US20230173085A1 - Saponin Conjugates - Google Patents

Saponin Conjugates Download PDF

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Publication number
US20230173085A1
US20230173085A1 US17/312,311 US201917312311A US2023173085A1 US 20230173085 A1 US20230173085 A1 US 20230173085A1 US 201917312311 A US201917312311 A US 201917312311A US 2023173085 A1 US2023173085 A1 US 2023173085A1
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Prior art keywords
saponin
cell
molecule
proteinaceous molecule
proteinaceous
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US17/312,311
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Inventor
Ruben Postel
Hendrik Fuchs
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Sapreme Technologies BV
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Sapreme Technologies BV
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Assigned to CHARITÉ - UNIVERSITÄTSMEDIZIN BERLIN, SAPREME TECHNOLOGIES B.V. reassignment CHARITÉ - UNIVERSITÄTSMEDIZIN BERLIN ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: FUCHS, HENDRIK, POSTEL, Ruben
Assigned to SAPREME TECHNOLOGIES B.V. reassignment SAPREME TECHNOLOGIES B.V. ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: CHARITÉ - UNIVERSITÄTSMEDIZIN BERLIN
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Definitions

  • the invention relates to a therapeutic combination for use as a medicament, wherein the therapeutic combination comprises: (a) a first pharmaceutical composition comprising a first proteinaceous molecule and at least one saponin covalently bound to said first proteinaceous molecule; and (b) a second pharmaceutical composition comprising a second proteinaceous molecule, comprising an effector moiety, wherein the binding site of the first proteinaceous molecule and the binding site of the second proteinaceous molecule are the same.
  • the invention also relates to the first pharmaceutical composition for use as a medicament.
  • the invention also relates to the first pharmaceutical composition, further comprising the second proteinaceous molecule.
  • the invention also relates to the first pharmaceutical composition, further comprising the second proteinaceous molecule, for use as a medicament.
  • the invention relates to the first pharmaceutical composition, further comprising the second proteinaceous molecule, for use in the treatment or prophylaxis of cancer in a patient in need thereof.
  • Molecules with a therapeutic biological activity are in many occasions in theory suitable for application as an effective therapeutic drug for the treatment of a disease such as a cancer in human patients in need thereof.
  • a typical example are small-molecule biologically active moieties.
  • therapeutically active molecules may exert off-target effects, in addition to the biologically activity directed to an aspect underlying a to-be-treated disease or health problem. Such off-target effects are undesired and bear a risk for induction of health- or even life-threatening side effects of the administered molecule.
  • the administered drug molecule should reach the targeted site in the human patient within a certain time frame and should remain at the targeted site for a certain time frame), and/or (6) have sufficiently long lasting therapeutic activity in the patient's body, amongst others.
  • ‘ideal’ therapeutics with many or even all of the beneficial characteristics here above outlined, are not available to the patients, despite already long-lasting and intensive research and despite the impressive progress made in several areas of the individually addressed encountered difficulties and drawbacks.
  • Chemotherapy is one of the most important therapeutic options for cancer treatment. However, it is often associated with a low therapeutic window because it has no specificity towards cancer cells over dividing cells in healthy tissue.
  • the invention of monoclonal antibodies offered the possibility of exploiting their specific binding properties as a mechanism for the targeted delivery of cytotoxic agents to cancer cells, while sparing normal cells. This can be achieved by chemical conjugation of cytotoxic effectors (also known as payloads or warheads) to antibodies, to create antibody-drug conjugates (ADCs).
  • cytotoxic effectors also known as payloads or warheads
  • ADCs antibody-drug conjugates
  • very potent payloads such as emtansine (DM1) are used which have a limited therapeutic index (a ratio that compares toxic dose to efficacious dose) in their unconjugated forms.
  • Mylotarg was however, withdrawn from the market at the request of the Federal Drug Administration (FDA) due to a number of concerns including its safety profile. Patients treated with Mylotarg were more often found to die than patients treated with conventional chemotherapy. Mylotarg was admitted to the market again in 2017 with a lower recommended dose, a different schedule in combination with chemotherapy or on its own, and a new patient population. To date, only five ADCs have been approved for clinical use, and meanwhile clinical development of approximately fifty-five ADCs has been halted. However, interest remains high and approximately eighty ADCs are still in clinical development in nearly six-hundred clinical trials at present.
  • FDA Federal Drug Administration
  • a low therapeutic index (a ratio that compares toxic dose to efficacious dose) is a major problem accounting for the discontinuance of many ADCs in clinical development, which can be caused by several mechanisms such as off-target toxicity on normal cells, development of resistance against the cytotoxic agents and premature release of drugs in the circulation.
  • a systematic review by the FDA of ADCs found that the toxicity profiles of most ADCs could be categorized according to the payload used, but not the antibody used, suggesting that toxicity is mostly determined by premature release of the payload. Of the approximately fifty-five ADCs that were discontinued, it is estimated that at least twenty-three were due to a poor therapeutic index.
  • trastuzumab tesirine conjugate ADCT-502, HER-2 targeted, ADC therapeutics
  • ADCT-502, HER-2 targeted, ADC therapeutics were recently discontinued due to a narrow therapeutic index, possibly due to an on-target, off-tissue effect in pulmonary tissue which expresses considerable levels of HER2.
  • ADCs in phase 3 trials have been discontinued due to missing primary endpoint.
  • ABT-414 EGFR targeted, AbbVie
  • IMGN853 folate receptor alpha
  • FR ⁇ folate receptor alpha
  • ImmunoGen immunogen
  • the clinically used dose of some ADCs may not be sufficient for its full anticancer activity.
  • ado-trastuzumab emtansine has an MTD of 3.6 mg/kg in humans.
  • ado-trastuzumab emtansine induced tumor regression at dose levels at or above 3 mg/kg, but more potent efficacy was observed at 15 mg/kg. This suggests that at the clinically administered dose, ado-trastuzumab emtansine may not exert its maximal potential anti-tumor effect.
  • ADCs are mainly composed of an antibody, a cytotoxic moiety such as a payload, and a linker.
  • the antibody component by identification and validation of adequate antigenic targets for the antibody component, by selecting antigens which have high expression levels in tumor and little or no expression in normal tissues, antigens which are present on the cell surface to be accessible to the circulating ADCs, and antigens which allows internalizing of ADCs into the cell after binding; and alternative mechanisms of activity; design and optimize linkers which enhance the solubility and the drug-to-antibody ratio (DAR) of ADCs and overcome resistance induced by proteins that can transport the chemotherapeutic agent out of the cells; enhance the DAR ratio by inclusion of more payloads, select and optimize antibodies to improve antibody homogeneity and developability.
  • DAR drug-to-antibody ratio
  • new clinical and translational strategies are also being deployed to maximize the therapeutic index, such as, change dosing schedules through fractionated dosing; perform biodistribution studies; include biomarkers to optimize patient selection, to capture response signals early and monitor the duration and depth of response, and to inform combination studies.
  • ADCs with clinical potential are those ADCs such as brentuximab vedotin, inotuzumab ozogamicin, moxetumomab pasudotox, and polatuzumab vedotin, which are evaluated as a treatment option for lymphoid malignancies and multiple myeloma.
  • Polatuzumab vedotin, binding to CD79b on (malignant) B-cells, and pinatuzumab vedotin, binding to CD22 are tested in clinical trials wherein the ADCs each were combined with co-administered rituximab, a monoclonal antibody binding to CD20 and not provided with a payload [B. Yu and D. Liu, Antibody - drug conjugates in clinical trials for lymphoid malignancies and multiple myeloma; Journal of Hematology & Oncology (2019) 12:94]. Combinations of monoclonal antibodies such as these examples are yet a further approach and attempt to arrive at the ‘magic bullet’ which combines many or even all of the aforementioned desired characteristics of ADCs.
  • nucleic acid-based therapeutics are under development.
  • Therapeutic nucleic acids can be based on deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), Anti-sense oligonucleotides (ASOs, AONs), and short interfering RNAs (siRNAs), MicroRNAs, and DNA and RNA aptamers, for approaches such as gene therapy, RNA interference (RNAi).
  • RNAi RNA interference
  • Many of them share the same fundamental basis of action by inhibition of either DNA or RNA expression, thereby preventing expression of disease-related abnormal proteins.
  • the largest number of clinical trials is being carried out in the field of gene therapy, with almost 2600 ongoing or completed clinical trials worldwide but with only about 4% entering phase 3.
  • ASOs peptide nucleic acid
  • PMO phosphoramidate morpholino oligomer
  • LNA locked nucleic acid
  • BNA bridged nucleic acid
  • ASOs as potential therapeutic agents
  • the application of ASOs as potential therapeutic agents requires safe and effective methods for their delivery to the cytoplasm and/or nucleus of the target cells and tissues.
  • inefficient cellular uptake both in vitro and in vivo, limit the efficacy of ASOs and has been a barrier to therapeutic development.
  • Cellular uptake can be ⁇ 2% of the dose resulting in too low ASO concentration at the active site for an effective and sustained outcome. This consequently requires an increase of the administered dose which induces off-target effects.
  • Most common side-effects are activation of the complement cascade, the inhibition of the clotting cascade and toll-like receptor mediated stimulation of the immune system.
  • Chemotherapeutics are most commonly small molecules, however, their efficacy is hampered by the severe off-target side toxicity, as well as their poor solubility, rapid clearance and limited tumor exposure.
  • Scaffold-small-molecule drug conjugates such as polymer-drug conjugates (PDCs) are macromolecular constructs with pharmacologically activity, which comprises one or more molecules of a small-molecule drug bound to a carrier scaffold (e.g. polyethylene glycol (PEG)).
  • PDCs polymer-drug conjugates
  • PK1 N-(2-hydroxypropyl)methacrylamide (HPMA) copolymer doxorubicin; development by Pharmacia, Pfizer
  • HPMA 2-hydroxypropyl)methacrylamide copolymer doxorubicin
  • scaffold-small-molecule drug conjugates is at least partially attributed to its poor accumulation at the tumor site.
  • PK1 showed 45-250 times higher accumulation in the tumor than in healthy tissues (liver, kidney, lung, spleen, and heart), accumulation in tumor was only observed in a small subset of patients in the clinical trial.
  • Liposomes are sphere-shaped vesicles consisting of one or more phospholipid bilayers, which are spontaneously formed when phospholipids are dispersed in water.
  • the amphiphilicity characteristics of the phospholipids provide it with the properties of self-assembly, emulsifying and wetting characteristics, and these properties can be employed in the design of new drugs and new drug delivery systems.
  • Drug encapsulated in a liposomal delivery system may convey several advantages over a direct administration of the drug, such as an improvement and control over pharmacokinetics and pharmacodynamics, tissue targeting property, decreased toxicity and enhanced drug activity.
  • doxorubicin a small molecule chemotherapy agent doxorubicin
  • Doxil a pegylated liposome-encapsulated form of doxorubicin
  • Myocet a non-pegylated liposomal doxorubicin
  • At least one of the above objectives of embodiments of the invention is achieved by providing a therapeutic combination of the invention, also suitable for use as a medicament, according to the invention.
  • the therapeutic combination comprises a first molecule comprising covalently bound saponin and comprises a second molecule comprising an effector molecule, wherein both the first and second molecule comprise a binding site for the same epitope exposed on the same cell-surface molecule of a targeted cell.
  • An aspect of the invention relates to a therapeutic combination, wherein the therapeutic combination comprises: (a) a first pharmaceutical composition comprising a first proteinaceous molecule comprising a binding site for binding to an epitope on a cell-surface molecule and at least one saponin covalently bound to said first proteinaceous molecule preferably to an amino-acid residue of said first proteinaceous molecule, the first pharmaceutical composition optionally further comprising a pharmaceutically acceptable excipient; and (b) a second pharmaceutical composition comprising a second proteinaceous molecule, the second proteinaceous molecule comprising a binding site for binding to the epitope on the cell-surface molecule of (a) and an effector moiety, the second pharmaceutical composition optionally further comprising a pharmaceutically acceptable excipient, wherein the binding site of the first proteinaceous molecule and the binding site of the second proteinaceous molecule are the same, and wherein the cell-surface molecule and the epitope on the cell-surface molecule, to which the first proteinaceous molecule can bind,
  • the first proteinaceous molecule is a conjugate comprising a binding site for binding to an epitope on a cell-surface molecule and comprising at least one saponin covalently bound to said first proteinaceous molecule preferably to an amino-acid residue of said first proteinaceous molecule.
  • the second proteinaceous molecule is a conjugate comprising the binding site for binding to the epitope on the same cell-surface molecule and comprising an effector moiety.
  • An aspect of the invention relates to a therapeutic combination for use as a medicament, wherein the therapeutic combination comprises: (a) a first pharmaceutical composition comprising a first proteinaceous molecule comprising a binding site for binding to an epitope on a cell-surface molecule and at least one saponin covalently bound to said first proteinaceous molecule preferably to an amino-acid residue of said first proteinaceous molecule, the first pharmaceutical composition optionally further comprising a pharmaceutically acceptable excipient; and (b) a second pharmaceutical composition comprising a second proteinaceous molecule, the second proteinaceous molecule comprising a binding site for binding to the epitope on the cell-surface molecule of (a) and an effector moiety, the second pharmaceutical composition optionally further comprising a pharmaceutically acceptable excipient, wherein the binding site of the first proteinaceous molecule and the binding site of the second proteinaceous molecule are the same, and wherein the cell-surface molecule and the epitope on the cell-surface molecule, to which the first proteinaceous
  • An aspect of the invention relates to said first pharmaceutical composition of the invention.
  • An aspect of the invention relates to said first pharmaceutical composition of the invention for use as a medicament.
  • An embodiment is the therapeutic combination of the invention or the therapeutic combination of the invention for use in the treatment or prevention of a cancer in a human subject, wherein the therapeutic combination comprises: (a) the first pharmaceutical composition of the invention; and (b) the second pharmaceutical composition of the invention, wherein the cell-surface molecule is expressed on a tumor cell surface, and preferably the cell-surface molecule is a tumor cell-specific surface molecule, and wherein preferably the epitope is a tumor-cell specific epitope.
  • An embodiment is the therapeutic combination of the invention, or the first pharmaceutical composition according to the invention or the therapeutic combination for use of the invention, or the first pharmaceutical composition for use according to the invention, wherein the binding site of the first proteinaceous molecule and the second proteinaceous molecule comprises or consists of an immunoglobulin or a binding fragment or binding domain of said immunoglobulin, such as any one or more of an antibody, an IgG, a molecule comprising or consisting of a Vhh domain or Vh domain, a Fab, an scFv, an Fv, a dAb, an F(ab)2, Fcab fragment, and/or comprises or consists of at least one ligand, the ligand for binding to a cell-surface molecule such as EGF or a cytokine.
  • an immunoglobulin or a binding fragment or binding domain of said immunoglobulin such as any one or more of an antibody, an IgG, a molecule comprising or consisting of a Vhh domain or Vh domain,
  • An embodiment is the therapeutic combination of the invention, or the first pharmaceutical composition according to the invention or the therapeutic combination for use of the invention, or the first pharmaceutical composition for use according to the invention, wherein the tumor-cell surface molecule is a cell-surface receptor specifically present at a tumor cell, and wherein preferably the epitope is a tumor-cell specific epitope.
  • An embodiment is the therapeutic combination of the invention, or the first pharmaceutical composition according to the invention or the therapeutic combination for use of the invention, or the first pharmaceutical composition for use according to the invention, wherein the at least one saponin is a triterpenoid saponin and/or a bisdesmosidic triterpene saponin belonging to the type of a 12,13-dehydrooleanane with an aldehyde function in position C-23 and optionally comprising a glucuronic acid function in a carbohydrate substituent at the C-3beta-OH group of the saponin, and/or a saponin isolated from a Gypsophila species and/or a Saponaria species and/or an Agrostemma species and/or a Quillaja species such as Quillaja saponaria.
  • the at least one saponin is a triterpenoid saponin and/or a bisdesmosidic triterpene saponin belonging to the type of a 12,13-dehydroo
  • An embodiment is the therapeutic combination the invention, or the first pharmaceutical composition according to the invention or the therapeutic combination for use of the invention, or the first pharmaceutical composition for use according to the invention, wherein the epitope is an epitope on a tumor-cell receptor, preferably a tumor-cell specific epitope, and wherein the receptor is preferably a tumor-cell specific receptor, more preferably a receptor selected from CD71, CA125, EpCAM(17-1A), CD52, CEA, CD44v6, FAP, EGF-IR, integrin, syndecan-1, vascular integrin alpha-V beta-3, HER2, EGFR, CD20, CD22, Folate receptor 1, CD146, CD56, CD19, CD138, CD27L receptor, PSMA, CanAg, integrin-alphaV, CA6, CD33, mesothelin, Cripto, CD3, CD30, CD239, CD70, CD123, CD352, DLL3, CD25, ephrinA4, MUC1, Trop2, CEACAM5, CE
  • an embodiment is the therapeutic combination of the invention or the therapeutic combination for use of the invention, wherein the effector moiety comprised by the second proteinaceous molecule comprises or consists of at least one proteinaceous molecule, preferably selected from any one or more of a peptide, a protein, an enzyme such as urease and Cre-recombinase, a proteinaceous toxin, a ribosome-inactivating protein, a protein toxin selected from Table A5 and/or a bacterial toxin, a plant toxin; preferably the protein toxin is dianthin and/or saporin.
  • the effector moiety comprised by the second proteinaceous molecule comprises or consists of at least one proteinaceous molecule, preferably selected from any one or more of a peptide, a protein, an enzyme such as urease and Cre-recombinase, a proteinaceous toxin, a ribosome-inactivating protein, a protein toxin selected from Table A5
  • An embodiment is the therapeutic combination of the invention or the therapeutic combination for use of the invention, wherein the first proteinaceous molecule comprises more than one covalently bound saponin, preferably 2, 3, 4, 5, 6, 8, 10, 16, 32, 64, 128 or 1-100 saponins, or any number of saponins therein between, such as 7, 9, 12 saponins.
  • An embodiment is the therapeutic combination of the invention or the therapeutic combination for use of the invention, wherein the first pharmaceutical composition and the second pharmaceutical composition are administered to the patient in need thereof.
  • An aspect of the invention relates to the first pharmaceutical composition of the invention, further comprising the second proteinaceous molecule of the invention.
  • An aspect of the invention relates to the first pharmaceutical composition of the invention, further comprising the second proteinaceous molecule of the invention, for use as a medicament.
  • An aspect of the invention relates to the first pharmaceutical composition of the invention, further comprising the second proteinaceous molecule of the invention, for use in the treatment or prophylaxis of cancer in a patient in need thereof.
  • An aspect of the invention relates to any of the following first proteinaceous molecules or any of the following second proteinaceous molecules, or any of the following semi-finished products consisting of any of the first proteinaceous molecules or any of the second proteinaceous molecules, comprising the binding site of the invention and either comprising at least one effector moiety of the invention when the second proteinaceous molecule is considered or comprising at least one saponin of the invention, when the first proteinaceous molecule is considered, wherein the semi-finished products are suitable for application in the manufacture of an antibody-drug conjugate conjugated with a saponin of the invention or an antibody-oligonucleotide conjugate conjugated with a saponin of the invention:
  • An embodiment is the semi-finished product consisting of any one of the first proteinaceous molecules or second proteinaceous molecules, covalently coupled to at least one oligonucleotide when the first proteinaceous molecule is considered or covalently coupled to at least one effector moiety when the second proteinaceous molecules is considered, preferably selected from:
  • An embodiment is the semi-finished conjugate of the invention or the conjugate of the invention, wherein the binding site is selected from cetuximab, trastuzumab, OKT-9, and/or wherein the effector moiety is selected from dianthin, saporin and antisense BNA(HSP27), and/or wherein the saponin is selected from SO1861, GE1741, SA1641, Quil-A, QS-21, and saponins in water soluble saponin fraction of Quillaja saponaria.
  • An embodiment is the conjugate according to the invention, wherein the binding site is selected from cetuximab, trastuzumab, OKT-9, and/or wherein the effector moiety is selected from dianthin, saporin and antisense BNA(HSP27), and/or wherein the saponin is selected from SO1861, GE1741, SA1641, Quil-A, QS-21, and saponins in water soluble saponin fraction of Quillaja saponaria.
  • An aspect of the invention relates to an ADC or an AOCs or a semi-finished ADC conjugate or a semi-finished AOC conjugate comprising the binding site of the invention and comprising at least one effector moiety of the invention and/or comprising at least one saponin of the invention, of Structure C:
  • An embodiment is the Structure C of the invention, wherein A is an anti-EGFR antibody such as cetuximab, an anti-HER2 antibody such as trastuzumab, an anti-CD71 antibody such as OKT-9, and/or wherein S is any one or more of a saponin, a triterpenoid saponin and/or a bisdesmosidic triterpene saponin belonging to the type of a 12,13-dehydrooleanane with an aldehyde function in position C-23 and optionally comprising a glucuronic acid function in a carbohydrate substituent at the C-3beta-OH group of the saponin, SO1861, GE1741, SA1641, Quil-A, QS-21, and saponins in water soluble saponin fraction of Quillaja saponaria, and/or wherein E is any one or more of an oligonucleotide, an antisense oligonucleotide, an siRNA, an antisense BNA
  • An embodiment is the Structure C of the invention, the conjugate of the invention or the semi-finished conjugate of the invention, wherein the saponin, if present, and/or the effector moiety, if present, is covalently coupled via at least one linker, such as a cleavable linker, and/or via at least one oligomeric or polymeric scaffold, such as a linker based on N-E-maleimidocaproic acid hydrazide (EMCH) succinimidyl 3-(2-pyridyldithio)propionate or 3-(2-Pyridyldithio)propionic acid N-hydroxysuccinimide ester (SPDP), and 1-[Bis(dimethylamino)methylene]-1H-1,2,3-triazolo[4,5-b]pyridinium 3-oxid hexafluorophosphate (HATU), and such as a scaffold based on a Dendron such as a G4-Dendron or a tri-functional link
  • An aspect of the invention relates to the use of any of the aforementioned conjugates, ADC-saponin conjugates, AOC-saponin conjugates, semi-finished products, semi-finished conjugate, as a medicament.
  • An aspect of the invention relates to the use of any of the aforementioned conjugates, ADC-saponin conjugates, AOC-saponin conjugates, semi-finished products, semi-finished conjugate, for use in the treatment or prophylaxis of a cancer or an auto-immune disease.
  • linker has its regular scientific meaning, and here refers to a chemical moiety or a linear stretch of amino-acid residues complexed through peptide bonds, which attaches a molecule or an atom to another molecule, e.g. to a ligand or to an effector molecule or to a scaffold.
  • the linker comprises a chain of atoms linked by chemical bonds.
  • Any linker molecule or linker technology known in the art can be used in the present disclosure.
  • the linker is a linker for covalently binding of molecules through a chemical group on such a molecule suitable for forming a covalent linkage or bond with the linker.
  • the linker may be a non-cleavable linker, e.g., the linker is stable in physiological conditions.
  • the linker may be a cleavable linker, e.g. a linker that is cleavable, in the presence of an enzyme or at a particular pH range or value, or under physiological conditions such as intracellular conditions in the endosomes such as the late endosomes and the lysosomes of mammalian cells such as human cells.
  • linkers that can be used in the context of the present disclosure includes, but is not limited to, N-E-maleimidocaproic acid hydrazide (EMCH), succinimidyl 3-(2-pyridyldithio)propionate or 3-(2-Pyridyldithio)propionic acid N-hydroxysuccinimide ester (SPDP), and 1-[Bis(dimethylamino)methylene]-1H-1,2,3-triazolo[4,5-b]pyridinium 3-oxid hexafluorophosphate (HATU).
  • EMCH N-E-maleimidocaproic acid hydrazide
  • SPDP succinimidyl 3-(2-pyridyldithio)propionate or 3-(2-Pyridyldithio)propionic acid N-hydroxysuccinimide ester
  • HATU 1-[Bis(dimethylamino)methylene]-1H-1,2,3-triazolo[4,5-b
  • tri-functional linker has its regular scientific meaning, and here refers to a linker which attaches three molecules via a chemical group on each of the three molecules.
  • the skilled person is able to design such tri-functional linkers, based on the present disclosure and the common general knowledge.
  • Such tri-functional linker can exhibit, for instance, a maleimido group that can be used for conjugation to targeting ligands that exhibit thiol groups to perform a thiol-ene reaction.
  • the tri-functional linker could exhibit a dibenzocyclooctyne (DBCO) group to perform the so-called strain-promoted alkyne-azide cycloaddition (SPAAC, click chemistry) with an azido bearing saponin.
  • DBCO dibenzocyclooctyne
  • SPAAC strain-promoted alkyne-azide cycloaddition
  • the tri-functional linker could obtain a third functional group such as a trans-cyclooctene (TCO) group to perform the so-called inverse electron demand Diels-Alder (IEDDA) reaction with a tetrazine (Tz) bearing effector molecule.
  • TCO trans-cyclooctene
  • IEDDA inverse electron demand Diels-Alder
  • the chemical groups of the tri-functional linker can be all three the same, or different, or the linker may comprise two of the same chemical groups for linking a molecule to the tri-functional linker.
  • the formed bonds between the tri-functional linker can be covalent or non-covalent, and covalent bonds are preferred.
  • the formed bonds between the tri-functional linker and the one or two or three bound molecules via respective chemical groups can be cleavable (labile) bonds, such as cleavable under acidic conditions inside cells such as endosomes and lysosomes of mammalian cells such as human cells, or can be non-cleavable bonds.
  • the tri-functional linker may encompass one or two chemical groups for forming covalent bonds while the further two or one chemical group(s), respectively, are/is for forming a non-covalent bond.
  • the tri-functional linker may encompass one or two chemical groups for forming cleavable bonds while the further two or one chemical group(s), respectively, are/is for forming a non-cleavable bond.
  • cleavable such as used in the term “cleavable linker” or “cleavable bond” has its regular scientific meaning, and here refers to being subject to cleavage under acidic conditions, reductive conditions, enzymatic conditions or light-induced conditions.
  • a cleavable linker may be subject to cleavage under acidic conditions, preferably said cleavable linker is subject to cleavage in vivo under acidic conditions as present in endosomes and/or lysosomes of mammalian cells, preferably human cells, preferably at pH 4.0-6.5, and more preferably at pH 5.5.
  • a cleavable linker may be subject to cleavage by an enzyme, e.g. by cathepsin.
  • an example of a covalent bond cleavable under reductive conditions is a disulphide bond.
  • oligomer and “polymer” in the context of an oligomeric or polymeric scaffold has its regular scientific meaning.
  • a polymer here refers to a substance which has a molecular structure built up chiefly or completely from a large number of equal or similar units bonded together; an oligomer here refers to a polymer whose molecules consist of relatively few repeating units.
  • a structure comprising 5-10 or less equal or similar units may be called an oligomeric structure
  • a structure comprising 10-50 monomeric units or more may be called a polymeric structure
  • a structure of 10 monomeric units may be called either oligomeric or polymeric.
  • binding site has its regular scientific meaning, and here refers to a region or an epitope on a molecule, e.g. a protein, DNA or RNA, to which another molecule can bind.
  • scaffold has its regular scientific meaning, and here refers to an oligomeric or polymeric template or a carrier or a base (base molecule or base structure), to which one or more molecules, e.g. ligand molecule, glycoside, saponin of the invention, effector molecule, can be covalently bound, either directly, or via a linker, such as a cleavable linker.
  • a scaffold may have a structurally ordered formation such as a polymer, oligomer, dendrimer, dendronized polymer, or dendronized oligomer or have an assembled polymeric structure such as a hydrogel, microgel, nanogel, stabilized polymeric micelle or liposome, but excludes structures that are composed of non-covalent assemblies of monomers such as cholesterol/phospholipid mixtures.
  • a scaffold may comprise a polymeric or oligomeric structure, such as poly- or oligo(amines), e.g., polyethylenimine and poly(amidoamine); or structures such as polyethylene glycol, poly- or oligo(esters), such as poly(lactids), poly(lactams), polylactide-co-glycolide copolymers; or poly(dextrin), poly- or oligosaccharides, such as cyclodextrin or polydextrose; or structures such as natural and/or artificial poly- or oligoamino acids such as poly-lysine or a peptide or a protein, DNA oligo- or polymers, stabilized RNA polymers or PNA (peptide nucleic acid) polymers.
  • polymeric or oligomeric structure such as poly- or oligo(amines), e.g., polyethylenimine and poly(amidoamine); or structures such as polyethylene glycol, poly- or
  • the polymeric or oligomeric structures are biocompatible, wherein biocompatible means that the polymeric or oligomeric structure does not show substantial acute or chronic toxicity in organisms and can be either excreted as it is or fully degraded to excretable and/or physiological compounds by the body's metabolism.
  • ligand has its regular scientific meaning, and here refers to any molecule or molecules which may selectively bind to a target cell-surface molecule or target cell-surface receptor expressed at target cells, e.g. target cancer cells or target auto-immune cells.
  • the ligand may bind to an epitope comprised by receptors or other antigens on the target cells.
  • the cell-binding ligands are antibodies.
  • antibody as used herein is used in the broadest sense, which may refer to an immunoglobulin (Ig) defined as a protein belonging to the class IgG, IgM, IgE, IgA, or IgD (or any subclass thereof), or a functional binding fragment or binding domain of an immunoglobulin.
  • Ig immunoglobulin
  • a “binding fragment” or a “binding domain” of an immunoglobulin is defined as antigen-binding fragment or -domain or other derivative of a parental immunoglobulin that essentially maintains the antigen binding activity of such parental immunoglobulin.
  • Functional fragments and functional domains are antibodies in the sense of the present invention even if their affinity to the antigen is lower than that of the parental immunoglobulin.
  • “Functional fragments and -domains” in accordance with the invention include, but are not limited to, F(ab′)2 fragments, Fab′ fragments, Fab fragments, scFv, dsFv, single-domain antibody (sdAb), monovalent IgG, scFv-Fc, reduced IgG (rlgG), minibody, diabodies, triabodies, tetrabodies, Fc fusion proteins, nanobodies, variable V domains such as VHH, Vh, and other types of antigen recognizing immunoglobulin fragments and domains.
  • the fragments and domains may be engineered to minimize or completely remove the intermolecular disulphide interactions that occur between the CH1 and CL domains.
  • Functional fragment and -domains offer the advantage of greater tumor penetration because of their smaller size. In addition, the functional fragment or -domain can be more evenly distributed throughout the tumor mass as compared to whole immunoglobulin.
  • the antibodies (immunoglobulins) of the present invention may be bi- or multifunctional.
  • a bifunctional antibody has one arm having a specificity for one receptor or antigen, while the other arm recognizes a different receptor or antigen.
  • each arm of the bifunctional antibody may have specificity for a different epitope of the same receptor or antigen of the target cell.
  • the antibodies (immunoglobulins) of the present invention may be, but are not limited to, polyclonal antibodies, monoclonal antibodies, human antibodies, humanized antibodies, chimeric antibodies, resurfaced antibodies, anti-idiotypic antibodies, mouse antibodies, rat antibodies, rat/mouse hybrid antibodies, llama antibodies, llama heavy-chain only antibodies, heavy-chain only antibodies, and veterinary antibodies.
  • the antibody (immunoglobulin) of the present invention is a monoclonal antibody.
  • the resurfaced, chimeric, humanized and fully human antibodies are also more preferred because they are less likely to cause immunogenicity in humans.
  • the antibodies of the ADC of the present invention preferably specifically binds to an antigen expressed on the surface of a cancer cell, an autoimmune cell, a diseased cell, an aberrant cell, while leaving any healthy cell essentially unaltered (e.g. by not binding to such normal cell, or by binding to a lesser extent in number and/or affinity to such healthy cell).
  • anti-HER2 monoclonal antibody such as trastuzumab and pertuzumab
  • anti-CD20 monoclonal antibody such as rituximab, ofatumumab, tositumomab and ibritumomab
  • anti-CA125 monoclonal antibody such as oregovomab
  • anti-EpCAM (17-1A) monoclonal antibody such as edrecolomab
  • anti-EGFR monoclonal antibody such as cetuximab, panitumumab and nimotuzumab
  • anti-CD30 monoclonal antibody such brentuximab
  • anti-CD33 monoclonal antibody such as gemtuzumab and huMy9-6
  • anti-vascular integrin alpha-v beta-3 monoclonal antibody such as etaracizumab
  • anti-CD52 monoclonal antibody such as alemtuzumab
  • An embodiment is the protein-toxin conjugate of Stemline: ELZONRISTM (tagraxofusp, SL-401)-ELZONRIS is a novel targeted therapy directed to the interleukin-3 (IL-3) receptor- ⁇ (CD123), a target present on a wide range of malignancies.
  • ELZONRISTM tagraxofusp, SL-401
  • IL-3 interleukin-3 receptor- ⁇
  • any other molecules than antibodies that bind to a cell receptor or antigen of a target cell can also be used as the cell-binding ligand for the ligand-drug conjugates of the present invention and the ligands provided with covalently bound saponin according to the invention.
  • These ligands include, but are not limited to, proteins, polypeptides, peptides, small molecules. Examples of these non-antibody ligands are interferons (e.g.
  • IFN- ⁇ , IFN- ⁇ , and IFN- ⁇ transferrins, lectins, epidermal growth factors (EGF) and EGF-like domains, gastrin-releasing peptides (GRP), platelet-derived growth factors (PDGF), transforming growth factors (TGF), vaccinia growth factor (VGF), insulin and insulin-like growth factors (IGF, e.g. IGF-1 and IGF-2), other suitable hormones such as thyrotropin releasing hormones (TRH), melanocyte-stimulating hormones (MSH), steroid hormones (e.g. estrogen and androgen), somatostatin, lymphokines (e.g.
  • CSF colony-stimulating factors
  • M-CSF and GM-CSF colony-stimulating factors
  • aptamers e.g. AS-1411, GBI-10, RNA aptamers against HIV glycoprotein
  • small molecules e.g. folate, anisamide phenylboronic acid
  • vitamins e.g., vitamin D
  • carbohydrates e.g. hyaluronic acid, galactose
  • effector molecule or “effector moiety” or “payload” has its regular scientific meaning and in the context of this invention is any substance that affects the metabolism of a cell by interaction with an intracellular effector molecule target, wherein this effector molecule target is any molecule or structure inside cells excluding the lumen of compartments and vesicles of the endocytic and recycling pathway but including the membranes of these compartments and vesicles.
  • Said structures inside cells thus include the nucleus, mitochondria, chloroplasts, endoplasmic reticulum, Golgi apparatus, other transport vesicles, the inner part of the plasma membrane and the cytosol.
  • the effector molecule or -moiety is a pharmaceutically active substance, such as a toxin such as a proteinaceous toxin, a drug, a polypeptide or a polynucleotide.
  • a pharmaceutically active substance in this invention is an effector molecule or -moiety that is used to achieve a beneficial outcome in an organism, preferably a vertebrate, more preferably a mammal such as non-human subjects or a human being/subject. Benefits include diagnosis, prognosis, treatment, cure and prevention (prophylaxis) of diseases and/or symptoms and/or health problems.
  • the pharmaceutically active substance may also lead to undesired and sometimes even harmful side effects (adverse events such as observed during clinical trials).
  • pros and cons must be weighed to decide whether the pharmaceutically active substance is suitable in the particular case. If the effect of the pharmaceutically active substance inside a cell is predominantly beneficial for the organism as a whole, the cell is called a target cell. If the effect inside a cell is predominantly harmful for the organism as a whole, the cell is called an off-target cell. In artificial systems such as cell cultures and bioreactors, target cells and off-target cells depend on the purpose and are defined by the user. Examples of effector molecules and -moieties are a drug, a toxin, a polypeptide (such as an enzyme), a polynucleotide (including polypeptides and polynucleotides that comprise non-natural amino acids or nucleic acids), and any combination thereof.
  • an effector molecule or effector moiety that is a drug may include, but not limited to, anti-cancer agents, anti-inflammatory agents, and anti-infective (e.g., anti-fungal, antibacterial, anti-parasitic, anti-viral) agents.
  • the drug molecule of the present invention is an anti-cancer agent or an anti-auto-immune agent.
  • Suitable anti-cancer agents include, but are not limited to, alkylating agents, antimetabolites, spindle poison plant alkaloids, cytotoxic/antitumor antibiotics, topoisomerase inhibitors, photosensitizers, and kinase inhibitors. Also included in the definition of “anti-cancer agent” are: e.g.
  • anti-hormonal agents that act to regulate or inhibit hormone action on tumors such as anti-estrogens and selective estrogen receptor modulators;
  • aromatase inhibitors that inhibit the enzyme aromatase, which regulates estrogen production in the adrenal glands;
  • anti-androgens iv
  • protein kinase inhibitors iii
  • lipid kinase inhibitors iii) antisense oligonucleotides, particularly those which inhibit expression of genes in signaling pathways implicated in aberrant cell proliferation
  • ribozymes such as VEGF expression inhibitors and HER2 expression inhibitors;
  • vaccines such as gene therapy vaccines; topoisomerase 1 inhibitors;
  • anti-angiogenic agents such as anti-angiogenic agents; and pharmaceutically acceptable salts, acids, solvates and derivatives of any of the above.
  • An effector molecule or -moiety that is a toxin may include, but is not limited to, proteinaceous toxins (e.g. bacterial-derived toxins, and plant-derived toxins), toxins targeting tubulin filaments, toxins targeting DNA, toxins targeting RNA.
  • proteinaceous toxins are saporin, dianthin, ricin, modeccin, abrin, volkensin, viscumin, shiga toxin, shiga-like toxin, pseudomonas exotoxin (PE, also known as exotoxin A), diphtheria toxin (DT), and cholera toxin.
  • tubulin filaments-targeting toxins are maytansinoids (e.g.
  • DM1 and DM4 auristatins (e.g. Monomethyl auristatin E (MMAE) and Monomethyl auristatin F (MMAF)), toxoids, tubulysins, cryptophycins, rhizoxin.
  • DNA-targeting toxins are calicheamicins: N-Acetyl- ⁇ -calicheamicin, CC-1065 analogs, duocarmycins, doxorubicin, methotrexate, benzodiazepines, camptothecin analogues, and anthracyclines.
  • DNA-targeting toxins are amanitins, spliceostatins, and thailanstatins.
  • a toxin is defined as a pharmaceutically active substance that is able to kill or inactivate a cell.
  • a targeted toxin is a toxin that is only, or at least predominantly, toxic for target cells but not for off-target cells. The net effect of the targeted toxin is preferably beneficial for the organism as a whole.
  • An effector molecule or -moiety that is a polypeptide may be, e.g., a polypeptide that recover a lost function, such as for instance enzyme replacement, gene regulating functions, or a toxin.
  • polypeptides as effector molecules are, e.g., Cas9; toxins (e.g. saporin, dianthin, gelonin, (de)bouganin, agrostin, ricin (toxin A chain); pokeweed antiviral protein, apoptin, diphtheria toxin, pseudomonas exotoxin) metabolic enzymes (e.g.
  • argininosuccinate lyase argininosuccinate synthetase
  • enzymes of the coagulation cascade repairing enzymes
  • enzymes for cell signaling cell cycle regulation factors
  • gene regulating factors transcription factors such as NF- ⁇ B or gene repressors such as methionine repressor
  • An effector molecule or an effector moiety that is a polynucleotide may, e.g., be a polynucleotide that comprises coding information, such as a gene or an open reading frame encoding a protein. It may also comprise regulatory information, e.g. promotor or regulatory element binding regions, or sequences coding for micro RNAs.
  • Such polynucleotide may comprise natural and artificial nucleic acids. Artificial nucleic acids include, e.g. peptide nucleic acid (PNA), Morpholino and locked nucleic acid (LNA), as well as glycol nucleic acid (GNA) and threose nucleic acid (TNA).
  • nucleotides as effector molecules are, but not limited to, e.g., DNA: single stranded DNA (e.g. DNA for adenine phosphoribosyltransferase); linear double stranded DNA (e.g. clotting factor IX gene); circular double stranded DNA (e.g. plasmids); RNA: mRNA (e.g. TAL effector molecule nucleases), tRNA, rRNA, siRNA, miRNA, antisense RNA; anti-sense oligonucleotides (ASOs, AONs e.g. PNA, PMO, LNA and BNA).
  • DNA single stranded DNA
  • linear double stranded DNA e.g. clotting factor IX gene
  • circular double stranded DNA e.g. plasmids
  • RNA mRNA (e.g. TAL effector molecule nucleases), tRNA, rRNA, siRNA,
  • proteinaceous used in e.g. “proteinaceous molecule” and “proteinaceous toxin”, are molecules and toxins comprising at least a string of amino acid residues that can be obtained as an expression product from a single mRNA.
  • Such a molecule or toxin may further comprise any post-translational modifications, a carbohydrate such as an N- or O-linked carbohydrate, disulphide bonds, phosphorylations, sulphatations, etc., as a result of any post-translational modification, and/or may further comprise any other modification such as those resulting from chemical modifications (e.g., linking of effector moieties, saponin, scaffolds, ligands, etc., either directly to e.g.
  • proteinaceous also encompasses and includes assemblies of such molecules, e.g. homodimers, heterotrimers, heterohexamers or complex assemblies such as ribosomes.
  • the number of receptors or molecular targets is considered, of a cell-surface receptor or molecular target on the surface of a first type of cell such as a tumor cell, autoimmune cell, diseased cell, aberrant cell, relative to the extent of expression of the same receptor or molecular target at a second type of cell such as a healthy cell, etc., wherein expression at the second type of cell can be fully absent or very low, relative to any extent of expression on the tumor cell, etc.
  • the term “specific”, for example in “specific binding”, has its normal scientific meaning known in the art, and here has the meaning of indicating a molecule that can have an interaction with another molecule with higher binding affinity than background interactions between molecules.
  • binding molecules such as immunoglobulins bind via their binding site such as immunoglobulin variable regions of the immunoglobulin, to binding sites on molecules, such as epitopes, cell-surface receptors, etc., with a higher binding affinity than background interactions between molecules.
  • background interactions are typically interactions with an affinity lower than a K D of 10E-4 M.
  • specific binding domains are domains that preferentially bind to binding sites on molecules, such as epitopes, cell-surface receptors, etc., with a higher binding affinity than background interactions between molecules.
  • background interactions are typically interactions with an affinity lower than a K D of 10E-4 M.
  • specific binding domains bind with an affinity higher than a K D of about 10E-5 M.
  • binding is defined as interactions between molecules that can be distinguished from background interactions.
  • fragment refers to an amino acid sequence which is part of a protein domain or which builds up an intact protein domain. Binding fragments according to the invention must have binding specificity for the respective target such as a cell-surface receptor, e.g. on the surface of a diseased cell such as a tumor cell.
  • ADC or “antibody-drug conjugate” has its regular scientific meaning known to the skilled person, and here refers to a class of biopharmaceutical drugs designed as a targeted therapy for treating e.g. cancer. Unlike chemotherapy, ADCs are intended to target and kill tumor cells while sparing healthy cells. ADCs are composed of an antibody linked to a biologically active cytotoxic (anticancer) payload or drug. ADCs combine the targeting capabilities of monoclonal antibodies with the cancer-killing ability of cytotoxic drugs. They are designed with the intention to discriminate between healthy cells and diseased tissue such as tumor cells in a tumor.
  • Saponinum album has its normal meaning and here refers to a mixture of saponins produced by Merck KGaA (Darmstadt, Germany) containing saponins from Gypsophila paniculata and Gypsophila arostii, containing SA1657 and mainly SA1641.
  • Quillajasaponin has its normal meaning and here refers to the saponin fraction of Quillaja saponaria and thus the source for all other QS saponins, mainly containing QS-18 and QS-21.
  • QS-21 or “QS21” has its regular scientific meaning and here refers to a mixture of QS-21 A-apio ( ⁇ 63%), QS-21 A-xylo ( ⁇ 32%), QS-21 B-apio ( ⁇ 3.3%), and QS-21 B-xylo ( ⁇ 1.7%).
  • QS-21A has its regular scientific meaning and here refers to a mixture of QS-21 A-apio ( ⁇ 65%) and QS-21 A-xylo ( ⁇ 35%).
  • QS-21B has its regular scientific meaning and here refers to a mixture of QS-21 B-apio ( ⁇ 65%) and QS-21 B-xylo ( ⁇ 35%).
  • Quil-A refers to a commercially available semi-purified extract from Quillaja saponaria and contains variable quantities of more than 50 distinct saponins, many of which incorporate the triterpene-trisaccharide substructure Gal-(1 ⁇ 2)-[Xyl-(1 ⁇ 3)]-GlcA- at the C-3beta-OH group found in QS-7, QS-17, QS18, and QS-21.
  • the saponins found in Quil-A are listed in van Setten (1995), Table 2 [Dirk C. van Setten, Gerrit van de Maschinenen, Gijsbert Zomer and Gideon F. A.
  • Quil-A and also Quillajasaponin are fractions of saponins from Quillaja saponaria and both contain a large variety of different saponins with largely overlapping content. The two fractions differ in their specific composition as the two fractions are gained by different purification procedures.
  • QS1861 and the term “QS1862” refer to QS-7 and QS-7 api.
  • QS1861 has a molecular mass of 1861 Dalton
  • QS1862 has a molecular mass of 1862 Dalton.
  • QS1862 is described in Fleck et al. (2019) in Table 1, row no.
  • a method comprising step A and step B should not be limited to a method consisting only of steps A and B, rather with respect to the present invention, the only enumerated steps of the method are A and B, and further the claim should be interpreted as including equivalents of those steps.
  • indefinite article “a” or “an” does not exclude the possibility that more than one of the features such as for example a component, excipient, saponin, etc. are present, unless the context clearly requires that there is one and only one of the features.
  • the indefinite article “a” or “an” thus usually means “at least one”.
  • FIG. 1 1T2C in vivo activity.
  • the 1T2C combination of 50 mg/kg cetuximab-(Cys-L-SO1861) 4 +25 mg/kg cetuximab-(-L-HSP27BNA) 4 in A431 tumor bearing mice reveals strong tumor targeted gene silencing, compared to the controls.
  • FIG. 2 1T2C in vivo activity.
  • the 1T2C combination of 40 mg/kg trastuzumab-(Cys-L-SO1861) 4 +0.02/0.03 mg/kg trastuzumab-saporin in a PDX tumor mouse model (high HER2 expression) shows effective tumor growth inhibition.
  • FIG. 3 1-target 2-component. EGFR targeted cell killing in A431 cells (EGFR ++ ) (A, C) and CaSKi cells (EGFR + ) (B, D) by a therapeutic combination according to the invention.
  • C, D Cetuximab-saporin titration+fixed concentration of 75 nM cetuximab-(Cys-L-SO1861) 3,7 and controls on A431 (C) and CaSKi (D) cells.
  • FIG. 4 1-target 2-component. EGFR targeted cell killing in HeLa cells (EGFR +/ ⁇ ) (A, C) and A2058 cells (EGFR ⁇ ) (B, D) by a therapeutic combination according to the invention.
  • C, D Cetuximab-saporin titration+fixed concentration of 75 nM cetuximab-(Cys-L-SO1861) 3,7 and controls on Hela (C) and A2058 (D) cells.
  • FIG. 5 1-target 2-component.
  • HER2 targeted cell killing in SKBR3 cells (HER2 ++ ) (A, B) by a therapeutic combination according to the invention.
  • A) Trastuzumab-(Cys-L-SO1861) 4 titration+fixed concentration 50 pM trastuzumab-saporin and controls on SKBR3 cells.
  • B) Trastuzumab-saporin titration+fixed concentration of 2.5 nM trastuzumab-(Cys-L-SO1861) 4 and controls on SKBR3 cells.
  • Remark For target receptor expression data of each cell line (determined by FACS analysis) see table 19.
  • FIG. 6 1-target 2-component.
  • HER2 targeted cell killing in JIMT-1 cells (HER2 +/ ⁇ ) (A, C) and MDA-MB-468 cells (HER2 ⁇ ) (B, D) by a therapeutic combination according to the invention.
  • A, B) Trastuzumab-(Cys-L-SO1861) 4 titration+fixed concentration of 50 pM trastuzumab-saporin and controls on JIMT-1 (A) and MDA-MB-468 (B) cells.
  • C, D Trastuzumab-saporin titration+fixed concentration of 2.5 nM trastuzumab-(Cys-L-SO1861) 4 and controls on JIMT-1 (C) and MDA-MB-468 (D) cells.
  • FIG. 8 Chloroquine inhibits the 1-target 2-component.
  • HER2 and EGFR targeted cell killing in SK-BR-3 (HER2 ++ ) and A431 cells (EGFR ++ ), by a therapeutic combination according to the invention+chloroquine.
  • A) Trastuzumab-saporin titration+fixed concentration of 5 nM trastuzumab-(Cys-L-SO1861) 4 +0.5 pM chloroquine and control on SK-BR-3 cells.
  • FIG. 9 1-target 2-component.
  • EGFR targeted gene silencing in A431 cells (EGFR ++ ) and A2058 cells (EGFR ⁇ ) by a therapeutic combination according to the invention.
  • A,B Cetuximab-(Cys-L-SO1861) 3,8 titration+fixed concentration of 100 nM Cetuximab-(Lys-L-HSP27BNA) 4 and control on A431 cells (A) and A2058 cells (B).
  • FIG. 10 2-target 2-component.
  • C,D Trastuzumab-Cys-(dendron(-L-SO1861) 4 ) 4 titration+fixed concentration 50 pM trastuzumab-saporin and controls on SK-BR-3 cells (C) and JIMT-1 cells (D).
  • FIG. 11 1-target 2-component.
  • SK-BR-3 cells HER2 +/ ⁇
  • Tratuzumab-saporin+2.5 nM trastuzumab-(Cys-L-SO1861) 4 can efficiently be killed with the therapeutic combination according to the invention, Tratuzumab-saporin+2.5 nM trastuzumab-(Cys-L-SO1861) 4 , however titration of T-DM1+2.5 nM trastuzumab-(Cys-L-SO1861) 4 is not effective at such low toxin concentrations.
  • T-DM1 is Trastuzumab-emtansine (Kadcyla®), carrying ⁇ 3.5 emtansine (DM1) toxin molecules per antibody (DAR3.5).
  • FIG. 12 Control treatments on all cell lines.
  • A-D Cell viability when trastuzumab (A), cetuximab (B), T-DM1, (C) free toxins: saporin and dianthin (D) or saporin coupled to a non-cell binding IgG (D) are treated with the indicated cell lines SK-BR-3, JIMT-1, MDA-MB-468, A431, CaSki, HeLa, A2058, BT-474.
  • Remark For target receptor expression data of each cell line (determined by FACS analysis) see table 19.
  • FIG. 13 1-target 2-component. EGFR targeted cell killing in A431 cells (EGFR ++ ) (A) and CaSKi cells (EGFR + ) (B) and A2058 cells (EGFR ⁇ ) by a therapeutic combination according to the invention.
  • A, B, C Cetuximab-(Cys-L-QSmix) 4, 1 titration+fixed concentration 10 pM cetuximab-saporin or 10 pM cetuximab-dianthin and controls in A431 cells (A), CaSKi cells (B) and A2058 cells (C).
  • QSmix is a mixture of saponins from an extract Quillaja Saponaria. Remark: For target receptor expression data of each cell line (determined by FACS analysis) see table 19.
  • FIG. 14 1-target 2-component concept: mAb1-SO1861+mAb1-protein toxin.
  • SO1861 and toxin are each, independently, conjugated to an antibody (mAb1) for delivery and internalization into target cells.
  • mAb1-SO1861 and mAb1-protein toxin bind to the cell surface receptor, 2) receptor-mediated endocytosis of both conjugates occurs, 3) at low endolysosomal pH and appropriate concentration, SO1861 becomes active to enable endolysosomal escape, 4) release of toxin into cytoplasm occurs and 5) toxin induces cell death
  • FIG. 15 1-target 2-component concept: mAb1-SO1861+mAb2-BNA oligo.
  • SO1861 and antisense BNA oligo nucleotide are each, independently, conjugated to an antibody (mAb1) for delivery and internalization into target cells.
  • mAb1-SO1861 and mAb1-BNAoligo bind to the cell surface receptor, 2) receptor-mediated endocytosis of both conjugates occurs, 3) at low endolysosomal pH and appropriate concentration, SO1861 becomes active to enable endolysosomal escape, 4) release of BNA oligo into cytoplasm occurs and 5) target gene silencing.
  • FIG. 16 1-target 2-component concept: mAb1-(scaffold(-SO1861) n ) n +mAb1-protein toxin.
  • Dendron(-SO1861) n and protein toxin are each, independently, conjugated to an antibody (mAb1) for delivery and internalization into target cells.
  • mAb1-dendron(-SO1861) 4 and mAb1-protein toxin bind to the cell surface receptor, 2) receptor-mediated endocytosis of both conjugates occurs, 3) at low endolysosomal pH and appropriate concentration, SO1861 becomes active to enable endolysosomal escape, 4) release of toxin into cytoplasm occurs and 5) toxin induces cell death
  • FIG. 17 Antibody-SO1861 conjugation procedure. Shown is the coupling reaction of the linking of four moieties of a plant-derived saponin SO1861 to the four cysteines in the light chain of an antibody. First, the disulphide bonds in the IgG are disrupted under influence of exposure to TCEP (Tris(2-carboxyethyl)phosphine); second, the saponin SO1861 comprising a chemical linker bound to it, is added together with trifluoro acetic acid, and four saponin moieties are linked to the IgG.
  • TCEP Tris(2-carboxyethyl)phosphine
  • the aldehyde group of SO1861 was reacted with an EMCH ( ⁇ -maleimidocaproic acid hydrazide) linker.
  • the hydrazide group of EMCH forms an acid cleavable hydrazone bond with the aldehyde of SO1861.
  • the EMCH linker presents a maleimide group that is thiol (sulfhydryl group) reactive and thus can be conjugated to thiols of the IgG, i.e. the ligand moiety.
  • an endosomal escape enhancing conjugate of the invention is provided, and/or a first binding molecule of the invention is provided.
  • FIG. 18 SO1861-EMCH synthesis
  • FIG. 19 Dendron+L-SO1861) 4 synthesis
  • FIG. 20 Dendron-(-L-SO1861) 8 synthesis
  • FIG. 21 SO1861-L-trifcuntional linker-L-HSP27BNA synthesis
  • FIG. 22 HSP27BNA-dendron+L-SO1861) 4 synthesis
  • FIG. 23 Dendron(NEM) 4 synthesis synthesis
  • FIG. 24 SO1861-EMCH synthesis
  • FIG. 25 Scaffold precursor with four amino groups for saponin linkage and an azide group for click chemistry.
  • FIG. 26 Evidence for the coupling of saponins to the model scaffold.
  • the inset shows the theoretically expected peeks and intensity distribution for coupled saponins.
  • the experimental data obtained by LC-MS/ESI-MS show almost exactly the same peaks at m/z 758-760 Da proving successful saponin coupling.
  • FIG. 27 Cytotoxicity assays using the targeted toxin dianthin-Epidermal Growth Factor (dianthin-EGF). Untreated cells were normalized to 1.
  • the polymeric structure (Pentrimer) has no influence on cell viability neither in the presence nor in the absence of Dianthin-EGF and saponin (SA1641) indicating no intrinsic cytotoxicity of the polymeric structure.
  • the clickable targeted toxin (Dianthin-EGF-Alkyne) has a markedly reduced activity, which is a result of the toxin modification but does not have any relation to the scaffold.
  • the functionalized polymeric structure has the same activity as the unclicked targeted toxin, indicating that the functionalization of the scaffold does not impair effector molecule activity.
  • the effect of saponins is identical in the presence and absence of the polymeric structure showing that the polymeric structure does not impair the efficacy of the saponins in the two-component system.
  • the absence of the signal at 9.43 ppm indicates a quantitative conversion of the aldehyde group.
  • FIG. 29 (A) MALDI-TOF-MS spectrum of SO1861-EMCH and (B) SO1861-EMCH-mercaptoethanol. (A) RP mode: m/z 2124 Da ([M+K] + , saponin-EMCH), m/z 2109 Da ([M+K] + , SO1861-EMCH), m/z 2094 Da ([M+Na] + , SO1861-EMCH).
  • FIG. 30 SO1861 structure with highlighted chemical groups for conjugation of endosomal escape enhancing saponins to a polymeric structure. Highlighted groups are aldehyde (black circle), carboxylic acid (dashed circle), alkene (dashed pentagon), and alcohol (dashed box). The aldehyde group (arrow) is most suitable group for chemoselective and reversible conjugation reactions.
  • FIG. 31 Strategy for producing (A) stable and (B) cleavable ‘ready-to conjugate’ endosomal escape enhancer saponins.
  • FIG. 32 Hydrolysis of the hydrazone bond of SO1861-EMCH under acidic conditions.
  • FIG. 33 SO1861-EMCH structure.
  • A Standard molecular structure
  • B 3D model. Maleimide group is marked with a circle.
  • FIG. 34 (A) SO1861-EMCH synthesis scheme. (B) MALDI-TOF-MS spectra of SO1861 (m/z 1861 Da) and (C) SO1861-EMCH (m/z 2068 Da) in negative reflector mode. TFA: trifluoroacetic acid, r.t: room temperature, h: hours, and MW: molecular weight.
  • FIG. 35 MALDI-TOF-MS spectra of SO1861-EMCH (A) before and (B) after hydrolysis in HCl solution at pH 3.
  • FIG. 36 Reaction scheme of SO1861-EMCH conjugation to any amine-bearing polymeric structure.
  • FIG. 37 MALDI-TOF-MS spectra of (A) BSA-SO1861 (m/z 70.0 kDa, 72.1 kDa, 74.2 kDa), and (B) BSA (m/z 66.6 kDa).
  • HATU 1-[Bis(dimethylamino)methylene]-1H-1,2,3-triazolo[4,5-b]pyridinium 3-oxid hexafluorophosphate
  • FIG. 39 MALDI-TOF-MS spectra of (A) Cy3-PAMAM, (B-D) Cy3-PAMAM-SO1861 with increasing SO1861-EMCH feed equivalents from (B) up to bottom (D).
  • (B) corresponds to Cy3-PAMAM-SO1861 with 5 SO1861 attached per PAMAM
  • (C) corresponds to Cy3-PAMAM-SO1861 with 13 SO1861 attached per PAMAM
  • (D) corresponds to Cy3-PAMAM-SO1861 with 51 SO1861 attached per PAMAM.
  • FIG. 40 MALDI-TOF-MS spectra of (A) Cy3-PAMAM-SO1861 with 5 equivalents feed SO1861-EMCH and (B) Cy3-PAMAM-SO1861 with 30 equivalents feed SO1861-EMCH.
  • FIG. 42 (A) Reaction scheme and MALDI-TOF-MS spectra of (B) Cy3-PAMAM-NC-SO1861-Dibenzocyclooctyne (DBCO), (C) Cy3-PAMAM-(SO1861) 5 -DBCO, and (D) Cy3-PAMAM-(SO1861) 27 -DBCO.
  • B Cy3-PAMAM-NC-SO1861-Dibenzocyclooctyne
  • C Cy3-PAMAM-(SO1861) 5 -DBCO
  • D Cy3-PAMAM-(SO1861) 27 -DBCO.
  • FIG. 43 Reaction scheme of (A) dianthin-EGF-Alexa488 and (B) dianthin-EGF-Alexa488-SS-PEG-N 3 .
  • FIG. 44 Reaction scheme of (A) dianthin-Alexa488 and (B) dianthin-Alexa488-SS-PEG-N 3 .
  • FIG. 45 Fluorescence images of SDS-PAGE gel performed on a VersaDoc imaging system.
  • M marker
  • P Cy3-PAMAM-(SO1861) 27 -DBCO
  • D dianthin-EGF-Alexa488-SS-PEG-N 3
  • C1 Cy3-PAMAM-(SO1861) 5 -Dianthin-EGF-Alexa488,
  • C2 Cy3-PAMAM-NC-SO1861-Dianthin-EGF-Alexa488, and
  • C3 Cy3-PAMAM-(SO1861) 27 -Dianthin-EGF-Alexa488.
  • FIG. 46 (A) Synthesis scheme of Cy3-PAMAM-NC-SO1861 via reductive amination. (B, and C) Respective MALDI-TOF-MS spectra.
  • FIG. 47 Reaction scheme for the generation of poly(SO1861) using SO1861-EMCH as monomer, the APS/TMEDA system as polymerization initiator, and aminopropanethiol as radical quencher.
  • FIG. 48 MALDI-TOF-MS spectra of poly(SO1861) reaction batches.
  • A SO1861-EMCH at 60° C.
  • B SO1861-EMCH+11 ⁇ 3 equivalents APS at 60° C.
  • C SO1861-EMCH+11 ⁇ 3 equivalents APS/TMEDA at 60° C.
  • FIG. 49 DNA approach. Usage of the principle of DNA-origami to generate a DNA based scaffold that is able to conjugate and release glycoside molecules. In addition, one of the DNA strands obtains a click chemistry moiety that can be used for conjugation to a targeted toxin to form a functionalized scaffold.
  • bp base pair.
  • FIG. 50 Poly(peptide-SO1861) approach. Usage of a peptide sequence that can conjugate and release glycoside molecules and which can react with itself to form a poly(peptide-SO1861) construct.
  • the poly(peptide) chain endings can be further modified with click chemistry moieties (e.g., BCN-NHS linker) that can be used for conjugation to a toxin.
  • click chemistry moieties e.g., BCN-NHS linker
  • FIG. 51 MALDI-TOF-MS spectra of (A) native peptide, (B) peptide-SO1861 conjugate.
  • FIG. 52 Molecular structure of G4-dendron with protected amino groups.
  • FIG. 53 Synthesis scheme for the generation of dendron based scaffolds and functional scaffolds.
  • FIG. 54 (A) Reaction scheme for partial dye labeling and deprotection of the G4-dendron. (B) MALDI-TOF-MS spectrum of deprotected and partially dye labeled G4-dendron.
  • FIG. 55 MALDI-TOF-MS spectra of G4-dendron-SO1861 scaffolds with (A) 22 feed equivalents of SO1861-EMCH, (B) 10 feed equivalents of SO1861-EMCH, and (C) 3 feed equivalents of SO1861-EMCH.
  • FIG. 56 Cell viability curves of HeLa cells treated with (A) EGFR cell surface expression as determined by FACS analyses of HeLa cells (B, see Table 19), cell viability of HeLa cells treated with SO1861+dianthin-EGF (Dia-EGF), SO1861+dianthin-EGF+500 nM chloroquine, SO1861+dianthin-EGF+500 nM PAMAM, SO1861+dianthin-EGF+667 nM dendron (C) cell viability of HeLa cells treated with SO1861+dianthin-EGF, SO1861+dianthin-EGF+500 nM chloroquine, SO1861+dianthin-EGF+500 nM PAMAM, SO1861+dianthin-EGF+500 nM PAMAM-(SH) 16 , SO1861+dianthin-EGF+500 nM PAMAM-(SH) 65 , SO1861+dianthin-EGF+500 nM PAMAM-(
  • FIG. 57 (A) Reaction scheme of the thiolation of PAMAM using the thiolation reagent 2-iminothiolane. MALDI-TOF-MS spectra of (B) native PAMAM, (C) thiolated PAMAM-(SH) 16 , (D) thiolated PAMAM-(SH) 65 , and (E) thiolated PAMAM-(SH) 108 .
  • FIG. 58 (A) Reaction scheme of the PEGylation of PAMAM using the PEGylating reagent mPEG 2k -NHS. MALDI-TOF-MS spectra of (B) native PAMAM, (C) PEGylated PAMAM-(mPEG 2k ) 3 , (D) PEGylated PAMAM-(mPEG 2k ) 8 , and (E) PEGylated PAMAM-(mPEG 2k ) 18 .
  • FIG. 59 Basic scaffold with click chemistry function to link any desired effector molecule. The user determines the position of the click chemistry position in the effector molecule and all further properties of the effector molecule, e.g. choice and position of an optional ligand.
  • FIG. 60 Functionalized scaffold with pre-bound effector molecule and click chemistry function to link any desired ligand.
  • a pH-sensitive linkage can be provided to release the effector molecule from the scaffold after reaching the endosomes.
  • the molecule In order for a bioactive molecule to work, the molecule must be able to engage with its target, e.g. in the blood serum, on the outside of the cell surface or inside a cell or an organelle.
  • the active moiety of almost all protein-based targeted toxins e.g., must enter the cytosol of the target cell to mediate its target modulatory effect.
  • the toxin remains ineffective since (1) the targeting moiety is poorly internalized and remains bound to the outside of the cells, (2) is recycled back to the cell surface after internalization or (3) transported to the endolysosomes where it is degraded.
  • An aspect of the invention relates to a therapeutic combination or a therapeutic combination for use as a medicament, wherein the therapeutic combination comprises: (a) a first pharmaceutical composition comprising a first proteinaceous molecule comprising a binding site for binding to an epitope on a cell-surface molecule and at least one saponin covalently bound to said first proteinaceous molecule preferably to an amino-acid residue of said first proteinaceous molecule, the first pharmaceutical composition optionally further comprising a pharmaceutically acceptable excipient; and (b) a second pharmaceutical composition comprising a second proteinaceous molecule, the second proteinaceous molecule comprising a binding site for binding to the epitope on the cell-surface molecule of (a) and an effector moiety, the second pharmaceutical composition optionally further comprising a pharmaceutically acceptable excipient, wherein the binding site of the first proteinaceous molecule and the binding site of the second proteinaceous molecule are the same, and wherein the cell-surface molecule and the epitope on the cell-surface molecule, to which
  • the first proteinaceous protein has at least one glycoside such as a saponin bound thereto, preferably covalently, more preferably via a cleavable linker.
  • the saponin augments the therapeutic efficacy of the effector moiety bound to the second proteinaceous molecule, likely by enhancing the endosomal escape of the effector moiety into the cytosol where the activity of the effector moiety is desired. This way, already at a lower dose than the conventional dose of the ADC, i.e.
  • the second proteinaceous molecule, therapeutic effect is established under influence of the presence of the first proteinaceous molecule comprising the saponin near, at and inside the targeted cell.
  • the targeted cell is for example a diseased cell such as a tumor cell or an auto-immune cell or a B-cell disease related B-cell, etc.
  • the effector moiety is for example a toxin as part of an ADC or an oligonucleotide such as a BNA according to the invention.
  • the delivery of the saponin and the effector molecule at and inside the cytosol of the very same targeted cell is improved and more specific.
  • An aberrant cell selected for targeting by the binding site of the first and second proteinaceous molecule ideally bears the cell-surface molecule to a high extent and/or specifically, when (neighboring) healthy cells in a patient are considered.
  • the epitope on the targeted cell-surface molecule is ideally unique to the targeted diseases cells, and is at least specifically present and exposed at the surface of the targeted cells.
  • Binding of the first and second proteinaceous molecules is followed by endocytosis of the complexes of the first proteinaceous molecule and the target cell-surface molecule and the second proteinaceous molecule and the target cell-surface molecule. Since the first and second proteinaceous molecules have to enter the same target cell through binding interaction with the very same cell-surface molecules, accumulation of a therapeutically active amount of first and second proteinaceous molecules inside the target cells is only possible and occurring if expression levels of the targeted cell-surface molecule is above a certain minimal expression threshold. At the same time, the fact that the effector moiety bound to the second proteinaceous molecule is only capable of exerting its intracellular (e.g.
  • cytotoxic or gene silencing activity in the presence of the first proteinaceous molecule bearing the covalently bound saponin, when both the first and second proteinaceous molecules were capable to enter the target cell in sufficient amounts by binding to sufficiently exposed and expressed cell-surface molecule also provides a safeguard against negative and undesired side effects of the effector moiety towards e.g. healthy cells and healthy tissue not meant to be targeted and affected by the effector moiety, when expression of the targeted cell-surface molecule is sufficiently low at the healthy cells.
  • low expression of the cell-surface molecule bound by the binding site of the first and second proteinaceous molecules does not allow entrance of both the first and second proteinaceous molecules to amounts that would in concert result in endosomal escape of the effector moiety under influence of the saponin bound to the first proteinaceous molecule.
  • the ADC can be used at lower dose compared to when the first proteinaceous molecule was not added to the therapeutic regimen, ADC entrance in healthy cells to low extent already bears a lower risk for occurrence of unwanted side effects when for example the targeting and killing of target diseased cells such as tumor cells and auto-immune cells is considered.
  • An aspect of the invention relates to the first pharmaceutical composition of the invention or to the first pharmaceutical composition of the invention for use as a medicament.
  • An aspect of the invention relates to a therapeutic combination for use in the treatment or prevention of a cancer in a human subject, wherein the therapeutic combination comprises: (a) the first pharmaceutical composition of the invention; and (b) the second pharmaceutical composition of the invention, wherein the cell-surface molecule is expressed on a tumor cell surface, and preferably the cell-surface molecule is a tumor cell-specific surface molecule, and wherein preferably the epitope is a tumor-cell specific epitope.
  • An aspect of the invention relates to the first pharmaceutical composition of the invention, for use in the treatment or prophylaxis of a cancer in a patient in need thereof, wherein the cell-surface molecule is expressed on a tumor cell surface, and preferably the cell-surface molecule is a tumor cell-specific surface molecule, and wherein preferably the epitope is a tumor-cell specific epitope.
  • An aspect of the invention relates to the first pharmaceutical composition for use according to the invention or the therapeutic combination for use of the invention, wherein the second pharmaceutical composition of the invention and the first pharmaceutical composition are administered to the patient in need thereof.
  • a solution provided for by the invention comprises the covalent binding of at least one saponin to the first proteinaceous molecule.
  • a further solution provided for by the invention comprises (first) polymerizing the glycoside molecules (saponins) using an oligomeric or polymeric scaffold, and providing the first proteinaceous molecule with a cluster of covalently bound saponins, enabling re-monomerization of the one or more saponins at the intracellular site where the mode of action of the saponin is desired, e.g. after endocytosis.
  • Polymerizes in this context means the reversible and/or irreversible multiple conjugation of saponin molecules to the first proteinaceous molecule, either via linker, or directly or via a polymeric or oligomeric structure to form a scaffold or the reversible and/or irreversible multiple conjugation of (modified) saponins thereby forming a polymeric or oligomeric structure to form a scaffold.
  • Re-monomerization in this context means the cleavage of the saponins from the first proteinaceous molecule, from the linker linking the saponin(s) to the first proteinaceous molecule or from the scaffold, for example after endocytosis, and regaining the (native) chemical state of the unbound saponins, which unbound saponins may or may not comprise additional chemical groups such as a chemical group for linking the saponin to a linker, an amino-acid residue of the first proteinaceous molecule or to the scaffold, and/or a (chemical) linker bound to a chemical group of the saponin such as an aldehyde group or carboxylic acid group.
  • the complex chemistry of the saponins for example the ‘polymerization’ of saponins at a scaffold or other linking linker and their ‘re-monomerization’ at a desired location such as intracellularly e.g. after endocytosis, was a challenging task.
  • the chemical reactions used for providing the linkers and the scaffold comprising covalently linked glycosides for covalent binding to the first proteinaceous molecule e.g. triterpenoid saponins (polymerization of the glycosides)
  • saponins and for example biocompatible polymers applied as a scaffold for bearing bound saponins are water-soluble molecules.
  • Embodiments of the present invention solves at least one of these drawbacks.
  • An embodiment is the therapeutic combination of the invention or the therapeutic combination for use of the invention, or the first pharmaceutical composition according to the invention or the first pharmaceutical composition for use according to the invention, wherein the binding site of the first proteinaceous molecule and the second proteinaceous molecule comprises or consists of an immunoglobulin or a binding fragment or binding domain of said immunoglobulin, such as any one or more of an antibody, an IgG, a molecule comprising or consisting of a Vhh domain or Vh domain, a Fab, an scFv, an Fv, a dAb, an F(ab)2, Fcab fragment, and/or comprises or consists of at least one ligand, the ligand for binding to a cell-surface molecule such as EGF or a cytokine.
  • an immunoglobulin or a binding fragment or binding domain of said immunoglobulin such as any one or more of an antibody, an IgG, a molecule comprising or consisting of a Vhh domain or Vh domain,
  • immunoglobulins, domains thereof, ligands, etc. are particularly suitable for application as the binding site of the first (and second) proteinaceous molecule comprising the binding site.
  • antibodies and binding domains of antibodies are suitable for targeting an epitope on the exposed surface of a selected cell-surface molecule, resulting in targeting the first (and second) proteinaceous molecule to cells expressing the cell-surface molecule and having said cell-surface molecule on their cell surface.
  • ligands such as EGF, targeting the EGFR on target cells, are suitable for application as the binding site in the first and second proteinaceous molecules.
  • binding sites for the epitope which are specific for the binding to the cell-surface molecule.
  • Binding sites based on antibodies or domains or binding fragments thereof for example provide for such desired specificity for a selected epitope on a selected cell-surface molecule of a selected cell for targeting such as a diseased cell, a tumor cell, an auto-immune cell, etc. Therefore, binding sites based on antibodies or binding molecules (fragments, domains) are preferred for the first and second proteinaceous molecules.
  • An embodiment is the therapeutic combination of the invention or the therapeutic combination for use of the invention, or the first pharmaceutical composition according to the invention or the first pharmaceutical composition for use according to the invention, wherein the tumor-cell surface molecule is a cell-surface receptor specifically present at a tumor cell, and wherein preferably the epitope is a tumor-cell specific epitope.
  • Tables A2, A3 and A4 list such preferred examples of cell-surface molecules comprising the epitope for the binding site of the first and second proteinaceous molecule.
  • the cell-surface molecule When the cell-surface molecule is specifically expressed on the target cell, and when the epitope on the cell-surface molecule, to which the binding site can bind, is specifically present in the cell-surface molecule, specific targeting of the first and second proteinaceous molecule to the desired cell such as a tumor cell exposing the tumor-cell surface molecule, is facilitated, whereas other cells such as healthy cells, which do not express the cell-surface molecule or do express the cell-surface molecule to a lower extent, are not targeted by the first and second proteinaceous molecule or are targeted to a lower extent.
  • An embodiment is the therapeutic combination of the invention or the therapeutic combination for use of the invention, or the first pharmaceutical composition according to the invention or the first pharmaceutical composition for use according to the invention, wherein the at least one saponin is a triterpenoid saponin and/or a bisdesmosidic triterpene saponin belonging to the type of a 12,13-dehydrooleanane with an aldehyde function in position C-23 and optionally comprising a glucuronic acid function in a carbohydrate substituent at the C-3beta-OH group of the saponin, and/or a saponin isolated from a Gypsophila species and/or a Saponaria species and/or an Agrostemma species and/or a Quillaja species such as Quillaja saponaria.
  • the at least one saponin is a triterpenoid saponin and/or a bisdesmosidic triterpene saponin belonging to the type of a 12,13-dehydroole
  • An embodiment is the therapeutic combination of the invention or the therapeutic combination for use of the invention, or the first pharmaceutical composition according to the invention or the first pharmaceutical composition for use according to the invention, wherein the at least one saponin is a single specific saponin or is a mixture of two or more different saponins, such as one or more of the saponins in Table A1 or Scheme I, SO1861, SA1657, GE1741, SA1641, QS-21, QS-21A, QS-21 A-api, QS-21 A-xyl, QS-21B, QS-21 B-api, QS-21 B-xyl, QS-7-xyl, QS-7-api, QS-17-api, QS-17-xyl, QS1861, QS1862, Quillajasaponin, Saponinum album, QS-18, Quil-A, Gyp1, gypsoside A, AG1, AG2, SO1542, SO1584, SO1658, SO1674, SO1832, or any of their stereomers and/or any combinations thereof
  • An embodiment is the therapeutic combination of the invention or the therapeutic combination for use of the invention, or the first pharmaceutical composition according to the invention or the first pharmaceutical composition for use according to the invention, wherein the at least one saponin is a bisdesmosidic saponin having a molecular mass of at least 1.500 Dalton and comprising an oleanan-type triterpene containing an aldehyde group at the C-23 position and optionally a hydroxyl group at the C-16 position, with a first branched carbohydrate side chain at the C-3 position which first branched carbohydrate side chain optionally contains glucuronic acid, wherein the saponin contains an ester group with a second branched carbohydrate side chain at the C-28 position which second branched carbohydrate chain preferably comprises at least four carbohydrate units, optionally containing at least one acetyl residue such as two acetyl residues and/or optionally at least one deoxy carbohydrate and/or a quinovose and/or
  • An embodiment is the therapeutic combination of the invention or the therapeutic combination for use of the invention, or the first pharmaceutical composition according to the invention or the first pharmaceutical composition for use according to the invention, wherein the at least one saponin is a bisdesmosidic triterpene saponin belonging to the type of a 12,13-dehydrooleanane with an aldehyde function in position C-23, wherein the saponin is covalently coupled to the first proteinaceous molecule, preferably covalently coupled to an amino-acid residue of the first proteinaceous molecule, via an aldehyde function in the saponin, preferably said aldehyde function in position C-23, preferably via at least one linker, and/or via at least one cleavable linker, wherein the amino-acid residue preferably is selected from cysteine and lysine.
  • the at least one saponin is a bisdesmosidic triterpene saponin belonging to the type of a 12,13-dehydrooleanan
  • Table A1 and Scheme I and the above embodiments summarize a series of saponins that have been identified for their endosomal escape enhancing activity when contacted to mammalian cells, in particular human tumor cells, in free form together with a second molecule (e.g. an effector moiety or effector molecule, such as a toxin, an oligonucleotide).
  • a second molecule e.g. an effector moiety or effector molecule, such as a toxin, an oligonucleotide.
  • a second molecule such as a nucleic acid and/or a toxin such as a protein toxin (e.g. one or more of the protein toxins listed in Table A5), bound to the second proteinaceous molecule, is delivered into the cytosol with increased efficiency and/or efficacy, presumably through intracellular release from the (late) endosomes and lysosomes.
  • a water-soluble saponin fraction from Quillaja saponaria comprising QS-21 and its family members QS-21A, QS-21 A-api, QS-21 A-xyl, QS-21B, QS-21 B-api, QS-21 B-xyl, QS-7-xyl, QS-7-api, QS-17-api, QS-17-xyl, QS1861, QS1862, QS-18 and Quil-A, also exhibits the ability to potentiate a biological effect in vitro of e.g.
  • a nucleic acid bound to a monoclonal antibody or a protein toxin bound to a monoclonal antibody examples of a second proteinaceous molecule of the invention comprising covalently bound oligonucleotide or payload such as a (protein) toxin
  • a second proteinaceous molecule of the invention comprising covalently bound oligonucleotide or payload such as a (protein) toxin
  • first proteinaceous molecule of the invention in the form of a covalent conjugate comprising a monoclonal antibody (first proteinaceous molecule of the invention)
  • the second proteinaceous molecule comprising the effector moiety the aforementioned second proteinaceous molecule
  • the at least one glycoside such as the QS-21 and its family member saponins encompassed by such QS-21 preparation
  • water soluble fraction of Quillaja saponaria comprised by the first proteinaceous molecule as a covalent conjugate, wherein the effector molecule and the glycoside, e.g. saponin fraction of Quillaja saponaria, QS-21, SO1861, SA1641, GE1741, are covalently bound to for example the proteinaceous molecules directly or via a linker or via a polymeric or oligomeric scaffold, either directly or via at least one linker.
  • the observed stimulation or potentiation of for example antisense BNA mediated reduction of tumor-cell HSP27 expression (HSP27 gene silencing) in the presence of saponins derived from Quillaja saponaria in vitro may (also) relate to activation of the inflammasome in the tumor cell by the saponins, for example resulting in tumor cell pyroptosis.
  • second proteinaceous molecules conjugated to for example antisense BNA or dianthin or saporin exerted any anti-tumor cell activity in vitro at all or improved anti-tumor cell activity when contacted with cells in bio-based cell assays, when in the presence of the first proteinaceous molecule of the invention, comprising the saponin, and targeted to the same binding site on the same tumor cells as the cell surface molecule targeted by the second proteinaceous molecule.
  • QS-21 and also the water-soluble saponins fraction comprising QS-21 from Quillaja saponaria is already for a long time known and previously intensively applied for its immune-potentiating abilities, e.g. as an adjuvant in e.g. sub-unit vaccines.
  • QS-21 is applied in two phase III clinical trials with human patients, who were vaccinated with a sub-unit vaccine mixed with an adjuvant comprising QS-21 (Glaxo-Smith-Kline, MAGRIT trial, DERMA study), wherein the sub-unit was MAGE-A3 protein, which is specifically expressed and presented by tumor cells.
  • the anti-tumor vaccinations potentiated with QS-21, aimed for extension of disease-free survival of the cancer patients (melanoma; non-small cell lung cancer).
  • QS-21 has been tested as an adjuvant in clinical trials for developing anti-cancer vaccine treatment, for vaccines for HIV-1 infection, in development of a vaccine against hepatitis B, and for anti-malaria vaccine development using QS-21 comprising adjuvants ASO1 and ASO2 of Glaxo-Smith-Kline.
  • Previous studies revealed an immune response elicited against MAGE-A3 peptides presented at the cancer cell surface, under influence of the QS-21 saponin comprising adjuvant (AS15; GSK).
  • the saponin fraction of Quillaja saponaria potentiates the anti-tumor cell activity of e.g. a payload such as a protein toxin (dianthin), bound to the second proteinaceous molecule (e.g. the ligand EGF).
  • a payload such as a protein toxin (dianthin)
  • the second proteinaceous molecule e.g. the ligand EGF
  • a tumor-cell targeting monoclonal antibody provided with covalently coupled antisense BNA such as BNA(HSP27), and contacted with the tumor cells together with a first proteinaceous molecule of the invention with covalently coupled saponin (e.g. SO1861, QS-21), both the BNA and the saponin coupled to the respective antibody (e.g. cetuximab) of the first and second proteinaceous molecule via a cleavable bond is capable of silencing HSP27 in vivo in tumors, compared to control and compared to ADC only, without presence of first proteinaceous molecule with coupled saponin.
  • Co-administering an ADC or an antibody-oligonucleotide conjugate (AOC), such as an antibody-BNA conjugate, with a first proteinaceous molecule with a saponin thus endows the ADC or AOC with anti-tumor cell activity not seen with only the ADC or only the AOC at the same dose.
  • the AOC the second proteinaceous molecule
  • the monoclonal antibody with covalently coupled saponin first proteinaceous molecule
  • increase HSP27 expression in tumor cells when administered to tumor-bearing mice separately in separate groups of mice, compared to a control group (vehicle administered, only).
  • the antisense BNA was BNA with oligo nucleic acid sequence 5′-GGCacagccagtgGCG-3′ according to Zhang et al. (2011) [Y Zhang, Z Qu, S Kim, V Shi, B Liao1, P Kraft, R Bandaru, Y Wu, L M Greenberger and I D Horak, Down - modulation of cancer targets using locked nucleic acid ( LNA )- based antisense oligonucleotides without transfection, Gene Therapy (2011) 18, 326-333].
  • BNA is designed for application as a free nucleic acid.
  • the inventors are now the first to demonstrate that the antisense BNA can be covalently coupled through a (non-)cleavable linker with a ligand or an antibody, in a way that gene-silencing activity is retained in vitro and more importantly in vivo in the tumor cells of a tumor-bearing animal.
  • This approach of providing BNA based AOCs opens new ways to administer targeted BNA to human (cancer) patients in need thereof.
  • the inventors demonstrate here that covalently coupling saponins such as saponins in the water-soluble fraction of Quillaja saponaria, QS-21, SA1641, SO1861, Table A1, Scheme I, to a first proteinaceous molecule, such as via a tri-functional linker, e.g. the tri-functional linker of Scheme II and Structure B, or via an oligomeric or polymeric structure of a scaffold comprising covalently bound saponins, results in improved cell toxicity exerted by the effector moiety such as a toxin, comprised by the second proteinaceous molecule, under influence of the covalently coupled saponin in the first proteinaceous molecule.
  • saponins such as saponins in the water-soluble fraction of Quillaja saponaria, QS-21, SA1641, SO1861, Table A1, Scheme I
  • a first proteinaceous molecule such as via a tri-functional linker, e.g. the tri-functional linker of Scheme II and Structure B, or via
  • An embodiment is the first proteinaceous molecule of the invention comprising a saponin comprising one or several or all of the indicated structural features of the saponin of Structure A in Scheme I, and/or a saponin selected from any one or more of the further saponins in Scheme I:
  • a glycoside, such as a saponin according to the invention, bound to the first proteinaceous molecule of the invention, which has the ‘ideal’ structure for the purpose of enhancing endosomal escape of an effector molecule bound to the second proteinaceous molecule of the invention is a bisdesmosidic saponin according to Structure A of Scheme I, having a molecular mass of at least 1.500 Dalton and comprising an oleanan-type triterpene containing an aldehyde group at the C-23 position and optionally a hydroxyl group at the C-16 position, with a first branched carbohydrate side chain at the C-3 position which first branched carbohydrate side chain optionally contains glucuronic acid, wherein the saponin contains an ester group with a second branched carbohydrate side chain at the C-28 position which second branched carbohydrate chain preferably comprises at least four carbohydrate units, optionally containing at least one acetyl residue such as two acety
  • SO1861 is different from the “ideal structure” displayed in Scheme I, Structure A, only in having only one acetyl residue at the quinovose and having an additional xylose.
  • the “ideal structure” of a saponin for enhancing endosomal escape of an effector molecule or effector moiety is a saponin which preferably has the Structure A of Scheme I, and saponins which display the endosomal escape enhancing activity have one or more of the structural features displayed in Structure A of Scheme I.
  • the QS-21 saponin and some of the saponins in the water soluble fraction of Quillaja saponaria differ in the carbohydrate modification at C-28 when the ideal structure of Structure A in Scheme I is considered: presence of an acyl chain in QS-21 for example.
  • saponins such as QS-7, QS1862, are similar to the ideal Structure A, and are similar to SO1861.
  • An embodiment is the therapeutic combination of the invention or the therapeutic combination for use of the invention, or the first pharmaceutical composition according to the invention or the first pharmaceutical composition for use according to the invention, wherein the aldehyde function in position C-23 of the at least one saponin is covalently coupled to linker N-E-maleimidocaproic acid hydrazide, which linker is covalently coupled via a thio-ether bond to a sulfhydryl group in the first proteinaceous molecule, such as a sulfhydryl group of a cysteine.
  • An embodiment is the therapeutic combination of the invention or the therapeutic combination for use of the invention, or the first pharmaceutical composition according to the invention or the first pharmaceutical composition for use according to the invention, wherein the at least one saponin is a bisdesmosidic triterpene saponin belonging to the type of a 12,13-dehydrooleanane with an aldehyde function in position C-23 and comprising a glucuronic acid function in a carbohydrate substituent at the C-3beta-OH group of the saponin, wherein the saponin is covalently coupled to an amino-acid residue of the first proteinaceous molecule via the glucuronic acid function in the carbohydrate substituent at the C-3beta-OH group of the saponin, preferably via at least one linker, wherein the amino-acid residue preferably is selected from cysteine and lysine.
  • the at least one saponin is a bisdesmosidic triterpene saponin belonging to the type of a 12,13-dehydr
  • An embodiment is the therapeutic combination of the invention or the therapeutic combination for use of the invention, or the first pharmaceutical composition according to the invention or the first pharmaceutical composition for use according to the invention, wherein the glucuronic acid function in the carbohydrate substituent at the C-3beta-OH group of the at least one saponin is covalently coupled to linker 1-[Bis(dimethylamino)methylene]-1H-1,2,3-triazolo[4,5-b]pyridinium 3-oxid hexafluorophosphate, which linker is covalently coupled via an amide bond to an amine group in the first proteinaceous molecule, such as an amine group of a lysine or an N-terminus of the first proteinaceous molecule.
  • the inventors established that covalent coupling, preferably via cleavable bonds or linkers, of the saponin to the first proteinaceous molecule, according to any of the embodiments here above, provides efficient and cell-targeted potentiation of the activity of an effector moiety bound to the second proteinaceous molecule, wherein the first and second proteinaceous molecules comprise the same binding site.
  • Coupling saponin to a cysteine side chain or a lysine side chain of the first proteinaceous molecule such as a monoclonal antibody, directly or via a linker proved to be a beneficial way of specific and efficient delivery of effector-moiety potentiating activity inside the target cell, when also the effector moiety is delivered in the same target cell by using the second proteinaceous molecule comprising the same binding site as the first proteinaceous molecule.
  • the uptake of extracellular substances into a cell by vesicle budding is called endocytosis.
  • Said vesicle budding can be characterized by (1) receptor-dependent ligand uptake mediated by the cytosolic protein clathrin, (2) lipid-raft uptake mediated by the cholesterol-binding protein caveolin, (3) unspecific fluid uptake (pinocytosis), or (4) unspecific particle uptake (phagocytosis). All types of endocytosis run into the following cellular processes of vesicle transport and substance sorting called the endocytic pathways.
  • organelles may be formed de novo and mature into the next organelle along the endocytic pathway. It is however, now hypothesized that the endocytic pathways involve stable compartments that are connected by vesicular traffic.
  • a compartment is a complex, multifunctional membrane organelle that is specialized for a particular set of essential functions for the cell. Vesicles are considered to be transient organelles, simpler in composition, and are defined as membrane-enclosed containers that form de novo by budding from a preexisting compartment. In contrast to compartments, vesicles can undergo maturation, which is a physiologically irreversible series of biochemical changes.
  • Early endosomes and late endosomes represent stable compartments in the endocytic pathway while primary endocytic vesicles, phagosomes, multivesicular bodies (also called endosome carrier vesicles), secretory granules, and even lysosomes represent vesicles.
  • the endocytic vesicle which arises at the plasma membrane, most prominently from clathrin-coated pits, first fuses with the early endosome, which is a major sorting compartment of approximately pH 6.5. A large part of the cargo and membranes internalized are recycled back to the plasma membrane through recycling vesicles (recycling pathway).
  • Lysosomes are vesicles that can store mature lysosomal enzymes and deliver them to a late endosomal compartment when needed.
  • the resulting organelle is called the hybrid organelle or endolysosome.
  • Lysosomes bud off the hybrid organelle in a process referred to as lysosome reformation.
  • Late endosomes, lysosomes, and hybrid organelles are extremely dynamic organelles, and distinction between them is often difficult. Degradation of an endocytosed molecule occurs inside an endolysosome or lysosome.
  • Endosomal escape is the active or passive release of a substance from the inner lumen of any kind of compartment or vesicle from the endocytic pathway, preferably from clathrin-mediated endocytosis, or recycling pathway into the cytosol. Endosomal escape thus includes but is not limited to release from endosomes, endolysosomes or lysosomes, including their intermediate and hybrid organelles.
  • endosome or “endosomal escape” is used herein, it also includes the endolysosome and lysosome, and escape from the endolysosome and lysosome, respectively. After entering the cytosol, said substance might move to other cell units such as the nucleus.
  • a glycoside is any molecule in which a sugar group is bound through its anomeric carbon to another group via a glycosidic bond.
  • Glycoside molecules such as saponins, in the context of the invention are such molecules that are further able to enhance the effect of an effector moiety, without wishing to be bound by any theory, in particular by facilitating the endosomal escape of the effector moiety.
  • the glycoside molecules (saponins, such as those listed in Table A1) interact with the membranes of compartments and vesicles of the endocytic and recycling pathway and make them leaky for said effector moieties resulting in augmented endosomal escape.
  • the scaffold is able to augment endosomal escape of the effector moiety
  • the at least one saponin (glycoside molecule) which is coupled to the polymeric or oligomeric structure of the scaffold, is able to enhance endosomal escape of an effector moiety when both molecules are within an endosome, e.g.
  • a late endosome optionally and preferably after the at least one glycoside such as a saponin is released from the first proteinaceous molecule such as from a linker or polymeric or oligomeric structure comprised by said first proteinaceous molecule, e.g., by cleavage of a cleavable bond between the at least one glycoside (saponin) and the first proteinaceous molecule (for example via a polymeric or oligomeric structure of a scaffold and/or via a linker).
  • the first proteinaceous molecule such as from a linker or polymeric or oligomeric structure comprised by said first proteinaceous molecule, e.g., by cleavage of a cleavable bond between the at least one glycoside (saponin) and the first proteinaceous molecule (for example via a polymeric or oligomeric structure of a scaffold and/or via a linker).
  • a bond between the at least one glycoside such as a saponin according to the invention and the first proteinaceous molecule, optionally via a linker or a scaffold may be a “stable bond”, that does not mean that such bond cannot be cleaved in the endosomes by, e.g., enzymes.
  • the glycoside or saponin optionally together with a linker or a part of the oligomeric or polymeric structure of a scaffold, may be cleaved off from the remaining linker fragment or oligomeric or polymeric structure.
  • a protease cuts a (proteinaceous) linker or proteinaceous polymeric structure, e.g., albumin, thereby releasing the at least one glycoside, saponin.
  • the glycoside molecule preferably saponin
  • the glycoside molecule is released in an active form, preferably in the original form that it had before it was (prepared to be) coupled to the first proteinaceous molecule optionally via a linker and/or an oligomeric or polymeric scaffold; thus the glycoside (saponin) has its natural structure after such cleavage or the glycoside (saponin) has (part of) a chemical group or linker bound thereto, after such cleavage, while glycoside biological activity (saponin biological activity), e.g.
  • endosomal/lysosomal escape enhancing activity towards an effector moiety present in the same endosome or lysosome is maintained or restored upon said cleavage of the bond between the glycoside (saponin) and the carrier molecule, i.e. the first proteinaceous molecule optionally comprising a linker and/or a scaffold of the invention.
  • saponins and amino-acid residues of the first proteinaceous molecule, a linker, a polymeric or oligomeric structures (of the scaffold), ligands, (monoclonal) immunoglobulins or binding domains or—fragments thereof, and/or effectors (effector moieties, effector molecules), is meant that the bond is not readily broken or at least not designed to be readily broken by, e.g., pH differences, salt concentrations, or UV-light, reductive conditions.
  • saponins and the first proteinaceous molecule, linkers, amino-acid residues, polymeric or oligomeric structures of the scaffold, ligands, antibodies and/or effectors is meant that the bond is designed to be readily broken by, e.g., pH differences, salt concentrations, under reductive conditions, and the like.
  • the skilled person is well aware of such cleavable bonds and how to prepare them.
  • An embodiment is the therapeutic combination of the invention or the therapeutic combination for use of the invention, or the first pharmaceutical composition according to the invention or the first pharmaceutical composition for use according to the invention, wherein the epitope is an epitope on a tumor-cell receptor, preferably a tumor-cell specific epitope, and wherein the receptor is preferably a tumor-cell specific receptor, more preferably a receptor selected from CD71, CA125, EpCAM(17-1A), CD52, CEA, CD44v6, FAP, EGF-IR, integrin, syndecan-1, vascular integrin alpha-V beta-3, HER2, EGFR, CD20, CD22, Folate receptor 1, CD146, CD56, CD19, CD138, CD27L receptor, PSMA, CanAg, integrin-alphaV, CA6, CD33, mesothelin, Cripto, CD3, CD30, CD239, CD70, CD123, CD352, DLL3, CD25, ephrinA4, MUC1, Trop2, CEACAM5, CE
  • An embodiment is the therapeutic combination of the invention or the therapeutic combination for use of the invention, or the first pharmaceutical composition according to the invention or the first pharmaceutical composition for use according to the invention, wherein the tumor-cell receptor, preferably the tumor-cell specific receptor, is internalized by the tumor cell after binding to the first proteinaceous molecule of the invention and/or after binding to the second proteinaceous molecule of the invention, and wherein preferably binding of the first proteinaceous molecule and/or the second proteinaceous molecule to the tumor-cell receptor, such as the tumor-cell specific receptor, is followed by tumor-cell receptor-mediated internalization, e.g. via endocytosis, of a complex of the first proteinaceous molecule and the tumor-cell receptor and of a complex of the second proteinaceous molecule and the tumor-cell receptor.
  • the tumor-cell receptor preferably the tumor-cell specific receptor
  • An embodiment is the therapeutic combination of the invention or the therapeutic combination for use of the invention, or the first pharmaceutical composition according to the invention or the first pharmaceutical composition for use according to the invention, wherein the binding site of the first proteinaceous molecule and the second proteinaceous molecule comprises a monoclonal antibody or at least one of a cell-surface molecule binding domain and/or -fragment thereof, and preferably comprise or consist of any one of cetuximab, daratumumab, gemtuzumab, trastuzumab, panitumumab, brentuximab, inotuzumab, moxetumomab, polatuzumab, obinutuzumab, OKT-9 anti-CD71 monoclonal antibody of the IgG type, pertuzumab, rituximab, ofatumumab, Herceptin, alemtuzumab, pinatuzumab, OKT-10 anti-CD38 monoclonal antibody, an antibody of Table
  • an effector molecule, or effector moiety, in the context of this invention is any substance that affects the metabolism of a cell by interaction with an intracellular effector molecule target, wherein this effector molecule target is any molecule or structure inside cells excluding the lumen of compartments and vesicles of the endocytic and recycling pathway but including the membranes of these compartments and vesicles.
  • Said structures inside cells thus include the nucleus, mitochondria, chloroplasts, endoplasmic reticulum, Golgi apparatus, other transport vesicles, the inner part of the plasma membrane and the cytosol.
  • Cytosolic delivery of an effector moiety in the context of the invention preferably means that the effector moiety is able to escape the endosome (and/or lysosome), which, as defined previously, also includes escaping the endolysosome and the lysosome, and is preferably able to reach the effector moiety target as described herein.
  • the invention also encompasses a new type of molecule, referred to as scaffold that serves to bring both an effector moiety and at least one glycoside molecule such as a saponin of the invention in an endosome at the same time in a pre-defined ratio, when the effector moiety is comprised by the second proteinaceous molecule of the invention and the saponin is comprised by the first proteinaceous molecule.
  • the polymeric or oligomeric structure of the scaffold is a structurally ordered formation such as a polymer, oligomer, dendrimer, dendronized polymer, or dendronized oligomer or it is an assembled polymeric structure such as a hydrogel, microgel, nanogel, stabilized polymeric micelle or liposome, but excludes structures that are composed of non-covalent assemblies of monomers such as cholesterol/phospholipid mixtures.
  • polymer, oligomer, dendrimer, dendronized polymer, or dendronized oligomer have their ordinary meaning.
  • a polymer is a substance which has a molecular structure built up chiefly or completely from a large number of equal or similar units bonded together and an oligomer is a polymer whose molecules consist of relatively few repeating units.
  • an oligomer is a polymer whose molecules consist of relatively few repeating units.
  • the scaffold may comprise a polymeric or an oligomeric structure, or both, the full range of numbers of similar units bonded together applies to such structure. i.e. from 2 monomeric units to 100 monomeric units, 1000 monomeric units, and more.
  • a structure of 10 monomeric units maybe called either oligomeric or polymeric.
  • a scaffold as defined herein, further comprises at least one glycoside molecule such as a saponin of the invention.
  • a scaffold preferably includes a polymeric or oligomeric structure such as poly- or oligo(amines), e.g., polyethylenimine and poly(amidoamine), and biocompatible structures such as polyethylene glycol, poly- or oligo(esters), such as poly(lactids), poly(lactams), polylactide-co-glycolide copolymers, and poly(dextrin), poly- or oligosaccharides, such as cyclodextrin or polydextrose, and poly- or oligoamino acids, such as poly-lysine or a peptide or a protein, or DNA oligo- or polymers.
  • polymeric or oligomeric structure such as poly- or oligo(amines), e.g., polyethylenimine and poly(amidoamine), and biocompatible structures such as polyethylene glycol, poly- or oligo(esters), such as poly(lactids), poly(lactams
  • An assembled polymeric structure as defined herein comprises at least one scaffold and, optionally, other individual polymeric or oligomeric structures.
  • Other individual polymeric or oligomeric structures of said assembly may be (a) scaffolds (thus comprising at least one glycoside molecule such as a saponin of the invention), (b) functionalized scaffolds (thus comprising at least one glycoside molecule such as a saponin, and a ligand, antibody, etc. as the first proteinaceous molecule, (c) polymeric or oligomeric structures without a glycoside molecule such as a saponin of the invention (See Table A1 for example), without a ligand, antibody, etc., as the first proteinaceous molecule.
  • a functionalized assembled polymeric structure is an assembled polymeric structure that contains (a) at least one functionalized scaffold or (b) at least one scaffold and at least one polymeric structure comprising at least one ligand, antibody, etc. as the first proteinaceous molecule.
  • Polymeric or oligomeric structures within an assembled polymeric structure that do not comprise any of the above mentioned molecules i.e. no glycosides such as saponins, no first proteinaceous molecule such as ligands, antibodies
  • the acidic environment seems to be a prerequisite for the synergistic action between glycoside (saponin) and effector moiety.
  • a first proteinaceous molecule comprising saponins is able to disturb the acidic environment and inhibit the endosomal escape function of the at least one glycoside (saponin) can be easily determined with an assay as described in Example 3 and as known in the art.
  • the inhibition is described as “fold amount increases of glycoside necessary to induced 50% cell killing”. It is preferred that the scaffold does not lead to an increase that is at least the increase in glycoside molecules (saponins) necessary to obtain 50% cell killing observed when using Chloroquine as a positive control.
  • the first proteinaceous molecule comprising saponins, either or not further comprising one or more (cleavable) linkers and/or optionally a scaffold does not lead to an at least 4-fold increase of glycoside molecules to induce 50% cell killing, more preferably does not lead to an at least 2-fold increase.
  • the fold increase is to be measured in assay, essentially as described in Example 4, wherein Chloroquine, as a positive control, induces a 2-fold increase in glycoside amount, preferably saponin amount wherein the saponin is any one or more of the saponins of the invention (see Table A1, Scheme I, previous embodiments) to observe 50% cell killing.
  • the glycoside molecule preferably a saponin of the invention, increases the functional efficacy of that effector moiety (e.g. the therapeutic index of a toxin or a drug or an oligonucleotide such as a BNA; the metabolic efficacy of a modifier in biotechnological processes; the transfection efficacy of genes in cell culture research experiments), preferably by enabling or improving its target engagement. Acceleration, prolongation, or enhancement of antigen-specific immune responses are preferably not included. Therapeutic efficacy includes but is not limited to a stronger therapeutic effect, preferably with lower dosing and/or with less side effects.
  • “Improving an effect of an effector moiety” can also mean that an effector moiety, which could not be used because of lack of effect (and was e.g. not known as being an effector moiety), becomes effective when used in combination with the present invention. Any other effect, which is beneficial or desired and can be attributed to the combination of effector moiety and the second proteinaceous molecule, as provided by the invention is considered to be “an improved effect”.
  • the scaffold comprising bound saponin(s) and comprised by the first proteinaceous molecule enhances an effect of the effector moiety comprised by the second proteinaceous molecule which effect is intended and/or desired.
  • the proteinaceous polymeric structure of the scaffold as such may have, for instance, an effect on colloid osmotic pressure in the blood stream. If such effect is not the intended or desired effect of such a functionalized scaffold comprised by the first proteinaceous molecule, the proteinaceous structure of the scaffold is not an effector moiety as defined in the invention. Or, for instance in case of a DNA- or RNA-based scaffold carrying bound saponins and comprised by the first proteinaceous molecule, parts of that DNA or RNA may have an (unintended) function, e.g., by interfering with expression. If such interference is not the intended or desired effect of the ultimate functionalized scaffold, the DNA- or RNA polymeric structure of the scaffold is not the effector moiety as defined in the invention.
  • a number of preferred features can be formulated for endosomal escape enhancers comprised by the first proteinaceous molecule, i.e. a glycoside, preferably a saponin according to the invention: (1) they are preferably not toxic and do not invoke an immune response, (2) they preferably do not mediate the cytosolic uptake of the effector moiety into off-target cells, (3) their presence at the site of action is preferably synchronized with the presence of the effector moiety, (4) they are preferably biodegradable or excretable, and (5) they preferably do not substantially interfere with biological processes of the organism unrelated to the biological activity of the effector molecule with which the endosomal escape enhancer is combined with, e.g. interact with hormones.
  • glycoside molecules such as saponins of the invention that fulfill the before mentioned criteria, at least to some extent, are bisdesmosidic triterpenes, preferably bisdesmosidic triterpene saponins, such as SO1861, SA1641, QS-21, GE1741, and the saponins in Table A1, Scheme I.
  • An embodiment is the first proteinaceous molecule according to the invention, wherein the at least one saponin is covalently bound to the first proteinaceous molecule via a linker and/or via a polymeric or oligomeric structure, via a non-cleavable bond or via a cleavable bond, wherein preferably said cleavable bond is subject to cleavage under acidic conditions, reductive conditions, enzymatic conditions or light-induced conditions, more preferably the cleavable bond is a hydrazone bond or a hydrazide bond subject to cleavage under acidic conditions, and/or is a bond susceptible to proteolysis, for example proteolysis by Cathepsin B, and/or is a bond susceptible for cleavage under reductive conditions such as a disulphide bond.
  • the saponin is a saponin listed in Table A1, Scheme I. It has been proven beneficial for the activity of the saponin, e.g. the endosomal escape enhancing activity inside cells when the entry into the cell and the accumulation inside the cytosol of an effector moiety covalently coupled to the second proteinaceous molecule, is considered, when the saponin is covalently coupled to the first proteinaceous molecule involving a hydrazone bond, and/or a hydrazide bond, and/or a disulphide bond.
  • Such bond types readily cleave under the acidic conditions inside (late) endosomes and lysosomes of mammalian cells, e.g.
  • the inventors demonstrate that covalent coupling of saponin to the first proteinaceous molecule via a bond that is not readily cleavable under the physiological conditions inside cells, e.g. (late) endosomes, lysosomes, cytosol, is also beneficial to the potentiating activity of the saponin on the biological effect of e.g. an effector moiety such as a nucleic acid (e.g. BNA silencing HSP27) and a proteinaceous toxin such as saporin.
  • an effector moiety such as a nucleic acid (e.g. BNA silencing HSP27) and a proteinaceous toxin such as saporin.
  • cleavable linker is also referred to as ‘labile linker’ (‘L’) and ‘labile bond’, for example in the context of cleavage of such a bond or linker in the (late) endosome and/or lysosome when a conjugate of the invention, e.g. a first proteinaceous molecule optionally comprising a scaffold with saponins coupled to the first proteinaceous molecule through a linker and/or via the scaffold via hydrazone bonds or disulphide bonds, is referred to.
  • a conjugate of the invention e.g. a first proteinaceous molecule optionally comprising a scaffold with saponins coupled to the first proteinaceous molecule through a linker and/or via the scaffold via hydrazone bonds or disulphide bonds
  • FIG. 1 shows the in vivo HSP27 gene silencing in human tumors in mice.
  • the tumor-bearing mice were treated with a first proteinaceous molecule consisting of monoclonal antibody with saponin bound thereto via a labile linker (hydrazone bond) according to the invention, whereas the second proteinaceous molecule comprised bound antisense BNA for silencing the HSP27 gene in the tumor cells, covalently coupled to the monoclonal antibody (same type as the first monoclonal antibody) via a a disulphide bond.
  • a first proteinaceous molecule consisting of monoclonal antibody with saponin bound thereto via a labile linker (hydrazone bond) according to the invention
  • the second proteinaceous molecule comprised bound antisense BNA for silencing the HSP27 gene in the tumor cells, covalently coupled to the monoclonal antibody (same type as the first monoclonal antibody) via a a disulphide bond.
  • the hydrazone bond and the disulphide bond are cleaved in the (late) endosomes and/or lysosomes of the targeted tumor cells that express the epitope on the targeted cell-surface molecule, here the EGFR, at the cell surface, once the therapeutic combination of the invention is internalized by e.g. endocytosis.
  • Cleavage of the bonds likely contributes to the endosomal escape enhancing activity of the saponin when the entry of the BNA from the endosome and/or lysosome into the cytosol is considered, although such cleavage is not a necessity for observing the gene silencing effect of the combination of the cetuximab-SO1861 conjugate and the cetuximab-BNA conjugate of the invention.
  • a tri-functional linker is a scaffold of the invention suitable for covalently coupling one, two or three saponin moieties.
  • covalent coupling of one or two saponin moieties is preferred.
  • the second and/or third binding site is for example suitable for covalent coupling a proteinaceous ligand such as the first proteinaceous molecule.
  • Typical proteinaceous ligands are EGF for targeting (tumor) cells expressing EGFR at the cell surface, and cytokines for targeting tumor cells or autoimmune cells.
  • the second or third binding site of the tri-functional linker is suitable for covalent coupling of an immunoglobulin such as a monoclonal antibody, i.e.
  • the first proteinaceous molecule for binding to a cell surface molecule such as a tumor cell surface molecule, preferably a tumor-cell specific molecule, more preferably a tumor cell receptor that is specifically (over-)expressed at the surface of the tumor cell.
  • a cell surface molecule such as a tumor cell surface molecule, preferably a tumor-cell specific molecule, more preferably a tumor cell receptor that is specifically (over-)expressed at the surface of the tumor cell.
  • the immunoglobulin, or any fragment(s) and/or domain(s) thereof which encompass the binding specificity of the immunoglobulin is suitable for binding to a cell surface molecule such as a receptor, expressed at the surface of an autoimmune cell.
  • the first proteinaceous molecule comprises the tri-functional linker, said linker comprises or consists of a covalently bound saponin, e.g.
  • QS-21, SO1861, and the covalently bound binding site such as a cell targeting moiety such as a ligand or an antibody for (specific) binding to a tumor cell, an auto-immune cell, a diseased cell, an aberrant cell, a non-healthy cell, a B-cell disease.
  • a cell targeting moiety such as a ligand or an antibody for (specific) binding to a tumor cell, an auto-immune cell, a diseased cell, an aberrant cell, a non-healthy cell, a B-cell disease.
  • An embodiment is the first proteinaceous molecule of the invention, comprising the oligomeric tri-functional linker as the scaffold core structure, according to Scheme II:
  • cysteines such as 1, 2, 3 or 4 cysteines such that 1-4 scaffolds are covalently bound to a single e.g. antibody such as a monoclonal antibody.
  • An embodiment is the first proteinaceous molecule of the invention wherein the glycoside molecule is a saponin and the linkage between saponin and the first proteinaceous molecule preferably occurs via an acid-labile bond that is stable at pH 7.4 and, preferably releases the saponin below pH 6.5, more preferably between pH 6.5 and 5.0.
  • This is, e.g., realized via an imine formed by an amino group of a linker linking the saponin and the first proteinaceous molecule and the aldehyde group of the saponin.
  • Other chemical bonds that fulfill the pH-condition can also be used for aldehyde coupling, e.g.
  • a saponin is preferably attached to the polymeric or oligomeric structure of a scaffold via an aldehyde function or via one of the carboxyl groups in saponin, more preferably through the aldehyde function, preferably an aldehyde function in position 23.
  • a saponin is preferably attached to the first proteinaceous molecule via the polymeric or oligomeric structure of the scaffold via a linker that connects the polymeric or oligomeric structure of the scaffold either via the aldehyde function or via the carboxylic acid function of the glycoside molecule, i.e. the saponin.
  • an embodiment is the first proteinaceous molecule of the invention, wherein the at least one saponin is bound to the first proteinaceous molecule via a stable bond.
  • the stable bond between saponin first proteinaceous molecule preferably occurs via an amide coupling or amine formation. This is, e.g., realized via carbodiimide mediated amide bond formation by an amino group of a polymeric or oligomeric scaffold structure linking the saponin and the first proteinaceous molecule together, and the activated glucuronic acid group of the saponin.
  • Chemical bonds that fulfill the stable bond definition can also be used for aldehyde coupling, e.g.
  • the bond is a stable bond
  • the saponin is preferably attached to a linker or a scaffold via one of the carboxyl groups of the saponin, the linker or scaffold further linked to the first proteinaceous molecule.
  • An embodiment is the first proteinaceous molecule of the invention wherein the saponin is coupled to the binding site via a scaffold according to the invention, wherein the chemical group for covalently coupling of the scaffold to the binding site is a click chemistry group.
  • An embodiment is the first proteinaceous molecule of the invention wherein the saponin is coupled to the binding site via a scaffold according to the invention, wherein the click chemistry group is a tetrazine, an azide, an alkene or an alkyne, or a cyclic derivative of any of these groups, preferably an azide.
  • a click chemistry group is a functional chemical group suitable for click chemistry, which is defined as a reaction that is modular, wide in scope, gives very high yields, generates only inoffensive byproducts, offers high selectivity, and high tolerance over different functional groups, and is stereospecific.
  • the required process characteristics include simple reaction conditions, readily available starting materials and reagents, the use of no solvent or a solvent that is benign (such as water) or easily removed, and simple product isolation.
  • the click chemistry group for coupling the saponin to the binding site in the first proteinaceous molecule optionally via a scaffold or a linker is preferably a tetrazine, azide, alkene, or alkyne, or reactive derivates of them such as methyl-tetrazine or maleimide (alkene), more preferably an alkyne, or a cyclic derivative of these groups, such as cyclooctyne (e.g. aza-dibenzocyclooctyne, difluorocyclooctyne, bicyclo[6.1.0]non-4-yne, dibenzocyclooctyne).
  • cyclooctyne e.g. aza-dibenzocyclooct
  • a first proteinaceous molecule according to the invention thus comprises at least one saponin.
  • the first proteinaceous molecule comprises one saponin molecule but may also comprise a couple (e.g. two, three or four) of saponins or a multitude (e.g. 10, 20 or 100) of saponins.
  • the first proteinaceous molecule may comprise a covalently bound scaffold with covalently bound saponins, wherein the scaffold may be designed such that it comprises a defined number of saponins.
  • a first proteinaceous molecule according to the invention comprises a defined number or range of saponins, rather than a random number. This is especially advantageous for drug development in relation to marketing authorization.
  • a defined number in this respect means that a first proteinaceous molecule preferably comprises a previously defined number of saponins. This is, e.g., achieved by designing a scaffold comprising a polymeric structure with a certain number of possible moieties for the saponin(s) to attach. Under ideal circumstances, all of these moieties are coupled to a saponin and the scaffold than comprises the prior defined number of saponins. It is envisaged to offer a standard set of scaffolds, comprising, e.g., two, four, eight, sixteen, thirty-two, sixty-four, etc., saponins so that the optimal number can be easily tested by the user according to his needs.
  • An embodiment is the first proteinaceous molecule of the invention comprising the scaffold of the invention, wherein the saponin is present in a defined range as, e.g., under non-ideal circumstances, not all moieties present in a polymeric structure bind a saponin.
  • a defined range may for instance be 2-4 saponin molecules per scaffold, 3-6 saponin molecules per scaffold, 4-8 saponin molecules per scaffold, 6-8 saponin molecules per scaffold, 6-12 saponin molecules per scaffold and so on.
  • a first proteinaceous molecule comprising a scaffold according to the invention thus comprises 2, 3 or 4 saponins if the range is defined as 2-4.
  • the scaffold is fundamentally independent of the type of saponin covalently bound to the scaffold, the scaffold subsequently (in sequential order) covalently coupled to the first proteinaceous molecule.
  • first proteinaceous molecule comprising the scaffold is the basis product for a new platform technology. Since the at least one covalently bound saponin mediates intracellular delivery of the effector moiety bound to the second proteinaceous molecule, the scaffold technology according to the invention is the first system known that mediates controlled intracellular effector moiety delivery by saponins.
  • the scaffold provides an optimized and functionally active unit that can be linked to the saponin(s) and to the binding site comprised by the first proteinaceous molecule, e.g. a ligand, an antibody, etc., at a single and defined position.
  • an embodiment is the first proteinaceous molecule comprising a scaffold according to the invention, wherein the number of monomers of the polymeric or oligomeric structure is an exactly defined number or range.
  • the polymeric or oligomeric structure comprises structures such as poly(amines), e.g., polyethylenimine and poly(amidoamine), or structures such as polyethylene glycol, poly(esters), such as poly(lactides), poly(lactams), polylactide-co-glycolide copolymers, poly(dextrin), or a peptide or a protein, or structures such as natural and/or artificial polyamino acids, e.g.
  • poly-lysine DNA polymers, stabilized RNA polymers or PNA (peptide nucleic acid) polymers, either appearing as linear, branched or cyclic polymer, oligomer, dendrimer, dendron, dendronized polymer, dendronized oligomer or assemblies of these structures, either sheer or mixed.
  • the polymeric or oligomeric structures are biocompatible, wherein biocompatible means that the polymeric or oligomeric structure does not show substantial acute or chronic toxicity in organisms and can be either excreted as it is or fully degraded to excretable and/or physiological compounds by the body's metabolism. Assemblies can be built up by covalent cross-linking or non-covalent bonds and/or attraction.
  • nanogels can therefore also form nanogels, microgels, or hydrogels, or they can be attached to carriers such as inorganic nanoparticles, colloids, liposomes, micelles or particle-like structures comprising cholesterol and/or phospholipids.
  • Said polymeric or oligomeric structures preferably bear an exactly defined number or range of coupling moieties for the coupling of glycoside molecules (and/or effector molecules and/or carrier molecules such as a ligand, monoclonal antibody or a fragment thereof).
  • a dendron is a branched, clearly defined tree-like polymer with a single chemically addressable group at the origin of the tree, called the focal point.
  • a dendrimer is a connection of two or more dendrons at their focal point.
  • a dendronized polymer is a connection of the focal point of one or more dendrons to a polymer.
  • a scaffold according to the invention wherein the polymeric or oligomeric structure comprises a linear, branched or cyclic polymer, oligomer, dendrimer, dendron, dendronized polymer, dendronized oligomer or assemblies of these structures, either sheer or mixed, wherein assemblies can be built up by covalent cross-linking or non-covalent attraction and can form nanogels, microgels, or hydrogels, and wherein, preferably, the polymer is a derivative of a poly(amine), e.g., polyethylenimine and poly(amidoamine), and structures such as polyethylene glycol, poly(esters), such as poly(lactids), poly(lactams), polylactide-co-glycolide copolymers, and poly(dextrin), and structures such as natural and/or artificial polyamino acids such as poly-lysine, or a peptide or a protein or DNA polymers, stabilized RNA polymers or
  • An embodiment is the therapeutic combination of the invention or the therapeutic combination for use according to the invention, wherein the first proteinaceous molecule comprises more than one covalently bound saponin, preferably 2, 3, 4, 5, 6, 8, 10, 16, 32, 64, 128 or 1-100 saponins, or any number of saponins therein between, such as 7, 9, 12 saponins.
  • an embodiment is the therapeutic combination of the invention or the therapeutic combination for use according to the invention, wherein the second proteinaceous molecule comprises the effector moiety, wherein said effector moiety is a pharmaceutically active substance, such as a toxin, a drug, a polypeptide and/or a polynucleotide.
  • an embodiment is the second proteinaceous molecule of the invention wherein the effector moiety is a toxin, a micro RNA, or a polynucleotide encoding a protein.
  • the first and second proteinaceous molecule comprises the binding site for targeting the saponin or the effector moiety respectively, to e.g. a tumor cell or an auto-immune cell or a cell related to a B-cell disease.
  • the binding site of the first and second proteinaceous molecule comprises an immunoglobulin or at least one or more binding domains and/or binding fragments thereof, such immunoglobulin preferably selected from any of the monoclonal antibodies of any of Tables A2-A4, such as cetuximab, OKT-9, trastuzumab.
  • a pharmaceutically active substance in this invention is an effector moiety that is used to achieve a beneficial outcome in an organism, preferably a vertebrate, more preferably a human being such as a cancer patient or an auto-immune patient.
  • Benefit includes diagnosis, prognosis, treatment, cure and/or prevention of diseases and/or symptoms.
  • the pharmaceutically active substance may also lead to undesired harmful side effects.
  • pros and cons must be weighed to decide whether the pharmaceutically active substance is suitable in the particular case. If the effect of the pharmaceutically active substance inside a cell is predominantly beneficial for the whole organism, the cell is called a target cell. If the effect inside a cell is predominantly harmful for the whole organism, the cell is called an off-target cell. In artificial systems such as cell cultures and bioreactors, target cells and off-target cells depend on the purpose and are defined by the user.
  • An effector moiety that is a polypeptide may be, e.g., a polypeptide that recover a lost function, such as for instance enzyme replacement, gene regulating functions, or a toxin.
  • an embodiment is the therapeutic combination of the invention or the therapeutic combination for use of the invention, wherein the effector moiety comprised by the second proteinaceous molecule comprises or consists of any one or more of an oligonucleotide, a nucleic acid and a xeno nucleic acid, preferably selected from any one or more of a vector, a gene, a cell suicide inducing transgene, deoxyribonucleic acid (DNA), ribonucleic acid (RNA), anti-sense oligonucleotide (ASO, AON), short interfering RNA (siRNA), microRNA (miRNA), DNA aptamer, RNA aptamer, mRNA, mini-circle DNA, peptide nucleic acid (PNA), phosphoramidate morpholino oligomer (PMO), locked nucleic acid (LNA), bridged nucleic acid (BNA), 2′-deoxy-2′-fluoroarabino nucleic acid (FANA), 2′-
  • an embodiment is the therapeutic combination of the invention or the therapeutic combination for use of the invention, wherein the effector moiety comprised by the second proteinaceous molecule comprises or consists of at least one proteinaceous molecule, preferably selected from any one or more of a peptide, a protein, an enzyme such as urease and Cre-recombinase, a proteinaceous toxin, a ribosome-inactivating protein, a protein toxin selected from Table A5 and/or a bacterial toxin, a plant toxin, more preferably selected from any one or more of a viral toxin such as apoptin; a bacterial toxin such as Shiga toxin, Shiga-like toxin, Pseudomonas aeruginosa exotoxin (PE) or exotoxin A of PE, full-length or truncated diphtheria toxin (DT), cholera toxin; a fungal toxin such as alpha
  • dianthin-30 or dianthin-32 saporin e.g. saporin-S3 or saporin-S6, bouganin or de-immunized derivative debouganin of bouganin, shiga-like toxin A, pokeweed antiviral protein, ricin, ricin A chain, modeccin, modeccin A chain, abrin, abrin A chain, volkensin, volkensin A chain, viscumin, viscumin A chain; or an animal or human toxin such as frog RNase, or granzyme B or angiogenin from humans, or any fragment or derivative thereof; preferably the protein toxin is dianthin and/or saporin.
  • saporin e.g. saporin-S3 or saporin-S6, bouganin or de-immunized derivative debouganin of bouganin, shiga-like toxin A, pokeweed antiviral protein, ricin, ricin A chain, modeccin, modeccin A
  • an embodiment is the therapeutic combination of the invention or the therapeutic combination for use of the invention, wherein the effector moiety comprised by the second proteinaceous molecule comprises or consists of at least one payload, preferably selected from any one or more of a toxin targeting ribosomes, a toxin targeting elongation factors, a toxin targeting tubulin, a toxin targeting DNA and a toxin targeting RNA, more preferably any one or more of emtansine, pasudotox, maytansinoid derivative DM1, maytansinoid derivative DM4, monomethyl auristatin E (MMAE, vedotin), monomethyl auristatin F (MMAF, mafodotin), a Calicheamicin, N-Acetyl- ⁇ -calicheamicin, a pyrrolobenzodiazepine (PBD) dimer, a benzodiazepine, a CC-1065 analogue, a duocarmycin
  • An embodiment is the therapeutic combination of the invention or the therapeutic combination for use of the invention, wherein the second proteinaceous molecule comprises or consists of any one of Gemtuzumab ozogamicin, Brentuximab vedotin, Trastuzumab emtansine, Inotuzumab ozogamicin, Moxetumomab pasudotox and Polatuzumab vedotin and an antibody-drug conjugate of Table A2 and Table A3, or at least one tumor-cell receptor binding-domain thereof and/or at least one tumor-cell receptor binding-fragment thereof, wherein said domain(s) or fragment(s) comprise(s) the effector moiety and are preferably (a) tumor-cell specific receptor binding-domain(s) and/or (a) tumor-cell specific receptor binding-fragment(s).
  • Synchronization is the missing link between a very successful delivery strategy for mice and its application in humans. Indeed, the inventors established in a series of in vivo mouse tumor models that separately administering to the mice a dose of free saponin and a dose of ADC (second proteinaceous molecule according to the invention) did not result in any desired anti-tumor activity such as delayed tumor growth, tumor regression, diminished and slower tumor growth, compared to control animals not treated with the ADC and free saponin.
  • the free saponin was administered using various routes of administration and using various time points of administering the free saponin compared to the moment of administering the ADC (administering free saponin before, during and after administering the ADC).
  • the ADC tested in in vivo tumor models was cetuximab-dianthin (with free SO1861), or trastuzumab-saporin (with free SO1861). Varying the dose of free saponin did not provide for an efficacious anti-tumor activity.
  • the ADCs referred to were administered at a dose that in itself did not inflict any beneficial anti-tumor effect on the tumor-bearing animals.
  • beneficial anti-tumor activity in various in vitro mammalian cell-based bioassays and/or in various in vivo animal tumor models can be achieved by treating the animals with conjugates according to the invention, comprising a scaffold according to the invention.
  • the scaffold for example being a tri-functional linker with a covalently bound saponin (e.g. SO1861, QS-21) via a cleavable or non-cleavable linkage, and with a covalently bound effector moiety (e.g.
  • a covalently bound saponin e.g. SO1861, QS-21
  • a covalently bound effector moiety e.g.
  • a dendron such as a dendron to which for example four moieties can bind such as four saponin molecules, or a dendron for binding for example two saponins and two effector molecules, the dendron comprising a chemical group for (covalent) coupling to a ligand or an antibody or fragment or domain thereof.
  • the invention preferably solves at least the following problem with respect to combining the effector moiety comprised by the second proteinaceous molecule and the saponins comprised by the first proteinaceous molecule: without wishing to be bound by any theory the only reasonable chemical group within, e.g., the saponins that can be used for (covalent), in particular single and cleavable, retainable coupling is required for the endosomal escape activity.
  • saponins previously applied for their immune-potentiating activity in the vaccination context involving saponins as adjuvant component are now also suitably for (covalent) coupling to the first proteinaceous molecule of the invention, for anti-tumor activity in vitro and in vivo.
  • An effector molecule useful in the present invention preferably relies on late endosomal escape for exerting its effect.
  • Some effectors such as, e.g., a pseudomonas exotoxin, are rerouted to other organelles prior to the “late endosomal stage” and, thus, would normally not benefit from coupling to the second proteinaceous molecule according to the present invention.
  • toxin may be adapted for use with the present invention, e.g., by deleting the signal peptide responsible rerouting.
  • toxins that are highly toxic and would require only one molecule to escape the endosomes to kill a cell maybe modified to be less potent.
  • a second proteinaceous molecule of the invention comprises a covalently conjugated functionalized scaffold, i.e. a scaffold comprising covalently bound effector moietie(s) for targeting the scaffold comprising the bound effector moietie(s) at a target cell such as a tumor cell or an auto-immune cell.
  • a target cell such as a tumor cell or an auto-immune cell.
  • cell membrane non-permeable small molecule toxins are preferred effector molecules over cell membrane permeable toxins.
  • ligand as used in this invention has its ordinary meaning and preferably means a molecule or structure that is able to bind another molecule or structure on the cell surface of a target cell, wherein said molecule or structure on the cell surface can be endocytosed and is preferably absent or less prominent on off-target cells.
  • said molecule or structure on the cell surface is constitutively endocytosed.
  • a ligand in this invention induces endocytosis of said molecule or structure on the cell surface of target cells after binding to said molecule or structure. This is for instance the case for Epidermal Growth Factor Receptor (EGFR), present on the surface of a variety of cancer cells.
  • EGFR Epidermal Growth Factor Receptor
  • Examples of molecules or structures on the cell surface of target cells that are constitutively endocytosed are for instance Claudin-1 or major histocompatibility complex class II glycoproteins.
  • a ligand can, e.g., be an antibody, a growth factor or a cytokine. Combining in a carrier molecule a toxin with a ligand is one possibility to create a targeted toxin.
  • a toxin that is only toxic in a target cell because it interferes with processes that occur in target cells only can also be seen as a targeted toxin (as in off-target cells it cannot exert its toxic action, e.g. apoptin).
  • a targeted toxin is a toxin that is combined with a ligand or e.g. a monoclonal antibody in order to be active in target cells and not in off-target cells (as it is only bound to and endocytosed by target cells).
  • a functionalized scaffold comprising a carrier molecule comprising a ligand and an effector molecule
  • the ligand or the monoclonal antibody guides the effector molecule and scaffold to the target cells.
  • the at least one glycoside, preferably a saponin mediates the endosomal escape of the effector molecule.
  • the saponin is typically a saponin listed in Table A1 and Scheme I, and preferably the saponin is SO1861 and/or QS-21, and/or SA1641 and/or GE1741.
  • the effector moiety bound to the second proteinaceous molecule which effect is enhanced by the saponins bound to the first proteinaceous molecule, detaches from the second proteinaceous molecule, e.g. an antibody, when endocytosed.
  • This can be achieved by a cleavable bond that breaks, e.g. under acidic, reductive, enzymatic or light-induced conditions.
  • An embodiment is the therapeutic combination of the invention or is the therapeutic combination for use of the invention, wherein the first proteinaceous molecule comprises more than one covalently bound saponin, preferably 2, 3, 4, 5, 6, 8, 10, 16, 32, 64, 128 or 1-100 saponins, or any number of saponins therein between, such as 7, 9, 12 saponins.
  • An embodiment is the therapeutic combination of the invention or the therapeutic combination for use of the invention, wherein the at least one saponin is covalently bound directly to an amino-acid residue of the first proteinaceous molecule, preferably to a cysteine and/or to a lysine, and/or is covalently bound via at least one linker and/or via at least one cleavable linker and/or via at least one oligomeric or polymeric scaffold, preferably 1-8 of such scaffolds or 2-4 of such scaffolds, wherein the at least one scaffold is optionally based on a dendron, wherein 1-32 saponins, such as 2, 3, 4, 5, 6, 8, 10, 16, 32 saponins, or any number of saponins therein between, such as 7, 9, 12 saponins, are covalently bound to the at least one scaffold.
  • An embodiment is the therapeutic combination of the invention or the therapeutic combination for use of the invention, wherein the cleavable linker is subject to cleavage under acidic conditions, reductive conditions, enzymatic conditions or light-induced conditions, and preferably the cleavable linker comprises a cleavable bond selected from a hydrazone bond and a hydrazide bond subject to cleavage under acidic conditions, and/or a bond susceptible to proteolysis, for example proteolysis by Cathepsin B, and/or a bond susceptible for cleavage under reductive conditions such as a disulphide bond.
  • the cleavable linker comprises a cleavable bond selected from a hydrazone bond and a hydrazide bond subject to cleavage under acidic conditions, and/or a bond susceptible to proteolysis, for example proteolysis by Cathepsin B, and/or a bond susceptible for cleavage under reductive conditions such as a disulphide
  • An embodiment is the therapeutic combination of the invention or the therapeutic combination for use of the invention, wherein the cleavable linker is subject to cleavage in vivo under acidic conditions as present in endosomes and/or lysosomes of mammalian cells, preferably human cells, preferably at pH 4.0-6.5, and more preferably at pH 5.5.
  • An embodiment is the therapeutic combination of the invention or the therapeutic combination for use of the invention, wherein the oligomeric or polymeric scaffold comprises a polymeric or oligomeric structure and comprises at least one chemical group, the at least one chemical group for covalently coupling of the scaffold to the amino-acid residue of said first proteinaceous molecule.
  • An embodiment is the therapeutic combination of the invention or the therapeutic combination for use of the invention, wherein the at least one saponin is covalently bound to the polymeric or oligomeric structure of the scaffold via a cleavable linker according to the invention.
  • An embodiment is the therapeutic combination of the invention or the therapeutic combination for use of the invention, wherein the at least one saponin is covalently bound to the polymeric or oligomeric structure of the scaffold via any one or more of an imine bond, a hydrazone bond, a hydrazide bond, an oxime bond, a 1,3-dioxolane bond, a disulphide bond, a thio-ether bond, an amide bond, a peptide bond or an ester bond, preferably via at least one linker.
  • An embodiment is the therapeutic combination of the invention or the therapeutic combination for use of the invention, wherein the at least one saponin comprises an aldehyde function in position C-23 and optionally a glucuronic acid function in the carbohydrate substituent at the C-3beta-OH group of the at least one saponin, which aldehyde function is involved in the covalent bonding to the polymeric or oligomeric structure of the scaffold, and/or, if present, the glucuronic acid function is involved in the covalent bonding to the polymeric or oligomeric structure of the scaffold, either via direct binding or via at least one linker.
  • An embodiment is the therapeutic combination of the invention or the therapeutic combination for use of the invention, wherein the aldehyde function in position C-23 of the at least one saponin is covalently coupled to linker N-E-maleimidocaproic acid hydrazide, which linker is covalently coupled via a thio-ether bond to a sulfhydryl group in the polymeric or oligomeric structure of the scaffold, such as a sulfhydryl group of a cysteine.
  • An embodiment is the therapeutic combination of the invention or the therapeutic combination for use of the invention, wherein the glucuronic acid function in the carbohydrate substituent at the C-3beta-OH group of the at least one saponin is covalently coupled to linker 1-[Bis(dimethylamino)methylene]-1H-1,2,3-triazolo[4,5-b]pyridinium 3-oxid hexafluorophosphate, which linker is covalently coupled via an amide bond to an amine group in the polymeric or oligomeric structure of the scaffold, such as an amine group of a lysine or an N-terminus of a proteinaceous molecule.
  • linker 1-[Bis(dimethylamino)methylene]-1H-1,2,3-triazolo[4,5-b]pyridinium 3-oxid hexafluorophosphate which linker is covalently coupled via an amide bond to an amine group in the polymeric or oligomeric structure of the scaffold, such as an
  • An embodiment is the therapeutic combination of the invention or the therapeutic combination for use of the invention, wherein the at least one chemical group of the scaffold, for covalently coupling of the oligomeric or polymeric scaffold to the amino-acid residue of said first proteinaceous molecule, is a click chemistry group, preferably selected from a tetrazine, an azide, an alkene or an alkyne, or a cyclic derivative of these groups, more preferably the click chemistry group is an azide.
  • An embodiment is the therapeutic combination of the invention or the therapeutic combination for use of the invention, wherein the polymeric or oligomeric structure of the scaffold comprises a linear, branched and/or cyclic polymer, oligomer, dendrimer, dendron, dendronized polymer, dendronized oligomer, a DNA, a polypeptide, poly-lysine, a poly-ethylene glycol, or an assembly of these polymeric or oligomeric structures which assembly is preferably built up by covalent cross-linking.
  • An embodiment is the therapeutic combination of the invention or the therapeutic combination for use of the invention, wherein the first pharmaceutical composition and the second pharmaceutical composition are administered to the patient in need thereof.
  • An embodiment is the first pharmaceutical composition of the invention or the first pharmaceutical composition for use of the invention, further comprising the second proteinaceous molecule of the invention.
  • An embodiment is the first pharmaceutical composition of the invention or the first pharmaceutical composition for use of the invention, further comprising the second proteinaceous molecule of the invention, for use as a medicament.
  • An embodiment is the first pharmaceutical composition of the invention or the first pharmaceutical composition for use of the invention, further comprising the second proteinaceous molecule of the invention, for use in the treatment or prophylaxis of cancer in a patient in need thereof.
  • the at least one saponin that is comprised by the first proteinaceous molecule according to the invention increases the efficacy of at least current and new effector moieties as defined in this invention. Potential side-effects will be decreased due to lowering of dosing of the effector moiety comprised by the second proteinaceous molecule, without lowering the efficacy. Therefore, the invention provides a first proteinaceous molecule according to the invention for use in medicine or for use as a medicament.
  • an aspect of the invention relates to a first proteinaceous molecule according to the invention, the first proteinaceous molecule comprising at least a saponin, for use as a medicament. Also provided is the use of a first proteinaceous molecule according to the invention for manufacturing a medicament.
  • a therapeutic combination according to the invention is especially valuable for use as a medicament, in particular for use in a method of treating cancer.
  • the invention thus provides a therapeutic combination according to the invention or a first proteinaceous molecule of the invention for use in a method of treating cancer.
  • the invention also provides a therapeutic combination according to the invention or a first proteinaceous molecule of the invention for use in a method of treating acquired or hereditary disorders, in particular monogenic deficiency disorders.
  • an aspect of the invention relates to a therapeutic combination according to the invention, wherein the second proteinaceous molecule comprises a covalently bound effector moiety, for use in a method for the treatment of a cancer or an auto-immune disease.
  • An aspect of the invention relates to the therapeutic combination according to the invention wherein the first and second proteinaceous molecule comprises an antibody as the binding site for targeting a tumor cell, for use in the treatment or prophylaxis of a cancer, wherein the therapeutic combination is administered to a human subject in need thereof.
  • An aspect of the invention relates to the treatment of a human subject who suffers from a cancer or who is at risk of developing a cancer and who is in need of said treatment, the treatment comprising the step of administering to the human subject an effective dose of the therapeutic combination of the invention, wherein the first proteinaceous molecule comprises a saponin and the second proteinaceous molecule comprises an effector moiety.
  • An aspect of the invention relates to the therapeutic combination of the invention for use as a medicament.
  • An aspect of the invention relates to the therapeutic combination of the invention for use in a method for treatment or prophylaxis of a cancer or an auto-immune disease, in a human subject in need thereof.
  • An aspect of the invention relates to the use of the therapeutic combination of the invention or a pharmaceutical composition comprising the therapeutic combination, for the manufacture of a medicament for anti-cancer therapy or anti-auto-immune disease therapy.
  • a further application in medicine is the substitution of intracellular enzymes in target cells that produce these enzymes in insufficient amount or insufficient functionality.
  • the resulting disease might be hereditary or acquired. In most cases, only symptomatic treatment is possible and for a number of rare diseases, insufficient treatment options lead to a shortened life span of concerned patients.
  • An example for such a disease is phenylketonuria, which is an inborn error of metabolism that results in decreased metabolism of the amino acid phenylalanine.
  • the disease is characterized by mutations in the gene for the hepatic enzyme phenylalanine hydroxylase. Phenylketonuria is not curable to date. The incidence is approximately 1:10,000 with the highest known incidence in Turkey with 1:2,600.
  • a second proteinaceous molecule preferably an antibody, with bound phenylalanine hydroxylase or with a bound polynucleotide that encodes phenylalanine hydroxylase can be used to target liver cells by use of a suitable specific antibody, and to substitute the defect enzyme in hepatocytes.
  • This is one example of use of the therapeutic combination of the invention comprising a first proteinaceous molecule with a saponin bound thereto ad a second proteinaceous molecule with the enzyme or the oligonucleotide bound thereto according to the invention for substitution or gene therapy.
  • a therapeutic combination according to the invention for use in a method of gene therapy or substitution therapy is provided.
  • the present invention also provides a method of treating cancer, the method comprising administering a medicament comprising a therapeutic combination according to the invention to a patient in need thereof, preferably administering an effective dose of said medicament to a patient in need thereof, preferably a human cancer patient.
  • Suitable dosage forms in part depend upon the use or the route of entry, for example transdermal or by injection. Such dosage forms should allow the compound to reach a target cell whether the target cell is present in a multicellular host. Other factors are known in the art, and include considerations such as toxicity and dosage form which retard the compound or composition from exerting its effect.
  • An embodiment is the combination of an endosomal escape enhancing conjugate according to the invention, comprising the first proteinaceous molecule comprising at least one covalently bound saponin, and a binding moiety, wherein the binding moiety comprises at least one effector moiety, the binding moiety being the second proteinaceous molecule comprising the bound effector moiety, wherein the endosomal escape enhancing conjugate and the binding moiety are, independently from one another, able to specifically bind to a target cell-specific surface molecule or structure, thereby inducing receptor-mediated endocytosis of a complex of the endosomal escape enhancing conjugate and the target cell-specific surface molecule, and of the complex of the binding moiety and the target cell-specific surface molecule, wherein the endosomal escape enhancing conjugate and the binding moiety can bind to the same target cell-specific surface molecule via their same binding site.
  • An embodiment is the combination according to the invention, wherein the endosomal escape enhancing conjugate is able to compete with the binding moiety for binding to the target cell-specific surface molecule or structure.
  • An embodiment is the combination according to the invention, wherein the endosomal escape enhancing conjugate and the binding moiety are, independently from one another, able to specifically bind to the same epitope.
  • An embodiment is the combination for use in a method for the treatment of an aberrancy such as a cancer according to the invention, wherein said endosomal escape enhancing conjugate and said binding moiety are to be administered concomitant or sequentially, preferably concomitant.
  • An aspect of the invention relates to a kit comprising a first container containing an endosomal escape enhancing conjugate according to the invention (i.e. the first proteinaceous molecule) and a second container containing a binding moiety according to the invention (i.e. the second proteinaceous molecule), the kit further comprising instructions for using the binding molecules (i.e. the therapeutic combination comprising the first and second pharmaceutical compositions).
  • Target cell-surface receptor Example monoclonal antibodies HER2 anti-HER2 monoclonal antibody such as trastuzumab and pertuzumab CD20 anti-CD20 monoclonal antibody such as rituximab, ofatumumab, tositumomab and ibritumomab CA125 anti-CA125 monoclonal antibody such as oregovomab EpCAM (17-1A) anti-EpCAM (17-1A) monoclonal antibody such as edrecolomab EGFR anti-EGFR monoclonal antibody such as cetuximab, panitumumab and nimotuzuma
  • Nigrin b SNA-V
  • Nigrin f SNA-Vf
  • tristis Yucca leaf protein YLP RIP 1 Carrière [Syn.: Yucca recurvifolia Salisb.] Basellaceae Basella rubra L. Basella RIP 2a, Basella RIP 2b, Basella RIP 3 RIP 1 Caryophyllaceae Agrostemma githago L. Agrostin 2, Agrostin 5, Agrostin 6, Agrostin RIP 1 Dianthus barbatus L. Dianthin 29 RIP 1 Dianthus caryophyllus L. Dianthin 30, Dianthin 32 RIP 1 Dianthus chinensis L. [Syn.: D.
  • moschata RIP RIP 1 Duchesne
  • PRIP 1 Cucurbita Moschatin
  • PRIP 2 moschata Duchesne ex ⁇ -moschin, ⁇ -moschin sRIP 1 candidate Lam.
  • Duchesne ex Poir. Cucurbita pepo L.
  • Pepocin RIP 1 Cucurbita pepo var. texana Texanin RIP 1 (Scheele)
  • D. S. Decker [Syn.: Cucurbita texana (Scheele) A. Gray] Gynostemma pentaphyllum Gynostemmin RIP 1 (Thunb.) Makino Lagenaria siceraria (Molina) Lagenin RIP 1 candidate Standl.
  • Trichokirin, Trichomislin TCM
  • Trichokirin S1, S-Trichokirin, Trichosanthrip sRIP 1 TKL-1 Trichosanthes kirilowii lectin-1 lectin/RIP 2 candidate TK-I, TK-II, TK-III, Trichosanthes kirilowii lectin lectin Trichosanthes kirilowii Karasurin-A, Karasurin-B, Karasurin-C RIP 1 Maximovicz var.
  • Trichomaglin RIP 1 Trichosanthes dioica Roxb.
  • TDSL lectin/RIP 2 candidate Trichosanthes sp.
  • E. characias lectin lectin Suregada multiflora Gelonin GAP 31 RIP 1 (A. Juss.) Baill. [Syn.: Gelonium multiflorum A.
  • Boerhaavia inhibitor RIP 1 candidate Bougainvillea spectabilis BAP I, Bouganin Bougainvillea RIP I RIP 1 Willd. Bougainvillea ⁇ buttiana cv. BBP-24, BBP-28 RIP 1 Enid Lancester Bougainvillea ⁇ buttiana cv. BBAP1 RIP 1 Mahara Mirabilis expansa (Ruiz & ME1, ME2 RIP 1 Pav.) Standl. Mirabilis jalapa L. MAP, MAP-2, MAP-3, MAP-4, MAP-S RIP 1 Olacaceae Malania oleifera Chun & Malanin lectin/RIP 2 S. K. Lee candidate Ximenia americana L.
  • keramanthus lectin RIP 2 candidate Adenia lanceolata Engl. Lanceolin RIP 2 Adenia racemosa W. J. de A. racemosa lectin lectin Wilde Adenia spinosa Burtt Davy A. spinosa lectin RIP 2 candidate Adenia stenodactyla Harms Stenodactylin RIP 2 Adenia venenata Forssk.
  • Phytolacca heterotepala Heterotepalin 4 Heterotepalin 5b RIP 1 H.
  • the therapeutic combination, the first pharmaceutical composition, the first proteinaceous molecule, the second pharmaceutical composition or the second proteinaceous molecule of the invention is further combined with a covalent conjugate (complex) of a binding molecule or a binding moiety and a saponin, or is further combined with a pharmaceutical compound, an antibody, etc., therewith providing a composition comprising three or more enhancers, pharmaceutically active ingredients, etc., e.g. a conjugate of the invention (e.g.
  • a first proteinaceous molecule and/or a second proteinaceous molecule combined with a binding moiety complexed with an effector molecule, further combined with a pharmaceutical, which is either or not linked to a saponin, and which is either or not coupled to a ligand such as a targeting immunoglobulin, a domain or a fragment thereof.
  • a pharmaceutical which is either or not linked to a saponin, and which is either or not coupled to a ligand such as a targeting immunoglobulin, a domain or a fragment thereof.
  • an embodiment is the therapeutic combination, the first pharmaceutical composition, the first proteinaceous molecule, the second pharmaceutical composition or the second proteinaceous molecule of the invention, wherein the second proteinaceous molecule is provided with two or more effector moieties such as a toxin or immunotoxin, wherein the two or more effector moieties are the same or different.
  • An embodiment is the endosomal escape enhancing conjugate of the invention, wherein the saponin is a bisdesmosidic triterpene saponin belonging to the type of a 12,13-dehydrooleanane with an aldehyde function, in position 23, and wherein the saponin is preferably a saponin that can be isolated from Gypsophila or Saponaria species, more preferably the saponin is the saponin SO1861 or any of its diastereomers.
  • the saponin is a bisdesmosidic triterpene saponin belonging to the type of a 12,13-dehydrooleanane with an aldehyde function, in position 23, and wherein the saponin is preferably a saponin that can be isolated from Gypsophila or Saponaria species, more preferably the saponin is the saponin SO1861 or any of its diastereomers.
  • An embodiment is the endosomal escape enhancing conjugate of the invention, wherein the binding site is at least a ligand, such as an immunoglobulin, with at least an effector moiety bound thereto.
  • the binding site is at least a ligand, such as an immunoglobulin, with at least an effector moiety bound thereto.
  • An embodiment is the endosomal escape enhancing conjugate of the invention, wherein the binding site is an immunoglobulin or at least a binding domain thereof for binding to a cell surface molecule, wherein preferably the cell surface molecule is selected from any of HER2, EGFR, CD20, CD22, Folate receptor 1, CD146, CD56, CD19, CD138, CD27L, PSMA, CanAg, integrin-alphaV, CA6, CD33, mesothelin, Cripto, CD3, CD30, CD33, CD239, CD70, CD123, CD352, DLL3, CD25, ephrinA4, MUC1, Trop2, CEACAMS, HER3, CD74, PTK7, Notch3, FGF2, C4.4A, FLT3, CD71.
  • the cell surface molecule is selected from any of HER2, EGFR, CD20, CD22, Folate receptor 1, CD146, CD56, CD19, CD138, CD27L, PSMA, CanAg, integrin-alphaV,
  • An embodiment is the endosomal escape enhancing conjugate of the invention, wherein a linker is coupled to the glycoside via a cleavable bond, and wherein the ligand is an immunoglobulin, wherein preferably said cleavable bond is subject to cleavage under acidic, reductive, enzymatic or light-induced conditions, and preferably the cleavable bond is a covalent bond, preferably an imine bond, a hydrazone bond, an oxime bond, a 1,3-dioxolane bond or an ester bond, wherein preferably the cleavable bond is a disulfide bond or a peptide bond.
  • An embodiment is the endosomal escape enhancing conjugate of the invention, wherein the saponin moiety is a terminal saponin, preferably the saponin SO1861, the linker is a chemical linker covalently linking the saponin to the binding site of the first proteinaceous molecule, and the binding site of the second and first proteinaceous molecule is an immunoglobulin such as trastuzumab or cetuximab, the linker preferably providing a cleavable bond between the terminal saponin moiety and the binding site comprised by the first proteinaceous molecule.
  • the saponin moiety is a terminal saponin, preferably the saponin SO1861
  • the linker is a chemical linker covalently linking the saponin to the binding site of the first proteinaceous molecule
  • the binding site of the second and first proteinaceous molecule is an immunoglobulin such as trastuzumab or cetuximab
  • the linker preferably providing a cleavable bond between the terminal
  • An embodiment is the combination of an endosomal escape enhancing conjugate (i.e. the first proteinaceous molecule) according to the invention and a binding moiety (i.e. the second proteinaceous molecule), wherein the binding moiety comprises at least one effector moiety, wherein the endosomal escape enhancing conjugate and the binding moiety are, independently from one another, able to specifically bind to a target cell-specific surface molecule or structure, thereby inducing receptor-mediated endocytosis of a complex of the endosomal escape enhancing conjugate and the target cell-specific surface molecule, and of the complex of the binding moiety and the target cell-specific surface molecule.
  • An embodiment is the combination according to the invention, wherein the endosomal escape enhancing conjugate and the binding moiety are able to specifically bind to the same target cell-specific surface molecule or structure.
  • An embodiment is the combination according to the invention, wherein the endosomal escape enhancing conjugate is able to compete with the binding moiety for binding to the target cell-specific surface molecule or structure.
  • An embodiment is the combination according to the invention, wherein the endosomal escape enhancing conjugate and the binding moiety are, independently from one another, able to specifically bind to the same epitope.
  • An embodiment is the combination according to the invention, wherein the endosomal escape enhancing conjugate is able to specifically bind to a first epitope, which is the same as the first epitope to which the binding moiety is able to specifically bind.
  • An embodiment is the combination according to the invention, wherein the target cell-specific surface molecule or structure is selected from HER2, EGFR, CD20, CD22, Folate receptor 1, CD146, CD56, CD19, CD138, CD27L, PSMA, CanAg, integrin-alphaV, CA6, CD33, mesothelin, Cripto, CD3, CD30, CD33, CD239, CD70, CD123, CD352, DLL3, CD25, ephrinA4, MUC1, Trop2, CEACAM5, HER3, CD74, PTK7, Notch3, FGF2, C4.4A, FLT3, CD71.
  • the target cell-specific surface molecule or structure is selected from HER2, EGFR, CD20, CD22, Folate receptor 1, CD146, CD56, CD19, CD138, CD27L, PSMA, CanAg, integrin-alphaV, CA6, CD33, mesothelin, Cripto, CD3, CD30, CD33, CD239, CD70, CD
  • glycoside molecule is a bisdesmosidic triterpene, preferably a saponin.
  • glycoside molecule is a bisdesmosidic triterpene saponin.
  • An embodiment is the combination according to the invention, wherein the saponin is a bisdesmosidic triterpene saponin belonging to the type of a 12,13-dehydrooleanane with an aldehyde function in position 23.
  • An embodiment is the combination according to the invention, wherein the saponin is a saponin that can be isolated from Gypsophila or Saponaria species.
  • An embodiment is the combination according to the invention, wherein the saponin is a SO1861 or any of its diastereomers.
  • An embodiment is the combination according to the invention, wherein the at least one glycoside is bound to the ligand (binding site for the epitope on the cell-surface molecule) via a cleavable bond, wherein preferably said cleavable bond is subject to cleavage under acidic, reductive, enzymatic or light-induced conditions, and wherein the cleavable bond preferably is a disulfide bond or a peptide bond.
  • cleavable bond is a covalent bond, preferably an imine bond, a hydrazone bond, an oxime bond, a 1,3-dioxolane bond or an ester bond.
  • An embodiment is the combination according to the invention, wherein the endosomal escape enhancing conjugate comprises a defined number of glycosides or a defined range.
  • An embodiment is the combination according to the invention, wherein the defined range is between 1-30 glycoside(s), preferably between 1-20, more preferably between 1-10, more preferably between 1-6, more preferably between 2-6, more preferably between 2-5, more preferably between 3-5, more preferably between 3-4 glycosides.
  • an embodiment is the combination according to the invention, wherein the effector moiety is a pharmaceutically active substance, such as a toxin such as a proteinaceous toxin, a drug, a polypeptide or a polynucleotide.
  • a pharmaceutically active substance such as a toxin such as a proteinaceous toxin, a drug, a polypeptide or a polynucleotide.
  • an embodiment is the combination according to the invention, wherein the target cell is a diseased cell or a disease-related cell, preferably a tumor cell or a tumor-associated cell (e.g. tumor vascular cell), or an immune cell (e.g. a T regulatory cell), or an autoimmune cell.
  • a diseased cell or a disease-related cell preferably a tumor cell or a tumor-associated cell (e.g. tumor vascular cell), or an immune cell (e.g. a T regulatory cell), or an autoimmune cell.
  • An embodiment is the combination according to the invention, wherein the at least one effector moiety is bound to the binding moiety (second proteinaceous molecule) via a cleavable bond, wherein preferably said cleavable bond is subject to cleavage under acidic, reductive, enzymatic or light-induced conditions, and/or wherein the cleavable bond is a disulfide bond or a peptide bond.
  • An embodiment is the combination according to the invention, wherein the glycoside (saponin) is capable of augmenting endosomal escape of the effector molecule.
  • An embodiment is the combination according to the invention, for use as a medicament.
  • An embodiment is the pharmaceutical composition comprising a combination according to the invention (previous embodiments) and a pharmaceutically acceptable excipient.
  • An embodiment is the pharmaceutical composition according to the invention, further comprising at least one further active pharmaceutically ingredient, such as a further immunoglobulin.
  • An embodiment is the combination for use according to the invention, or pharmaceutical composition according to the invention, for use in a method of treating cancer or an autoimmune disease.
  • An embodiment is the combination for use according to the invention, wherein the endosomal escape enhancing conjugate (first proteinaceous molecule) and the binding moiety (second proteinaceous molecule) are to be administered concomitant or sequentially, preferably concomitant.
  • An embodiment is a method of treating cancer, the method comprising administering a combination according to the invention to a patient in need thereof.
  • An embodiment is the method of treating cancer, the method comprising administering a pharmaceutical composition according to the invention, to a patient in need thereof.
  • An embodiment is a kit comprising a first container containing an endosomal escape enhancing conjugate according to the invention and a second container containing a binding moiety according to the invention, the kit further comprising instructions for using the binding molecules.
  • Example A Treatment of a Mammalian Tumor-Bearing Animal with a Conjugate of the Invention in Combination with An ADC Results in Survival and Tumor Regression
  • mice Female Balb/c nude mice were injected subcutaneously with a suspension of human A431 tumor cells. Under the skin of the mice, a human epidermal carcinoma developed in the xenograft animal tumor model. After injection of the tumor cells, the xenograft tumor was allowed to develop to a size of approximately 170-180 mm 3 .
  • the A431 tumor cells have the following characteristics: high EGFR expressors, medium CD71 expressors, low HER2 expressors.
  • mice were treated with the indicated antibodies directed to either human Her2/neu, human EGFR, or human CD71, which are cell-surface receptors on the xenograft tumor.
  • Cetuximab was covalently conjugated with saponin SO1861.
  • the SO1861 was first provided with the linker EMCH (N- ⁇ -maleimidocaproic acid hydrazide), which EMCH is a maleimide-and-hydrazide crosslinker for covalently conjugating sulfhydryls (reduced cysteines of the antibody)) to carbonyls (aldehyde or ketones; here the carbonyl of the aldehyde at position C-23 of the saponin).
  • the saponin-EMCH was covalently coupled to reduced cysteines of the Cetuximab, forming a covalent thio-ether bond between the EMCH and the cysteine side chain.
  • the ADCs trastuzumab-saporin (covalent conjugate) and anti-CD71 mAb (OKT-9, IgG)-saporin (covalent conjugate) were tested for their tumor-attacking efficacy in the mice, measured as tumor volume in time after start of the treatment with the ADCs.
  • the dose of the ADCs was sub-optimal in the tumor model. That is to say, from previous experiments, it was established at which sub-optimal dose of the ADCs no tumor-regression or arrest of tumor growth would be observable.
  • the covalent conjugate administered to the mice suffering from cancer at a non-effective dose when administered alone (tumor growths, death of the mice is not prevented (euthanasia)), provides an efficient and efficacious treatment regimen, expressed as tumors in regression and prolonged survival of the treated animals (beyond the duration of the experiment).
  • the sub-optimal dose of ADC combined with a covalently bound saponin-comprising conjugate of the invention which has no anti-tumor activity when administered alone, thus provide for an effective treatment option for cancer patients, wherein a relative low dose of the ADC is efficacious.
  • a lower dose of ADC bears the promise of less risk for adverse events, or even no side effects at all.
  • the stimulatory effect of the saponin-bearing conjugate of the invention when the efficacy of the ADC is considered shows that ADCs which previously have proven to lack efficacy when tumor patient treatment is concerned, may gain renewed attention and value, since ADC efficacy is improved in combination therapy setting, as the current example demonstrated.
  • Table A2 and Table A3 summarizing ADCs which were previously investigated in the human clinical setting, but then were for some ADCs retracted from further clinical investigation.
  • ADCs which may gain renewed value for cancer patients when combined with a covalently bound saponin-comprising conjugate of the invention, such as the cetuximab-saponin tested.
  • Example B Seponins Mixture of Quillaja saponaria Comprising QS-21, with Endosomal/Lysosomal Escape Enhancing Activity
  • Scheme I displays the common molecular structure of a series of QS-21 saponins (in part adapted from: Conrado Pedebos, Laércio Pol-Fachin, Ramon Pons, Cilaine V. Teixeira Hugo Verli, Atomic Model and Micelle Dynamics of QS-21 Saponin, Molecules 2014, 19, 3744-3760).
  • a mixture of water-soluble saponins obtained from Quillaja saponaria (Sigma-Aldrich, product No. S4521; Roth, Item No.
  • product ‘Quil-A’ may be applied in the endosomal/lysosomal escape enhancing conjugate, composition, combination of the invention, based on endosomal/lysosomal escape enhancing properties of at least one individual saponin present in the mixture, e.g. QS-21, or based on a combination of two or more of the saponins comprised by the mixture, such as QS-21 and QS-7.
  • endosomal/lysosomal escape enhancing conjugate, composition, combination of the invention based on endosomal/lysosomal escape enhancing properties of at least one individual saponin present in the mixture, e.g. QS-21, or based on a combination of two or more of the saponins comprised by the mixture, such as QS-21 and QS-7.
  • the effector moiety exposed to the cells was dianthin covalently coupled to the ligand EGF: EGF-dianthin.
  • Cells tested were tumor cell lines HeLa for free saponins, and A431, MDA-MB-468, CaSki and A2058 for testing the saponins when covalently coupled to cetuximab.
  • the 1 target 2-components system (1T2C) is the combination treatment of mAb1-protein toxin and mAb1-SO1861, as illustrated in FIG. 14 .
  • SO1861-EMCH was conjugated via cysteine residues (Cys) and HSP27BNA oligo was conjugated via lysine residues to cetuximab (monoclonal antibody recognizing and binding human EGFR), both with a DAR 4 resulting in the production of 2 conjugates: cetuximab-(Cys-L-SO1861) 4 and cetuximab-(Lys-L-HSP27BNA) 4 .
  • cetuximab-(Cys-L-SO1861) 4 Intraperitoneal administration, (i.p.)
  • cetuximab-(Lys-L-HSP27BNA) 4 Intravenous administration, (i.v.)
  • A431 xenograph ‘mouse tumor model for EGFR tumor targeted gene silencing activity. Dosings started at day 12 when tumors reached ⁇ 150 mm 3 in size and tumor samples were collected at 72h after the first dosing and analysed for HSP27 gene expression compared to control gene mRNA expression levels (reference genes).
  • trastuzumab monoclonal antibody recognizing and binding human HER2
  • DAR 4 a DAR 4 resulting in the production of trastuzumab-(Cys-L-SO1861) 4 .
  • trastuzumab-(Cys-L-SO1861) 4 and trastuzumab-saporin were tested in a mouse tumor model (patient derived xenograph tumor model, PDX) with high HER2 expression levels and resistant for trastuzumab mono therapy.
  • trastuzumab-(Cys-L-SO1861) 4 intraperitoneal administration, (i.p.))+0.03 (Day1, 8)/0.02 (Day 15, 22, 30, 36,43) mg/kg trastuzumab-saporin (intravenous administration, (i.v.)) revealed strong tumor growth inhibition compared to the vehicle control and the 40 mg/kg trastuzumab-(Cys-L-SO1861) 4 or 0.03/0.02 mg/kg trastuzumab-saporin mono therapies ( FIG. 2 ).
  • FIG. 2 shows and enables that the 1T2C combination of trastuzumab conjugated SO1861+trastuzumab conjugated protein toxin induces efficient targeted delivery of a therapeutic protein toxin in the cytoplasm of solid tumor cells, thereby inducing tumor cell death and tumor growth inhibition, in vivo.
  • the 1 target 2-components system (1T2C) is the combination treatment of mAb1-SO1861 and mAb1-protein toxin ( FIG. 14 )
  • SO1861-EMCH was conjugated via cysteine residues (Cys) to cetuximab (monoclonal antibody recognizing and binding human EGFR), with a DAR 3,7 (cetuximab-(Cys-L-SO1861) 3,7 ).
  • Cetuximab-(Cys-L-SO1861) 3,7 was titrated on a fixed concentration of 10 pM cetuximab-saporin (cetuximab, conjugated to the protein toxin, saporin) and targeted protein toxin mediated cell killing on EGFR expressing cells (A431, EGFR ++ ; CaSKi, EGFR + ) was determined.
  • cetuximab conjugated SO1861 efficiently enhances endosomal escape of the cetuximab conjugated protein toxin (at non-effective concentrations), thereby inducing cell killing of EGFR expressing cells.
  • the cell killing activity in A431 is more effective compared to CaSki correlating with EGFR expression levels in these cell lines.
  • EGFR receptor binding competition between both conjugates within the 1T2C is also observed when cetuximab-(Cys-L-SO1861) 3,7 concentrations increase, cell killing activity declines due to outcompeting receptor binding and internalization of cetuximab-saporin ( FIG. 3 A, 3 B ).
  • cetuximab-(Cys-L-SO1861) 3,7 was titrated on a fixed concentration of 10 pM cetuximab-saporin and targeted protein toxin mediated cell killing on low EGFR expressing cells or cells without EGFR expression (HeLa, EGFR +/ ⁇ ; A2058, EGFR ⁇ ) was determined. Cells with low (HeLa) or no (A2058) EGFR expression were not sensitive at all for any combination of cetuximab-(Cys-L-SO1861) 3,7 +10 pM cetuximab-saporin (HeLa: IC50>1000 nM; A2058: IC50>1000 nM; FIG. 4 A, 4 B ).
  • cetuximab-saporin was titrated on a fixed concentration of 75 nM cetuximab-(Cys-L-SO1861) 3,7 and targeted protein toxin mediated cell killing on low (HeLa) or no (A2058) EGFR expressing cells was determined.
  • trastuzumab monoclonal antibody recognizing and binding human HER2, with a DAR 4, (trastuzumab-(Cys-L-SO1861) 4 ).
  • Trastuzumab-(Cys-L-SO1861) 4 was titrated on a fixed concentration of 50 pM trastuzumab-saporin (trastuzumab, conjugated to the protein toxin, saporin) and targeted protein toxin mediated cell killing on HER2 expressing cells (SK-BR-3, HER2 ++ ) was determined.
  • equivalent concentrations trastuzumab, trastuzumab-(Cys-L-SO1861) 4 or trastuzumab+50 pM trastuzumab-saporin could not induce any cell killing activity in HER2 expressing cells.
  • trastuzumab conjugated SO1861 efficiently enhances endosomal escape of the trastuzumab conjugated protein toxin (at non-effective concentrations), thereby inducing cell killing of HER2 expressing cells.
  • trastuzumab-(Cys-L-SO1861) 4 concentrations increase, cell killing activity declines due to outcompeting receptor binding and internalization of trastuzumab-saporin ( FIG. 5 A ).
  • trastuzumab-saporin alone or trastuzumab-saporin+2,5 nM trastuzumab showed cell killing only at high concentrations trastuzumab-saporin ( FIG. 5 B ). All this shows that relatively low concentrations of trastuzumab-saporin can be effective and induce cell killing only in combination with low trastuzumab-(Cys-L-SO1861) 4 concentrations in high HER2 expressing cells.
  • trastuzumab-(Cys-L-SO1861) 4 was titrated on a fixed concentration of 50 pM trastuzumab-saporin, according to the invention and targeted protein toxin mediated cell killing on low HER2 expressing cells (A431 HER2 +/ ⁇ ) or cells without HER2 expression (JIMT-1: HER2+; MDA-MB-468: HER2 ⁇ ) was determined.
  • trastuzumab-saporin was titrated on a fixed concentration of 2,5 nM trastuzumab-(Cys-L-SO1861) 4 and targeted protein toxin mediated cell killing on low or no HER2 expressing cells was determined.
  • Low HER2 expressing cells JIMT-1) showed cell killing only at high trastuzumab-saporin concentrations in combination with 2.5 nM trastuzumab-(Cys-L-SO1861) 4 (JIMT-1: IC50>10.000 pM; FIG. 6 C ), whereas MDA-MB-468 cells (HER2 ⁇ ) are not sensitive at any of the tested concentrations (MDA-MB-468: IC50>10.000 pM; FIG. 6 D ).
  • the 1T2C system was tested in combination with an endosomal acidification inhibitor, chloroquine.
  • Trastuzumab-saporin was titrated in combination with 5 nM trastuzumab-(Cys-L-SO1861) 4 in combination with or without chloroquine.
  • the 1 target 2-components system (1T2C) can also be the combination treatment of mAb1-SO1861 and mAb1-antisense BNA oligo nucleotide as illustrated in FIG. 15 .
  • HSP27 heat shock protein 27
  • the antisense BNA Upon release into the cytoplasm the antisense BNA recognizes and binds the mRNA encoding for HSP27, targeting the mRNA for destruction thereby depleting the HSP27 mRNA expression within the cancer cell.
  • HSP27BNA was conjugated to cetuximab with a DAR4 (Cetuximab-(Lys-L-HSP27BNA) 4 ) and tested in combination with cetuximab-(Cys-L-SO1861) 3,8 for enhanced HSP27 gene silencing activity in EGFR expressing cells (A431, EGFR ++ ) and non-expressing cells (A2058, EGFR), according to the invention ( FIG. 15 ).
  • DAR4 Cetuximab-(Lys-L-HSP27BNA) 4
  • cetuximab-(Cys-L-SO1861) 3,8 for enhanced HSP27 gene silencing activity in EGFR expressing cells (A431, EGFR ++ ) and non-expressing cells (A2058, EGFR), according to the invention ( FIG. 15 ).
  • A2058 cells (EGFR ⁇ ) no gene silencing activity was observed in the 1T2C combination ( FIG. 9 B ).
  • the 1 target 2-components system (1T2C) can also be the combination treatment of mAb1-(scaffold(-SO1861) n ) n and mAb1-protein toxin as illustrated in FIG. 16 .
  • Dendron(-L-SO1861) 4 was conjugated to cetuximab via cysteine residues (Cys) conjugation with a DAR3,9 and cetuximab-Cys-(dendron(-L-SO1861) 4 ) 3,9 was tested for enhanced cell killing activity in combination with an anti-EGFR antibody-protein toxin conjugate (cetuximab-saporin) in EGFR expressing cells (MDA-MB-468).
  • Cetuximab-Cys-(dendron(-L-SO1861) 4 ) 3,9 +10 pM cetuximab-saporin efficiently induces toxin-mediated cell killing in high EGFR expressing cells (IC50 0.4 nM; FIG. 10 A ), whereas this was not induced by cetuximab-Cys-(dendron(-L-SO1861) 4 ) 3,9 or cetuximab+10 pM cetuximab-saporin or cetuximab ( FIG. 10 A ).
  • cetuximab conjugated dendron(-L-SO1861) 4 efficiently enhances endosomal escape of the cetuximab conjugated protein toxin (at non-effective concentrations), thereby inducing cell killing of high HER2 expressing cells.
  • Similar 1T2C experiments were performed in cells that express low levels of EGFR (HeLa, EGFR +/ ⁇ ) and this revealed no cell killing activity when the 1T2C combination, according of the invention was used (IC50>100 pM; FIG. 10 B ) indicating that in the absence of sufficient EGFR receptor expression, effective intracellular SO1861 concentrations are not optimal (threshold) to induce cytoplasmic delivery of the protein toxin that results in toxin-mediated cell killing.
  • dendron(-L-SO1861) 4 was conjugated to the anti-HER2 antibody, trastuzumab via cysteine conjugation (Cys) with a DAR4, trastuzumab-Cys-(dendron(-L-SO1861) 4 ) 4 and tested for enhanced cell killing activity in combination with an anti-HER2 antibody-protein toxin conjugate (trastuzumab-saporin) in HER2 expressing cells (SK-BR-3, HER2++).
  • trastuzumab conjugated dendron(-L-SO1861) 4 efficiently enhances endosomal escape of the trastuzumab conjugated protein toxin (at non-effective concentrations), thereby inducing cell killing of high HER2 expressing cells.
  • T-DM1 trastuzuzmab-emtansine
  • DAR3.5 small molecule toxin emtansine
  • T-DM1 was titrated in combination with trastuzumab-(Cys-L-SO1861) 4 and compared with the antibody protein toxin conjugate, trastuzumab-saporin+Trastuzumab-(Cys-L-SO1861) 4 , according to the invention.
  • FIG. 12 A-D displays the relative cell viability when trastuzumab ( FIG. 12 A ), cetuximab ( FIG. 12 B ) or T-DM1 ( FIG. 12 C ), unconjugated protein toxins, saporin, dianthin and saporin conjugated to a (non-cell binding) IgG antibody ( FIG. 12 D ) are administrated to various cancer cell lines SK-BR-3, JIMT-1, MDA-MB-468, A431, CaSki, HeLa, A2058.
  • trastuzumab and cetuximab do not or hardly influence cell viability when exposed to most of the cell lines, with some effect on cell growth inhibition via blocking the function of the HER2 growth factor receptor when trastuzumab is exposed to SK-BR-3 cells at relatively high dose and with some effect on cell growth inhibition via blocking the function of the EGFR growth factor receptor when cetuximab is exposed to MDA-MB-468 cells at relatively high dose.
  • TDM-1 or ado-trastuzumab emtansine
  • HER2-positive metastatic breast cancer that has previously been treated with Herceptin (chemical name: trastuzumab) and taxane chemotherapy
  • Herceptin chemical name: trastuzumab
  • Taxane early-stage HER2-positive breast cancer after surgery if residual disease was found after neoadjuvant (before surgery) treatment with Herceptin and taxane chemotherapy.
  • the TDM-1 is a combination of Herceptin (Trastuzumab) and the chemotherapy medicine emtansine.
  • FIG. 12 C shows that the TDM-1 results in decreased cell viability for all cell lines tested at >1000 pM concentrations
  • the 1 target 2-components system (1T2C) can also be the combination treatment of mAb1-QSmix (mixture of saponins from Quillaja saponaria ) and mAb1-protein toxin.
  • QSmix-EMCH was conjugated via cysteine residues (Cys) to cetuximab (monoclonal antibody recognizing and binding human EGFR), with a DAR 4.1 (cetuximab-(Cys-L-QSmix) 4,1 ).
  • Cetuximab-(Cys-L-QSmix) 4,1 was titrated on a fixed concentration of 10 pM cetuximab-saporin or 10 pM cetuximab-dianthin and targeted protein toxin mediated cell killing on A431 (EGFR ++ ), CaSKi (EGFR + ) and A2058 (EGFR ⁇ ) cells was determined.
  • Apparatus Agilent 1260 Bin. Pump: G7112B, Multisampler, Column Comp, DAD: Agilent G7115A, 210, 220 and 220-320 nm, PDA: 210-320 nm, MSD: Agilent LC/MSD G6130B ESI, mass ranges depending on the molecular weight of the product:
  • Apparatus Waters IClass; Bin. Pump: UPIBSM, SM: UPISMFTN with SO; UPCMA, PDA: UPPDATC, 210-320 nm, SQD: ACQ-SQD2 ESI, mass ranges depending on the molecular weight of the product:
  • Detection DAD (220-320 nm); Detection: MSD (ESI pos/neg) mass range: 100-800; Fraction collection based on DAD.
  • MS instrument type Agilent Technologies G6130B Quadrupole
  • HPLC instrument type Agilent Technologies 1290 preparative LC
  • column Waters XBridge Shield (C18, 150 ⁇ 19 mm, 5 ⁇ ); Flow: 25 ml/min
  • Column temp room temperature
  • Eluent A 100% acetonitrile
  • 6-azidohexanoic acid (0.943 g, 6.00 mmol), EDCl.HCl (1.21 g, 6.30 mmol) and Oxyma Pure (0.938 g, 6.60 mmol) were dissolved in DMF (10.0 mL) and the mixture was stirred for 5 min.
  • a solution of di-tert-butyl (azanediylbis(ethane-2,1-diyl))dicarbamate (1.82 g, 6.00 mmol) in DMF (5.00 mL) was added and the reaction mixture was stirred at room temperature. After 5 hours the reaction mixture was evaporated in vacuo and the residue was dissolved in ethyl acetate (50 mL).
  • N,N-bis(2-aminoethyl)-6-azidohexanamide dihydrochloride (1.19 g, 3.76 mmol) in DMF (30.0 mL) and DIPEA (2.62 mL, 15.1 mmol) was added Boc-Lys(Boc)-ONp (3.69 g, 7.90 mmol) and the mixture was stirred at room temperature overnight. The reaction mixture was evaporated in vacuo and the residue was dissolved in ethyl acetate (100 mL).
  • N, N′-((9S,19S)-14-(6-aminohexanoyl)-1-mercapto-9-(3-mercaptopropanamido)-3,10,18-trioxo-4,11,14,17-tetraazatricosane-19,23-diyl)bis(3-mercaptopropanamide) formate (2.73 mg, 3.13 ⁇ mol) was dissolved in a mixture of 20 mM NH 4 HCO 3 with 0.5 mM TCEP/acetonitrile (3:1, v/v, 3.00 mL). Next, SO1861-EMCH (29.2 mg, 0.014 mmol) was added and the reaction mixture was stirred at room temperature.
  • Dendron(SO1861) 4 -amine (6.81 mg, 0.748 ⁇ mol) and 2,5-dioxopyrrolidin-1-yl 1-azido-3,6,9,12-tetraoxapentadecan-15-oate (2.90 mg, 7.48 ⁇ mol) were dissolved in DMF(1.00 mL).
  • DIPEA 1.302 ⁇ L, 7.48 ⁇ mol
  • 3C Fractions corresponding to the product were immediately pooled together, frozen and lyophilized overnight to give the title compound (5.86 mg, 84%) as a white fluffy solid. Purity based on LC-MS 90%.
  • the resulting residue was dissolved in a mixture of 20 mM NH 4 HCO 3 with 0.5 mM TCEP/acetonitrile (3:1, v/v, 3.242 mL). From this solution, directly, 1000 ⁇ L was added to SO1861-EMCH (14.4 mg, 6.94 ⁇ mol, 4.5 equiv. compared to the scaffold) and the mixture was shaken for 1 min and left standing at room temperature. After 10 min the reaction mixture was lyophilized overnight.
  • Trifunctional linker (DBCO, TCO, maleimide) was ordered at Bio-Synthesis Inc. (Lewisville, Tex.).
  • HSP27BNA(-thiol) oligos (sequence 5′-GGCacagccagtgGCG-3′) 39 were ordered at Bio-synthesis Inc. (Lewisville, Tex.)
  • HSP27 BNA oligo disulfide (70.0 mg, 0.012 mmol) was dissolved in 20 mM NH 4 HCO 3 (20.0 mL).
  • TCEP (14.3 mg, 0.050 mmol) was added and the reaction mixture was shaken for 1 min and left standing at room temperature.
  • the reaction mixture was filtered by using a centrifugal filter with a molecular weight cut-off of 3000 Da (5000 ⁇ g for 30 min).
  • a solution of 20 mM NH 4 HCO 3 with 2.5 mM TCEP (20.0 mL) was added to the residue solution and the resulting mixture was filtered again under the same conditions described above.
  • Methyltetrazine-BNA oligo (90.0 mg, 0.014 mmol) and SO1861-trifunctional linker (48.6 mg, 0.014 mmol) were dissolved in a mixture of water/acetonitrile (4:1, v/v, 12.0 mL). The reaction mixture was shaken for 1 min and left standing at room temperature. After 15 min the mixture was subjected to preparative LC-MS. 4A Fractions corresponding to the product were immediately pooled together, frozen and lyophilized overnight to give the title compound (82.0 mg, 60%) as a white fluffy solid. Purity based on LC-MS 92% (2 peaks with both m/z values corresponding to the title compound).
  • HSP27 BNA oligo disulfide (70.0 mg, 0.012 mmol) was dissolved in 20 mM NH 4 HCO 3 (20.0 mL).
  • TCEP (14.3 mg, 0.050 mmol) was added and the reaction mixture was shaken for 1 min and left standing at room temperature.
  • the reaction mixture was filtered by using a centrifugal filter with a molecular weight cut-off of 3000 Da (5000 ⁇ g for 30 min).
  • a solution of 20 mM NH 4 HCO 3 with 2.5 mM TCEP (20.0 mL) was added to the residue solution and the resulting mixture was filtered again under the same conditions described above.
  • Methyltetrazine-BNA oligo (90.0 mg, 0.014 mmol) and SO1861-trifunctional linker (48.6 mg, 0.014 mmol) were dissolved in a mixture of water/acetonitrile (4:1, v/v, 12.0 mL). The reaction mixture was shaken for 1 min and left standing at room temperature. After 15 min the mixture was subjected to preparative LC-MS. 4A Fractions corresponding to the product were immediately pooled together, frozen and lyophilized overnight to give the title compound (82.0 mg, 60%) as a white fluffy solid. Purity based on LC-MS 92% (2 peaks with both m/z values corresponding to the title compound).
  • HSP27 BNA oligo disulfide (1.10 mg, 0.187 ⁇ mol) was dissolved in 20 mM NH 4 HCO 3 with 1.0 mM TCEP (500 ⁇ L) and the mixture was shaken for 1 min and left standing at room temperature. After 1 hour the reaction mixture was filtered by using a centrifugal filter with a molecular weight cut-off of 3000 Da (14000 ⁇ g for 30 min). The residue solution was diluted with 20 mM NH 4 HCO 3 with 1.0 mM TCEP (500 ⁇ L) and the resulting mixture was filtered again under the same conditions described above.
  • HSP27 BNA oligo disulfide (1.1 mg, 0.187 ⁇ mol) was dissolved in 20 mM NH 4 HCO 3 with 1.0 mM TCEP (500 ⁇ L) and the mixture was shaken for 1 min and left standing at room temperature. After 1 hour the reaction mixture was filtered by using a centrifugal filter with a molecular weight cut-off of 3000 Da (14000 ⁇ g for 30 min). The residue solution was diluted with 20 mM NH 4 HCO 3 with 1.0 mM TCEP (500 ⁇ L) and the resulting mixture was filtered again under the same conditions described above.
  • HSP27BNA with linkers oligos (sequence 5′-GGCacagccagtgGCG-3′) 39 were ordered at Bio-Synthesis Inc. (Lewisville, Tex.)
  • RNA from cells was isolated and analysed according to standard protocols (Biorad)
  • Model Subcutaneous A431 Human Epidermoid Carcinoma Xenograft Model in female BALB/c nude Mice. Tumor volume was monitored and tumor samples were collected for gene silencing analysis (see below)
  • Random Hexamers Qiagen; final concentration 2 ⁇ M
  • a cDNA synthesis mix consisting of 4 pl 5xRT Buffer (Promega), 0.4 ⁇ l 25 mM dNTPs (Promega), 1 ⁇ l 200 U/ ⁇ L MMLV RT-enzyme (Promega), 0.5 ⁇ L 40 U/ ⁇ L RNAse Inhibitor (Promega) and 1.6 ⁇ L NFW.
  • the following cDNA synthesis protocol was used: 1) 10 minutes 25° C. 2) 60 minutes 37° C. 3) 5 minutes 85° C. 4) ⁇ 4° C.
  • HSP27 gene expression was calculated using 2 -(Ct Hsp27 -GEOMEAN(Ct ref1 ;Ct ref2 ;Ct ref3 ;Ct ref4 )) , where ref1, ref2, ref3 and ref4 are the reference genes IMMT, EIF2S2, GUSB and UBC for the analysis of the tumors.
  • ref1, ref2, ref3 and ref4 are the reference genes IMMT, EIF2S2, GUSB and UBC for the analysis of the tumors.
  • Four reference genes were chosen based on the performance of a GeNORM analysis among nine reference genes tested to choose the most ideal and stable reference gene for this tumor samples. To do so, qPCR results were imported in Qbase+software program by which two quality measures are calculated: the coefficient of variation of the normalized reference gene expression levels (V); and the geNorm stability M-value (M)1.
  • a reference gene with an M ⁇ 0.2 and a V ⁇ 0.15 is considered very stable. Based on this analysis IMMT and EIF2S2 were chosen as the most stable reference genes. However, UBC and GUSB were also added to the group of reference genes to further enhance the accuracy of the normalization. Each sample was analyzed as technical triplicate on a CFX96 Real-Time qPCR machine (Bio-Rad).
  • trastuzumab Herceptin®
  • cetuximab cetuximab
  • T-DM1 Kadcyla®
  • CD71 monoclonal antibody was purchased from BioCell (Okt9, #BE0023).
  • SO1861 was isolated and purified by Analyticon Discovery GmbH from raw plant extract obtained from Saponaria officinalis L. Quillaja saponaria saponin extract (QSmix) was purchased (Sigma Aldrich, #S4521)
  • Trastuzumab (Tras, Herceptin®, Roche), Cetuximab (Cet, Erbitux®, Merck KGaA), Tris(2-carboxyethyl)phosphine hydrochloride (TCEP, 98%, Sigma-Aldrich), 5,5-Dithiobis(2-nitrobenzoic acid) (DTNB, Ellman's reagent, 99%, Sigma-Aldrich), ZebaTM Spin Desalting Columns (2 mL, Thermo-Fisher), NuPAGETM 4-12% Bis-Tris Protein Gels (Thermo-Fisher), NuPAGETM MES SDS Running Buffer (Thermo-Fisher), NovexTM Sharp Pre-stained Protein Standard (Thermo-Fisher), PageBlueTM Protein Staining Solution (Thermo-Fischer), PierceTM BCA Protein Assay Kit (Thermo-Fisher), N-Ethylmaleimide (NEM, 98%, Sigma-
  • MALDI-TOF Matrix-assisted laser desorption/ionization time of flight
  • RP mode refers to reflector positive mode.
  • RN mode refers to reflector negative mode.
  • LP mode refers to linear positive mode.
  • Freeze-drying was performed on an Alpha 1-2 LD plus (Martin Christ Gefriertrocknungsanlagen GmbH). Typically, samples were frozen with liquid nitrogen and placed into the freeze-dryer at high vacuum.
  • Dia-Cys OD 280 0.57 (mg/ml) ⁇ 1 cm ⁇ 1
  • Nickel-nitrilotriacetic acid (Ni-NTA) chromatography was performed to purify histidine-tagged protein and protein-conjugates. Briefly, Ni-NTA agarose (10 mL) was pipetted into a gravity flow column for 5 mL bed volume. The resin was washed with 20 mL deionized water and recharged with 5 mL of 100 mM NiSO4 solution. The resin was washed again five times with 5 mL deionized water and equilibrated five times with DPBS. The protein solution was incubated with the washed Ni-NTA agarose rotating at 4° C. for 30 min. Afterwards, the Ni-NTA protein solution was pipetted back into the gravity flow column.
  • Ni-NTA Nickel-nitrilotriacetic acid
  • the flow through was collected and the resin was washed three times with 5 mL DPBS.
  • the immobilized sample was then eluted by increasing the imidazole concentration from 50 mL of 125 mM, pH 8 to 50 mL of 250 mM, pH 8. Elution fractions were dialyzed against PBS pH 7.4 to obtain the purified sample.
  • Size exclusion chromatography was carried out on an AKTA purifier. Samples were analyzed by SEC using either a Biosep SEC-53000 column or an Sephadex G50M column (10 ⁇ 40 cm) eluting with TBS/isopropyl alcohol solution (85:15 v/v). Sample purities were determined by integration of the antibody sample peak with respect to the trace aggregate peaks.
  • TNB 2-nitro-5-thiobenzoate
  • Dianthin was expressed in a bacterium culture and the protein was purified following conventional cell culturing and protein purification steps known in the art.
  • Custom trastuzumab-saporin cetuximab-saporin, CD71mab-saporin conjugates were produced and purchased from Advanced Targeting Systems (San Diego, Calif.). IgG-saporin and saporin was purchased from Advanced Targeting Systems
  • Ab Trastuzumab and Cetuximab are referred hereafter as “Ab”.
  • Ab was conjugated to dendritic saponin [dendron-(L-SO1861) 4 -maleimide] via a tetra(ethylene glycol) succinimidyl 3-(2-pyridyldithio)propionate (PEG 4 -SPDP) linker conducting a thiole-ene Michael-type reaction between Ab and dendritic saponin.
  • PEG 4 -SPDP tetra(ethylene glycol) succinimidyl 3-(2-pyridyldithio)propionate
  • Cetuximab was desalted into DPBS pH 7.5 buffer and then normalized to 2.50 mg/ml.
  • Ab 9.19 mg, 61 nmol
  • PEG 4 -SPDP solution 5.0 mg/ml, 6.70 mole equivalents, 411 nmol
  • the mixture vortexed briefly then incubated for 60 minutes at 20° C. with roller-mixing.
  • the reaction was quenched with the addition of glycine (20 mg/ml, 7.7 ⁇ l), then the SPDP moiety reduced in situ by the addition of TCEP (5.0 mg/ml, 4.0 mole equivalents per SPDP, 1.64 ⁇ mol).
  • Antibody-(L-SO1861) 4 (as Illustrated in FIG. 17 )
  • Trastuzumab, Cetuximab, are referred hereafter as “Ab”.
  • Ab was conjugated to the saponin SO18161-EMCH via Michael-type thiol-ene conjugation reaction at DARs of 1, 2, 3, 4, 5, and 6.
  • the SO1861-EMCH molecule obtains a labil (L) hydrazone bond between its structure and its maleimide function generating a labil bond between the saponin and Ab.
  • the procedure is exemplary described for Trastuzumab-(L-SO1861) 4 :
  • Tris concentrate 127 mg/ml, 1.05M
  • Tris.HCl concentrate 623 mg/ml, 3.95M
  • EDTA-Na 2 concentrate 95 mg/ml, 0.26M
  • SO1861 from Saponaria officinalis L (15.4 mg, 8.28 ⁇ mol) and HATU (140 mg, 368 ⁇ mol, 44.5 mole equivalents) were placed as solid into a 20 mL glas vial with magnetic stirrer and 5 mL DMSO was added to dissolve the materials. The dissolved mixture was stirred for 30 min at room temperature. After 30 min, 1 mL of freshly prepared AEM solution (65 mg, 256 ⁇ mol, 31 mole equivalents) in DMSO was added to the stirring SO1861-HATU mixture. The reaction mixture was stirred for 17 hours at room temperature.
  • Ab Trastuzumab and Cetuximab are referred hereafter as “Ab”.
  • Ab was conjugated to the saponin SO18161-S-Mal via Michael-type thiol-ene conjugation reaction.
  • the saponin obtains a stable (S) amide bond between its structure and its maleimide function generating a stable bond between the saponin and Ab.
  • Trastuzumab, Cetuximab, are referred hereafter as “Ab”.
  • Ab was conjugated to HSP27 BNA disulfide via a tetra(ethylene glycol) succinimidyl 3-(2-pyridyldithio)propionate (PEG 4 -SPDP) linker forming a labil (L) disulfide bond between Ab and HSP27 BNA .
  • PEG 4 -SPDP tetra(ethylene glycol) succinimidyl 3-(2-pyridyldithio)propionate
  • Trastuzumab (1.5 mg, 10.3 nmol, 2.50 mg/ml) was reacted with an aliquot of freshly prepared PEG 4 -SPDP solution (6.81 mole equivalents, 70.1 nmol, 39 ⁇ g) in DMSO (1 mg/ml) for 60 minutes at 20° C. with roller mixing. After, the reaction was quenched with glycine (15.1 ⁇ l of 2 mg/ml freshly prepared solution in TBS pH 7.5) and then desalted via zeba desalting column eluting with TBS pH 7.5. An aliquot of the resulting Tras-S-PEG 4 -SPDP was taken out and tested by UV-Vis analysis.
  • SPDP incorporation was determined using TCEP to liberate pyridiyl-2-thione (PDT) and by UV-vis analysis at 343 nm (SPDP to Ab ratio: 4).
  • the remaining Tras-(S-PEG 4 -SPDP) 4 was reacted with an aliquot of freshly prepared HSP27 oligonucleotide (oligo-SH) (8 mole equivalents, 82.4 nmol, 1.24 mg/ml) and incubated overnight at 20° C. with roller mixing. After 17 hours, the conjugate was analysed by UV-vis analysis to ascertain incorporation of HSP27 by displacement of pyridiyl-2-thione (PDT) at 343 nm.
  • HSP27-Mal maleimido bearing HSP27 derivate which is referred hereafter as “HSP27-Mal”.
  • Ab was conjugated to the HSP27-Mal via Michael-type thiol-ene conjugation reaction.
  • the HSP17-Mal obtains a labile (L) hydrazone bond between its structure and its maleimide function generating a labile bond between the HSP27 BNA and Ab.
  • L labile
  • Trastuzumab was reconstituted to 21 mg/ml with deionized water (DI), then diluted to 5 mg/ml using histidine buffer pH 6. To a 20 mg (4.0 ml) aliquot was added 10 ⁇ l/ml each of Tris concentrate (127 mg/ml, 1.05M), Tris.HCl concentrate (623 mg/ml, 3.95M) and EDTA-Na 2 concentrate (95 mg/ml, 0.26M) to give a 50 mM TBS, 2.5 mM EDTA buffer pH 7.5.
  • DI deionized water
  • HSP27-Mal HSP27 BNA derivatives which are referred hereafter as “HSP27-Mal”. These HSP27-Mal derivatives were namely: 1) Mal-Trifunctional linker-(L-SO1861)-(L-HSP27), 2) Mal-Trifunctional linker-(blocked)-(L-HSP27).
  • S-Trifunctional linker-(L-SO1861)-(L-HSP27 BNA)] 4 The procedure is exemplary described for Trastuzumab-[S-Trifunctional linker-(L-SO1861)-(L-HSP27 BNA)] 4 :
  • Trastuzumab was reconstituted to 21 mg/ml with deionized water (DI), then diluted to 5 mg/ml using histidine buffer pH 6. To a 20 mg (4.0 ml) aliquot was added 10 ⁇ l/ml each of Tris concentrate (127 mg/ml, 1.05M), Tris.HCl concentrate (623 mg/ml, 3.95M) and EDTA-Na 2 concentrate (95 mg/ml, 0.26M) to give a 50 mM TBS, 2.5 mM EDTA buffer pH 7.5.
  • DI deionized water
  • the bulk Ab-SH was split into two aliquots (1.1 mg, 7.6 nmol and 1.2 mg, 8.3 nmol), and to each aliquot was added an aliquot of each of the HSP27 BNA-Mal derivatives 1-2 (freshly prepared in TBS pH 7.5, 2 mg/ml, 1.3 mole equivalents per ‘thiol’, 40 nmol and 43 nmol), the mixtures vortexed briefly then incubated for 120 minutes at 20° C.
  • Trastuzumab-(L-SO1861) 4 , Cetuximab-(L-SO1861) 4 are referred hereafter as “Ab”.
  • Ab was conjugated to HSP27 BNA disulfide via a tetra(ethylene glycol) succinimidyl 3-(2 pyridyldithio)propionate (PEG 4 -SPDP) linker forming a labil (L) disulfide bond between Ab and HSP27 BNA.
  • PEG 4 -SPDP tetra(ethylene glycol) succinimidyl 3-(2 pyridyldithio)propionate
  • Trastuzumab-(L-SO1861) 4 (1.3 mg, 8.7 nmol, 2.50 mg/ml) was reacted with an aliquot of freshly prepared PEG 4 -SPDP solution (9.26 mole equivalents, 80.3 nmol, 45 ⁇ g) in DMSO (1 mg/ml) for 60 minutes at 20° C. with roller mixing. After, the reaction was quenched with glycine (15.1 ⁇ l of 2 mg/ml freshly prepared solution in TBS pH 7.5) and then desalted via zeba desalting column eluting with TBS pH 7.5. An aliquot of the resulting Tras-(L-SO1861)-(L-PEG 4 -SPDP) was taken out and tested by UV-Vis analysis. SPDP incorporation
  • Trastuzumab, Cetuximab, are referred hereafter as “Ab”. Ab was conjugated to the saponin QS Mix-EMCH via Michael-type thiol-ene conjugation reaction. The procedure is exemplary described for Trastuzumab-L-QS Mix:
  • Trastuzumab (“Ab”, 600 mg) was reconstituted to 21 mg/mL with deionized water (DI), then diluted to 5 mg/mL using freshly prepared histidine buffer pH 6 (5 mM histidine pH 6, 2% trehalose, 0.01% Tween 20). 10 ⁇ L/mL each of Tris concentrate (127 mg/mL, 1.05M), Tris.HCL concentrate (623 mg/mL, 3.95M) and EDTA-Na2 concentrate (95 mg/ml, 0.26M) was added to give a 50 mM TBS, 2.5 mM EDTA buffer pH 7.5.
  • DI deionized water
  • the conjugate was purified by 10 ⁇ 40 cm Sephadex G50M column eluting with DPBS pH 7.5 to give purified Trastuzumab-(L-QS Mix) conjugate.
  • the product as a whole was concentrated then normalized to 5 mg/mL using a vivacell 100 concentrator (2,000 g, 4° C., 200 minutes).
  • Trastuzumab and Cetuximab are referred hereafter as “Ab”.
  • Ab was conjugated a saponin SO1861 and maleimido (Mal) bearing HSP27 derivate which is referred hereafter as “HSP27-Mal”.
  • Ab was conjugated to the HSP27-Mal via Michael-type thiol-ene conjugation reaction.
  • the HSP17-Mal obtains a labile (L) hydrazone bond between its structure and its maleimide function generating a labile bond between the HSP27 BNA and Ab.
  • L labile
  • the procedure is exemplary described for Trastuzumab-(L-HSP27 BNA-L-SO1861) 4 :
  • Trastuzumab was reconstituted to 21 mg/ml with deionized water (DI), then diluted to 5 mg/ml using histidine buffer pH 6. To a 20 mg (4.0 ml) aliquot was added 10 ⁇ l/ml each of Tris concentrate (127 mg/ml, 1.05M), Tris.HCl concentrate (623 mg/ml, 3.95M) and EDTA-Na2 concentrate (95 mg/ml, 0.26M) to give a 50 mM TBS, 2.5 mM EDTA buffer pH 7.5.
  • DI deionized water
  • FIG. 25 shows a basic scaffold with click chemistry function to link any desired effector molecule. The user determines the position of the click chemistry position in the effector molecule and all further properties of the effector molecule, e.g. choice and position of an optional ligand.
  • the saponin in this example SA1641 was purified from a saponin composite raw extract from Gypsophila species called Saponinum album obtained from Merck (Darmstadt, Germany).
  • the powdered raw extract (2.5 g) was hydrolyzed in water (100 mL) with sodium hydroxide (0.2 g).
  • the solution was stirred for 20 h at 40° C. and then supplemented with glacial acetic acid until pH 5.0 was reached.
  • the solution was shaken in a separatory funnel with 30 mL butanol.
  • the aqueous phase was recaptured and butanol extraction repeated two times.
  • the butanol phases were supplemented with anhydrous sodium sulfate, filtered and pooled.
  • HPLC high performance liquid chromatography
  • Saponins were applied to the column and eluted with a methanol gradient (20% methanol to 70% methanol within 30 min at 1.5 mL/min in water supplemented with 0.01% trifluoroacetic acid followed by 70% methanol for further 60 min) [31]. Aliquots of the fractions were analyzed for their SA1641 content by electrospray ionization mass spectrometry (ESI-MS). Fractions containing pure SA1641 were pooled and methanol evaporated. The aqueous solution was frozen as a thin film in a rotating round-bottom flask by use of dry ice. After storage for 16 h at ⁇ 80° C., the sample was lyophilized.
  • ESI-MS electrospray ionization mass spectrometry
  • the polymeric structure (0.2 mM) and SA1641 (3.2 mM) were solved in water (approx. pH 8) and equal volumes mixed and shaken for 24 h at 26° C. Then sodium cyanoborohydride (NaCNBH 3 ; 0,1 M) was added in 4-fold molar excess referred to SA1641 and the sample incubated for further 24 h. The structure was then verified by ultra performance liquid chromatography (UPLC)/ESI-MS.
  • UPLC ultra performance liquid chromatography
  • the samples were applied to a RP-C4-column and eluted with a methanol gradient (25% methanol to 80% methanol within 15 min in water supplemented with 0.01% trifluoroacetic acid followed by 80% methanol for further 10 min).
  • the fractions were analyzed by use of LockSprayTM that is an ion source designed specifically for exact mass measurement with electrospray ionization using LC-time-of-flight (LC-TOF) mass spectrometers from Waters Corporation.
  • LockSprayTM that is an ion source designed specifically for exact mass measurement with electrospray ionization using LC-time-of-flight (LC-TOF) mass spectrometers from Waters Corporation.
  • FIG. 26 relates to a functionalized scaffold with pre-bound effector molecule and click chemistry function to link any desired ligand.
  • a pH-sensitive linkage can be provided to release the effector molecule from the scaffold after reaching the endosomes.
  • the inset of FIG. 26 shows the theoretically expected mass spectrum obtained from a calculation with the isotope pattern calculator enviPat Web 2.0. The pattern considers the charge of the molecule and the natural occurrence of isotopes, which is the reason that more than one peek is expected for a single substance.
  • the experimental data ( FIG. 26 ) obtained by UPLC/ESI-MS show almost exactly the same peaks at m/z 758-760 with same intensity as predicted, thus proving successful SA1641 coupling to the polymeric structure.
  • dianthin-EGF targeted toxin dianthin-Epidermal Growth Factor
  • the plasmid His-dianthin-EGF-pET11d [20] (100 ng) was added to 20 ⁇ L Escherichia coli RosettaTM 2 (DE3) pLysS Competent Cells (Novagen, San Diego, Calif., USA). Cells were transformed by a heat-shock (30 min on ice, 90 s at 42° C. and 1 min on ice). Thereafter, 300 ⁇ L lysogeny broth (LB) was added and the suspension incubated for 1 h at 37° C. while shaking at 200 rpm.
  • LB lysogeny broth
  • a preheated lysogeny broth agar plate with 50 ⁇ g/mL ampicillin was inoculated with 100 ⁇ l bacteria suspension and the plate incubated overnight at 37° C.
  • Lysogeny broth (3 mL) with 50 ⁇ g/mL ampicillin was inoculated with a colony from the plate and the bacteria were incubated for 8 h at 37° C. and 200 rpm.
  • the suspension (50 ⁇ L) was added to 500 mL of lysogeny broth with 50 ⁇ g/mL ampicillin and incubated overnight at 37° C. and 200 rpm. Subsequently, the volume was scaled-up to 2.0 L and bacteria grew under the same conditions until an optical density at wavelength 600 nm of 0.9 was reached.
  • Lysates were centrifuged (15,800 ⁇ g, 4° C., 30 min) and imidazole added to a final concentration of 20 mM. The supernatant was incubated with 2 mL of Ni-nitrilotriacetic acid agarose under continuous shaking for 30 min at 4° C. in the presence of 20 mM imidazole.
  • the material was poured into a 20-mL-column and washed three times with 10 mL wash buffer (50 mM NaH 2 PO 4 , 300 mM NaCl, 20 mM imidazole) and dianthin-EGF eluted by 10-mL-portions of increasing concentrations of imidazole (31, 65, 125 and 250 mM) in wash buffer. Eluate fractions (2 mL) were dialyzed overnight at 4° C. against 2.0 L PBS. Desalted dianthin-EGF was concentrated by an Amicon® Ultra-15 (10 kDa) and the protein concentration quantified.
  • wash buffer 50 mM NaH 2 PO 4 , 300 mM NaCl, 20 mM imidazole
  • dianthin-EGF eluted by 10-mL-portions of increasing concentrations of imidazole (31, 65, 125 and 250 mM) in wash buffer. Eluate fractions (2 mL) were dialyzed overnight
  • alkyne-PEG 5 -N-hydroxysuccinimidyl ester in 8-fold molar excess referred to dianthin-EGF was solved in dimethyl sulfoxide and added to 9 volumes of dianthin-EGF (1 mg in 0.2 M NaH 2 PO 4 /Na 2 HPO 4 , pH 8). After incubation at room temperature for 4 h, non-bound alkyne was separated by use of a PD10 column (GE-Healthcare, Freiburg, Germany). Click chemistry with the polymeric structure was conducted by copper(I)-catalyzed alkyne-azide cycloaddition.
  • Alkyne-dianthin-EGF (0.02 mM), dendrimer (0.05 mM), CuSO 4 (0.1 mM), tris(3-hydroxypropyltriazolylmethyl)amine (0.5 mM) and sodium ascorbate (5 mM) were incubated under gentle agitation for 1 h at room temperature in 0.1 M NaH 2 PO 4 /Na 2 HPO 4 , pH 8. Low molecular mass substances were then separated using a PD10 column.
  • HER14 cells are fibroblasts stably transfected with the human epidermal growth factor receptor and therefore target cells for the targeted toxin dianthin-EGF.
  • HER14 cells (2,000 cells/100 ⁇ L/well) were seeded into wells of 96-well-cell culture plates and incubated for 24 h in DMEM medium supplemented with 10% fetal calf serum and 1% penicillin/streptomycin at 37° C., 5% CO 2 and 98% humidity.
  • the different test substances (see results and FIG. 27 ) were then added in triplicates in a volume of 25 ⁇ L and supplemented with further 25 ⁇ L of medium.
  • 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (0.5 mg/mL in water) was added per well and incubated for 2 h. Thereafter, the medium was carefully removed and replaced by an aqueous solution containing 10% (v/v) isopropanol, 5% (w/v) sodium dodecyl sulfate and 400 mM HCl, and incubated for 5 min. Solubilized formazan was photometrically quantitated at 570 nM in a microplate reader (Spectra MAX 340 PC, Molecular Devices, Sunnyvale, Calif., USA). Untreated cells were normalized to 1 and all samples referred to the untreated control. Significance was determined by unpaired two-sample t-tests.
  • the polymeric structure in the example a pentameric dendrimer (pentrimer), does not have any cytotoxic effect on the target cells, neither in absence nor in presence of SA1641 ( FIG. 27 , column 2 and 3).
  • the targeted toxin (dianthin-EGF) shows half maximal toxicity at a concentration of 0.1 nM (column 4).
  • the same concentration results in death of all cells indicating the general ability of SA1641 to act as an enhancer of the endosomal escape (column 5).
  • the presence of the polymeric structure does not affect the toxicity of dianthin-EGF neither in the presence nor in the absence of SA1641 (columns 6 and 7), indicating that the scaffold does not affect the toxicity of dianthin-EGF.
  • To couple the model polymeric structure via click chemistry to the example pharmaceutically active substance of dianthin-EGF the substance had to be coupled with an alkyne group before.
  • dianthin-EGF lost some activity (compare columns 8 and 9 with 6 and 7, respectively), however, the undirected alkyne modification does not affect the idea of the invention and is also not required in future applications.
  • MALDI-TOF spectra were recorded on a MALDI-Mass Spectrometer (Bruker Ultrafex III). Typically, the sample dissolved in MilliQ water in nanomolar to micromolar range was spotted on the target (MTP 384 target plate polished steel T F, Bruker Daltons) using either super-DHB (99%, Fluka) or sinapinic acid (SA, 99%, Sigma-Aldrich) as the matrix dissolved in acetonitrile (MADLI-TOF-MS tested, Sigma)/0.1% TFA (7:3 v/v) via the dried-droplet-method.
  • RP mode refers to reflector positive mode.
  • RN mode refers to reflector negative mode.
  • LP mode refers to linear positive mode.
  • UV-Vis measurements were performed on a NanoDrop ND-1000 spectrophotometer in the spectral range of 200-750 nm.
  • Size exclusion chromatography was performed with Sephadex G 25 Superfine from GE Healthcare and on prepacked PD10 columns (GE Healthcare, Sephadex G 25 M). The material was activated by swelling in the respective eluent prior to performing chromatography.
  • Freeze-drying was performed on an Alpha 1-2 LD plus (Martin Christ Gefriertrocknungsanlagen GmbH). Typically, samples were frozen with liquid nitrogen and placed into the freeze-dryer at high vacuum.
  • MALDI-TOF-MS (RP mode) ( FIG. 29 A ): m/z 2124 Da ([M+K] + , saponin-EMCH), m/z 2109 Da ([M+K] + , SO1861-EMCH), m/z 2094 Da ([M+Na] + , SO1861-EMCH)
  • MALDI-TOF-MS (RN mode) ( FIG. 34 C ): m/z 2275 Da ([M ⁇ H] ⁇ , saponin-EMCH conjugate), 2244 Da ([M ⁇ H] ⁇ , saponin-EMCH conjugate), 2222 Da ([M ⁇ H] ⁇ , saponin-EMCH conjugate), 2178 Da ([M ⁇ H] ⁇ , saponin-EMCH conjugate), 2144 Da ([M ⁇ H] ⁇ , saponin-EMCH conjugate), 2122 Da ([M ⁇ H] ⁇ , saponin-EMCH conjugate), 2092 Da ([M ⁇ H] ⁇ , saponin-EMCH conjugate), 2070 Da ([M ⁇ H] ⁇ , SO1861-EMCH), 2038 Da ([M ⁇ H] ⁇ , SO1832-EMCH), 1936 Da ([M ⁇ H] ⁇ , SO1730-EMCH), 1861 Da ([M ⁇ H] ⁇ , SO1861).
  • MALDI-TOF-MS ( FIG. 29 B ) (RP mode): m/z 2193 Da ([M+K] + , SO1861-EMCH-mercaptoethanol), m/z 2185 Da ([M+K] + , SO1861-EMCH-mercaptoethanol), m/z 2170 Da ([M+Na] + , SO1861-EMCH-mercaptoethanol).
  • the reaction mixture was shaken for 12 h at 800 rpm and room temperature on a ThermoMixer C (Eppendorf). After shaking for 12 h the BSA-SO1861 concentrated using centrifugal filtration at 4,000 rpm (15° C.) via Amicon Ultra 15 filters with a MWCO of 3 kDa. The conjugate was stored as solution in the fridge and aliquots were taken for analysis. Yield: not determined.
  • MALDI-TOF-MS ( FIG. 37 A ) (LP mode): m/z 74.2 kDa ([M+H] + , BSA-SO1861 with 4 SO1861 attached), 72.2 kDa ([M+H] + , BSA-SO1861 with 3 SO1861 attached), 70.2 kDa ([M+H] + , BSA-SO1861 with 2 SO1861 attached), 37.0 kDa ([M+H] 2+ , BSA-SO1861 with 4 SO1861 attached), 35.9 kDa ([M+H] 2+ , BSA-SO1861 with 3 SO1861 attached), 34.7 kDa ([M+H] 2+ , BSA-SO1861 with 2 SO1861 attached).
  • the HATU-Cy3 solution was added to the stirring PAMAM solution and the reaction mix was stirred for 12 h at room temperature. After stirring for 12 h, the reaction mix was diluted with MilliQ water and dialyzed extensively for 24 h against MilliQ water using regenerated cellulose membrane tubes (Spectra/Por 6) with a MWCO of 2 kDa. After dialysis, the volume of the conjugate solution was reduced via a rotary evaporator (20 mbar, 60° C.) and the concentrated conjugate solution was run through a Sephadex G25 superfine size exclusion column (16 mL column volume). The first fraction was collected and lyophilized to obtain the viscous pink PAMAM-Cy3 conjugate.
  • PAMAM-Cy3 conjugate formation was confirmed by chromatography on thin layer chromatography (methanol/water, v/v 1:1), and the appearance of a faster band on a Sephadex G 25 superfine column. Yield 21.3 mg (63%).
  • the dye per PAMAM molar ratio determined by UV-Vis spectrophotometry was 0.43.
  • MALDI-TOF-MS ( FIG. 39 A ) (LP mode): m/z 28.0 kDa ([M+H] + , Cy3-PAMAM).
  • the reaction mixture was shaken for 12 h at 800 rpm and room temperature on a ThermoMixer C (Eppendorf). After shaking for 12 h, the reaction mix was diluted with MilliQ water and dialyzed extensively for 24 h against MilliQ water using regenerated cellulose membrane tubes (ZelluTrans, Carl Roth) with a MWCO of 12 -14 kDa. After dialysis, the Cy3-PAMAM-SO1861 solution was concentrated using centrifugal filtration at 4000 rpm (15° C.) via Amicon Ultra 15 filters with a MWCO of 3 kDa. The conjugate was stored as solution in the fridge and aliquots were taken for analysis. Yield: 0.5 mg (75%).
  • MALDI-TOF-MS spectra are illustrated in FIGS. 39 B-D , and FIG. 40 .
  • MALDI-TOF-MS of Cy3-PAMAM-(SO1861) 6 ( FIG. 39 B ) (LP mode): m/z 38.4 kDa ([M+H] + , Cy3-PAMAM-SO1861), 17.9 kDa ([M+H] 2+ , Cy3-PAMAM-SO1861).
  • Cy3-PAMAM (0.5 mg, 18 nmol), SO1861 (2.3 mg, 1.24 ⁇ mol), and HATU (64.6 mg, 170 ⁇ mol) were dissolved separately in 200 ⁇ L DMSO.
  • SO1861 and HATU solutions were mixed and shaken for 20 min at 800 rpm and room temperature on a ThermoMixer C (Eppendorf).
  • Cy3-PAMAM solution was added to the shaking SO1861-HATU solution and the reaction mixture was allowed to shake for 12 h at 800 rpm and room temperature on a ThermoMixer C (Eppendorf).
  • the reaction mix was diluted with MilliQ water and dialyzed extensively for 24 h against MilliQ water using regenerated cellulose membrane tubes (ZelluTrans, Carl Roth) with a MWCO of 12-14 kDa.
  • the Cy3-PAMAM-NC-SO1861 solution was concentrated using centrifugal filtration at 4,000 rpm (15° C.) via Amicon Ultra 15 filters with a MWCO of 3 kDa.
  • the Cy3-PAMAM-NC-(SO1861) 17 conjugate was stored as solution in the fridge and aliquots were taken for analysis. Yield: 0.77 mg (69%).
  • MALDI-TOF-MS ( FIG. 41 ) (LP mode): m/z 62.3 kDa ([M+H] + , Cy3-PAMAM-NC-SO1861), 35.7 kDa ([M+H] 2+ , Cy3-PAMAM-NC-SO1861).
  • PFd-G4-Azide-NH-BOC (G4-dendron) (9.75 mg, 2.11 ⁇ mol) was placed into a 2 mL reaction tube (Eppendorf) and dissolved in 200 ⁇ L DMSO. 100 ⁇ L of a Cy5-DBCO solution in DMSO (1.72 ⁇ mol*mL ⁇ 1 , 170 nmol) was added to the G4-dendron solution and the mix was shaken for 12 hours at room temperature and 800 rpm on a ThermoMixer C (Eppendorf).
  • the reaction mix was diluted with MilliQ water and dialyzed extensively for 24 h against MilliQ water using regenerated cellulose membrane tubes (Spectra/Por 7) with a MWCO of 1 kDa. After dialysis, the solution was lyophilized to obtain a blue powder. The crude product was used as obtained from lyophilization for the deprotection step.
  • MALDI-TOF-MS ( FIG. 54 B ) (RP mode): m/z 3956 Da ([M+Na] + , Cy5-G4-dendron+PF 6 ⁇ counterion), 3820 Da ([M+Na] + , Cy5-G4-dendron-PF 6 ⁇ counterion), 3617 Da ([M+H] + , G4-dendron impurity), 3017 ([M+H] + , G4-dendron).
  • the reaction mixture was shaken for 12 h at 800 rpm and room temperature on a ThermoMixer C (Eppendorf). After shaking for 12 h, the reaction mix was concentrated via centrifugal filtration using Amicon Ultra centrifugal filters (3 kDa MWCO). The conjugate was stored as solution in the fridge and aliquots were taken for analysis. Yield: 90 nmol (47%).
  • MALDI-TOF-MS spectra are illustrated in FIG. 55 .
  • MALDI-TOF-MS of G4-dendron-SO1861 ( FIG. 55 C ) (LP mode): m/z 10.19 kDa ([M+H] + , Cy5-G4-dendron-[SO1861] 3 ), 9.27 kDa ([M+H] + , G4-dendron-[SO1861] 3 ), 7.92 kDa ([M+H] + , Cy5-G4-dendron-[SO1861] 2 ), 7.14 kDa ([M+H] + , G4-dendron-[SO1861] 2 ), 5.86 kDa ([M+H] + , Cy5-G4-dendron-[SO1861] 1 ), 5.07 kDa ([M+H] + , G4-dendron-[SO1861] 1 ).
  • MALDI-TOF-MS spectra are illustrated in FIG. 57 .
  • MALDI-TOF-MS of PAMAM-(SH) 108 ( FIG. 57 E ) (LP mode): m/z 41.5 kDa ([M+H] + , PAMAM-[SH] 108 ).
  • the batch was concentrated via centrifugal filtration using Amicon Ultra 15 mL centrifugal filters (10 kDa MWCO). The concentrated batch was run through a PD10 size exclusion column followed by lyophilization to obtain a white fluffy powder. Yield was not determined.
  • MALDI-TOF-MS spectra are illustrated in FIG. 58 .
  • MALDI-TOF-MS of PAMAM-(mPEG 2k ) 3 ( FIG. 58 C ) (LP mode): m/z 33.46 kDa ([M+H] + , PAMAM-[mPEG 2k ] 3 ).
  • Cy3-PAMAM-(SO1861) 27 -(DBCO) 10 Procedure is described exemplary for Cy3-PAMAM-(SO1861) 27 -(DBCO) 10 .
  • Cy3-PAMAM-(SO1861) 27 (0.41 mg, 4.71 nmol) was freeze-fried and dissolved in 100 ⁇ L DMSO.
  • DBCO-PEG 13 -NHS ester (0.197 mg, 188 nmol) dissolved in DMSO was added to the Cy3-PAMAM-SO1861 solution and the mixture was shaken at 800 rpm and room temperature on a ThermoMixer C (Eppendorf).
  • the reaction mix was diluted with MilliQ water and dialyzed extensively for 24 h against MilliQ water using regenerated cellulose membrane tubes (ZelluTrans, Carl Roth) with a MWCO of 12-14 kDa.
  • the Cy3-PAMAM-SO1861-DBCO solution was concentrated using centrifugal filtration at 4,000 rpm (15° C.) via Amicon Ultra 15 filters with a MWCO of 3 kDa.
  • the conjugate was stored as solution in the fridge and aliquots were taken for analysis. Yield: 0.1 mg (22%).
  • MALDI-TOF-MS ( FIG. 42 D) (LP mode): m/z 92.5 kDa ([M+H] + , Cy3-PAMAM-SO1861-DBCO), 53.0 kDa ([M+H] 2+ , Cy3-PAMAM-SO1861-DBCO).
  • Cy3-PAMAM-NC-(SO1861) 17 (0.3 mg, 4.8 nmol) was freeze-fried and dissolved in 100 ⁇ L DMSO.
  • DBCO-PEG 13 -NHS ester (0.202 mg, 194 nmol) dissolved in DMSO was added to the Cy3-PAMAM-NC-SO1861 solution and the mixture was shaken at 800 rpm and room temperature on a ThermoMixer C (Eppendorf). After shaking for 3 h, the reaction mix was diluted with MilliQ water and dialyzed extensively for 24 h against MilliQ water using regenerated cellulose membrane tubes (ZelluTrans, Carl Roth) with a MWCO of 12-14 kDa.
  • MALDI-TOF-MS ( FIG. 42 B ) (LP mode): m/z 93.2 kDa ([M+H] + , Cy3-PAMAM-NC-SO1861-DBCO), 49.6 kDa ([M+H] 2+ , Cy3-PAMAM-NC-SO1861-DBCO).
  • Plasmid-DNA (His-dianthin-EGF-pET11d or His-dianthin-pET11d) [20] was transformed into chemically competent Escherichia coli NiCo21 (DE3) (New England Biolabs®, Inc.) and grown in 3 mL lysogeny broth supplemented with 50 ⁇ g/mL ampicillin at 37° C. for 5 h at 200 rpm. These bacteria were used to inoculate 500 mL lysogeny broth supplemented with 50 ⁇ g/mL ampicillin for overnight culture at 37° C. Subsequently, the culture volume was scaled up to 2 L and bacteria were grown until an optical density (A600) of 0.9.
  • A600 optical density
  • IPTG isopropyl ⁇ -D-1-thiogalactopyranoside
  • Cells were further grown for 3 h at 37° C. and 200 rpm. After centrifugation (5 min, 5,000 g, 4° C.) cell pellets were resuspended in 20 mL phosphate buffered saline (Dulbecco's phosphate-buffered saline (PBS) with Ca 2+ and Mg 2+ , pH 7.4) and stored at ⁇ 20° C. After thawing, proteins were released by ultrasound device (Branson Sonifier 250, G. Heinemann).
  • PBS phosphate buffered saline
  • the solution was centrifuged (15,800 ⁇ g, 30 min, 4° C.) and adjusted to 20 mM imidazole concentration.
  • the construct contained an N-terminal His-tag and was purified by nickel nitrilotriacetic acid chromatography (Ni-NTA Agarose, Qiagen, Hilden, Germany). After elution with imidazole (20-250 mM) the eluates were analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) (12%).
  • Fractions containing dianthin-EGF or dianthin were dialyzed against 2 L chitin binding domain buffer (20 mM tris(hydroxymethyl)-aminomethane/HCl, 500 mM NaCl, 1 mM EDTA, 0.1% Tween-20, pH 8.0) at 4° C. Further purification by chitin column affinity chromatography served to remove bacterial proteins with binding activity for Ni-NTA agarose. After elution with chitin binding domain buffer, the fractions were analyzed by SDS-PAGE (12%). Fractions containing dianthin-EGF or dianthin were dialyzed against 5 L PBS at 4° C. Purified proteins were concentrated by Amicon centrifugal filter devices (10 kDa, Millipore, Eschborn, Germany). The protein concentration was determined by a bicinchoninic acid assay (Pierce, Rockford, USA).
  • Dianthin-EGF (240 ⁇ g, 6.7 nmol) solution in PBS was placed into an Amicon Ultra 15 filter with a MWCO of 3 kDa and centrifuged at 4,000 rpm and 4° C. for 30 min three times. After each cycle, the Amicon filter was refilled with 0.1 M sodium carbonate buffer at pH 9. After the third centrifugation cycle, the volume was reduced to 0.5 mL via centrifugation. The dianthin-EGF sodium carbonate solution was placed into a 2 mL reaction tube and Alexa FluorTM 488 5-TFP (50 ⁇ g, 56 nmol) dissolved in 10 ⁇ L DMSO was added to the protein solution.
  • Alexa FluorTM 488 5-TFP 50 ⁇ g, 56 nmol
  • the mix was shaken at 800 rpm and room temperature on a ThermoMixer C (Eppendorf) for 80 min. After shaking, the mix was run through a Sephadex G25 M size exclusion column (GE Healthcare, PD10 column). The dianthin-EGF-Alexa488 conjugate was stored in solution in 0.1 M sodium carbonate buffer at pH 9 in the fridge and aliquots were taken for analysis. Yield: 210 ⁇ g (85%).
  • MALDI-TOF-MS ( FIG. 43 D ) (LP mode): m/z 36.8 kDa ([M+H] + , dianthin-EGF-Alexa488), m/z 33.6 kDa ([M+H] + , dianthin-EGF-Alexa488), 18.8 kDa ([M+H] 2+ , dianthin-EGF-Alexa488), 16.6 kDa ([M+H] 2+ , dianthin-EGF-Alexa488).
  • Dianthin (184 ⁇ g, 6.2 nmol) solution in PBS was placed into an Amicon Ultra 15 filter with a MWCO of 3 kDa and centrifuged at 4,000 rpm and 4° C. for 30 min three times. After each cycle, the Amicon filter was refilled with 0.1 M sodium carbonate buffer at pH 9. After the third centrifugation cycle, the volume was reduced to 0.5 mL via centrifugation. The dianthin sodium carbonate solution was placed into a 2 mL reaction tube and Alexa FluorTM 488 5-TFP (16.7 ⁇ g, 19 nmol) dissolved in 3.5 ⁇ L DMSO was added to the protein solution.
  • the mix was shaken at 800 rpm and room temperature on a ThermoMixer C (Eppendorf) for 80 min. After shaking, the mix was run through a Sephadex G25 M size exclusion column (GE Healthcare, PD 10 column).
  • the dianthin-Alexa488 conjugate was stored in solution in 0.1 M sodium carbonate buffer at pH 9 in the fridge and aliquots were taken for analysis. Yield: not determined MALDI-TOF-MS ( FIG. 44 D ) (LP mode): m/z 30.7 kDa ([M+H] + , dianthin-Alexa488).
  • MALDI-TOF-MS ( FIG. 43 E ) (LP mode): m/z 40.8 kDa ([M+H] + , dianthin-EGF-Alexa488-S-S-PEG-N 3 ), m/z 37.5 kDa ([M+H] + , dianthin-EGF-Alexa488-S-S-PEG-N 3 ).
  • Dianthin-Alexa488 (24.5 ⁇ g, 0.8 nmol) sodium carbonate solution was placed into a 2 mL reaction tube and azido-PEG 3 -S-S-NHS (34 ⁇ g, 78 nmol) dissolved in 9 ⁇ L DMSO was added to the protein solution.
  • the mix was shaken at 800 rpm and 15° C. on a ThermoMixer C (Eppendorf) for 12 h. After shaking, the reaction mix was diluted with PBS and was washed with PBS via centrifugal filtration at 4,000 rpm and 4° C. using Amicon Ultra 15 filter with a MWCO of 3 kDa.
  • MALDI-TOF-MS ( FIG. 44 E ) (LP mode): m/z 32.9 kDa ([M+H] + , dianthin-Alexa488-S-S-PEG-N 3 ).
  • Cy3-PAMAM-(SO1861) 27 -DBCO Procedure is described exemplary for Cy3-PAMAM-(SO1861) 27 -DBCO.
  • Cy3-PAMAM-(SO1861) 27 -DBCO (17 ⁇ g, 0.184 nmol) solution in MilliQ water was mixed with a dianthin-EGF-Alexa488-SS-PEG3-N 3 (3.6 ⁇ g, 0.089 nmol) solution in PBS in a 1.5 mL reaction tube and the reaction mix was shaken at 800 rpm and 15° C. on a ThermoMixer C (Eppendorf) for 2 h. After shaking, small aliquots were taken out for analysis via SDS-PAGE and fluorescence imaging on a Molecular Imager® VersaDocTM MP 4000 imaging system (Bio-Rad) ( FIG. 45 ).
  • Cy3-PAMAM (0.19 mg, 13 nmol) and SO1861 (0.73 mg, 0.39 ⁇ mol) were dissolved separately in 200 ⁇ L 0.1 M acetate buffer at pH 5.
  • SO1861 and Cy3-PAMAM solutions were mixed and shaken for 20 min at 800 rpm and room temperature on a ThermoMixer C (Eppendorf).
  • NaCNBH 3 5 mg, 81 ⁇ mol was added to the shaking reaction solution and the reaction mixture was allowed to shake for 12 h at 800 rpm and room temperature on a ThermoMixer C (Eppendorf).
  • the reaction mix was diluted with MilliQ water and dialyzed extensively for 24 h against MilliQ water using regenerated cellulose membrane tubes (ZelluTrans, Carl Roth) with a MWCO of 12-14 kDa.
  • the Cy3-PAMAM-NC-SO1861 solution was concentrated using centrifugal filtration at 4,000 rpm (15° C.) via Amicon Ultra 15 filters with a MWCO of 3 kDa.
  • the conjugate was stored as solution in the fridge and aliquots were taken for analysis. Yield: not determined
  • MALDI-TOF-MS ( FIG. 46 B , C) (LP mode): m/z 88.7 kDa ([M+H] + , Cy3-PAMAM-NC-SO1861), 49.2 kDa ([M+H] 2+ , Cy3-PAMAM-NC-SO1861).
  • SO1861-EMCH (0.13 mg, 63 nmol) was dissolved in 30 ⁇ L degased MilliQ water.
  • APS 0.2 ⁇ g, 0.8 nmol
  • 4 ⁇ L degased MilliQ water was added to the SO1861-EMCH solution and the solution was placed into a ThermoMixer C (Eppendorf) at 60° C.
  • TMEDA cat., 0.5 ⁇ L
  • MALDI-TOF-MS ( FIG. 48 C ) (LP mode): m/z 18.2 kDa ([M+H] + , poly(SO1861) 9 ), 16.0 kDa ([M+H] + , poly(SO1861) 8 ), 14.2 kDa ([M+H] + , poly(SO1861) 7 ), 12.2 kDa ([M+H] + , poly(SO1861) 6 ), 10.2 kDa ([M+H] + , poly(SO1861) 5 ), 8.2 kDa ([M+H] + , poly(SO1861) 4 ), 6.2 kDa ([M+H] + , poly(SO1861) 3 ).
  • Customized peptide with the sequence SESDDAMFCDAMDESDSK (0.6 mg, 0.3 ⁇ mol) and SO1861-EMCH (0.8 mg, 0.39 ⁇ mol) were dissolved separately in 200 ⁇ L PBS.
  • SO1861-EMCH and peptide solutions were mixed and shaken for 12 h at 800 rpm and room temperature on a ThermoMixer C (Eppendorf). After shaking small aliquots were taken out for analysis. Yield: not determined
  • MALDI-TOF-MS ( FIG. 51 B ) (RN mode): m/z 4.05 kDa ([M+H] ⁇ , peptide-SO1861), 3.92 kDa ([M+H] ⁇ , peptide-SO1730), 1.98 kDa ([M+H] ⁇ , peptide), 1.86 kDa ([M+H] ⁇ , SO1861).
  • HeLa cells were seeded in DMEM (PAN-Biotech GmbH) supplemented with 10% fetal bovine serum (PAN-Biotech GmbH) and 1% penicillin/streptomycin (PAN-Biotech GmbH), in a 96 well plate at 5,000 c/w in 100 ⁇ L/well and incubated overnight at 37° C. and 5% CO 2 .
  • DMEM fetal bovine serum
  • PAN-Biotech GmbH penicillin/streptomycin
  • the media was removed from the cell culture plate and replaced by 160 ⁇ L culture media, followed by the addition of 10 ⁇ L sample/well (from the 20 ⁇ concentrated stocks) and a 45 min incubation at 37° C. During this incubation the SO1861 concentration curve was prepared.
  • the SO1861 master stock was heated for 10 min at 50° C., while shaking at 1,250 rpm.
  • a serial dilution of SO1861 was prepared in PBS.
  • the SO1861 concentration curve was prepared as 10x concentrated stock, from which 20 ⁇ L was added/well.
  • the cells were incubated for 72 hr at 37° C. before the cell viability was determined by a MTS-assay, performed according to the manufacturer's instruction (CellTiter 96® AQueous One Solution Cell Proliferation Assay, Promega). Briefly, the MTS solution was diluted 20 ⁇ in DMEM without phenol red (PAN-Biotech GmbH) supplemented with 10% FBS. The cells were washed once with 200 ⁇ L/PBS well, after which 100 ⁇ L diluted MTS solution was added/well. The plate was incubated for approximately 20-30 minutes at 37° C. Subsequently, the OD at 492 nm was measured on a Thermo Scientific Multiskan FC plate reader (Thermo Scientific).
  • the background signal of ‘medium only’ wells was subtracted from all other wells, before the cell viability percentage of treated/untreated cells was calculated, by dividing the background corrected signal of treated wells over the background corrected signal of the untreated wells ( ⁇ 100).
  • HeLa cells were seeded in DMEM (PAN-Biotech GmbH) supplemented with 10% fetal calf serum (PAN-Biotech GmbH) and 1% penicillin/streptomycin (PAN-Biotech GmbH), at 500,000 c/plate in 10 cm dishes and incubated for 48 hrs (5% CO2, 37° C.), until a confluency of 90% was reached.
  • the cells were trypsinized (TryplE Express, Gibco Thermo Scientific) to single cells. 0.75 ⁇ 10 6 Cells were transferred to a 15 mL falcon tube and centrifuged (1,400 rpm, 3 min). The supernatant was discarded while leaving the cell pellet submerged.
  • the pellet was dissociated by gentle tapping the falcon tube on a vortex shaker and the cells were washed with 4 mL cold PBS (Mg 2+ and Ca 2+ free, 2% FBS). After washing the cells were resuspended in 3 mL cold PBS (Mg 2+ and Ca 2+ free, 2% FBS) and divided equally over 3 round bottom FACS tubes (1 mL/tube). The cells were centrifuged again and resuspended in 200 ⁇ L cold PBS (Mg 2+ and Ca 2+ free, 2% FBS) or 200 ⁇ L antibody solution; containing 5 ⁇ L antibody in 195 ⁇ L cold PBS (Mg 2+ and Ca 2+ free, 2% FBS).
  • APC Mouse IgG1, ⁇ Isotype Ctrl FC (#400122, Biolegend) was used as isotype control, and APC anti-human EGFR (#352906, Biolegend) was used to stain the EGFR receptor.
  • Samples were incubated for 30 min at 4° C. on a tube roller mixer. Afterwards, the cells were washed 3 ⁇ with cold PBS (Mg 2+ and Ca 2+ free, 2% FBS) and fixated for 20 min at room temperature using a 2% PFA solution in PBS. Cells were washed 2 ⁇ with cold PBS, and resuspended in 250-350 ⁇ L cold PBS for FACS analysis. Samples were analyzed with a BD FACSCanto II flow cytometry system (BD Biosciences) and FlowJo software. Table 19 shows the eExpression levels of EGFR, HER2 and CD71 of various cells.
  • aldehyde and alcohol groups are best suitable for reversible conjugation reactions, while the alkene and the carboxylic acid (glucuronic acid) are the groups best suitable for irreversible/stable conjugation reactions.
  • the aldehyde group within the molecule structure of SO1861, however, is the most suitable for reversible conjugation reactions over the alcohols. On the one hand, because there is only one aldehyde present in the structure that allows chemoselective reactions.
  • the aldehyde can perform reversible conjugation reactions with a variety of chemical groups such as amines, hydrazides, and hydroxylamines forming acid-cleavable moieties like imines, hydrazones, and oximes.
  • This factor enables a freedom of choice over the chemical group for the desired reversible conjugation reaction.
  • the alcohols are good candidates for reversible conjugation reaction via the formation of acetals and ketals as well, but lack in chemoselectivity since they are present in a large quantity on the glycosidic structure.
  • carboxylic acid is the most suitable since it can form amides and esters with the common tools used in peptide chemistry (e.g. reaction with amines via carbodiimide mediated amide formation).
  • an endosomal escape enhancing saponin such as SO1861
  • a methodology has been established that allows the generation of a non-cleavable and cleavable ‘ready to conjugate’ saponins ( FIG. 31 ) using the most suitable chemical groups present on SO1861.
  • the carboxylic group of SO1861 is activated via a reagent used in peptide coupling chemistry to generate an active ester (e.g. 1-[Bis(dimethylamino)methylene]-1H-1,2,3-triazolo[4,5-b]pyridinium 3-oxide hexafluorophosphate, HATU).
  • the resulting active ester of SO1861 is able to react with amines forming stable amide bonded conjugates ( FIG. 31 A ).
  • the aldehyde group of SO1861 is reacted with an EMCH (E-maleimidocaproic acid hydrazide) linker.
  • EMCH E-maleimidocaproic acid hydrazide
  • the hydrazide group of EMCH forms an acid cleavable hydrazone bond with the aldehyde of SO1861.
  • the EMCH linker presents a maleimide group that is thiol (sulfhydryl group) reactive and thus can be conjugated to thiols ( FIG. 31 B ).
  • the maleimide group of SO1861-EMCH performs a rapid and specific Michael addition reaction with thiols and thiol bearing polymeric structures when carried out in a pH range of 6.5-7.5 ( FIG. 31 B ).
  • the acid sensitive hydrazone linkage between the SO1861 and EMCH can be utilized to perform saponin release from a scaffold in acidic environment ( FIG. 32 ).
  • the EMCH linker fulfills both the need for a pH cleavable strategy and a conjugation strategy to a polymeric structure.
  • FIG. 34 A To synthesize the SO1861-EMCH, a strategy has been developed that allows the conversion of the aldehyde group on the SO1861 to EMCH ( FIG. 34 A ).
  • the SO1861-EMCH conjugate was isolated and successfully characterized via nuclear magnetic resonance spectroscopy (see materials and methods section, FIG. 28 ) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) as shown on FIGS. 34 B and 34 C , and FIG. 28 A .
  • MALDI-TOF-MS matrix-assisted laser desorption/ionization time-of-flight mass spectrometry
  • the three different feeds corresponded to an obtained mass of m/z 38.4 kDa, m/z 53.9 kDa and m/z 133.8 kDa for the Cy3-PAMAM-SO1861 conjugates that correspond to 6, 13 and 51 SO1861 molecules attached per PAMAM dendrimer as shown on FIG. 39 B-D .
  • the carboxylic acid of SO1861 was activated with HATU and then reacted with the amines of Cy3-PAMAM forming a pH stable amide bound between Cy3-PAMAM and SO1861.
  • the saponin conjugated scaffolds were conjugated to linking points for a possible conjugation to targeted therapeutics (e.g. targeted toxins) via the so-called strain-promoted alkyne-azide cycloaddition (SPAAC, click chemistry) to obtain a functionalized scaffold.
  • targeted therapeutics e.g. targeted toxins
  • SPAAC strain-promoted alkyne-azide cycloaddition
  • the NHS N Hydroxysuccinimide
  • the resulting DBCO dibenzocyclooctyne moiety on the conjugates is able to perform SPAAC with corresponding azides on the targeted therapeutics.
  • Dianthin-EGF served as a model targeted toxin and dianthin served as a non-targeted toxin. Both toxins were labeled with Alexa FluorTM 488 using the tetrafluorophenyl ester (TFP) derivative of the dye. The dye labeled proteins were then conjugated to a heterobifunctional NHS-SS-PEGS-azide linker to obtain the corresponding chemical moiety for the SPAAC to the PAMAM-saponin conjugates. Maldi-TOF-MS measurements showed that one Alexa FluorTM 488 dye and 9 NHS-SS-PEG 3 -azide molecules were attached per dianthin-EGF molecule ( FIG. 43 , FIG. 44 ).
  • Alexa FluorTM 488 labeled dianthin-EGF was conjugated to a heterobifunctional NHS-PEG 12 -azide linker that lacked the disulfide bond and would thus generate a non-toxin-cleavable construct.
  • Cy3-PAMAM-NC-SO1861-DBCO and Cy3-PAMAM-SO1861-DBCO conjugates were reacted with Alexa FluorTM 488 labeled azido-toxins to perform a strain-promoted alkyne-azide cycloaddition.
  • the conjugation between the reacting agents was indicated via gel electrophoresis and the co-localization of the fluorescent signals of Cy3 that is only attached on the PAMAM polymer and Alexa FluorTM 488 that is only attached on the toxins on a polyacrylamide gel after gel electrophoresis ( FIG. 45 ).
  • a G4-dendron (PFd-G4-Azide-NH-BOC, Polymer Factory) with 16 functional amino end groups and an azido group at the focal point was utilized for the conjugation to SO1861 ( FIG. 52 ).
  • the advantage of using a dendron over a dendrimer is the focal point that the dendron structure is exhibiting. This focal point allows the direct conjugation to a targeted toxin without the need of its post-modification with orthogonal click functions ( FIG. 53 ).
  • the dendron underwent the same methodology as described for the PAMAM dendrimer. Briefly, after partial dye labeling and deprotection ( FIG.
  • the amino groups of the dendron were converted into thiols using the thiolating reagent 2-iminothiolane followed by conjugation to SO1861-EMCH.
  • SO1861-EMCH three different feed equivalents of SO1861-EMCH were used.
  • the dendron-SO1861 conjugates were analyzed via MALDI-TOF-MS. As expected, the conjugate species of 1 and 2 SO1861 molecules per dendron molecule were obtained when low SO1861-EMCH feed equivalents of 3 and 10 were used ( FIG. 55 B , C). Higher dendron-SO1861 conjugate species of up to 9 SO1861 molecules per dendron were obtained ( FIG. 55 A ) when using a feed equivalent of 22 SO1861-EMCH molecules per dendron molecule.
  • the saponin functionalized dendron will be conjugated to targeted toxins over its focal point to yield a functionalized scaffold and will be evaluated biologically.
  • poly(SO1861) approach Another approach for the development of a SO1861 scaffold among the discussed polymer, and protein approach is the poly(SO1861) approach.
  • the idea of this approach is to generate a polymer that consists of SO1861 molecules only, with pH sensitive cleavable bonds that release the SO1861.
  • the poly(SO1861) should be able to perform conjugation reactions to toxins and biopolymers.
  • the main goal with this approach is to keep it as simple and cost effective as possible.
  • the generated SO1861 polymers could be quenched with a radical quencher that not only quenches the reaction but also generates a functional group for toxin or biopolymer conjugation.
  • a radical quencher that not only quenches the reaction but also generates a functional group for toxin or biopolymer conjugation.
  • FIG. 47 Such a reaction scheme is illustrated in FIG. 47 .
  • the system of ammonium persulfate (APS) and tetramethylethylenediamine (TMEDA) is shown in an exemplary way as radical generator and aminopropanethiol serves as a model radical quencher.
  • aminopropanethiol as a quencher exemplary, the generated amine group could be specifically further modified to a click-able group or being used to directly conjugate the poly(SO1861) to a toxin.
  • azo-initiators like 2,2′-azobis[2-methyl-N-(2-hydroxyethyl)propionamide] and azobisisobutyronitrile will be tested, as well as other polymerization techniques such as controlled radical polymerization (atom-transfer radical-polymerization, reversible addition-fragmentation chain transfer, etc).
  • hydrazide linker as a substitute for EMCH could be considered which obtains a functional group (such as an acryl or acrolyol residue) that is more suitable for radical polymerization than the maleimide group.
  • DNA-origami As the polymeric or assembled polymeric structure to conjugate saponins to it, can offer several inherent advantages including stability, scalability, and precise control of the final size and shape of the resulting DNA-saponin scaffold. Since these DNA nanocarriers are comprised of natural DNA, they are biocompatible and do not show toxicity to living cells, and can ease the release of cargo from internal cellular compartments. The multivalency of such a structure can further allow fine-tuning targeting capabilities and high capacity for a variety of payloads such as fluorophores and toxins.
  • DNA strands are identified that offer chemical functional groups on the 3′ and 5′ endings respectively, and that are able to hybridize only in certain wanted areas of the sequence that allow a control over the final shape of the construct.
  • the chemical groups should be utilized to couple saponins, for instance though a thiol-ene reaction between the already developed SO1861-EMCH and a thiol group on one of the 3′ and 5′ DNA strands.
  • the complementary DNA strand can offer a click function group that can be used for coupling to a targeted toxin. The concept is illustrated in FIG. 49 .
  • a similar approach is imaginable by using a specific peptide sequence instead of DNA strands that is able to bind and release saponins and that can be polymerized forming a large poly(peptide)-like structure.
  • a peptide sequence has been identified and purchased that has a length fitting the calculated size of a SO1861-EMCH molecule, that offers a cysteine residue in the middle of the sequence, and that obtains an amine group at both the N-terminus and C-terminus.
  • the cysteine residue can be utilized to conjugate SO1861-EMCH via a thiol-ene reaction of the maleimide group of SO1861-EMCH and the thiol group of the cysteine residue.
  • the two amine groups can be utilized to polymerize the peptide-SO1861 conjugate with a suitable crosslinker as shown on FIG. 50 .

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