Patent Application
20250164485
This non-Provisional US patent application claims priority to EP Patent Application EP23210793.8 filed in European Patent Office on Nov. 20, 2023. This prior application is incorporated by reference in its entirety.
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Antibodies and antibody fragments thereof e.g. VHHs, are an important class of biomolecules for immunotherapy. Due to their unique molecular properties e.g. small size, simple folding, and improved tissue penetration, VHHs are becoming more important towards new therapeutic approaches. One potential novel application for VHHs, is their use as adapter molecules in combination with AdCAR™ T cells.
Therefore, VHHs need to be modified or tagged for such purposes. One approach is chemical conjugation to a chemical tag, e.g. biotin, thiamine, peptides, DBCO, oligonucleotides, peptide nucleic acids (PNAs) to name a few, to get recognized by the AdCAR™ T cells in order to crosslink tumor cells and CAR T cells for tumor cell killing. The use of adapter molecules in conjunction with AdCAR™ T cells is the ability to control dosing, and the consequential safety as in case it is needed, it can be easily removed featuring minimal risks to patients. To be suitable as pharmaceutical, adapter molecules' chemical conjugation must be site-specific and result in a homogenous and well-defined product that is stable under physiological conditions after injection.
One opportunity to enable site-specific conjugation is the incorporation of engineered cysteines. However, free cysteines can form disulfide bonds leading to the aggregation of the protein during production or purification. Another strategy that is used currently is maleimide-based conjugation of free cysteines. The limitation of this approach is that maleimide thiol adducts can generate labile chemical conjugation under physiologically reducing conditions. The occurring retro Michal-addition would lead to adapter Molecules that are non-functional and potential block epitopes for conjugated adapter molecules.
There are many known methods for the site-specific conjugation of single domain antibody fragments, e.g. maleimide addition to engineered cysteine or Sortase reaction.
For example, U.S. Ser. No. 11/021,544B2 discloses the use of the ETAC system (Thiobridging) to dimerize VHHs, wherein VHHs featuring a C-terminal extension comprising a cysteine moiety are linked via the ETAC system (Thiobridging) to yield chemically linked Nanobody dimers introducing a diagnostic, therapeutic or labelling agent.
Further, conjugation by bis-alkylation using reagents can be equilibrium controlled via an addition-elimination reaction that is reliant on the Michael reaction. Covalent conjugation occurs with 2 amino acids close in space (e.g. the two cysteine thiols from a disulfide or two histidines in a C- or N-terminal his-tag).
The modification of His tags by ETAC reagents has been documented for the possibility to give rise to multiple additions of the reagents. The modification of the His tag is not stable against strong Michael donors like DTT. To stabilize the conjugate, a reduction of the introduced ketone in the ETAC linker is achieved using triacetoxy borohydride which might not be compatible with the stability of the protein.
Accordingly, there is a need for a conjugation method is needed that is site-specific, stable under physiological conditions, and not prone to protein aggregation as seen with disulfide bonds.
Here it is demonstrated that the ETAC-biotin linker can specifically mono-label single VHHs units by linking one terminal cysteine with a histidine residue that is in direct proximity to the terminal cysteine, thus targeting a cysteine-histidine motif. By providing an excess of ETAC-biotin linker the ETAC linker reacted with multiple Michael acceptors within the VHH. We were able to remove ETAC-biotin labels crosslinking single histidine residue under the addition of competing nucleophilic agent (e.g. TCEP) leading to an enrichment of single-site mono-specific conjugated VHHs. No further processing was needed to remove the non-conjugated product (confirmed by LC-MS experiments). To the best of our knowledge, a double Michael addition reaction targeting one cysteine and one neighboring histidine in the same sequence followed by selective enrichment of site-specific single-label VHHs via elimination of multi-label targets using a nucleophile such as TCEP is a unique approach and has not been yet reported.
An object of the invention is a method for providing a polypetide with a detectable label, wherein the polypetide comprises at least 5 amino acids of which a first amino acid is C (Cysteine) and at least one second amino acid is selected from the group consisting of S (Serine), T (Threonine), Y (Tyrosine), K (Lysine), H (Histidine) and R (Arginine) characterized by the steps
The term “polypeptide” refers to any molecule comprised of a chain of at least 5 amino acids. This includes molecules ranging from small peptides, which are polypeptides with a molecular weight from 300 Da to 7 kDa, to larger forms such as single-domain antibodies (VHHs) that have a molecular weight between 8-15 kDa, antibody fragments typically in the range of 20-50 kDa, and full-sized antibodies like the IgG species, which have a molecular weight of approximately 140-160 kDa.
ETAC-biotin-linked VHHs showed specific binding to their respective tumor antigens indicating correct folding and function. Furthermore, ETAC-biotin conjugated VHHs induced tumor cell lysis and cytokine secretion of biotin-specific adapter CAR.
Compared to a single attachment site, e.g. via a maleimide, the bridged modification of the VHH might provide better stability against de-conjugation and higher rigidity of the introduced labeling agent possibly enhancing binding to a secondary reagent (e.g. CAR T cell).
A polypeptide with at least one a reduced Cysteine (C) and at least one nucleophilic amino acid (X) is treated with the ETAC reagent. The ETAC compound reacts in a Michael addition either with a C and amino acid X or with amino acid X and second amino acid X. By treating this reaction products with a Michael donor e.g. a reducing agent, ETAC conjugated to amino acid X and second amino acid X are removed.
The VHH contains a terminal cysteine and sequence of histidines. To enable the conjugation of the VHH with the ETAC reagent the terminal cysteine is reduced leaving the intramolecular disulfide bridge intact. Next, the ETAC compound reacts in a Michael addition with the terminal reduced cysteine and with one of the histidines. In addition, the ETAC compounds is conjugated to only histidines. By treating this reaction product with a Michael donor e.g. a reducing agent, ETAC compounds crosslinked with only histidines are removed from the VHH. ETAC compounds linked to cysteines and histidine are stable in presence of a Michael donor and remain crosslinked.
In an embodiment of the invention, the at least one second amino acid is provided at the C-terminus of the polypeptide.
The nucleophilic agent may be selected from the group consisting of Dithiothreitol (DTT), Tris(2-carboxyethyl)phosphine (TCEP), Triphenylphosphine (PPh3), Hydrazine (N2H4), Tetrakis(dimethylamino)ethylene (TDAE), Mercaptoethanol, Formic acid, Trichlorosilane (HSiCl3), Phosphine (PH3), Dimethyl sulfide borane (Me2S·BH3), Thioacetic acid, Tris(trimethylsilyl)phosphine, Tri-n-hexylphosphine, Ammonia (NH3), Cysteine, Selenocysteine, Thiophenole, Glutathione (GSH), Iodide, Methylamine, Hydrogen sulfide
Preferable, the reagent has formula (II)
Or formula (III)
Most preferred, the reagent has one of the formulas (IV) to (VII)
The method of the invention is especially useful to provide polypetides with in CAR-Adapter molecules, in Cell staining reagents, in cell separation/labeling/enrichment/depletion processes, in protein purification and for Cell activation with a detectable label.
1.1 Conjugation of EGFR Specific VHHs with Multiple ETAC-Biotin-Linker
As a model VHH we were using an anti-EGFR specific VHH with a C-terminal histidine tag followed by flexible glycine serin linker and a glycine capped cysteine residue as Michael donors.
The terminally introduced cysteine of the EGFR VHH was reduced with 3 molar equivalents of TCEP for 1h at 21° C. The reaction was done in PBS buffer with 5 mM EDTA (PE-buffer) at pH 7.8. Next, TCEP was removed via a desalting column contain Sephadex G-25 resin and PE-buffer. Afterwards, the ETAC-biotin labeling molecule was added to the reduced and purified EGFR VHH. The ETAC-biotin labeling molecule was previously dissolved in DMSO and added at 4 molar equivalents to the EGFR VHH. DMSO was added in sufficient amount to the reaction mixture in order to reach a final concentration of 10% DMSO in the final reaction mixture. The conjugation reaction was kept for 2 h at 21° C. Next, the reaction mixture was applied to a previously PBS buffer equilibrated molecular weight cut off column (Merck Millipore) and washed with four column volumes of 1×PBS. The protein concentration of the final product was analyzed via absorption at 280 nanometers.
The product of the coupling reaction was analyzed via liquid chromatography coupled to mass spectrometry (
ETAC-biotin labels that did not react with one cysteine were selectively removed via a retro Michael reaction by adding a nucleophilic reducing agent. Therefore, 250 mM TCEP were added per 13 μL VHH for 10 min at 37° C. This led to a VHH polypeptide containing a single ETAC-Biotin label with a MW of 15905 Da as confirmed by mass spectrometry (
The sites of the conjugation of the ETAC-biotin to the EGFR specific VHH was analyzed via peptide mass fingerprint (PMF) (
To show the application of ETAC-biotin labeled EGFR-specific VHHs for flow cytometry, EGFR-specific VHH molecules were used to detect tumor cells that are known to express EGFR. Therefor, 10 g/mL of ETAC-biotin labeled EGFR specific VHHs were incubated with EGFR positive tumor cells for 1h at 4° C. Cell suspension was washed with PE-buffer containing 0.5% BSA (PEB-buffer) and a secondary staining with a PE labeled biotin specific secondary antibody was done (REA746). Next, the cell suspension was washed with PEB. Binding of ETAC-biotin labeled EGFR specific VHHs to EGFR positive tumor cells and the presence of the ETAC-biotin-linker was detected via secondary staining with a PE labeled biotin-specific secondary antibody. Signal intensity of unstained tumor cells (
CAR T cells are immune cells that are genetically engineered to express a chimeric antigen receptor (CAR) that does not occur naturally in T cells. This receptor is specific for a certain antigen expressed on the surface of a tumor cell. After engaging the tumor cells the CAR T cell will induce tumor cell lysis. In contrast, an adapter CAR T cell expresses a CAR that is specific for tagged polypeptide and not for an antigen expressed by a tumor cell. This polypeptide e.g. a VHH will mediate the biding between the adapter CAR T cell and the tumor cells. In absence of this adapter no tumor cell lysis will be induced. By using different adapter molecules one CAR T cell can target more than one tumor antigen. This mode of action increases the safety and therapeutic efficacy.
ETAC-biotin CAR T cells contained an biotin specific scFv as binding moiety. The scFv was linked to human CD8 transmembrane domain via hIgG4 hinge domain. The signaling domain was composed of 4-1BB and CD3ζ.
Lentiviral vector particles were manufactured via transient transfection of HEK-293T cells. The lentiviral vector particles were pseudotyped with VSV-G. For transfection HEK-293T cells were seeded in T175 culture flasks in DMEM supplemented with 2 mM L-Glutamine and 10% FCS 3 days prior to transfection. At the day of transfection the culture medium was removed and replaced by DMEM supplemented with 2 mM L-Glutamine. The cells were transfected with a three-plasmid system encoding for VSV-G, gag/pol/rev and the psi positive transfer vector.
After 48 h the supernatant was collected and centrifuged for 10 min at 1000 rpm to remove cellular debris. In addition, the supernatant was filtrated trough a 0.45 μm filter. The pellet was re-suspended in ice cold PBS and stored at −80° C.
Anti-biotin adapter CAR T cells were manufactured using primary T cells from healthy donors. T cells were isolated from PBMC with the PAN T cell isolation Kit (Miltenyi Biotec) according to the manufactures protocol. Prior to transduction 2E6 T cells were seeded in a 24 well plate with 2 mL TexMACS medium (Miltenyi) supplemented with IL-7 (Miltenyi Biotec), IL-15 (Miltenyi Biotec) and Transact (Miltenyi Biotec).
After 24 h T cells were transduced with an MOI of 5 by adding the corresponding volume of lentiviral vector particles. On day 3 post activation the culture medium was removed and replaced by TexMACS medium (Miltenyi Biotec) supplemented with IL-7 (Miltenyi Biotec), IL-15 (Miltenyi Biotec).
Frequency of anti-biotin adapter CAR positive T cells was analyzed on day 6 after transduction via flow cytometry using a biotinylated PE conjugate (Miltenyi Biotec). Anti-biotin adapter CAR T cells were used for functional assays on day 10 after transduction.
To test the application of ETAC biotin conjugated EGFR specific VHHs as adapter molecules for biotin specific anti-biotin adapter CAR T cells, antigen positive tumor cells and ETAC-biotin labeled EGFR specific VHHs were cultured either in presence or absence of biotin-specific adapter CAR T cells. Therefore, 20.000 biotin specific adapter CAR T cells and 5.000 tumor cells were seeded in RPMI with 2 mM L-glutamine and 10% FCS in a 96 well flat bottom plate.
Next, 50 μL ETAC-biotin labeled EGFR specific VHH was added to a final concentration of 5 nM. As a positive control a functional tumor specific adapter molecule was used. The co culture was incubated at 37° C. and 5% CO2. Tumor cell lysis was analyzed via live cell fluorescent microscopy of tumor cells using the IncuCyte® S3 system. Data shown were obtained from (n=3) independent donors and plotted with mean and ±1 standard deviation (
In summary, this shows that ETAC-biotin-linker labeled EGFR-specific VHHs are functional adapter molecules for biotin-specific adapter CAR T cells.
As a model VHH we were using an anti-CD56 specific VHH with a C-terminal histidine tag followed by flexible glycine serin linker and a glycine capped cysteine residue as Michael donors.
The terminally introduced cysteine of the CD56 VHH was reduced with 3 molar equivalents of TCEP for 1 h at 21° C. The reaction was done in PBS buffer with 5 mM EDTA (PE-buffer) at pH 7.8. Next, TCEP was removed via a desalting column contain Sephadex G-25 resin and PE-buffer. Afterwards, the ETAC-biotin labeling molecule was added to the reduced and purified CD56 VHH. The ETAC-biotin labeling molecule was previously dissolved in DMSO and added at 4 molar equivalents to the CD56 VHH. DMSO was added in sufficient amount to the reaction mixture in order to reach a final concentration of 10% DMSO in the final reaction mixture. The conjugation reaction was kept for 2 h at 21° C. Next, the reaction mixture was applied to a previously PBS buffer equilibrated molecular weight cut off column (Merck Millipore) and washed with four column volumes of 1×PBS. The protein concentration of the final product was analyzed via absorption at 280 nanometers. The product of the coupling reaction was analyzed via liquid chromatography coupled to mass spectrometry (
ETAC-biotin labels that did not react with one cysteine were selectively removed via a retro Michael reaction by adding a nucleophilic reducing agent. Therefore, 250 mM TCEP were added per 13 μL VHH for 10 min at 37° C. This led to a VHH polypeptide containing a single ETAC-Biotin label with a MW of 16240 Da as confirmed by mass spectrometry (
To show the application of ETAC-biotin labeled CD56 VHHs for flow cytometry, CD56-specific VHH molecules were used to detect tumor cells that are known to express CD56. To show the specific binding of ETAC-biotin labeled CD56 specific VHHs, 5 μg/mL of the conjugated VHH were incubated with CD56 positive tumor cells and CD56 negative cells for 1 h at 4° C. The cell suspension was washed with PEB. Binding of ETAC-biotin labeled CD56 specific VHHs was detected via secondary staining with a PE labeled biotin-specific secondary antibody (REA746).A CD56 specific IgG1 (REA196-PE) was used as a positive control. Next, the cell suspension was washed with PEB. Signal intensity of PE positive tumor cells was analyzed via flow cytometry on antigen positive cells and on antigen negative cells. Frequency of CD56 positive cells was plotted for antigen positive and antigen negative cells after incubation with either ETAC-biotin labeled CD56 specific VHHs or a CD56 specific IgG1 (REA196-PE) as positive control. Specific binding of ETAC-biotin labeled VHHs was detected (
While various details have been described in conjunction with the exemplary implementations outlined above, various alternatives, modifications, variations, improvements, and/or substantial equivalents, whether known or that are or may be presently unforeseen, may become apparent upon reviewing the foregoing disclosure. Accordingly, the exemplary implementations set forth above, are intended to be illustrative, not limiting.
| Number | Date | Country | Kind |
|---|---|---|---|
| EP23210793.8 | Nov 2023 | EP | regional |
