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Generation of potent anti-HER1/2 immunotoxins by protein ligation using split inteins Thomas Pirzer, Kira-Sophie Becher, Marcel Rieker, Tobias Meckel, Henning D. Mootz, and Harald Kolmar ACS Chem. Biol., Just Accepted Manuscript • DOI: 10.1021/acschembio.8b00222 • Publication Date (Web): 19 Jun 2018 Downloaded from http://pubs.acs.org on June 20, 2018

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ACS Chemical Biology

79x39mm (300 x 300 DPI)

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Figure 1: Scheme of the protein trans-splicing reactions and final immunotoxins. a) Antibodies were coupled to protein A agarose first and incubated with MBP-toxins in the presence of the reducing agent TCEP at 25 °C for 24 h. Subsequently, uncoupled toxins and TCEP were washed off, antibodies were re-oxidized and eluted with citrate buffer pH 3 from the solid support. b) Final immunotoxins: Trast-Gelonin, Trast-PE24, 7D9G-Gelonin and 7D9G-PE24. 7D9G stands for the two camelid nanobodies 7D12 and 9G8. Molecular masses of all four ITs were calculated from primary sequences. 139x86mm (300 x 300 DPI)


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Figure 2: Protein trans-splicing reactions and subsequent purification. a) PTS reaction on protein A beads of 7D9G-Fc-IntN with MBP-Gelonin (top) and MBP-PE24 (bottom). The reaction was carried out in the presence of 2 mM TCEP for 24 h at 25 °C. Molecular masses of Ab-toxins are close to the MBP-Toxin educts and are marked accordingly. Lane 1 = Ab load; 2 = Ab flow-through; 3 = Toxin load; 4 = Toxin flow-through; 5 = Toxin wash; 6 = after oxidation; 7–8 = elutions 1–2. b) Exemplary IMAC purification of generated TrastGelonin immunotoxin. Unconjugated HC can be seen in the flow-through. Enriched HC-Toxin is eluted with an approximately 2:1 ratio of conjugated to unconjugated HC. Lane 1 = IT input; 2 = flow-through; 3 = wash; 4–6 = elution fractions 1–3. c) Final ITs after PTS and IMAC purification with a TAR of approximately 1.3. Lane 1 = 7D9G-Gelonin; 2 = Trast-Gelonin; 3 = 7D9G-PE24; 4 = Trast-PE24. d) Table showing all protein fragments depicted in a)–c) with respective abbreviations and molecular masses. 138x96mm (300 x 300 DPI)



Figure 3: Determination of binding affinities of ITs on cells. Antigen over-expressing cells were incubated with varying concentrations of parental antibodies or immunotoxins and analyzed by flow cytometry. The relative mean fluorescence was plotted against antibody concentrations and KD values were determined using sigmoidal fitting with GraphPad Prism software (GraphPad Software, Inc.). 41x66mm (300 x 300 DPI)


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Figure 4: Cytotoxicity assay shows high toxicity for PE24 ITs and lower toxicity for gelonin derivatives. Different antigen presenting cells were treated for 72 h with antibodies, immunotoxins and toxins alone. The upper row shows data of cell lines treated with HER1 targeting 7D9G conjugates and the lower row shows data of HER2 targeting trastuzumab conjugates. CHO cells were used as negative control because of their lack of HER1 or HER2 expression. The assay was performed in triplicate. The relative survival to untreated cells was plotted against antibody concentrations and IC50 values were determined using sigmoidal fitting with GraphPad Prism (GraphPad Software, Inc.). 139x69mm (300 x 300 DPI)



Figure 5: Immunotoxins are endocytosed efficiently as shown by confocal microscopy. MDA-MB-468 cells (HER1 overexpressing) cells were treated for 1h with 7D9G ITs, washed with low pH glycine buffer to remove surface bound conjugates and stained directly or incubated for another 3h before staining. CHO cells were used as negative cell line. Anti-hIgG Fab-Alexa 488 (1:500) and anti-His6 Alexa 647 antibody (1:1000) were used to specifically visualize the antibody fraction and the toxin fraction of the ITs, respectively. Scale bar = 10 µm. 139x73mm (300 x 300 DPI)


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Generation of potent anti-HER1/2 immunotoxins by protein ligation using

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split inteins

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Thomas Pirzer1, Kira-Sophie Becher2, Marcel Rieker3, Tobias Meckel4, Henning D. Mootz2,

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Harald Kolmar1*

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Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-

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Weiss-Strasse 4, D-64287 Darmstadt, Germany

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Germany

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250, D-64293 Darmstadt, Germany

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64293 Darmstadt, Germany

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Universität Darmstadt, Alarich-Weiss-Str. 8, D-64287 Darmstadt, Germany

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*

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Harald Kolmar: Institute for Organic Chemistry and Biochemistry, Technische Universität

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Darmstadt, Alarich-Weiss-Strasse 4, D-64287 Darmstadt, Germany

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E-Mail: [email protected]

Institute of Biochemistry, University of Münster, Wilhelm-Klemm-Str. 2, D-48149 Münster, Antibody Drug Conjugates and Targeted NBE Therapeutics, Merck KGaA, Frankfurter Straße Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Straße 250, DMacromolecular Chemistry & Paper Chemistry, Department of Chemistry, Technische

To whom correspondence should be addressed:

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Keywords: Immunotoxin, split intein, protein ligation, antibody conjugation, protein

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engineering,

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Abstract

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Cell targeting protein toxins have gained increasing interest for cancer therapy, aimed at

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increasing the therapeutic window and to reduce systemic toxicity. Since recombinant

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expression of immunotoxins consisting of a receptor-binding and a cell-killing moiety is

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hampered by their high toxicity in an eukaryotic production host, most applications rely on

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recombinant production of fusion proteins consisting of an antibody fragment and a protein

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toxin in bacterial hosts such as Escherichia coli (E. coli). These fusions often lack beneficial

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properties of whole antibodies like extended serum half-life or efficient endocytic uptake via

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receptor clustering. Here we describe the production of full-length antibody immunotoxins

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using self-splicing split inteins. To this end, the short (11 amino acids) N-terminal intein part

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of the artificially designed split intein M86, a derivative of the Ssp DnaB intein, was

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recombinantly fused to the heavy chain of trastuzumab, a human epidermal growth factor

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receptor 2 (HER2) receptor targeting antibody and to a nanobody-Fc fusion targeting the HER1

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receptor, respectively. Both antibodies were produced in Expi293F cells. The longer C-terminal

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counterpart of the intein was genetically fused to the protein toxins gelonin or Pseudomonas

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Exotoxin A, respectively and expressed in E. coli via fusion to maltose binding protein. Using

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optimized in vitro splicing conditions we were able to generate a set of specific and potent

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immunotoxins with IC50 values in the mid- to subpicomolar range.

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Introduction

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Antibodies (Abs) are currently widely used for therapy of several indications like inflammatory

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diseases, haemophilia, autoimmune diseases and cancer. Besides classical antibodies that rely

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on their agonistic/antagonistic properties or intrinsic effector functions, i.e. antibody-dependent

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cellular cytotoxicity (ADCC) and complement-dependent cytotoxicity (CDC), antibodies can

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be modified resulting in antibody-drug conjugates (ADCs).1 These combine the specific

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targeting properties of antibodies with highly toxic small molecules. Upon binding to a

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malignant cell, the ADC is internalized by receptor-mediated endocytosis and guided to the

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lysosome, where the toxic payload is released, either by proteolysis of the antibody or the

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cleavage of a designed linker. Different classes of toxins are currently used, among them

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microtubule inhibitors (e.g. auristatins) or DNA alkylating agents (e.g. duocarmycins).2,3

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Beside small molecules, bacterial and plant protein toxins can be conjugated to antibody

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fragments and the resulting immunotoxins (ITs) have been investigated for their potential

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application in therapy.4 Compared to their small molecule counterparts, protein toxins can cause

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over-stoichiometric cell damage due to their inherent enzymatic activities, thereby reducing the -2ACS Paragon Plus Environment

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necessary amount of molecules to reach the cytosol.5 The translation inhibiting Pseudomonas

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Exotoxin A (PE) is one of the most prominent proteins in this class, mainly because of its good

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producibility in Escherichia coli and its effective translocation mechanisms into the cytosol of

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the target cell.6 In recent years five PE constructs entered clinical trials and currently at least

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two next generation ITs are still under clinical investigation.4,7,8 One of the main problems is

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still the high immunogenicity, although de-immunized variants have been developed to

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circumvent this issue. The most recent de-immunized variant is a 24 kD large fragment of PE

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(PE24) that encompasses an improved furin cleavage site and the cytotoxic domain III.9 After

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tumor-specific uptake that is mediated by the fused antibody or antibody fragment the toxin is

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released in the endosome by endosomal proteases and translocated into the cytoplasm, where it

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induces cell killing via inhibition of ribosomal protein synthesis. Due to their high toxicity and

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blockage of the translational machinery in an eukaryotic expression host, most immunotoxins

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(ITs) are produced in bacterial hosts as fusions to antibody fragments like antigen binding

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fragments (Fabs) or single chain variable fragments (scFvs), which limits their use.10–12

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Besides bacterial toxins such as PE, some ribosome inactivating plant toxins were intensively

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studied to be used as immunotoxins. They all belong to the family of ribosome inactivating

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proteins (RIPs) that are divided in class 1 and 2, depending whether or not they contain a cell

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targeting domain in addition to the ribosome inactivating domain. Class 1 RIPs like gelonin

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have the advantage of a very low off-target toxicity since they are naturally lacking a cell

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recognition domain.13 Gelonin inhibits cellular protein translation in eukaryotes by hydrolyzing

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the 28S rRNA of the 60S ribosomal subunit.13 As for PE this is a catalytic process so that only

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a few molecules are needed to kill a cell. Nevertheless it has been observed that a certain

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threshold concentration has to be reached intracellularly for effective cell killing. 14 Transfer

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from the endosomal lumen into the cytosol is still a major obstacle since gelonin has no active

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translocation mechanism. Nevertheless, alternative ways for efficient endosomal release have

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been investigated in the last years.15–17

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For the generation of immunotoxins fusion protein expression can be considered or,

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alternatively, chemical conjugation strategies as well as site-specific enzymatic conjugation

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methods can be applied aimed at linking an antibody and a protein toxin. An elegant way of

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generating protein-protein conjugates uses inteins, which are self-excising proteins that are

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found in all domains of life (archaea, bacteria and eukaryotes).18 They are naturally flanked by

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exteins, which are assembled through the splicing event. Because of their unique mechanism,

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inteins can be regarded as single turnover enzymes that do not rely on an energy source or

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cofactors.19 Besides classical inteins, buried in a pre-protein, naturally occurring split inteins -3ACS Paragon Plus Environment


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have been reported that reassemble after mixing both N- and C-terminal intein parts (IntN and

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IntC) and therefore perform the splicing reaction in trans.20–23 Designed artificial split inteins

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have opened new possibilities for protein ligation.24–26 We have chosen an artificially evolved

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split intein with an unusual short N-terminal part that showed very good splicing yields in a

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previous study.27 This intein was chosen for this work since we expected not only good yields

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but also minor effects of the shortened IntN on antibody production and stability.

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In this study a truncated, optimized variant of Pseudomonas Exotoxin A and gelonin obtained

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by expression in E. coli were used for the generation of immunotoxins derived from the full-

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length antibody trastuzumab as well as a single-chain antibody targeting human epidermal

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growth factor receptors HER2 and HER1/EGFR, respectively (Figure 1B). Upon optimization

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of splicing conditions immunotoxins with high potency were obtained that also showed

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selectivity.

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RESULTS AND DISCUSSION

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Antibody and toxin constructs. Two antibodies were used to generate immunotoxins and

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evaluate their functionality. Trastuzumab is a well characterized HER2 binding antibody that

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is approved by the FDA as single treatment as well as in the form of the ADC trastuzumab-

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emtansin (T-DM1) for the treatment of aggressive breast tumors.28 A glycine serine linker

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(GGGSGGG), followed by the 11 amino acids (aa) of the IntN, was attached to the C-terminus

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of the heavy chain (Supplementary Figure S1). The second targeting antibody was constructed

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from two camelid heavy-chain antibody domains (VHHs) targeting HER1 (EGFR) that were

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already described and well characterized in literature. The 7D12 and 9G8 nanobodies bind to

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HER1/EGFR with an affinity in the double digit nanomolar range on cells and were used in the

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optimized 7D12-9G8 orientation (later called 7D9G) with a linker length of 10 aa, which leads

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to an optimized KD in the single digit nanomolar range.29 The VHH domains were shown to

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bind different epitopes in the domain III and in the junction of domain II and III of HER1 and

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induce rapid internalization by receptor clustering.30,31 Both VHH domains were placed on an

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IgG1 Fc domain and terminated with a slightly longer C-terminal glycine serine linker

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((GGGGS)3) and the IntN sequence (Supplementary Figure S1).

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Both antibodies were then expressed in Expi293F cells and purified from the supernatant by

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protein A chromatography. Both antibodies showed a monomer content >95 % in size exclusion

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chromatography (SEC) analysis (Supplementary Figure S2). The toxin constructs were

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composed of a maltose binding protein for better solubility and producibility in E. coli followed

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by the 143 aa long C-terminal intein part (IntC) and the toxin itself (Supplementary Figures S1 -4ACS Paragon Plus Environment

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and S5). PE24 already contained an optimized furin cleavable sequence, which was also

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inserted into the gelonin construct to provide efficient proteolytic release in the

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endosome/lysosome.9 Both toxins were produced in E. coli BL21 (DE3) and purified by

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immobilized metal ion affinity chromatography (IMAC) and SEC (Supplementary Figure S3).

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The monomeric fractions were then used for the trans-splicing reaction.

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Protein trans-splicing (PTS) on protein A beads. Antibodies were coupled to protein A

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agarose beads for 30 min at room temperature (RT). The toxins were added at an approximately

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6-fold molar excess (3-fold relative to each heavy chain) together with 2 mM TCEP to achieve

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complete reduction of the splicing-active N-terminal cysteine in the IntN. The reaction was

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stopped after 24 h by column wash and immunotoxins were eluted after antibody re-oxidation

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with dehydroascorbic acid. The whole procedure is depicted in Figure 1A. Since coupling

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efficiencies were in the range of 50–70 %, as determined by densitometry of SDS-PAGE gels

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(Figure 2A), unconjugated antibody was removed by a subsequent IMAC (Figure 2B). It was

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not possible to distinguish molecules with a toxin/antibody ratio (TAR) of 2 from those with an

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incomplete coupling. The resulting final constructs showed a TAR of approximately 1.3, as

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determined by densitometry from a reducing SDS-PAGE gel and were used for further analysis

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(Figure 2C).

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Immunotoxins retain enzymatic function and inhibit protein translation in vitro. Since

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elution from protein A includes a low pH step that might harm the structural and functional

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integrity of the respective toxin protein, the activity of ITs was assessed in a protein translation

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assay in vitro using rabbit reticulocyte lysate. Various concentrations were added to the lysate

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and the translation of luciferase was analyzed by measuring the luminescence of a chromogenic

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substrate. While gelonin showed inhibition in the picomolar range (IC50 = 251 pM) as reported

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before (Supplementary Figure S4), PE24 did not show inhibition of rabbit ribosomal protein

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synthesis in this assay (data not shown). This is probably due to the fact that NAD+ is needed

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for activity of PE24 and not enough of this co-factor may be included in the rabbit lysate.32

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Both trastuzumab and 7D9G conjugates to gelonin showed IC50 values in the same range

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compared to the parental toxin with half maximal inhibitions at 183 pM and 84 pM, respectively

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(Supplementary Figure S4). The IC50 values of ITs were expected to be slightly lower than for

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the parental toxins because of a stoichiometry of 1–2 toxins per antibody.

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Immunotoxins retain cell binding properties of parental antibodies. To study whether

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attached toxins have an influence on the binding affinities of the antibody, both parental

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antibodies and respective immunotoxins were titrated on target protein expressing cells to

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determine binding constants. Both gelonin and PE24 ITs showed only slight deviations in KD -5ACS Paragon Plus Environment


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values compared to the parental antibodies (Figure 3). 7D9G binding to MDA-MB-468 cells

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showed an expected high affinity binding with a KD of 4.5 ± 1.0 nM. The gelonin and PE24

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conjugates had slightly decreased binding affinities of 5.9 ± 0.6 nM and 6.1 ± 0.4 nM,

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respectively. The same was observed for trastuzumab. While the parental antibody bound to

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HER2 overexpressing SK-BR-3 cells with a KD of 8.2 ± 0.3 nM, the gelonin and PE24

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conjugates showed dissociation constants of 9.1 ± 1.3 and 9.7 ± 0.4, respectively. Thus, the

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attachment of such bulky additives at the C-terminus of both antibodies does not impair their

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binding properties.

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High toxicity for both PE24 and gelonin derived immunotoxins. As biochemical properties

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of all ITs looked promising, they were tested in cellular assays to assess their cytotoxicity and

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specificity. Four different cell lines with different receptor densities on their surfaces were used.

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A549 have low to medium EGFR expression, MDA-MB-468 show high EGFR expression, SK-

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BR-3 are HER2 high-expressing cells and CHO-KI were used as negative cell line. Antibodies,

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toxins and ITs were incubated with the cells for 72h before measuring cell viability in a standard

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MTS assay. Different concentration scales had to be used for gelonin and PE24 in the

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nanomolar and picomolar range, respectively, because of different inherent toxicities.

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On the negative cell line CHO, none of the investigated ITs and controls displayed growth

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inhibition up to the maximal tested concentrations (Figure 4 left). The single-chain IT with

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7D9G targeting HER1 showed potent cell killing of MDA-MB-468 cells compared to the

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antibody and the toxin alone (Figure 4 upper middle). The effective ratio (ER) of IC50 value

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(IC50 of IT divided by that of the toxin, Table 1) of 7D9G-Gelonin to MBP-Gelonin of about

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771 showed the high selectivity and enhanced uptake of the antibody-toxin conjugate. With a

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half-maximal inhibition at only 68.0 ± 4.2 pM, this conjugate is highly toxic to this target cell

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line. Interestingly, the same IT did not show any toxicity in the other EGFR expressing cell line

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A549, which has a receptor density about 50–fold lower than that of MDA-MB-468.33 The

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HER2 targeting Trast-Gelonin conjugate showed an even lower inhibitory constant of 11.8 ±

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1.6 pM (Table 1) on overexpressing SK-BR-3. Combined with an ER of over 2.5*107 this is

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the highest gap between toxin and antibody-toxin conjugates in this whole data set.

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198 199 200


Table 1: Cytotoxicity of immunotoxins on target and control cell lines. Antibodies, toxins and immunotoxins were tested for cytotoxicity in a MTS cell viability assay. IC50 values were calculated by sigmoidal curve fitting using GraphPad Prism (GraphPad Software, Inc.). Values were calculated from triplicate samples. CHO Target

HER1

HER2

A549

MDA-MB-468

SK-BR-3

Protein

IC50 (nM)

ER

IC50 (pM)

ER

IC50 (pM)

ER

IC50 (pM)

ER

7D9G-Fc

>300

n.d.

>300000

n.d.

>300000

n.d.

n.d.

n.d.

7D9G-Gelonin

>300

n.d.

>300000

n.d.

68.0 ± 4.2

771

n.d.

n.d.

7D9G-PE24

>1

n.d.

3.9 ± 0.5

412

0.8 ± 0.1

290

n.d.

n.d.

Trastuzumab

>300

n.d.

n.d.

n.d.

>300000

n.d.

>300000

n.d.

Trast-Gelonin

>300

n.d.

n.d.

n.d.

n.d.

n.d.

11.8 ± 1.6

>2.5E+7

Trast-PE24

>10

n.d.

n.d.

n.d.

59.9 ± 3.2

4

2.4 ± 0.1

233

MBP-Gelonin

>300

1

>300000

1

5244 ± 1316

1

>300000

1

MBP-PE24

>10

1

1644 ± 247

1

239 ± 26

1

568 ± 58

1

201 202

Similar results were obtained for the PE24 ITs. In the analyzed concentration range up to

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10 nM, no toxicity can be observed in CHO cells for all analytes (Figure 4 lower panel). The

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7D9G-PE24 constructs show high potency in both EGFR positive cell lines A549 and MDA-

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MB-468 compared to the toxin alone with IC50 values of 3.9 ± 0.5 and 0.8 ± 0.1 pM, respectively

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(Table 1, Figure 4). Effective ratios of 412 and 290 for A549 and MDA-MB-468, respectively,

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show a high contribution of receptor mediated internalization of the antibody fraction to the

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ultimate toxicity. The sub-picomolar IC50 value of 7D9G-PE24 of 0.8 ± 0.1 pM depicts the

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highest toxicity in this study. In this case, the lower number of surface exposed receptors on

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A549 cells did not have such a high impact as for the gelonin construct which indicates that

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also the efficiency of endosomal escape may play an important role for IT efficacy.

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Additionally, the Trast-PE24 IT showed a 233-fold decreased IC50 of 2.4 ± 0.1 pM compared

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to the toxin alone.

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Time-resolved toxin internalization to target cells. To investigate why PE24 is several orders

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of magnitude more efficient in cell killing, confocal microscopy was applied aimed at

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monitoring a time-dependent release of the toxin into the cytosol. Cells were treated with ITs

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for one or four hours and the respective route of the IgG and the toxin were followed by staining

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them with specific antibodies. The antibody fraction was visualized using an Alexa488 labeled

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-IgG Fab fragment and the toxin was stained with an Alexa647 labelled -His6 antibody.

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HER1 positive MDA-MB-468 cells showed endocytic uptake of 7D9G-Gelonin and 7D9G-

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PE24 after 1h of incubation, marked by a punctate pattern in the 488-channel inside the cell

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(Figure 5). This was also confirmed for the trastuzumab ITs on SK-BR-3 cells (Supplementary

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Figure S5). Additionally, after 1 h, signals for the antibody part and the toxin part colocalize

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for both the gelonin and PE24 IT. After four hours, however, the toxin fluorescence of the PE24

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IT is clearly reduced in the vesicles. Gelonin still seems to be attached to the antibody at this -7ACS Paragon Plus Environment


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time point as a high degree of colocalization of antibody and gelonin is observed. This may be

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explained by the retrograde transport mechanism of PE246 that may result in a more efficient

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and faster transport to the cytosol than gelonin.

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Discussion. In this study we showed the conjugation of two toxic proteins to two antibody

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scaffolds by protein trans-splicing. With this site-specific ligation, four immunotoxins were

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produced, which retained their target binding and toxic properties, hence being highly toxic on

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tumor cells expressing the target receptors. Although the intein splicing reaction was not

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quantitative, the purified ITs contained at least one toxin molecule per antibody.

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Different protein conjugation strategies have been reported in previous years, ranging from

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enzymatic reactions using sortase A34, microbial transglutaminase (mTG)35, or SpyLigase36.

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Although sortase A has a high substrate specificity and has already been used to fuse the

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trastuzumab Fab fragment to gelonin to increase its potency11, generally a high excess (10-20

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fold) of the oligoglycine containing substrate is needed to drive the equilibrium reaction to the

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side of the desired product.37 Microbial transglutaminase forms a stable isopeptide bond

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between the -carboxamide group of glutamine and the primary -amino group of lysine.35,38,39

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Although mTG has been used successfully in the generation of ADCs40 it shows to be highly

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promiscuous towards the acyl acceptor41 and thus makes coupling of proteins with several

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superficial lysines a trial and error approach. Furthermore, it showed to have a substrate

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preference for glutamines in special sequence and structural context that is currently little

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understood. While IgG1 antibodies have no acyl donor glutamine, they can be specifically

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conjugated with mTG after deglycosylation or by introduction of a glutamine containing

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tag.42,43 In human growth hormone two of several available glutamines are addressed resulting

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in a heterogeneous reaction product.44 The SpyTag/SpyCatcher technology proved to be highly

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specific with no or only a slight excess of one reaction partner over the other needed for a

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quantitative turnover to the final product. This method nevertheless has the disadvantage of

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significant peptide tags (23 aa) remaining in the product.36,45 Protein trans-splicing thus offers

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an advantageous combination of specificity, efficiency and speed without inserting large

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foreign sequences into the final construct.

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A PTS efficiency of up to 70 % was achieved, which is fairly high considering the molecular

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sizes of both splicing partners of 150 and 90 kDa. In the original assay, the evolved M86 split

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intein showed up to 90 % splicing efficiency, which was performed with a 30 kDa IntC and an

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IntN peptide with less than 2 kDa.27 While trastuzumab contained a shorter linker of only 7 aa

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and glycine at the –1 position of the IntN, which is favored for the M86 intein, the 7D9G

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antibody contained a longer linker of 15 aa providing more flexibility but has a serine at the –1 -8ACS Paragon Plus Environment

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position, possibly decreasing PTS efficiency.27,46 Thus, optimization of linker length and amino

261

acids composition could further improve the splicing reaction. Besides that, increasing the

262

equivalents of the toxin portion to the antibody could also help increasing the coupling

263

efficiency, although protein solubility could be a limiting factor. Protein solubility of the IntC

264

containing splicing partner was also critical because inefficient splicing was observed for

265

aggregated portions after concentrating the protein. Choosing a different split intein could also

266

be an alternative, as shown for the generation of bispecific antibodies by Han and coworkers in

267

2017.26 They used a split Npu DnaE intein which was reported to have extremely fast splicing

268

kinetics and could achieve efficient conjugations of antibody scaffolds in the same size range

269

as they were used here.47 Another engineered Npu DnaE split intein was used for direct labelling

270

of antibodies in culture medium.48 However, the much larger IntN domain (123 amino acids

271

compared to 11) might impact antibody production yields and stability.

272

To date, mostly antibody fragments have been linked to toxic proteins to target them to receptor

273

expressing cells.11,49–51 This was mainly driven by the fact that the complete immunotoxin can

274

be produced in prokaryotes and can thus be generated in larger amounts. There are also reports

275

that made use of toxins containing Fc binding domains from protein A or G which proved to

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induce cell-specific toxicity when bound to a full antibody.49,52 Nevertheless, this approach is

277

useful only in screening campaigns and not for therapeutic purposes. Full-length antibodies

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have other advantages over antibody fragments such as an extended half-life in blood53, low

279

immunogenicity and increased stability mediated through the glycosylated Fc domain.54

280

Additionally, an antibody is naturally bivalent and therefore in the position to trigger efficient

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cellular uptake through receptor clustering.31,55 The VHH antibody format that was applied in

282

this study may combine the benefits of both antibody fragments and conventional antibodies.

283

The glycosylated Fc domain adds physicochemical stability and increases the serum half-life.

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The VHH construct has a more simple structure due to the lack of an additional light chain and

285

retains a bivalent, or in this case, even tetravalent binding to its antigen, leading to an increased

286

receptor-mediated uptake. This may also be the reason for an increased efficacy of the generated

287

ITs in this study, compared to previously reported conjugates. All produced Pseudomonas

288

Exotoxin A conjugates in this study were more potent than the most toxic PE IT reported to

289

date, with an IC50 of 7D9G-PE24 of 0.8 pM on MDA-MB-468 cells being more potent by a

290

factor of 24.56 Although the toxic moiety is comparable in this case, different receptors were

291

targeted and ITs were tested on different cell lines, which may account for some difference in

292

efficacy. More comparability is given for the gelonin conjugates to trastuzumab that were tested

293

on SK-BR-3 cells. The same combination was tested with a Fab-toxin conjugates in 2014 with -9ACS Paragon Plus Environment


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an EC50 of 600 pM on the same cell line which is less potent by a factor of 50 compared to the

295

tested full-length Trast-Gelonin in this study.11 The endosomal escape mechanism may also

296

play a role in the differences of toxicities between gelonin and PE24. For the latter, a defined

297

escape mechanism via a retrograde ER transport has been described in detail,57 while for

298

gelonin no such mechanism is known. As a consequence, PE24 has the advantage over gelonin

299

of an active transport mechanism that likely contributes to its remarkable potency. To sum up,

300

we generated highly potent immunotoxins by applying protein trans-splicing with split inteins.

301

This method is fast and yields site-specific conjugates with minimal changes to the native

302

sequences.

303 304

METHODS

305

Detailed information on used cell lines and cultivation conditions, protein productions and

306

purifications, cloning of expression plasmids, immunostainings, confocal microscopy and in

307

vitro protein translation assay are available in the Supplementary.

308

Protein trans-splicing on protein A agarose beads. Protein splicing reactions were performed

309

on a solid support as described previously for coupling cytotoxic agents to reduced cysteines of

310

antibodies.58 Abs were first incubated with protein A agarose (protein A HP SpinTrap, GE

311

Healthcare) for 30 min under shaking in intein buffer (50 mM Tris/HCl, 300 mM NaCl, pH 7).

312

The supernatant was removed by centrifugation and the slurry washed 2x with intein buffer.

313

Toxin at 6-fold molar excess towards the antibody was then added with 2 mM TCEP as reducing

314

agent and incubated with the beads for 18–24 h at 25 °C under continuous shaking. Unreacted

315

toxin was removed by centrifugation and residual reducing agent was washed away 3x with

316

PBS. Immunotoxins were re-oxidized in PBS with 100 eq. of dehydroascorbic acid for 2 h at

317

37 °C. ITs were eluted after 2 washing steps with elution buffer, diluted in IMAC A buffer and

318

subjected to IMAC.

319

Cytotoxicity assay. Cell viability after addition of immunotoxins was assessed with the

320

CellTiter 96® AQueous One Solution Cell Proliferation Assay. 5,000 cells were seeded per

321

well in a 96-well plate in the corresponding medium with additional pen/strep solution and

322

incubated for 24 h. Cells were then treated in triplicate with varying concentrations of

323

antibodies, toxins or immunotoxins. After 72 h, 20 µl of the MTS solution were added per well

324

and the plates were incubated for 0.5 to 3 h under standard conditions. Last, the absorption was

325

measured at 485 nm in a Tecan reader. IC50 values were calculated by using sigmoidal fitting

326

with GraphPad Prism software (GraphPad Software, Inc.) and were not normalized to the TAR - 10 ACS Paragon Plus Environment

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327

since all ITs displayed the same TAR of 1.3. Cell viability of reference wells with untreated

328

cells was set to 100 %.

329

Determination of KD by flow cytometry. Receptor over-expressing cells were incubated with

330

the analytes at different concentrations and subsequently with specific fluorogenic secondary

331

antibodies. Cells were then conducted to flow cytometry. For more details, see Supplementary

332

section 2.

333 334

ASSOCIATED CONTENT

335

Supporting Information

336

The Supporting Information is available free of charge on the ACS Publications website.

337

Supporting figures (S1–S5), protein sequences and supplemental methods (PDF).

338 339

ACKNOWLEDGEMENTS

340

This work was supported by Deutsche Forschungsgemeinschaft in the course of priority program

341

SPP 1623.

342 343

AUTHOR CONTRIBUTIONS

344

T.P. wrote the manuscript, conducted the cloning of antibody constructs, produced all proteins

345

and conducted all biochemical and cell biological characterizations. H.K. and H.M. directed

346

and supervised the project. K.-S.B. provided the intein sequences and performed cloning of

347

MBP-Gelonin vector. M.R. provided pTT5 expression plasmids for trastuzumab and gave

348

advices for the cytotoxicity assays, antibody analytics and cell culture. T.M. performed confocal

349

microscopy. All authors reviewed the manuscript.

350 351

Corresponding autor:

352

*E-Mail: [email protected]

353 354

- 11 ACS Paragon Plus Environment


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