
LNCaP cell lysate (Figure S7a,b).
Finally, the use of iBodies is not limited to enzymes.
Theoretically, iBodies can be designed to target any molecule
of interest for which a ligand is known. To demonstrate this
general principle, we set out to target proteins containing
a polyhistidine tag (His-tag), the most common affinity tag
used for protein purification and visualization. Because the
His-tag is bound by nickel-loaded nitrilotriacetic acid (NTA)
derivatives, we prepared tris-NTA connected to a linker[15]
(compound 4, Figure 1g) and subsequently iBody 4 (Fig-
ure S6). iBody 4 was decorated with the fluorophore
ATTO488 for visualization and biotin for both visualization
and immobilization. As a negative control, iBody 5, which
bears only the fluorophore ATTO488 and biotin, was used.
We compared the sensitivity and specificity of iBody 4
with that of commercially available peroxidase-conjugated
anti-polyhistidine antibody by western blot. iBody 4 exhibited
slightly increased sensitivity and equal specificity in compar-
ison to the commercial antibody (Figure 3a,b). When using
iBody 4, we detected as little as 100 pg of the His-tagged
DNA damage protein 1 (Ddi1-His). Additionally, we specif-
ically pulled down the protein from an E. coli lysate (Fig-
ure 3c). To quantify the binding, we analyzed the interaction
between iBody 4 and Ddi1-His by SPR, which indicated KD =
3.5 nm (Figure 3d).
Figure 3. Application of iBody 4, which targets His-tagged proteins.
a) Comparison of iBody 4 and anti-polyhistidine antibody sensitivity for
the visualization of purified Ddi1-His by western blot. b) Comparison
of iBody 4 and the anti-polyhistidine antibody for the visualization of
Ddi1-His in a cell lysate by western blot. c) Affinity isolation of Ddi1-
His by using iBody 4. iBody 5 (which does not possess the tris-NTA
ligand), and blank resin (NC) were used as negative controls.
MWM=molecular-weight marker. d) Binding of Ddi1-His to immobi-
lized iBody 4 as analyzed by SPR.
prepared iBodies targeting various proteins of interest are
efficient substitutes for the corresponding antibodies in
standard immunochemical methods. Overall, iBodies offer
an inexpensive, non-animal-based alternative for antibodies
in biochemical methods involving the isolation and visual-
ization of proteins, cells, and tissues.
Our approach has two major advantages. First, the system
is remarkably modular: any compound, functional group, or
tag for any specific purpose can be added to form the final
polymer conjugate. For the targeting of a specific protein with
an iBody, simple replacement of the targeting moiety (the
inhibitor) is sufficient to yield a new specific polymer
conjugate. To some extent, this resembles the concept of
molecularly imprinted polymers (MIPs). MIPs rely on lock-
and-key interaction with the target, which makes them more
suitable for the extraction of target compounds/proteins, even
though the targeting of proteins on the cell surface has been
reported.[16] Second, the system is truly versatile: a single
iBody can be used for several methods, as we have shown for
GCPII. One potential limitation of the system is the need for
a ligand that specifically binds to the target protein. More-
over, for attachment to the polymer backbone, the ligand
must be modified with a linker that does not significantly
compromise its binding affinity. Nonetheless, if a potent
ligand is known and the attachment of the linker does not lead
to a dramatic loss of potency, the preparation of a specific
iBody is rather straightforward.
Acknowledgements
ˇ
We thank Jana Starkovµ and Karolína Srµmkovµ for their
technical support, Marco Colombatti for the D2B antibody,
Michal Svoboda for expression of Ddi1-His and Stanislava
ˇ
Matejkovµ for ICP-OES analysis. This work was supported by
Grant No. P208-12-G016 (Center of Excellence) from the
Grant Agency of the Czech Republic and InterBioMed
project LO 1302 from the Ministry of Education of the Czech
Republic.
Keywords: antibody mimetics · HPMA · molecular recognition ·
polymer conjugates · protein targeting
How to cite: Angew. Chem. Int. Ed. 2016, 55, 2356–2360
Angew. Chem. 2016, 128, 2402–2406
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Received: September 18, 2015
Published online: January 8, 2016
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