WO2024050648A1 - Treatment of chemo-resistant tumors using multabodies - Google Patents
Treatment of chemo-resistant tumors using multabodies Download PDFInfo
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- WO2024050648A1 WO2024050648A1 PCT/CA2023/051200 CA2023051200W WO2024050648A1 WO 2024050648 A1 WO2024050648 A1 WO 2024050648A1 CA 2023051200 W CA2023051200 W CA 2023051200W WO 2024050648 A1 WO2024050648 A1 WO 2024050648A1
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Classifications
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P35/00—Antineoplastic agents
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- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
- C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
- C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
- C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
- C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
- C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
- C07K16/2878—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the NGF-receptor/TNF-receptor superfamily, e.g. CD27, CD30, CD40, CD95
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K39/00—Medicinal preparations containing antigens or antibodies
- A61K2039/505—Medicinal preparations containing antigens or antibodies comprising antibodies
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K39/00—Medicinal preparations containing antigens or antibodies
- A61K2039/545—Medicinal preparations containing antigens or antibodies characterised by the dose, timing or administration schedule
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- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K2317/00—Immunoglobulins specific features
- C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
- C07K2317/73—Inducing cell death, e.g. apoptosis, necrosis or inhibition of cell proliferation
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K2319/00—Fusion polypeptide
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K2319/00—Fusion polypeptide
- C07K2319/30—Non-immunoglobulin-derived peptide or protein having an immunoglobulin constant or Fc region, or a fragment thereof, attached thereto
Definitions
- chemotherapeutic agents have greatly improved therapeutic options for cancer patients.
- patients may respond favorably to chemotherapeutics only to experience relapse and recurrence as their tumors develop chemo-resistance.
- no favorable response is observed even initially.
- SUMMARY [0005] The present invention addresses this need with the provision of methods of treating chemo-resistant tumors and related uses.
- a pharmaceutical composition comprising a self-assembled polypeptide complex to the subject, wherein the self-assembled polypeptide complex comprises: a plurality of first fusion polypeptides, each first fusion polypeptide comprising (1) an antibody or antibody fragment that is capable of binding to a tumor-associated antigen expressed on the chemo-resistant tumor and (2) a nanocage monomer or subunit thereof.
- a pharmaceutical composition comprising self-assembled polypeptide complex to treat a 1 IPTS/124242861.1 Attorney Docket No.90702160 chemo-resistant tumor in a subject who has or is at risk of having a chemo-resistant tumor
- the self-assembled polypeptide complex comprises: a plurality of first fusion polypeptides, each first fusion polypeptide comprising (1) an antibody or antibody fragment that is capable of binding to a tumor-associated antigen expressed on the chemo-resistant tumor and (2) a nanocage monomer or subunit thereof.
- the complex further comprises: a plurality of second fusion polypeptides, each second fusion polypeptide comprising (1) an Fc polypeptide and (2) a nanocage monomer or subunit thereof.
- each second fusion polypeptide comprises the Fc polypeptide linked to the nanocage monomer or subunit thereof via an amino acid linker.
- the amino acid linker comprises a (G n S) m linker, e.g., a (GGGGS) m (SEQ ID NO:50) linker.
- the Fc polypeptide comprises a single-chain Fc (scFc) comprising two Fc chains, wherein the two Fc chains are linked via an amino acid linker, e.g., a (G n S) m linker such as a (GGGGS) m (SEQ ID NO:50) linker.
- the Fc polypeptide comprises an IgG1 Fc chain.
- the IgG1 Fc chain comprises (1) an amino acid residue other than glycine at position 237; and (2) a proline residue at position 329, according to EU numbering.
- the IgG1 Fc chain comprises an alanine at position 237 according to EU numbering.
- the IgG1 Fc chain comprises: an alanine at position 234, an alanine at position 235, an arginine at position 236, and a leucine at position 330, according to EU numbering.
- the nanocage monomer or subunit thereof is a ferritin monomer or subunit thereof, such as a ferritin light chain or subunit thereof and/or a human ferritin or subunit thereof.
- the self-assembled polypeptide complex does not comprise any ferritin heavy chains or subunits of ferritin heavy chains.
- each first fusion polypeptide comprises a C-half-ferritin
- each second fusion polypeptide comprises an N-half-ferritin
- each first fusion 2 IPTS/124242861.1 Attorney Docket No.90702160 polypeptide comprises an N-half ferritin
- each second fusion polypeptide comprises a C- half-ferritin.
- the self-assembled polypeptide complex is characterized by a 1:1 ratio of first fusion polypeptides to second fusion polypeptides.
- the total number of fusion polypeptides in each self- assembled polypeptide complex is at least 24 or at least 32.
- the total number of fusion polypeptides in each self- assembled polypeptide complex is about 24 or about 32.
- the total number of fusion polypeptides in each self- assembled polypeptide complex is between 24 and 48.
- the antibody or antibody fragment is linked to the N-terminus of the nanocage monomer or subunit thereof.
- each first fusion polypeptide comprises (1) a Fab fragment and (2) a nanocage monomer or subunit thereof. In some embodiments, each first fusion polypeptide does not comprise any antibody CH2 or CH3 domains.
- the tumor-associated antigen is a TNF receptor superfamily member, e.g., a death receptor, such as DR5 (also known as TRAIL receptor 2 (TRAILR2).
- DR5 also known as TRAIL receptor 2 (TRAILR2).
- the antibody or antibody fragment is conatumumab, tigatuzumab, lexatumumab, drozitumab, or a DR5-binding fragment of any of the foregoing.
- the antibody or antibody fragment is conatumumab or a DR5-binding fragment thereof.
- the antibody or antibody fragment comprises (1) a heavy chain comprising CDR-H1, CDR-H2, and CDR-H3 and (2) a light chain comprising CDR- L1, CDR-L2, and CDR-L3, wherein [0027] (a) (i) the CDR-H1 has a sequence of SEQ ID NO:23 or a sequence differing by one or two amino acids therefrom; (ii) the CDR-H2 has a sequence of SEQ ID NO:24 or a sequence differing by one or two amino acids therefrom; (iii) the CDR-H3 has a sequence of SEQ ID NO:25 or a sequence differing by one or two amino acids therefrom; (iv) the CDR-L1 has a sequence of SEQ ID NO:20 or a sequence differing by one or two amino acids therefrom; 3 IPTS/12424286
- the antibody fragment comprises (1) a heavy chain comprising CDR-H1, CDR-H2, and CDR-H3 and (2) a light chain comprising CDR-L1, CDR-L2, and CDR-L3, wherein [0032] (a) (i) the CDR-H1 has a sequence of SEQ ID NO:23, (ii) the CDR-H2 has a sequence of SEQ ID NO:24, (iii) the CDR-H3 has a sequence of SEQ ID NO:25, (iv) the CDR-L1 has a sequence of SEQ ID NO:20, (v) the CDR-L2 has a sequence of SEQ ID NO:21, and (vi) the CDR-L3 has a sequence of SEQ ID NO:22; [0033] (b) (i) the CDR-H1 has a sequence of SEQ ID NO:31, (ii) the CDR-H2 has a sequence of SEQ ID NO:32, (iii)
- the antibody fragment comprises (1) a heavy chain variable region having at least 85% identical to a reference VH sequence and (2) a light chain variable region having at least 85% identical to a reference VL sequence, wherein: (a) the reference VH sequence has a sequence of SEQ ID NO:19 and the reference VL sequence has a sequence of SEQ ID NO:18; (b) the reference VH sequence has a sequence of SEQ ID NO:27 and the reference VL sequence has a sequence of SEQ ID NO:26; (c) the reference VH sequence has a sequence of SEQ ID NO:35 and the reference VL sequence has a sequence of SEQ ID NO:34; or (d) the reference VH sequence has a sequence of SEQ ID NO:43 and the reference VL sequence has a sequence of SEQ ID NO:42.
- the subject is a mammal, e.g., a human.
- the tumor is a colon tumor.
- the subject has a chemo-resistant tumor, e.g., a tumor resistant to a taxane, a vinca alkaloid, an anthracycline, a platinum-containing compound, or any combination of the foregoing.
- the tumor may be resistant to a taxane, e.g., paclitaxel, taxane, or both; a vinca alkaloid, e.g., vincristine; an anthracycline, e.g., doxorubicin; and/or a platinum-containing compound, e.g., satraplatin, and oxaliplatin.
- the step of administering comprises administration by a systemic route, e.g., subcutaneous, intravenous, or intramuscular, inhalation, or intranasal administration.
- the step of administering comprises administering (or the subject is administered) more than one dose of the pharmaceutical composition.
- the pharmaceutical composition may be administered once a week for at least two weeks, at least three weeks, or more.
- the step of administering or the use results in slowing, inhibiting progression of, or regression of the tumor
- the method comprising a step of administering a pharmaceutical composition comprising a self-assembled polypeptide complex to the subject, wherein the self-assembled polypeptide complex comprises: (a) a plurality of first fusion polypeptides, each first fusion polypeptide comprising (1) an antibody fragment that is capable of binding to DR5 and (2) a ferritin monomer or subunit thereof; and (b) a plurality of second fusion polypeptides, each second fusion polypeptide comprising (1) an scFc and (2) a ferritin mono
- a pharmaceutical composition comprising a self-assembled polypeptide complex to treating a subject who has a chemo- resistant tumor or is at risk of having a chemo-resistant tumor
- the self-assembled polypeptide complex comprises: (a) a plurality of first fusion polypeptides, each first fusion polypeptide comprising (1) an antibody fragment that is capable of binding to DR5 and (2) a ferritin monomer or subunit thereof; and (b) a plurality of second fusion polypeptides, each second fusion polypeptide comprising (1) an scFc and (2) a ferritin monomer or subunit thereof, and, wherein the scFc comprises two IgG1 Fc chains, each IgG1 Fc chain comprising: an alanine at position 234, an alanine at position 235, an arginine at position 236, an alanine at position 237, a proline at position 329, and a leucine
- the step of administering or the use results in slowing, inhibiting progression of, or regression of the tumor
- the self-assembled polypeptide complex comprises: a plurality of first fusion polypeptides, each first fusion polypeptide comprising (1) an antibody or antibody fragment that is capable of binding to a 7 IPTS/124242861.1 Attorney Docket No.90702160 tumor-associated antigen expressed on the chemo-resistant tumor and (2) a nanocage monomer or subunit thereof.
- FIG.1A is a diagrammatic representation of human ferritin light chain (hFTL) and exemplary N-half ferritin (N-hFTL) and C-half ferritin (C-hFTL) molecules.
- FIG.1B is a diagrammatic representation of fusion polypeptides that together form exemplary Multabodies of the disclosure.
- FIG.2A depicts a tumor growth curve, showing tumor volume plotted against time after tumor cell injection in mice injected with vehicle (black curve), conatumumab (“parent IgG,” green curve), or a DR5-targeting Multabody (“MB,” orange curve). The red arrows indicate treatment time points.
- FIG.2B is a survival curve of HCT-15 xenograft mice for mice injected with vehicle (black curve), conatumumab (“parent IgG,” green curve), or a DR5-targeting Multabody (“MB,” orange curve).
- FIG.3 is a schematic depicting the design of a dose range efficacy study of a DR5- targeting Multabody in an HCT-15 xenograft mouse model. Experiments are described in Example 3.
- FIG.4A depicts a tumor growth curve, showing tumor volume plotted against time after treatment for HCT-15 xenograft mice administered vehicle or a DR5-targeting Multabody (“MB”) at 0.1 mg/kg, 0.25 mg/kg, 1 mg/kg, or 5 mg/kg. See Example 3.
- FIG.4B depicts the amount of Multabodies detected in blood of the mice from the dose range efficacy study described in Example 3, over time from the first dose.
- FIG.5 is a schematic depicting the design of a study of large tumor penetration and apoptosis induction by a DR5-targeting Multabody in an HCT-15 xenograft mouse model. Experiments are described in Example 4.
- FIGs.6A-6B depict representative tumor sections from mice that were untreated (FIGs.6A and 6B) or treated with a DR5-targeting Multabody (“MB”) (FIGs.6C and 6D). Sections were stained with an antibody against cleaved caspase-3, a marker of apoptosis. Experiments are described in Example 4. 8 IPTS/124242861.1 Attorney Docket No.90702160 DETAILED DESCRIPTION [0056] The present disclosure provides methods of treating a subject who has or is at risk of having a chemo-resistant tumor by administering to the subject a pharmaceutical composition comprising a self-assembled polypeptide complex (a “Multabody”) as described further herein.
- a pharmaceutical composition comprising a self-assembled polypeptide complex
- the terms “about” and “approximately” may encompass a range of values that fall within 25%, 20%, 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, or less of the referred value.
- the terms “alter,” “altered,” “decrease,” “decreased,” “increase,” “increased,” or “reduction,” “reduced,” have meanings relative to a reference level.
- the reference level is a level known or as determined with an IgG that does not contain the referenced mutation(s) in the Fc region.
- binding refers to a non- covalent association between or among two or more entities. "Direct" binding involves physical contact between entities or moieties; indirect binding involves physical interaction by way of physical contact with one or more intermediate entities.
- Binding between two or more entities can typically be assessed in any of a variety of contexts--including where interacting entities or moieties are studied in isolation or in the context of more complex systems (e.g., while covalently or otherwise associated with a carrier entity and/or in a biological system or cell).
- the phrases “non-binding” or “no binding,” or similar phrases, between two entities refers to 1) a lack of detectable binding or 2) binding below a set threshold that corresponds to no binding in an appropriate assay, e.g., an in vitro binding assay such as biolayer interferometry.
- chemo-resistant when used to describe a tumor, refers to the tumor’s characteristic of being poorly responsive to a chemotherapy drug.
- chemo-resistant encompasses both intrinsic resistance (i.e., resistance even without prior exposure) to one or more chemotherapy drugs and acquired resistance (i.e., resistance developed after exposure) to one or more chemotherapy drugs.
- a chemo-resistant tumor may be resistant to one or more chemotherapy drugs in the same class and/or to one or more classes of chemotherapy drugs.
- the terms “ferritin” and “apoferritin” are used interchangeably herein and generally refer to a polypeptide (e.g., a ferritin chain) that is capable of assembling into a ferritin complex which typically comprises 24 protein subunits.
- the ferritin is a human ferritin, e.g., a human ferritin light chain, e.g., a human ferritin light chain having at least 85% sequence identity to SEQ ID NO:1 or UniProt P02792.
- the ferritin is a wild-type ferritin.
- the ferritin may be a wild-type human ferritin.
- the term “ferritin monomer,” is used herein to refer to a single chain of a ferritin that, in the presence of other ferritin chains, is capable of self-assembling into a polypeptide complex comprising a plurality of ferritin chains, e.g., 24 or more ferritin chains.
- the term “linker” is used to refer to an entity that connects two or more elements to form a multi-element agent.
- a polypeptide e.g., fusion polypeptide
- a polypeptide comprising a linker element has an overall structure of the general form S1-L-S2, wherein S1 and S2 may be the same or different and represent two domains associated with one another by the linker (L).
- the linker is an “amino acid linker,” that is, it comprises amino acid residues, e.g., an amino acid linker may comprise at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100 or more amino acid residues.
- a linker is characterized in that it tends not to adopt a rigid three-dimensional structure, but rather provides flexibility to the polypeptide.
- multispecific refers to the characteristic of having at least two binding sites at which at least two different binding partners, e.g., an antigen or receptor (e.g., Fc receptor), can bind.
- an antigen or receptor e.g., Fc receptor
- a polypeptide complex that comprises at least two Fab fragments, wherein each of the two Fab fragments is capable of binding to a different antigen is “multispecific.”
- a polypeptide complex that comprises an Fc fragment (which is capable of binding to an Fc receptor) and a Fab fragment (which is capable of binding to an antigen) is “multispecific.”
- the term “multivalent,” as used herein, refers to the characteristic of having at least two binding sites at which a binding partner, e.g., an antigen or receptor (e.g., Fc receptor), can bind.
- the binding partners that can bind to at least two binding sites may be the same or different.
- nanocage monomer refers to a single chain of a polypeptide that is capable of self-assembling with other nanocage monomers to form a self- assembled polypeptide complex comprising a plurality of nanocage monomers.
- the nanocage monomer is selected from monomers of ferritin, apoferritin, encapsulin, sulfur oxygenase reductase (SOR), lumazine synthase, pyruvate dehydrogenase, carboxysome, vault proteins, GroEL, heat shock protein, E2P coat protein, MS2 coat protein, fragments thereof, and variants thereof.
- polypeptide generally has its art-recognized meaning of a polymer of at least three amino acids, e.g., linked to each other by peptide bonds.
- polypeptide is intended to be sufficiently general as to encompass not only polypeptides having a complete sequence recited herein, but also to encompass polypeptides that represent functional fragments (i.e., fragments retaining at least one activity) of such complete polypeptides.
- protein sequences generally tolerate some substitution without destroying activity.
- Polypeptides may contain L-amino acids, D-amino acids, or both and may contain any of a variety of amino acid modifications or analogs known in the art.
- IPTS/124242861.1 Attorney Docket No.90702160 include, e.g., terminal acetylation, amidation, methylation, glycosylation etc.
- proteins may comprise natural amino acids, non-natural amino acids, synthetic amino acids, and combinations thereof [0068]
- self-assembled when used in reference to a macromolecular complex (e.g., a polypeptide complex), refers to the spontaneous formation of that complex when sufficient constituents of the complex (e.g., fusion polypeptides) to be formed are present.
- complexes self-assemble in physiological conditions, or in a buffer (e.g., a solution) that corresponds to physiological conditions.
- a subject to an organism, typically a mammal (e.g., a human).
- a subject is suffering from or susceptible to a relevant disease, disorder or condition.
- a subject displays one or more symptoms or characteristics of a disease, disorder or condition.
- a subject is someone with one or more features characteristic of susceptibility to or risk of a disease, disorder, or condition.
- a subject is a patient.
- a subject is a subject to whom diagnosis and/or therapy is and/or has been administered.
- treatment refers to any administration of a therapy that partially or completely alleviates, ameliorates, relieves, inhibits, delays onset of, reduces severity of, and/or reduces incidence of one or more symptoms, features, and/or causes of a particular disease, disorder, and/or condition.
- such treatment may be of a subject who does not exhibit signs of the relevant disease, disorder and/or condition and/or of a subject who exhibits only early signs of the disease, disorder, and/or condition.
- such treatment may be of a subject who exhibits one or more established signs of the relevant disease, disorder and/or condition.
- treatment may be of a subject who has been diagnosed as suffering from the relevant disease, disorder, and/or condition. In some embodiments, treatment may be of a subject known to have one or more susceptibility factors that are statistically correlated with increased risk of development of the relevant disease, disorder, and/or condition.
- A. Fusion polypeptides [0071] In many embodiments, fusion polypeptides compatible with compositions and methods disclosed herein generally comprise a nanocage monomer or subunit thereof linked 12 IPTS/124242861.1 Attorney Docket No.90702160 to either an antibody fragment which is capable of binding to a tumor-associated antigen expressed on a chemo-resistant tumor or an “Fc polypeptide” as described herein.
- the antibody fragment or Fc polypeptide may be linked to the nanocage monomer or subunit thereof at a particular terminus of the nanocage monomer or subunit thereof, e.g., the N-terminus or the C-terminus.
- antibody fragment or Fc fragment is linked via an amino acid linker, such as a linker as described herein.
- Nanocage monomers and subunits thereof [0072] In some embodiments, the nanocage monomer is a ferritin monomer.
- ferritin monomer is used herein to refer to a single chain of a ferritin that, in the presence of other ferritin chains, is capable of self-assembling into a polypeptide complex comprising a plurality of ferritin chains, e.g., 24 or more ferritin chains.
- the ferritin monomer is a ferritin light chain.
- the ferritin monomer does not include a ferritin heavy chain or other ferritin components capable of binding to iron or capable of ferroxidase activity.
- each fusion polypeptide within the self-assembled polypeptide complex comprises a ferritin light chain or a subunit of a ferritin light chain.
- the self-assembled polypeptide complex does not comprise any ferritin heavy chains or subunits of ferritin heavy chains.
- the ferritin monomer is a human ferritin chain, e.g., a human ferritin light chain, e.g., a human ferritin light chain having the sequence of at least residues 2-175 of SEQ ID NO:1.
- a “subunit” of a ferritin monomer refers to a portion of a ferritin monomer that is capable of spontaneously associating with another, distinct subunit of a ferritin monomer, so that the subunits together form a ferritin monomer, which ferritin monomer, in turn, is capable of self-assembling with other ferritin monomers to form a polypeptide complex.
- the ferritin monomer subunit comprises approximately half of a ferritin monomer.
- the term “N-half ferritin” refers to approximately half of a ferritin chain, which half comprises the N-terminus of the ferritin chain.
- C-half ferritin refers to approximately half a ferritin chain, which half comprises the C-terminus of the ferritin chain.
- the exact point at which a ferritin chain may be divided to form the N-half ferritin and the C-half ferritin may vary depending on the embodiment.
- the 13 IPTS/124242861.1 Attorney Docket No.90702160 halves may be divided at a point that corresponds to a position between about position 75 to about position 100 of SEQ ID NO:1 (or a substantial portion thereof).
- an N-half ferritin based on a human ferritin light chain has an amino acid sequence corresponding to residues 1-95 of SEQ ID NO: 1 (or a substantial portion thereof, e.g., residues 2-95 of SEQ ID NO: 1)
- a C-half ferritin based on a human ferritin light chain has an amino acid sequence corresponding to residues 96-175 of SEQ ID NO: 1 (or a substantial portion thereof).
- the halves are divided at a point that corresponds to a position between about position 85 to about position 92 of SEQ ID NO: 1.
- an N-half ferritin based on a human ferritin light chain has an amino acid sequence corresponding to residues 1-90 of SEQ ID NO:1 (or a substantial portion thereof, e.g., residues 2-90 of SEQ ID NO: 1)
- a C-half ferritin based on a human ferritin light chain has an amino acid sequence corresponding to residues 91-175 of SEQ ID NO:1 (or a substantial portion thereof.
- Antibody fragments capable of binding to a tumor-associated antigen expressed on the chemo-resistant tumor [0079] Antibody fragments typically comprise a heavy chain variable region (e.g., a V H ).
- the antibody fragment comprises a heavy chain variable domain (e.g., VH) and a light chain variable domain (e.g., a VL or VK).
- the antibody fragment comprises a Fab which comprises a heavy chain variable domain (e.g., V H ) and a light chain variable domain (e.g., a V L or V K ).
- a fusion polypeptide e.g., the first fusion polypeptide
- the antibody fragment does not comprise any domains from the Fc region, e.g., does not comprise any CH2 or CH3 domains.
- the antibody fragment is a Fab.
- the antibody fragment is a single-chain Fab (scFab); for example, a fusion polypeptide comprising both the heavy and light chains of a Fab, optionally linked by a linker (e.g., amino acid linker as disclosed herein) is used.
- the tumor-associated antigen expressed on the chemo- resistant tumor is a tumor necrosis factor (TNF) receptor superfamily member.
- TNF tumor necrosis factor
- the TNF 14 IPTS/124242861.1 Attorney Docket No.90702160 receptor superfamily of cytokine receptors are able to bind TNFs via an extracellular domain and, when activated, typically form trimeric complexes in the plasma membrane.
- the tumor-associated antigen is a death receptor (e.g., TNFR1, Fas receptor, DR4 (also known as TRAIL receptor 1), or DR5 (also known as TRAIL receptor 2)), a class of receptors within the TNF receptor superfamily which comprise a “death domain.” Death receptors play a role in apoptosis.
- An antibody fragment can be assessed for its suitability for use in accordance with the methods disclosed herein using any of a variety of methods known in the art. For example, binding of an antibody or antibody fragment to a desired target, e.g., an antigen expressed on a chemo-resistant tumor, can be assessed using surface plasmon resonance or biolayer interferometry. Alternatively or additionally, when the tumor-associated antigen is a TNF receptor superfamily member, an antibody fragment can be assessed for its ability to induce trimerization of the TNF receptor. Alternatively or additionally, wherein the tumor- associated antigen is a death receptor, an antibody fragment can be assessed for its ability to induce apoptosis, e.g., in a cell-based apoptosis assay.
- a desired target e.g., an antigen expressed on a chemo-resistant tumor
- a desired target e.g., an antigen expressed on a chemo-resistant tumor
- an antibody fragment can be assessed for its ability to induce trimerization of
- the tumor-associated antigen is DR5.
- the antibody fragment may be capable of binding to an epitope within DR5, exemplary sequences of which are shown in SEQ ID NO:14 to SEQ ID NO:17.
- the antibody fragment capable of binding to DR5 is an antibody fragment of, or derived from, any of a variety of DR5 antibodies, including, e.g., fully human, humanized or chimeric DR5 antibodies.
- the DR5 antibody from which the antibody fragment is obtained or derived can be of any of a variety of antibody classes, including, e.g., an IgG1 antibody, an IgG2 antibody, an IgG4 antibody.
- the antibody fragment is obtained or derived from an agonistic DR5 antibody, e.g., an agonistic humanized DR5 antibody.
- DR5 antibodies include, e.g., conatumumab, tigatuzumab, lexatumumab, and drozitumab.
- antibody fragments capable of binding to DR5 comprises heavy chain and light chain CDRs having similar sequences (e.g., each CDR being identical, or having one or two amino acid substitutions) to that of the heavy and light chain CDRs of a DR5 antibody.
- antibody fragments capable of binding to DR5 comprise (1) a heavy chain comprising CDR-H1, CDR-H2, and CDR-H3 and (2) a light chain comprising CDR-L1, CDR-L2, and CDR-L3, wherein 15 IPTS/124242861.1 Attorney Docket No.90702160 (a) (i) the CDR-H1 has a sequence of SEQ ID NO:23 or a sequence differing by one or two amino acid residues therefrom, (ii) the CDR-H2 has a sequence of SEQ ID NO:24 or a sequence differing by one or two amino acid residues therefrom, (iii) the CDR-H3 has a sequence of SEQ ID NO:25 or a sequence differing by one or two amino acid residues therefrom, (iv) the CDR-L1 has a sequence of SEQ ID NO:20 or a sequence differing by one or two amino acid residues therefrom, (v) the CDR-L2 has a sequence
- antibody fragments capable of binding to DR5 comprises heavy and light chain CDRs having sequences identical to those of the heavy and light chain CDRs of a DR5 antibody, except for one or two amino acid substitutions total across all six CDRs.
- antibody fragments capable of binding to DR5 comprises heavy chain and light chain complementarity-determining regions (CDRs) having the same sequences as the CDRs of a DR5 antibody.
- antibody fragments capable of binding to DR5 comprise (1) a heavy chain comprising CDR-H1, CDR-H2, and CDR-H3 and (2) a light chain comprising CDR-L1, CDR-L2, and CDR-L3, wherein (a) (i) the CDR-H1 has a sequence of SEQ ID NO:23; (ii) the CDR-H2 has a sequence of SEQ ID NO:24; (iii) the CDR-H3 has a sequence of SEQ ID NO:25; (iv) the CDR-L1 has a sequence of SEQ ID NO:20; (v) the CDR-L2 has a sequence of SEQ ID NO:21; and (vi) the CDR-L3 has a sequence of SEQ ID NO:22; 17 IPTS/124242861.1 Attorney Docket No.90702160 (b) (i) the CDR-H1 has a sequence of SEQ ID NO:31, (ii) the CDR-H2
- the antibody fragment capable of binding to DR5 comprises (1) a heavy chain variable region having at least 85%, at least 87.5%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to a heavy chain variable region from a DR5 antibody and (2) a light chain variable region having at least 85%, at least 87.5%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to a light chain variable region from a DR5 antibody.
- the antibody fragment capable of binding to DR5 comprises 18 IPTS/124242861.1 Attorney Docket No.90702160 (1) a heavy chain variable region having at least 85%, at least 87.5%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to a reference VH sequence and (2) a light chain variable region having at least 85%, at least 87.5%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to a reference VL sequence, wherein: (a) the reference VH sequence has a sequence of SEQ ID NO:19 and the reference VL sequence has a sequence of SEQ ID NO:18, (b) the reference VH sequence has a sequence of SEQ ID NO
- fragment crystallizable (Fc) polypeptides comprise Fc chains that each have one or more mutations relative to a reference Fc chain of the same Ig class. As explained further herein below, the reference Fc chain may be of, e.g., the IgG1 class.
- the Fc polypeptide comprises one or more human IgG1 Fc chains that is, except for mutations noted herein, the Fc polypeptide comprises an Fc chain that is substantially similar to that of the Fc chains within a wild type human IgG1.
- the Fc polypeptide comprises one or more IgG1 Fc chains (e.g., human IgG1 Fc chains or a human Fc chains), that is, except for having particular residue(s) (which may be different than the residue(s) in the corresponding wild type Fc chains) at certain positions as noted herein, the Fc polypeptide comprises an Fc chain that has 19 IPTS/124242861.1 Attorney Docket No.90702160 an amino acid sequence that is substantially similar to that of the chains within a wild type IgG1 Fc.
- the wild type IgG1 Fc is a human IgG1 Fc, in which each Fc chain has an amino acid sequence of SEQ ID NO:4.
- an Fc polypeptide may comprise an Fc chain with an amino acid sequence that is at least 85%, at least 87.5%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to that of an Fc chain within a wild-type IgG1 Fc.
- an Fc polypeptide comprises an Fc chain that comprises the particular residue(s) at certain position(s) specifically described for that Fc chain, but has an amino acid sequence that is otherwise 100% identical to a corresponding Fc chain within a wild type Fc chain, e.g., wild type IgG1 Fc chain.
- the Fc polypeptide comprises an Fc chain that has an amino acid sequence that differs by at least one, at least two, at least three, or at least four amino acid residues from the sequence of SEQ ID NO:4. In some embodiments, the Fc polypeptide comprises an Fc chain that has an amino acid sequence that differs by no more than ten, no more than nine, no more than eight, no more than seven, no more than six, no more than five, or no more than four amino acid residues from the sequence of SEQ ID NO:4. [0097] In some embodiments, the Fc polypeptide is a single chain Fc (scFc), which comprises two Fc chains linked together by a covalent linker, e.g., via an amino acid linker.
- scFc single chain Fc
- the Fc chain comprises (1) an amino acid residue other than glycine at position 237; and (2) a proline residue at position 329. In some embodiments, the Fc chain comprises an alanine at position 237. In some embodiments, the Fc chain is an IgG1 Fc chain and further comprises a mutation or set of mutations at one or more positions selected from position 234, position 235, position 236, position 330, and combinations thereof.
- the Fc chain is an IgG1 Fc chain that comprises an alanine at position 234, an alanine at position 235, an arginine at position 236, an alanine at position 237, a proline at position 329, and a leucine at position 330.
- the Fc chain further comprises a mutation at a position associated with glycosylation, e.g., position 297 (e.g., by comprising a glutamine at position 297).
- the Fc chain comprises a mutation or set of mutations (relative to a corresponding wild type Fc chain) associated with an altered characteristic as further described herein.
- the altered characteristic e.g., altered binding to FcRn, altered effector function, etc.
- altered characteristic e.g., binding to an Fc receptor (e.g., an Fc ⁇ receptor or an FcRn)
- the altered characteristic comprises altered binding to an Fc receptor.
- the altered characteristic comprising altered binding to an Fc ⁇ receptor, e.g., a human Fc ⁇ R.
- the Fc ⁇ R is a human Fc ⁇ R selected from the group consisting of hFc ⁇ RI, hFc ⁇ RIIa, hFc ⁇ RIIb, hFc ⁇ RIIIa, hFc ⁇ RIIIb, and combinations thereof.
- the altered binding comprises no binding, or significantly reduced binding, relative to a corresponding control (e.g., binding levels typically observed under similar circumstances with a corresponding wild type chain), in an assay, e.g., an in vitro assay. 4.
- linkers are used within fusion polypeptides and/or within single-chain molecules such as scFcs.
- the linker is an amino acid linker.
- a linker as employed herein may comprise from about 1 to about 100 amino acid residues, e.g., about 1 to about 70, about 2 to about 70, about 1 to about 30, or about 2 to about 30 amino acid residues.
- the linker comprises at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, or at least 10 amino acid residues.
- the linker comprises a glycine-serine sequence, e.g., a (G n S) m sequence (e.g., GGS, GGGS, or GGGGS (SEQ ID NO:50) sequence) that is present in at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, or at least 14 copies within the linker.
- G n S m sequence
- SEQ ID NO:50 GGGGS
- IPTS/124242861.1 Attorney Docket No.90702160 polypeptide complexes comprise (a) a plurality of first fusion polypeptides, each first fusion polypeptide comprising (1) an Fc polypeptide linked to (2) a nanocage monomer or subunit thereof, wherein the Fc polypeptide comprises an Fc chain having one or more mutations relative to a reference Fc chain of the same Ig class, and (b) a plurality of second fusion polypeptides, each second fusion polypeptide comprising (1) an antigen-binding antibody fragment linked to (2) a nanocage monomer or subunit thereof.
- the nanocage monomer is a ferritin monomer
- each fusion polypeptide within the self-assembled polypeptide complex comprises a ferritin light chain or a subunit of a ferritin light chain.
- the self-assembled polypeptide complex does not comprise any ferritin heavy chains, subunits of ferritin heavy chains, or other ferritin components capable of binding to iron or capable of ferroxidase activity.
- the nanocage monomer or subunit thereof is a ferritin monomer subunit
- each first fusion polypeptide comprises a ferritin monomer subunit which is C-half-ferritin and each second fusion polypeptide comprises a ferritin monomer subunit which is N-half-ferritin; or (b) each first fusion polypeptide comprises a ferritin monomer subunit which is N-half ferritin and each second fusion polypeptide comprises a ferritin monomer subunit which is C-half-ferritin.
- the self-assembled polypeptide complex comprises between 24 and 48 fusion polypeptides in total.
- the self-assembled polypeptide complex comprises 24 fusion polypeptides in total. In some embodiments, the self-assembled polypeptide complex comprises more than 24 fusion polypeptides, e.g., at least 26, at least 28, at least 30, at least 32 fusion polypeptides, at least 34 fusion polypeptides, at least 36 fusion polypeptides, at least 38 fusion polypeptides, at least 40 fusion polypeptides, at least 42 fusion polypeptides, at least 44 fusion polypeptides, at least 46 fusion polypeptides, or at least 48 fusion polypeptides in total. In some embodiments, the self-assembled polypeptide complex comprises about 32 fusion polypeptides.
- the self-assembled polypeptide complex comprises at least 4, at least 5, least 6, at least 7, or at least 8 first fusion polypeptides. [0112] In some embodiments, the self-assembled polypeptide complex comprises at least 4, at least 5, least 6, at least 7, or at least 8 second fusion polypeptides. 22 IPTS/124242861.1 Attorney Docket No.90702160 [0113] In some embodiments, the self-assembled polypeptide complex further comprises at least 4, at least 5, least 6, at least 7, at least 8, at least 9, at least 10, least 11, at least 12, at least 13, at least 14, at least 15, or at least 16 third fusion polypeptides.
- the self-assembled polypeptide complex comprises a ratio of approximately 1:1, 11:13, 3:5, 1:2, 7:17, 1:3, 2:7, 5:19, 1:4, 1:5, 1:6, 1:7, 1:8, 1:12, 1:24 of first fusion polypeptides to all other fusion polypeptides.
- a provided self-assembled polypeptide complex is capable of inducing multimerization (e.g., trimerization) of TNF receptor super family receptors (e.g., death receptors, e.g., DR5 receptors) on a target cell (e.g., a cancer cell).
- administration of a self-assembled polypeptide complex as disclosed herein to a subject results in an improvement in a clinical outcome or metric in the subject.
- administration of the self-assembled polypeptide complex or a composition thereof may inhibit or slow progression of the tumor, e.g., cause regression of the tumor.
- administration of the self- assembled polypeptide complex results in complete regression of the tumor.
- methods that may be useful for treating, ameliorating, or preventing a disease or a condition (e.g., cancer, e.g., a chemo-resistant cancer), generally comprising a step of administering a composition comprising a self-assembled polypeptide complex as described herein to a subject.
- the subject is a mammal, e.g., a human.
- the subject has a chemo-resistant tumor or is at risk of having a chemo-resistant tumor.
- the subject has a chemo-resistant tumor at the time of administration of the pharmaceutical composition.
- the subject has not been previously treated with a chemotherapy agent.
- the subject may have or be at risk of having a tumor that is intrinsically chemo-resistant or has characteristics that suggest the tumor is likely to acquire chemo-resistance.
- 23 IPTS/124242861.1 Attorney Docket No.90702160 [0122]
- the subject carries, and/or a tumor sample in the subject carries, a genetic mutation or variation that is associated with intrinsic chemo-resistance or likelihood of acquiring chemo-resistance.
- the subject carries, and/or a tumor sample in the subject carries, an epigenetic alteration that is associated with intrinsic chemo-resistance or likelihood of acquiring chemo-resistance.
- the subject has or is at risk of having a tumor that is genetically heterogeneous.
- the subject has or is at risk of having a tumor that comprises cancer stem cells.
- the subject has one or more clinical markers associated with having or being at risk of having a tumor that is chemo-resistant.
- the subject has been previously treated with one or more chemotherapy drugs. In some such embodiments, the subject exhibits one or more clinical signs that the tumor has recurred or relapsed.
- compositions for administration to subjects generally comprise a self-assembled polypeptide complex as disclosed herein. In some embodiments, such compositions further comprise a pharmaceutically acceptable excipient.
- Compositions may be formulated for administration for any of a variety of routes of administration, including systemic routes (e.g., oral, inhalation, intranasal, intravenous, intraperitoneal, subcutaneous, or intramuscular administration).
- the step of administering results in improvement in one or more clinical outcomes or metrics in the subject. [0129] In some embodiments, the step of administering results in slowing or inhibiting progression of the tumor, e.g., regression of the tumor. In some embodiments, the step of administering results in complete regression of the tumor. EXAMPLES Example 1.
- DR5-targeting Multabodies comprising a combination of fusion proteins comprising a (1) human ferritin light chain or 24 IPTS/124242861.1 Attorney Docket No.90702160 subunit thereof and (2) a single-chain Fab (scFab) or a single chain Fc-dimer (scFc), fused via a linker, such as a (Glyn-Ser)m amino acid linker as described herein.
- scFab single-chain Fab
- scFc single chain Fc-dimer
- scFab of an anti-DR5 antibody fused to the N-terminus of hFTL (aDR5-hFTL, SEQ ID NO:9)
- scFab of an anti-DR5 antibody fused to the N-terminus of an N-half ferritin aDR5-N_hFTL, SEQ ID NO:11
- scFc-LLRAL fused to the N-terminus of a C-half ferritin
- scFc-LLRAL is a single-chain Fc-dimer based on an IgG1 Fc and having the following Fc mutations: L234A, L235A, G236R, G237A, and A330L. The residue at position 329 is proline. (Numbering is according to the EU numbering scheme). [0132] The resulting Multabody is a DR5-targeting Multabody hereinafter referred to as Cona MB IgG1 LLRAL. Example 2.
- HCT-15 colon adenocarcinoma
- paclitaxel docetaxel
- vincristine doxorubicin
- satraplatin doxorubicin
- satraplatin doxorubicin
- FIG.2A is a plot that depicts tumor volumes of mice in various groups over time since tumor injection. The red arrows indicate treatment time points. “MB” indicates the Cona MB IgG1 LLRAL group.
- FIG.4A is a plot that depicts tumor volumes of mice in various groups over time since the first dose.
- FIG. 4A indicates the Cona MB IgG1 LLRAL group.
- FIG. 4B is a plot that depicts that amount of Cona MB IgG1 LLRAL detectable in blood samples collected at various timepoints after the first dose was administered.
- Cona MB IgG1 LLRAL was detectable at all time points tested in the 0.25 mg/kg, 1 mg/kg/ and 5 mg/kg Cona MB IgG1 LLRAL treatment groups. 26 IPTS/124242861.1 Attorney Docket No.90702160 [0143] These results demonstrate that Cona MB IgG1 LLRAL exhibited therapeutic efficacy at multiple doses tested, including comparable efficacy at a dose level that was five- fold lower than that tested in Example 2.
- Exemplary Multabodies generated as described in Example 1 were evaluated for their ability to penetrate large tumors and induce apoptosis in a chemo-resistant xenograft model.
- 5 x 10 6 HCT-15 cells were injected subcutaneously in the flank of Balb/c SCID mice. Tumors were allowed to grow until well established ( ⁇ 31 days). Tumor volumes were estimated using calipers. Mice were randomly assigned to a vehicle or treatment groups such that the average tumor size was the same across the two groups, about 400 mm 3 in each group.
- FIG.5 depicts a schematic and timeline for these experiments.
- Tumors were fixed in formalin, embedded in paraffin, and sectioned. Tumor sections were stained immunohistochemically for cleaved caspase-3, a marker of apoptosis. Representative images of stained tissue sections are shown in FIGs.6A and 6B (vehicle- treated mice) and FIGs.6C and 6D (Cona MB IgG1 LLRAL-treated mice).
- Embodiment 2 The method of embodiment 1, wherein the complex further comprises: a plurality of second fusion polypeptides, each second fusion polypeptide comprising (1) an Fc polypeptide and (2) a nanocage monomer or subunit thereof.
- Embodiment 3 The method of embodiment 2, wherein each second fusion polypeptide comprises the Fc polypeptide linked to the nanocage monomer or subunit thereof via an amino acid linker.
- Embodiment 4 The method of embodiment 3, wherein the amino acid linker comprises a (GnS)m linker.
- Embodiment 5 The method of embodiment 4, wherein the (GnS)m linker is a (GGGGS) m (SEQ ID NO:50) linker.
- Embodiment 6 The method of any one of embodiments 2-5, wherein the Fc polypeptide comprises a single-chain Fc (scFc) comprising two Fc chains, wherein the two Fc chains are linked via an amino acid linker.
- Embodiment 7 The method of embodiment 6, wherein the amino acid linker that links the two Fc chains comprises a (GnS)m linker.
- Embodiment 8 The method of embodiment 12, wherein the (GnS)m linker is a (GGGGS) m (SEQ ID NO:50) linker.
- Embodiment 9 The method of any one of embodiments 2-8, wherein the Fc polypeptide comprises an IgG1 Fc chain.
- Embodiment 10 The method of embodiment 9, wherein the IgG1 Fc chain comprises (1) an amino acid residue other than glycine at position 237; and (2) a proline residue at position 329, according to EU numbering.
- Embodiment 11 The method of embodiment 10, wherein the IgG1 Fc chain comprises an alanine at position 237 according to EU numbering.
- Embodiment 12 The method of embodiment 10 or 11, wherein the IgG1 Fc chain comprises: an alanine at position 234, an alanine at position 235, an arginine at position 236, and a leucine at position 330, according to EU numbering.
- Embodiment 13 The method of any one of embodiments 1-12, wherein the nanocage monomer or subunit thereof is a ferritin monomer or subunit thereof.
- Embodiment 14 The method of embodiment 13, wherein the ferritin monomer or subunit thereof is a ferritin light chain or subunit thereof.
- Embodiment 15 The method of embodiment 13 or 14, wherein the ferritin monomer or subunit thereof is a human ferritin or subunit thereof.
- Embodiment 16 The method of any one of embodiments 13-15, wherein the self- assembled polypeptide complex does not comprise any ferritin heavy chains or subunits of ferritin heavy chains.
- Embodiment 17 The method of any one of embodiments 13-16, wherein at least a portion of the plurality of first fusion polypeptides and/or a portion of the plurality of second fusion polypeptides are fusion polypeptides which each comprise a ferritin monomer subunit.
- Embodiment 18 The method of embodiment 17, wherein (a) each first fusion polypeptide comprises a C-half-ferritin, and each second fusion polypeptide comprises an N- half-ferritin; or (b) each first fusion polypeptide comprises an N-half ferritin, and each second fusion polypeptide comprises a C-half-ferritin.
- Embodiment 19 The method of embodiment 18, wherein the self-assembled polypeptide complex is characterized by a 1:1 ratio of first fusion polypeptides to second fusion polypeptides.
- Embodiment 20 The method of any one of embodiments 1-19, wherein the total number of fusion polypeptides in each self-assembled polypeptide complex is at least 24.
- Embodiment 21 The method of claim 20, wherein the total number of fusion polypeptides in each self-assembled polypeptide complex is at least 32.
- Embodiment 22 The method of any one of embodiments 1-19, wherein the total number of fusion polypeptides in each self-assembled polypeptide complex is about 24.
- Embodiment 23 The method of any one of embodiments 1-19, wherein the total number of fusion polypeptides in each self-assembled polypeptide complex is about 32. 37 IPTS/124242861.1 Attorney Docket No.90702160 [0171]
- Embodiment 24 The method of any one of embodiments 1-19, wherein the total number of fusion polypeptides in each self-assembled polypeptide complex is between 24 and 48.
- Embodiment 25 The method of any one of embodiments 1-24, wherein, within each first fusion polypeptide, the antibody or antibody fragment is linked to the N-terminus of the nanocage monomer or subunit thereof.
- Embodiment 26 The method of any one of embodiments 1-25, wherein each first fusion polypeptide comprises (1) a Fab fragment and (2) a nanocage monomer or subunit thereof.
- Embodiment 27 The method of any one of embodiments 1-26, wherein each first fusion polypeptide does not comprise any antibody CH2 or CH3 domains.
- Embodiment 28 The method of any one of embodiments 1-27, wherein the tumor- associated antigen is a TNF receptor superfamily member.
- Embodiment 29 The method of embodiment 28, wherein the TNF receptor superfamily member is a death receptor.
- Embodiment 30 The method of embodiment 29, wherein the death receptor is DR5.
- Embodiment 31 The method of embodiment 30, wherein the antibody or antibody fragment is conatumumab, tigatuzumab, lexatumumab, drozitumab, or a DR5-binding fragment of any of the foregoing.
- Embodiment 32 The method of embodiment 31, wherein the antibody or antibody fragment is conatumumab or a DR5-binding fragment thereof.
- Embodiment 33 The method of embodiment 31, wherein the antibody or antibody fragment comprises (1) a heavy chain comprising CDR-H1, CDR-H2, and CDR-H3 and (2) a light chain comprising CDR-L1, CDR-L2, and CDR-L3, wherein (a) (i) the CDR-H1 has a sequence of SEQ ID NO:23 or a sequence differing by one or two amino acids therefrom; (ii) the CDR-H2 has a sequence of SEQ ID NO:24 or a sequence differing by one or two amino acids therefrom; (iii) the CDR-H3 has a sequence of SEQ ID NO:25 or a sequence differing by one or two amino acids therefrom; 38 IPTS/124242861.1 Attorney Docket No.90702160 (iv) the CDR-L1 has a sequence of SEQ ID NO:20 or a sequence differing by one or two amino acids therefrom; (v) the CDR-L2 has a sequence of SEQ ID NO
- Embodiment 34 The method of embodiment 33, wherein the antibody fragment comprises (1) a heavy chain comprising CDR-H1, CDR-H2, and CDR-H3 and (2) a light chain comprising CDR-L1, CDR-L2, and CDR-L3, wherein (a) (i) the CDR-H1 has a sequence of SEQ ID NO:23, (ii) the CDR-H2 has a sequence of SEQ ID NO:24, (iii) the CDR-H3 has a sequence of SEQ ID NO:25, (iv) the CDR-L1 has a sequence of SEQ ID NO:20, (v) the CDR-L2 has a sequence of SEQ ID NO:21, and (vi) the CDR-L3 has a sequence of SEQ ID NO:22; (b) (i) the CDR-H1 has a sequence of SEQ ID NO:31, (ii) the CDR-H2 has a sequence of SEQ ID NO:32, (iii
- Embodiment 35 The method of any one of embodiments 1-34, wherein the antibody fragment comprises (1) a heavy chain variable region having at least 85% identical to a reference VH sequence and (2) a light chain variable region having at least 85% identical to a reference VL sequence, wherein: (a) the reference VH sequence has a sequence of SEQ ID NO:19 and the reference VL sequence has a sequence of SEQ ID NO:18; (b) the reference VH sequence has a sequence of SEQ ID NO:27 and the reference VL sequence has a sequence of SEQ ID NO:26; (c) the reference VH sequence has a sequence of SEQ ID NO:35 and the reference VL sequence has a sequence of SEQ ID NO:34; or (d) the reference VH sequence has a sequence of SEQ ID NO:43 and the reference VL sequence has a sequence of SEQ ID NO:42.
- Embodiment 36 The method of any one of embodiments 1-35, wherein the subject is a mammal.
- Embodiment 37 The method of embodiment 36, wherein the subject is a human.
- Embodiment 38 The method of any one of embodiments 1-37, wherein the tumor is a colon tumor.
- Embodiment 39 The method of any one of embodiments 1-38, wherein the subject has a chemo-resistant tumor.
- Embodiment 40 The method of any one of embodiments 1-39, wherein the chemo- resistant tumor is resistant to a taxane, a vinca alkaloid, an anthracycline, or any combination of the foregoing.
- Embodiment 41 The method of embodiment 40, wherein the chemo-resistant tumor is resistant to a taxane.
- Embodiment 42 The method of embodiment 41, wherein the taxane is paclitaxel, taxane, or both.
- Embodiment 43 The method of embodiment 40, 41, or 42, wherein the chemo- resistant tumor is resistant to a vinca alkaloid.
- Embodiment 44 The method of embodiment 43, wherein the vinca alkaloid is vincristine.
- Embodiment 45 The method of any one of embodiment 41-44, wherein the chemo-resistant tumor is resistant to an anthracycline.
- Embodiment 46 The method of embodiment 45, wherein the anthracycline is doxorubicin.
- Embodiment 47 The method of any one of embodiment 41-46, wherein the chemo-resistant tumor is resistant to a platinum-containing compound.
- Embodiment 48 The method of embodiment 47, wherein the platinum-containing compound is satraplatin, oxaliplatin, or both.
- Embodiment 49 The method of any one of embodiments 1-46, wherein the administering comprises administration by a systemic route.
- Embodiment 50 The method of embodiment 47, wherein the systemic route comprises subcutaneous, intravenous, intramuscular, inhalation, or intranasal administration. 42 IPTS/124242861.1 Attorney Docket No.90702160
- Embodiment 51 The method of any one of embodiments 1-48, wherein the step of administering comprises administering more than one dose of the pharmaceutical composition.
- Embodiment 52 The method of embodiment 49, wherein the step of administering comprises administering the pharmaceutical composition once a week for at least two weeks.
- Embodiment 53 The method of embodiment 50, wherein the step of administering comprises administering the pharmaceutical composition once a week for at least three weeks.
- Embodiment 54 A method of treating a subject who has a chemo-resistant tumor or is at risk of having a chemo-resistant tumor, the method comprising a step of administering a pharmaceutical composition comprising a self- assembled polypeptide complex to the subject, wherein the self-assembled polypeptide complex comprises: (a) a plurality of first fusion polypeptides, each first fusion polypeptide comprising (1) an antibody fragment that is capable of binding to DR5 and (2) a ferritin monomer or subunit thereof; and (b) a plurality of second fusion polypeptides, each second fusion polypeptide comprising (1) an scFc and (2) a ferritin monomer or subunit thereof, and, wherein the scFc comprises two IgG1 Fc chains, each IgG1 Fc chain comprising: an
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Abstract
Methods of treating a subject who has or is at risk of having a chemo-resistant tumor comprising a step of administering a pharmaceutical composition comprising a self-assembled polypeptide complex, which methods result in slowing, inhibiting progression of, or regression of the tumor.
Description
Attorney Docket No.90702160 TREATMENT OF CHEMO-RESISTANT TUMORS USING MULTABODIES CROSS-REFERENCE TO RELATED APPLICATIONS [0001] This application claims the benefit of and priority to U.S. Provisional Patent Application No.63/375,242 filed on September 11, 2022, the disclosure of which is incorporated by reference herein in its entirety for all purposes. SEQUENCE LISTING [0002] The present specification makes reference to a Sequence Listing which has been submitted electronically in XML format and is hereby incorporated by reference in its entirety. Said XML file, created on September 11, 2023, is named RBT_055WO_ST26.xml and is 52 kb in size. BACKGROUND [0003] The development of anti-cancer agents such as chemotherapeutic agents have greatly improved therapeutic options for cancer patients. However, in many cases, patients may respond favorably to chemotherapeutics only to experience relapse and recurrence as their tumors develop chemo-resistance. In some cases, as with intrinsically resistant tumors, no favorable response is observed even initially. [0004] A need exists for improved compositions and methods for treating chemo-resistant tumors. SUMMARY [0005] The present invention addresses this need with the provision of methods of treating chemo-resistant tumors and related uses. [0006] In one aspect, provided are methods of treating a subject who has or is at risk of having a chemo-resistant tumor, the method comprising a step of administering to the subject a pharmaceutical composition comprising a self-assembled polypeptide complex to the subject, wherein the self-assembled polypeptide complex comprises: a plurality of first fusion polypeptides, each first fusion polypeptide comprising (1) an antibody or antibody fragment that is capable of binding to a tumor-associated antigen expressed on the chemo-resistant tumor and (2) a nanocage monomer or subunit thereof. Also provided are uses of a pharmaceutical composition comprising self-assembled polypeptide complex to treat a 1 IPTS/124242861.1
Attorney Docket No.90702160 chemo-resistant tumor in a subject who has or is at risk of having a chemo-resistant tumor, wherein the self-assembled polypeptide complex comprises: a plurality of first fusion polypeptides, each first fusion polypeptide comprising (1) an antibody or antibody fragment that is capable of binding to a tumor-associated antigen expressed on the chemo-resistant tumor and (2) a nanocage monomer or subunit thereof. [0007] In some embodiments, the complex further comprises: a plurality of second fusion polypeptides, each second fusion polypeptide comprising (1) an Fc polypeptide and (2) a nanocage monomer or subunit thereof. [0008] In some embodiments, each second fusion polypeptide comprises the Fc polypeptide linked to the nanocage monomer or subunit thereof via an amino acid linker. [0009] In some embodiments, the amino acid linker comprises a (GnS)m linker, e.g., a (GGGGS)m (SEQ ID NO:50) linker. [0010] In some embodiments, the Fc polypeptide comprises a single-chain Fc (scFc) comprising two Fc chains, wherein the two Fc chains are linked via an amino acid linker, e.g., a (GnS)m linker such as a (GGGGS)m (SEQ ID NO:50) linker. [0011] In some embodiments, the Fc polypeptide comprises an IgG1 Fc chain. In some embodiments, the IgG1 Fc chain comprises (1) an amino acid residue other than glycine at position 237; and (2) a proline residue at position 329, according to EU numbering. In some embodiments, the IgG1 Fc chain comprises an alanine at position 237 according to EU numbering. [0012] In some embodiments, the IgG1 Fc chain comprises: an alanine at position 234, an alanine at position 235, an arginine at position 236, and a leucine at position 330, according to EU numbering. [0013] In some embodiments, the nanocage monomer or subunit thereof is a ferritin monomer or subunit thereof, such as a ferritin light chain or subunit thereof and/or a human ferritin or subunit thereof. [0014] In some embodiments, the self-assembled polypeptide complex does not comprise any ferritin heavy chains or subunits of ferritin heavy chains. [0015] In some embodiments, at least a portion of the plurality of first fusion polypeptides and/or a portion of the plurality of second fusion polypeptides are fusion polypeptides which each comprise a ferritin monomer subunit. [0016] In some embodiments, (a) each first fusion polypeptide comprises a C-half-ferritin, and each second fusion polypeptide comprises an N-half-ferritin; or (b) each first fusion 2 IPTS/124242861.1
Attorney Docket No.90702160 polypeptide comprises an N-half ferritin, and each second fusion polypeptide comprises a C- half-ferritin. [0017] In some embodiments, the self-assembled polypeptide complex is characterized by a 1:1 ratio of first fusion polypeptides to second fusion polypeptides. [0018] In some embodiments, the total number of fusion polypeptides in each self- assembled polypeptide complex is at least 24 or at least 32. [0019] In some embodiments, the total number of fusion polypeptides in each self- assembled polypeptide complex is about 24 or about 32. [0020] In some embodiments, the total number of fusion polypeptides in each self- assembled polypeptide complex is between 24 and 48. [0021] In some embodiments, within each first fusion polypeptide, the antibody or antibody fragment is linked to the N-terminus of the nanocage monomer or subunit thereof. [0022] In some embodiments, each first fusion polypeptide comprises (1) a Fab fragment and (2) a nanocage monomer or subunit thereof. In some embodiments, each first fusion polypeptide does not comprise any antibody CH2 or CH3 domains. [0023] In some embodiments, the tumor-associated antigen is a TNF receptor superfamily member, e.g., a death receptor, such as DR5 (also known as TRAIL receptor 2 (TRAILR2). [0024] In some embodiments, the antibody or antibody fragment is conatumumab, tigatuzumab, lexatumumab, drozitumab, or a DR5-binding fragment of any of the foregoing. [0025] In some embodiments, the antibody or antibody fragment is conatumumab or a DR5-binding fragment thereof. [0026] In some embodiments, the antibody or antibody fragment comprises (1) a heavy chain comprising CDR-H1, CDR-H2, and CDR-H3 and (2) a light chain comprising CDR- L1, CDR-L2, and CDR-L3, wherein [0027] (a) (i) the CDR-H1 has a sequence of SEQ ID NO:23 or a sequence differing by one or two amino acids therefrom; (ii) the CDR-H2 has a sequence of SEQ ID NO:24 or a sequence differing by one or two amino acids therefrom; (iii) the CDR-H3 has a sequence of SEQ ID NO:25 or a sequence differing by one or two amino acids therefrom; (iv) the CDR-L1 has a sequence of SEQ ID NO:20 or a sequence differing by one or two amino acids therefrom; 3 IPTS/124242861.1
Attorney Docket No.90702160 (v) the CDR-L2 has a sequence of SEQ ID NO:21 or a sequence differing by one or two amino acids therefrom; and (vi) the CDR-L3 has a sequence of SEQ ID NO:22 or a sequence differing by one or two amino acids therefrom; [0028] (b) (i) the CDR-H1 has a sequence of SEQ ID NO:31 or a sequence differing by one or two amino acids therefrom; (ii) the CDR-H2 has a sequence of SEQ ID NO:32 or a sequence differing by one or two amino acids therefrom; (iii) the CDR-H3 has a sequence of SEQ ID NO:33 or a sequence differing by one or two amino acids therefrom; (iv) the CDR-L1 has a sequence of SEQ ID NO:28 or a sequence differing by one or two amino acids therefrom; (v) the CDR-L2 has a sequence of SEQ ID NO:29 or a sequence differing by one or two amino acids therefrom; and (vi) the CDR-L3 has a sequence of SEQ ID NO:30 or a sequence differing by one or two amino acids therefrom; [0029] (c) (i) the CDR-H1 has a sequence of SEQ ID NO:39 or a sequence differing by one or two amino acids therefrom; (ii) the CDR-H2 has a sequence of SEQ ID NO:40 or a sequence differing by one or two amino acids therefrom; (iii) the CDR-H3 has a sequence of SEQ ID NO:41 or a sequence differing by one or two amino acids therefrom; (iv) the CDR-L1 has a sequence of SEQ ID NO:36 or a sequence differing by one or two amino acids therefrom; (v) the CDR-L2 has a sequence of SEQ ID NO:37 or a sequence differing by one or two amino acids therefrom; and (vi) the CDR-L3 has a sequence of SEQ ID NO:38 or a sequence differing by one or two amino acids therefrom; or 4 IPTS/124242861.1
Attorney Docket No.90702160 [0030] (d) (i) the CDR-H1 has a sequence of SEQ ID NO:47 or a sequence differing by one or two amino acids therefrom; (ii) the CDR-H2 has a sequence of SEQ ID NO:48 or a sequence differing by one or two amino acids therefrom; (iii) the CDR-H3 has a sequence of SEQ ID NO:49 or a sequence differing by one or two amino acids therefrom; (iv) the CDR-L1 has a sequence of SEQ ID NO:44 or a sequence differing by one or two amino acids therefrom; (v) the CDR-L2 has a sequence of SEQ ID NO:45 or a sequence differing by one or two amino acids therefrom; and (vi) the CDR-L3 has a sequence of SEQ ID NO:46 or a sequence differing by one or two amino acids therefrom. [0031] In some embodiments, the antibody fragment comprises (1) a heavy chain comprising CDR-H1, CDR-H2, and CDR-H3 and (2) a light chain comprising CDR-L1, CDR-L2, and CDR-L3, wherein [0032] (a) (i) the CDR-H1 has a sequence of SEQ ID NO:23, (ii) the CDR-H2 has a sequence of SEQ ID NO:24, (iii) the CDR-H3 has a sequence of SEQ ID NO:25, (iv) the CDR-L1 has a sequence of SEQ ID NO:20, (v) the CDR-L2 has a sequence of SEQ ID NO:21, and (vi) the CDR-L3 has a sequence of SEQ ID NO:22; [0033] (b) (i) the CDR-H1 has a sequence of SEQ ID NO:31, (ii) the CDR-H2 has a sequence of SEQ ID NO:32, (iii) the CDR-H3 has a sequence of SEQ ID NO:33, (iv) the CDR-L1 has a sequence of SEQ ID NO:28, (v) the CDR-L2 has a sequence of SEQ ID NO:29, and (vi) the CDR-L3 has a sequence of SEQ ID NO:30; [0034] (c) (i) the CDR-H1 has a sequence of SEQ ID NO:39, (ii) the CDR-H2 has a sequence of SEQ ID NO:40, (iii) the CDR-H3 has a sequence of SEQ ID NO:41, (iv) the CDR-L1 has a sequence of SEQ ID NO:36, 5 IPTS/124242861.1
Attorney Docket No.90702160 (v) the CDR-L2 has a sequence of SEQ ID NO:37, and (vi) the CDR-L3 has a sequence of SEQ ID NO:38; or [0035] (d) (i) the CDR-H1 has a sequence of SEQ ID NO:47, (ii) the CDR-H2 has a sequence of SEQ ID NO:48, (iii) the CDR-H3 has a sequence of SEQ ID NO:49, (iv) the CDR-L1 has a sequence of SEQ ID NO:44, (v) the CDR-L2 has a sequence of SEQ ID NO:45, and (vi) the CDR-L3 has a sequence of SEQ ID NO:46. [0036] In some embodiments, the antibody fragment comprises (1) a heavy chain variable region having at least 85% identical to a reference VH sequence and (2) a light chain variable region having at least 85% identical to a reference VL sequence, wherein: (a) the reference VH sequence has a sequence of SEQ ID NO:19 and the reference VL sequence has a sequence of SEQ ID NO:18; (b) the reference VH sequence has a sequence of SEQ ID NO:27 and the reference VL sequence has a sequence of SEQ ID NO:26; (c) the reference VH sequence has a sequence of SEQ ID NO:35 and the reference VL sequence has a sequence of SEQ ID NO:34; or (d) the reference VH sequence has a sequence of SEQ ID NO:43 and the reference VL sequence has a sequence of SEQ ID NO:42. [0037] In some embodiments, the subject is a mammal, e.g., a human. [0038] In some embodiments, the tumor is a colon tumor. [0039] In some embodiments, the subject has a chemo-resistant tumor, e.g., a tumor resistant to a taxane, a vinca alkaloid, an anthracycline, a platinum-containing compound, or any combination of the foregoing. For example, the tumor may be resistant to a taxane, e.g., paclitaxel, taxane, or both; a vinca alkaloid, e.g., vincristine; an anthracycline, e.g., doxorubicin; and/or a platinum-containing compound, e.g., satraplatin, and oxaliplatin. [0040] In some embodiments, the step of administering comprises administration by a systemic route, e.g., subcutaneous, intravenous, or intramuscular, inhalation, or intranasal administration. [0041] In some embodiments, the step of administering comprises administering (or the subject is administered) more than one dose of the pharmaceutical composition. For example, 6 IPTS/124242861.1
Attorney Docket No.90702160 the pharmaceutical composition may be administered once a week for at least two weeks, at least three weeks, or more. [0042] In some embodiments, the step of administering or the use results in slowing, inhibiting progression of, or regression of the tumor [0043] In some embodiments, provided are methods of treating a subject who has a chemo- resistant tumor or is at risk of having a chemo-resistant tumor, the method comprising a step of administering a pharmaceutical composition comprising a self-assembled polypeptide complex to the subject, wherein the self-assembled polypeptide complex comprises: (a) a plurality of first fusion polypeptides, each first fusion polypeptide comprising (1) an antibody fragment that is capable of binding to DR5 and (2) a ferritin monomer or subunit thereof; and (b) a plurality of second fusion polypeptides, each second fusion polypeptide comprising (1) an scFc and (2) a ferritin monomer or subunit thereof, and, wherein the scFc comprises two IgG1 Fc chains, each IgG1 Fc chain comprising: an alanine at position 234, an alanine at position 235, an arginine at position 236, an alanine at position 237, a proline at position 329, and a leucine at position 330, according to EU numbering. [0044] In some embodiments, provided are uses of a pharmaceutical composition comprising a self-assembled polypeptide complex to treating a subject who has a chemo- resistant tumor or is at risk of having a chemo-resistant tumor, wherein the self-assembled polypeptide complex comprises: (a) a plurality of first fusion polypeptides, each first fusion polypeptide comprising (1) an antibody fragment that is capable of binding to DR5 and (2) a ferritin monomer or subunit thereof; and (b) a plurality of second fusion polypeptides, each second fusion polypeptide comprising (1) an scFc and (2) a ferritin monomer or subunit thereof, and, wherein the scFc comprises two IgG1 Fc chains, each IgG1 Fc chain comprising: an alanine at position 234, an alanine at position 235, an arginine at position 236, an alanine at position 237, a proline at position 329, and a leucine at position 330, according to EU numbering. [0045] In some embodiments, the step of administering or the use results in slowing, inhibiting progression of, or regression of the tumor [0046] In one aspect, provided are uses of a self-assembled polypeptide complex in the manufacture of a medicament to treat a chemo-resistant tumor, wherein the self-assembled polypeptide complex comprises: a plurality of first fusion polypeptides, each first fusion polypeptide comprising (1) an antibody or antibody fragment that is capable of binding to a 7 IPTS/124242861.1
Attorney Docket No.90702160 tumor-associated antigen expressed on the chemo-resistant tumor and (2) a nanocage monomer or subunit thereof. BRIEF DESCRIPTION OF THE DRAWINGS [0047] FIG.1A is a diagrammatic representation of human ferritin light chain (hFTL) and exemplary N-half ferritin (N-hFTL) and C-half ferritin (C-hFTL) molecules. [0048] FIG.1B is a diagrammatic representation of fusion polypeptides that together form exemplary Multabodies of the disclosure. [0049] FIG.2A depicts a tumor growth curve, showing tumor volume plotted against time after tumor cell injection in mice injected with vehicle (black curve), conatumumab (“parent IgG,” green curve), or a DR5-targeting Multabody (“MB,” orange curve). The red arrows indicate treatment time points. Experiments are described in Example 2. [0050] FIG.2B is a survival curve of HCT-15 xenograft mice for mice injected with vehicle (black curve), conatumumab (“parent IgG,” green curve), or a DR5-targeting Multabody (“MB,” orange curve). Experiments are described in Example 2. [0051] FIG.3 is a schematic depicting the design of a dose range efficacy study of a DR5- targeting Multabody in an HCT-15 xenograft mouse model. Experiments are described in Example 3. [0052] FIG.4A depicts a tumor growth curve, showing tumor volume plotted against time after treatment for HCT-15 xenograft mice administered vehicle or a DR5-targeting Multabody (“MB”) at 0.1 mg/kg, 0.25 mg/kg, 1 mg/kg, or 5 mg/kg. See Example 3. [0053] FIG.4B depicts the amount of Multabodies detected in blood of the mice from the dose range efficacy study described in Example 3, over time from the first dose. [0054] FIG.5 is a schematic depicting the design of a study of large tumor penetration and apoptosis induction by a DR5-targeting Multabody in an HCT-15 xenograft mouse model. Experiments are described in Example 4. [0055] FIGs.6A-6B depict representative tumor sections from mice that were untreated (FIGs.6A and 6B) or treated with a DR5-targeting Multabody (“MB”) (FIGs.6C and 6D). Sections were stained with an antibody against cleaved caspase-3, a marker of apoptosis. Experiments are described in Example 4. 8 IPTS/124242861.1
Attorney Docket No.90702160 DETAILED DESCRIPTION [0056] The present disclosure provides methods of treating a subject who has or is at risk of having a chemo-resistant tumor by administering to the subject a pharmaceutical composition comprising a self-assembled polypeptide complex (a “Multabody”) as described further herein. Methods disclosed herein have demonstrated therapeutic efficacy, e.g., ability to cause tumor suppression and/or regression at least over a period of time in a highly aggressive chemo-resistant xenograft tumor model. Definitions [0057] The terms “about” and “approximately,” when used herein in reference to a value, are used interchangeably and refer to a value that is similar to the referenced value. In general, those skilled in the art, familiar with the context, will appreciate the relevant degree of variation encompassed by “about” or “approximately” in that context. For example, in some embodiments, the terms “about” and “approximately” may encompass a range of values that fall within 25%, 20%, 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, or less of the referred value. [0058] As used herein, the terms “alter,” “altered,” “decrease,” “decreased,” “increase,” “increased,” or “reduction,” “reduced,” (e.g., in reference to certain outcomes or effects) have meanings relative to a reference level. In some embodiments, in the context of discussing mutations in an Fc chain or Fc polypeptide, the reference level is a level known or as determined with an IgG that does not contain the referenced mutation(s) in the Fc region. [0059] As used herein, the term “binding,” unless otherwise specified, refers to a non- covalent association between or among two or more entities. "Direct" binding involves physical contact between entities or moieties; indirect binding involves physical interaction by way of physical contact with one or more intermediate entities. Binding between two or more entities can typically be assessed in any of a variety of contexts--including where interacting entities or moieties are studied in isolation or in the context of more complex systems (e.g., while covalently or otherwise associated with a carrier entity and/or in a biological system or cell). As used herein, the phrases “non-binding” or “no binding,” or similar phrases, between two entities refers to 1) a lack of detectable binding or 2) binding below a set threshold that corresponds to no binding in an appropriate assay, e.g., an in vitro binding assay such as biolayer interferometry. For example, in some embodiments, in an in 9 IPTS/124242861.1
Attorney Docket No.90702160 vitro biolayer interferometry assay, a maximal association binding response of less than 0.1 nm after 180 seconds to a biosensor loaded with 0.8 nm of target when the test article is present at a concentration of 20 nM is classified as “non-binding.” [0060] As used herein, the term “chemo-resistant,” when used to describe a tumor, refers to the tumor’s characteristic of being poorly responsive to a chemotherapy drug. The term “chemo-resistant” encompasses both intrinsic resistance (i.e., resistance even without prior exposure) to one or more chemotherapy drugs and acquired resistance (i.e., resistance developed after exposure) to one or more chemotherapy drugs. A chemo-resistant tumor may be resistant to one or more chemotherapy drugs in the same class and/or to one or more classes of chemotherapy drugs. [0061] The terms “ferritin” and “apoferritin” are used interchangeably herein and generally refer to a polypeptide (e.g., a ferritin chain) that is capable of assembling into a ferritin complex which typically comprises 24 protein subunits. In some embodiments, the ferritin is a human ferritin, e.g., a human ferritin light chain, e.g., a human ferritin light chain having at least 85% sequence identity to SEQ ID NO:1 or UniProt P02792. In some embodiments, the ferritin is a wild-type ferritin. For example, the ferritin may be a wild-type human ferritin. [0062] The term “ferritin monomer,” is used herein to refer to a single chain of a ferritin that, in the presence of other ferritin chains, is capable of self-assembling into a polypeptide complex comprising a plurality of ferritin chains, e.g., 24 or more ferritin chains. [0063] As used herein, the term “linker” is used to refer to an entity that connects two or more elements to form a multi-element agent. For example, those of ordinary skill in the art appreciate that a polypeptide (e.g., fusion polypeptide) whose structure includes two or more functional or organizational domains often includes a stretch of amino acids between such domains that links them to one another. In some embodiments, a polypeptide comprising a linker element has an overall structure of the general form S1-L-S2, wherein S1 and S2 may be the same or different and represent two domains associated with one another by the linker (L). In some embodiments, the linker is an “amino acid linker,” that is, it comprises amino acid residues, e.g., an amino acid linker may comprise at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100 or more amino acid residues. In some embodiments, a linker is characterized in that it tends not to adopt a rigid three-dimensional structure, but rather provides flexibility to the polypeptide. 10 IPTS/124242861.1
Attorney Docket No.90702160 [0064] The term “multispecific,” as used herein, refers to the characteristic of having at least two binding sites at which at least two different binding partners, e.g., an antigen or receptor (e.g., Fc receptor), can bind. For example, a polypeptide complex that comprises at least two Fab fragments, wherein each of the two Fab fragments is capable of binding to a different antigen, is “multispecific.” As an additional example, a polypeptide complex that comprises an Fc fragment (which is capable of binding to an Fc receptor) and a Fab fragment (which is capable of binding to an antigen) is “multispecific.” [0065] The term “multivalent,” as used herein, refers to the characteristic of having at least two binding sites at which a binding partner, e.g., an antigen or receptor (e.g., Fc receptor), can bind. The binding partners that can bind to at least two binding sites may be the same or different. [0066] The term “nanocage monomer,” as used herein, refers to a single chain of a polypeptide that is capable of self-assembling with other nanocage monomers to form a self- assembled polypeptide complex comprising a plurality of nanocage monomers. In some embodiments, the nanocage monomer is selected from monomers of ferritin, apoferritin, encapsulin, sulfur oxygenase reductase (SOR), lumazine synthase, pyruvate dehydrogenase, carboxysome, vault proteins, GroEL, heat shock protein, E2P coat protein, MS2 coat protein, fragments thereof, and variants thereof. [0067] The term “polypeptide,” as used herein, generally has its art-recognized meaning of a polymer of at least three amino acids, e.g., linked to each other by peptide bonds. Those of ordinary skill in the art will appreciate that the term “polypeptide” is intended to be sufficiently general as to encompass not only polypeptides having a complete sequence recited herein, but also to encompass polypeptides that represent functional fragments (i.e., fragments retaining at least one activity) of such complete polypeptides. Moreover, those of ordinary skill in the art understand that protein sequences generally tolerate some substitution without destroying activity. Thus, any polypeptide that retains activity and shares at least about 30-40% overall sequence identity, often greater than about 50%, 60%, 70%, or 80%, and further usually including at least one region of much higher identity, often greater than 90% or even 95%, 96%, 97%, 98%, or 99% in one or more highly conserved regions, usually encompassing at least 3-4 and often up to 20 or more amino acids, with another polypeptide of the same class, is encompassed within the relevant term “polypeptide” as used herein. Polypeptides may contain L-amino acids, D-amino acids, or both and may contain any of a variety of amino acid modifications or analogs known in the art. Useful modifications 11 IPTS/124242861.1
Attorney Docket No.90702160 include, e.g., terminal acetylation, amidation, methylation, glycosylation etc. In some embodiments, proteins may comprise natural amino acids, non-natural amino acids, synthetic amino acids, and combinations thereof [0068] The term “self-assembled,” when used in reference to a macromolecular complex (e.g., a polypeptide complex), refers to the spontaneous formation of that complex when sufficient constituents of the complex (e.g., fusion polypeptides) to be formed are present. In some embodiments, complexes self-assemble in physiological conditions, or in a buffer (e.g., a solution) that corresponds to physiological conditions. [0069] As used herein, the term “subject” to an organism, typically a mammal (e.g., a human). In some embodiments, a subject is suffering from or susceptible to a relevant disease, disorder or condition. In some embodiments, a subject displays one or more symptoms or characteristics of a disease, disorder or condition. In some embodiments, a subject is someone with one or more features characteristic of susceptibility to or risk of a disease, disorder, or condition. In some embodiments, a subject is a patient. In some embodiments, a subject is a subject to whom diagnosis and/or therapy is and/or has been administered. [0070] As used herein, the term “treatment” (also “treat” or “treating”) refers to any administration of a therapy that partially or completely alleviates, ameliorates, relieves, inhibits, delays onset of, reduces severity of, and/or reduces incidence of one or more symptoms, features, and/or causes of a particular disease, disorder, and/or condition. In some embodiments, such treatment may be of a subject who does not exhibit signs of the relevant disease, disorder and/or condition and/or of a subject who exhibits only early signs of the disease, disorder, and/or condition. Alternatively, or additionally, such treatment may be of a subject who exhibits one or more established signs of the relevant disease, disorder and/or condition. In some embodiments, treatment may be of a subject who has been diagnosed as suffering from the relevant disease, disorder, and/or condition. In some embodiments, treatment may be of a subject known to have one or more susceptibility factors that are statistically correlated with increased risk of development of the relevant disease, disorder, and/or condition. A. Fusion polypeptides [0071] In many embodiments, fusion polypeptides compatible with compositions and methods disclosed herein generally comprise a nanocage monomer or subunit thereof linked 12 IPTS/124242861.1
Attorney Docket No.90702160 to either an antibody fragment which is capable of binding to a tumor-associated antigen expressed on a chemo-resistant tumor or an “Fc polypeptide” as described herein. Within the fusion polypeptide, the antibody fragment or Fc polypeptide may be linked to the nanocage monomer or subunit thereof at a particular terminus of the nanocage monomer or subunit thereof, e.g., the N-terminus or the C-terminus. In some embodiments, antibody fragment or Fc fragment is linked via an amino acid linker, such as a linker as described herein. 1. Nanocage monomers and subunits thereof [0072] In some embodiments, the nanocage monomer is a ferritin monomer. [0073] The term “ferritin monomer,” is used herein to refer to a single chain of a ferritin that, in the presence of other ferritin chains, is capable of self-assembling into a polypeptide complex comprising a plurality of ferritin chains, e.g., 24 or more ferritin chains. In some embodiments, the ferritin monomer is a ferritin light chain. In some embodiments, the ferritin monomer does not include a ferritin heavy chain or other ferritin components capable of binding to iron or capable of ferroxidase activity. [0074] In some embodiments, each fusion polypeptide within the self-assembled polypeptide complex comprises a ferritin light chain or a subunit of a ferritin light chain. In these embodiments, the self-assembled polypeptide complex does not comprise any ferritin heavy chains or subunits of ferritin heavy chains. [0075] In some embodiments, the ferritin monomer is a human ferritin chain, e.g., a human ferritin light chain, e.g., a human ferritin light chain having the sequence of at least residues 2-175 of SEQ ID NO:1. [0076] A “subunit” of a ferritin monomer refers to a portion of a ferritin monomer that is capable of spontaneously associating with another, distinct subunit of a ferritin monomer, so that the subunits together form a ferritin monomer, which ferritin monomer, in turn, is capable of self-assembling with other ferritin monomers to form a polypeptide complex. [0077] In some embodiments, the ferritin monomer subunit comprises approximately half of a ferritin monomer. As used herein, the term “N-half ferritin” refers to approximately half of a ferritin chain, which half comprises the N-terminus of the ferritin chain. As used herein, the term “C-half ferritin” refers to approximately half a ferritin chain, which half comprises the C-terminus of the ferritin chain. The exact point at which a ferritin chain may be divided to form the N-half ferritin and the C-half ferritin may vary depending on the embodiment. In the context of ferritin monomer subunits based on human ferritin light chain, for example, the 13 IPTS/124242861.1
Attorney Docket No.90702160 halves may be divided at a point that corresponds to a position between about position 75 to about position 100 of SEQ ID NO:1 (or a substantial portion thereof). For example, in some embodiments, an N-half ferritin based on a human ferritin light chain has an amino acid sequence corresponding to residues 1-95 of SEQ ID NO: 1 (or a substantial portion thereof, e.g., residues 2-95 of SEQ ID NO: 1), and a C-half ferritin based on a human ferritin light chain has an amino acid sequence corresponding to residues 96-175 of SEQ ID NO: 1 (or a substantial portion thereof). [0078] In some embodiments, the halves are divided at a point that corresponds to a position between about position 85 to about position 92 of SEQ ID NO: 1. For example, in some embodiments, an N-half ferritin based on a human ferritin light chain has an amino acid sequence corresponding to residues 1-90 of SEQ ID NO:1 (or a substantial portion thereof, e.g., residues 2-90 of SEQ ID NO: 1), and a C-half ferritin based on a human ferritin light chain has an amino acid sequence corresponding to residues 91-175 of SEQ ID NO:1 (or a substantial portion thereof. 2. Antibody fragments capable of binding to a tumor-associated antigen expressed on the chemo-resistant tumor [0079] Antibody fragments typically comprise a heavy chain variable region (e.g., a VH). In certain embodiments, the antibody fragment comprises a heavy chain variable domain (e.g., VH) and a light chain variable domain (e.g., a VL or VK). In certain embodiments, the antibody fragment comprises a Fab which comprises a heavy chain variable domain (e.g., VH) and a light chain variable domain (e.g., a VL or VK). [0080] In certain embodiments, a fusion polypeptide (e.g., the first fusion polypeptide) does not contain a full-length antibody, and contains an antibody fragment which is missing one or more domains from a full-length antibody. For example, in some embodiments, the antibody fragment does not comprise any domains from the Fc region, e.g., does not comprise any CH2 or CH3 domains. [0081] In some embodiments, the antibody fragment is a Fab. In some embodiments, the antibody fragment is a single-chain Fab (scFab); for example, a fusion polypeptide comprising both the heavy and light chains of a Fab, optionally linked by a linker (e.g., amino acid linker as disclosed herein) is used. [0082] In some embodiments, the tumor-associated antigen expressed on the chemo- resistant tumor is a tumor necrosis factor (TNF) receptor superfamily member. The TNF 14 IPTS/124242861.1
Attorney Docket No.90702160 receptor superfamily of cytokine receptors are able to bind TNFs via an extracellular domain and, when activated, typically form trimeric complexes in the plasma membrane. In some embodiments, the tumor-associated antigen is a death receptor (e.g., TNFR1, Fas receptor, DR4 (also known as TRAIL receptor 1), or DR5 (also known as TRAIL receptor 2)), a class of receptors within the TNF receptor superfamily which comprise a “death domain.” Death receptors play a role in apoptosis. [0083] An antibody fragment can be assessed for its suitability for use in accordance with the methods disclosed herein using any of a variety of methods known in the art. For example, binding of an antibody or antibody fragment to a desired target, e.g., an antigen expressed on a chemo-resistant tumor, can be assessed using surface plasmon resonance or biolayer interferometry. Alternatively or additionally, when the tumor-associated antigen is a TNF receptor superfamily member, an antibody fragment can be assessed for its ability to induce trimerization of the TNF receptor. Alternatively or additionally, wherein the tumor- associated antigen is a death receptor, an antibody fragment can be assessed for its ability to induce apoptosis, e.g., in a cell-based apoptosis assay. [0084] In some embodiments, the tumor-associated antigen is DR5. For example, the antibody fragment may be capable of binding to an epitope within DR5, exemplary sequences of which are shown in SEQ ID NO:14 to SEQ ID NO:17. In certain embodiments, the antibody fragment capable of binding to DR5 is an antibody fragment of, or derived from, any of a variety of DR5 antibodies, including, e.g., fully human, humanized or chimeric DR5 antibodies. The DR5 antibody from which the antibody fragment is obtained or derived can be of any of a variety of antibody classes, including, e.g., an IgG1 antibody, an IgG2 antibody, an IgG4 antibody. In some embodiments, the antibody fragment is obtained or derived from an agonistic DR5 antibody, e.g., an agonistic humanized DR5 antibody. [0085] Non-limiting examples of DR5 antibodies include, e.g., conatumumab, tigatuzumab, lexatumumab, and drozitumab. [0086] In some embodiments, antibody fragments capable of binding to DR5 comprises heavy chain and light chain CDRs having similar sequences (e.g., each CDR being identical, or having one or two amino acid substitutions) to that of the heavy and light chain CDRs of a DR5 antibody. [0087] In some embodiments, antibody fragments capable of binding to DR5 comprise (1) a heavy chain comprising CDR-H1, CDR-H2, and CDR-H3 and (2) a light chain comprising CDR-L1, CDR-L2, and CDR-L3, wherein 15 IPTS/124242861.1
Attorney Docket No.90702160 (a) (i) the CDR-H1 has a sequence of SEQ ID NO:23 or a sequence differing by one or two amino acid residues therefrom, (ii) the CDR-H2 has a sequence of SEQ ID NO:24 or a sequence differing by one or two amino acid residues therefrom, (iii) the CDR-H3 has a sequence of SEQ ID NO:25 or a sequence differing by one or two amino acid residues therefrom, (iv) the CDR-L1 has a sequence of SEQ ID NO:20 or a sequence differing by one or two amino acid residues therefrom, (v) the CDR-L2 has a sequence of SEQ ID NO:21 or a sequence differing by one or two amino acid residues therefrom, and (vi) the CDR-L3 has a sequence of SEQ ID NO:22 or a sequence differing by one or two amino acid residues therefrom; (b) (i) the CDR-H1 has a sequence of SEQ ID NO:31 or a sequence differing by one or two amino acid residues therefrom, (ii) the CDR-H2 has a sequence of SEQ ID NO:32 or a sequence differing by one or two amino acid residues therefrom, (iii) the CDR-H3 has a sequence of SEQ ID NO:33 or a sequence differing by one or two amino acid residues therefrom, (iv) the CDR-L1 has a sequence of SEQ ID NO:28 or a sequence differing by one or two amino acid residues therefrom, (v) the CDR-L2 has a sequence of SEQ ID NO:29 or a sequence differing by one or two amino acid residues therefrom, and (vi) the CDR-L3 has a sequence of SEQ ID NO:30 or a sequence differing by one or two amino acid residues therefrom, or (c) (i) the CDR-H1 has a sequence of SEQ ID NO:39 or a sequence differing by one or two amino acid residues therefrom, (ii) the CDR-H2 has a sequence of SEQ ID NO:40 or a sequence differing by one or two amino acid residues therefrom, (iii) the CDR-H3 has a sequence of SEQ ID NO:41 or a sequence differing by one or two amino acid residues therefrom, (iv) the CDR-L1 has a sequence of SEQ ID NO:36 or a sequence differing by one or two amino acid residues therefrom, 16 IPTS/124242861.1
Attorney Docket No.90702160 (v) the CDR-L2 has a sequence of SEQ ID NO:37 or a sequence differing by one or two amino acid residues therefrom, and (vi) the CDR-L3 has a sequence of SEQ ID NO:38 or a sequence differing by one or two amino acid residues therefrom; or (d) (i) the CDR-H1 has a sequence of SEQ ID NO:47 or a sequence differing by one or two amino acid residues therefrom, (ii) the CDR-H2 has a sequence of SEQ ID NO:48 or a sequence differing by one or two amino acid residues therefrom, (iii) the CDR-H3 has a sequence of SEQ ID NO:49 or a sequence differing by one or two amino acid residues therefrom, (iv) the CDR-L1 has a sequence of SEQ ID NO:44 or a sequence differing by one or two amino acid residues therefrom, (v) the CDR-L2 has a sequence of SEQ ID NO:45 or a sequence differing by one or two amino acid residues therefrom, and (vi) the CDR-L3 has a sequence of SEQ ID NO:46 or a sequence differing by one or two amino acid residues therefrom. [0088] In some embodiments, antibody fragments capable of binding to DR5 comprises heavy and light chain CDRs having sequences identical to those of the heavy and light chain CDRs of a DR5 antibody, except for one or two amino acid substitutions total across all six CDRs. [0089] In some embodiments, antibody fragments capable of binding to DR5 comprises heavy chain and light chain complementarity-determining regions (CDRs) having the same sequences as the CDRs of a DR5 antibody. [0090] In some embodiments, antibody fragments capable of binding to DR5 comprise (1) a heavy chain comprising CDR-H1, CDR-H2, and CDR-H3 and (2) a light chain comprising CDR-L1, CDR-L2, and CDR-L3, wherein (a) (i) the CDR-H1 has a sequence of SEQ ID NO:23; (ii) the CDR-H2 has a sequence of SEQ ID NO:24; (iii) the CDR-H3 has a sequence of SEQ ID NO:25; (iv) the CDR-L1 has a sequence of SEQ ID NO:20; (v) the CDR-L2 has a sequence of SEQ ID NO:21; and (vi) the CDR-L3 has a sequence of SEQ ID NO:22; 17 IPTS/124242861.1
Attorney Docket No.90702160 (b) (i) the CDR-H1 has a sequence of SEQ ID NO:31, (ii) the CDR-H2 has a sequence of SEQ ID NO:32, (iii) the CDR-H3 has a sequence of SEQ ID NO:33, (iv) the CDR-L1 has a sequence of SEQ ID NO:28, (v) the CDR-L2 has a sequence of SEQ ID NO:29, and (vi) the CDR-L3 has a sequence of SEQ ID NO:30; (c) (i) the CDR-H1 has a sequence of SEQ ID NO:39, (ii) the CDR-H2 has a sequence of SEQ ID NO:40, (iii) the CDR-H3 has a sequence of SEQ ID NO:41, (iv) the CDR-L1 has a sequence of SEQ ID NO:36, (v) the CDR-L2 has a sequence of SEQ ID NO:37, and (vi) the CDR-L3 has a sequence of SEQ ID NO:38; or (d) (i) the CDR-H1 has a sequence of SEQ ID NO:47, (ii) the CDR-H2 has a sequence of SEQ ID NO:48, (iii) the CDR-H3 has a sequence of SEQ ID NO:49, (iv) the CDR-L1 has a sequence of SEQ ID NO:44, (v) the CDR-L2 has a sequence of SEQ ID NO:45, and (vi) the CDR-L3 has a sequence of SEQ ID NO:46. [0091] In some embodiments, the antibody fragment capable of binding to DR5 comprises (1) a heavy chain variable region having at least 85%, at least 87.5%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to a heavy chain variable region from a DR5 antibody and (2) a light chain variable region having at least 85%, at least 87.5%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to a light chain variable region from a DR5 antibody. [0092] In some embodiments, the antibody fragment capable of binding to DR5 comprises 18 IPTS/124242861.1
Attorney Docket No.90702160 (1) a heavy chain variable region having at least 85%, at least 87.5%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to a reference VH sequence and (2) a light chain variable region having at least 85%, at least 87.5%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to a reference VL sequence, wherein: (a) the reference VH sequence has a sequence of SEQ ID NO:19 and the reference VL sequence has a sequence of SEQ ID NO:18, (b) the reference VH sequence has a sequence of SEQ ID NO:27 and the reference VL sequence has a sequence of SEQ ID NO:26, (c) the reference VH sequence has a sequence of SEQ ID NO:35 and the reference VL sequence has a sequence of SEQ ID NO:34, or (d) the reference VH sequence has a sequence of SEQ ID NO:43 and the reference VL sequence has a sequence of SEQ ID NO:42. [0093] In embodiments where multiple types of fusion polypeptides having antibody fragments are used, the antibody fragments in the various types of fusion polypeptides may be capable of binding to the same epitope on DR5, capable of binding to epitopes that are distinct and non-overlapping on DR5, or capable of binding to epitopes that are distinct but overlapping on DR5. 3. Fc polypeptides [0094] In certain embodiments, fragment crystallizable (Fc) polypeptides comprise Fc chains that each have one or more mutations relative to a reference Fc chain of the same Ig class. As explained further herein below, the reference Fc chain may be of, e.g., the IgG1 class. Unless otherwise noted, numbering of residues within an antibody fragment, e.g., an Fc chain, throughout this disclosure is according to the EU numbering. [0095] In some embodiments, the Fc polypeptide comprises one or more human IgG1 Fc chains that is, except for mutations noted herein, the Fc polypeptide comprises an Fc chain that is substantially similar to that of the Fc chains within a wild type human IgG1. [0096] In some embodiments, the Fc polypeptide comprises one or more IgG1 Fc chains (e.g., human IgG1 Fc chains or a human Fc chains), that is, except for having particular residue(s) (which may be different than the residue(s) in the corresponding wild type Fc chains) at certain positions as noted herein, the Fc polypeptide comprises an Fc chain that has 19 IPTS/124242861.1
Attorney Docket No.90702160 an amino acid sequence that is substantially similar to that of the chains within a wild type IgG1 Fc. In some embodiments, the wild type IgG1 Fc is a human IgG1 Fc, in which each Fc chain has an amino acid sequence of SEQ ID NO:4. For example, an Fc polypeptide may comprise an Fc chain with an amino acid sequence that is at least 85%, at least 87.5%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to that of an Fc chain within a wild-type IgG1 Fc. In some embodiments, an Fc polypeptide comprises an Fc chain that comprises the particular residue(s) at certain position(s) specifically described for that Fc chain, but has an amino acid sequence that is otherwise 100% identical to a corresponding Fc chain within a wild type Fc chain, e.g., wild type IgG1 Fc chain. In some embodiments, the Fc polypeptide comprises an Fc chain that has an amino acid sequence that differs by at least one, at least two, at least three, or at least four amino acid residues from the sequence of SEQ ID NO:4. In some embodiments, the Fc polypeptide comprises an Fc chain that has an amino acid sequence that differs by no more than ten, no more than nine, no more than eight, no more than seven, no more than six, no more than five, or no more than four amino acid residues from the sequence of SEQ ID NO:4. [0097] In some embodiments, the Fc polypeptide is a single chain Fc (scFc), which comprises two Fc chains linked together by a covalent linker, e.g., via an amino acid linker. [0098] In certain embodiments, the Fc chain comprises (1) an amino acid residue other than glycine at position 237; and (2) a proline residue at position 329. In some embodiments, the Fc chain comprises an alanine at position 237. In some embodiments, the Fc chain is an IgG1 Fc chain and further comprises a mutation or set of mutations at one or more positions selected from position 234, position 235, position 236, position 330, and combinations thereof. [0099] For example, in some embodiments, the Fc chain is an IgG1 Fc chain that comprises an alanine at position 234, an alanine at position 235, an arginine at position 236, an alanine at position 237, a proline at position 329, and a leucine at position 330. [0100] In some embodiments, the Fc chain further comprises a mutation at a position associated with glycosylation, e.g., position 297 (e.g., by comprising a glutamine at position 297). [0101] In some embodiments, the Fc chain comprises a mutation or set of mutations (relative to a corresponding wild type Fc chain) associated with an altered characteristic as further described herein. By “associated with,” it is meant that the mutation or set of 20 IPTS/124242861.1
Attorney Docket No.90702160 mutations has been previously characterized, in the context of antibodies such as IgG antibodies, as conferring the altered characteristic (e.g., altered binding to FcRn, altered effector function, etc.) By “altered” it is meant that the characteristic (e.g., binding to an Fc receptor (e.g., an Fcγ receptor or an FcRn)), is different than that observed without the mutation or set of mutations. [0102] For example, in some embodiments, the altered characteristic comprises altered binding to an Fc receptor. [0103] In some embodiments, the altered characteristic comprising altered binding to an Fcγ receptor, e.g., a human FcγR. In some embodiments, the FcγR is a human FcγR selected from the group consisting of hFcγRI, hFcγRIIa, hFcγRIIb, hFcγRIIIa, hFcγRIIIb, and combinations thereof. [0104] In some embodiments, the altered binding comprises no binding, or significantly reduced binding, relative to a corresponding control (e.g., binding levels typically observed under similar circumstances with a corresponding wild type chain), in an assay, e.g., an in vitro assay. 4. Linkers [0105] In certain embodiments, linkers are used within fusion polypeptides and/or within single-chain molecules such as scFcs. In some embodiments, the linker is an amino acid linker. For example, a linker as employed herein may comprise from about 1 to about 100 amino acid residues, e.g., about 1 to about 70, about 2 to about 70, about 1 to about 30, or about 2 to about 30 amino acid residues. In some embodiments, the linker comprises at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, or at least 10 amino acid residues. [0106] In certain embodiments, the linker comprises a glycine-serine sequence, e.g., a (GnS)m sequence (e.g., GGS, GGGS, or GGGGS (SEQ ID NO:50) sequence) that is present in at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, or at least 14 copies within the linker. B. Self-assembled polypeptide complexes [0107] In one aspect, provided are self-assembled polypeptide complexes comprising a plurality of fusion polypeptides as disclosed herein. Generally, provided self-assembled 21 IPTS/124242861.1
Attorney Docket No.90702160 polypeptide complexes comprise (a) a plurality of first fusion polypeptides, each first fusion polypeptide comprising (1) an Fc polypeptide linked to (2) a nanocage monomer or subunit thereof, wherein the Fc polypeptide comprises an Fc chain having one or more mutations relative to a reference Fc chain of the same Ig class, and (b) a plurality of second fusion polypeptides, each second fusion polypeptide comprising (1) an antigen-binding antibody fragment linked to (2) a nanocage monomer or subunit thereof. [0108] In some embodiments, the nanocage monomer is a ferritin monomer, and each fusion polypeptide within the self-assembled polypeptide complex comprises a ferritin light chain or a subunit of a ferritin light chain. In these embodiments, the self-assembled polypeptide complex does not comprise any ferritin heavy chains, subunits of ferritin heavy chains, or other ferritin components capable of binding to iron or capable of ferroxidase activity. [0109] In some embodiments, the nanocage monomer or subunit thereof is a ferritin monomer subunit, and (a) each first fusion polypeptide comprises a ferritin monomer subunit which is C-half-ferritin and each second fusion polypeptide comprises a ferritin monomer subunit which is N-half-ferritin; or (b) each first fusion polypeptide comprises a ferritin monomer subunit which is N-half ferritin and each second fusion polypeptide comprises a ferritin monomer subunit which is C-half-ferritin. [0110] In some embodiments, the self-assembled polypeptide complex comprises between 24 and 48 fusion polypeptides in total. In some embodiments, the self-assembled polypeptide complex comprises 24 fusion polypeptides in total. In some embodiments, the self-assembled polypeptide complex comprises more than 24 fusion polypeptides, e.g., at least 26, at least 28, at least 30, at least 32 fusion polypeptides, at least 34 fusion polypeptides, at least 36 fusion polypeptides, at least 38 fusion polypeptides, at least 40 fusion polypeptides, at least 42 fusion polypeptides, at least 44 fusion polypeptides, at least 46 fusion polypeptides, or at least 48 fusion polypeptides in total. In some embodiments, the self-assembled polypeptide complex comprises about 32 fusion polypeptides. [0111] In some embodiments, the self-assembled polypeptide complex comprises at least 4, at least 5, least 6, at least 7, or at least 8 first fusion polypeptides. [0112] In some embodiments, the self-assembled polypeptide complex comprises at least 4, at least 5, least 6, at least 7, or at least 8 second fusion polypeptides. 22 IPTS/124242861.1
Attorney Docket No.90702160 [0113] In some embodiments, the self-assembled polypeptide complex further comprises at least 4, at least 5, least 6, at least 7, at least 8, at least 9, at least 10, least 11, at least 12, at least 13, at least 14, at least 15, or at least 16 third fusion polypeptides. [0114] In some embodiments, the self-assembled polypeptide complex comprises a ratio of approximately 1:1, 11:13, 3:5, 1:2, 7:17, 1:3, 2:7, 5:19, 1:4, 1:5, 1:6, 1:7, 1:8, 1:12, 1:24 of first fusion polypeptides to all other fusion polypeptides. Effects [0115] In certain embodiments, a provided self-assembled polypeptide complex is capable of inducing multimerization (e.g., trimerization) of TNF receptor super family receptors (e.g., death receptors, e.g., DR5 receptors) on a target cell (e.g., a cancer cell). [0116] In some embodiments, administration of a self-assembled polypeptide complex as disclosed herein to a subject results in an improvement in a clinical outcome or metric in the subject. For example, in a subject with a tumor, administration of the self-assembled polypeptide complex or a composition thereof may inhibit or slow progression of the tumor, e.g., cause regression of the tumor. In some embodiments administration of the self- assembled polypeptide complex results in complete regression of the tumor. C. Methods of treatment [0117] In one aspect, provided are methods that may be useful for treating, ameliorating, or preventing a disease or a condition (e.g., cancer, e.g., a chemo-resistant cancer), generally comprising a step of administering a composition comprising a self-assembled polypeptide complex as described herein to a subject. [0118] In some embodiments, the subject is a mammal, e.g., a human. [0119] In many embodiments, the subject has a chemo-resistant tumor or is at risk of having a chemo-resistant tumor. [0120] In some embodiments, the subject has a chemo-resistant tumor at the time of administration of the pharmaceutical composition. [0121] In some embodiments, the subject has not been previously treated with a chemotherapy agent. For example, the subject may have or be at risk of having a tumor that is intrinsically chemo-resistant or has characteristics that suggest the tumor is likely to acquire chemo-resistance. 23 IPTS/124242861.1
Attorney Docket No.90702160 [0122] In some embodiments, the subject carries, and/or a tumor sample in the subject carries, a genetic mutation or variation that is associated with intrinsic chemo-resistance or likelihood of acquiring chemo-resistance. In some embodiments, the subject carries, and/or a tumor sample in the subject carries, an epigenetic alteration that is associated with intrinsic chemo-resistance or likelihood of acquiring chemo-resistance. In some embodiments, the subject has or is at risk of having a tumor that is genetically heterogeneous. In some embodiments, the subject has or is at risk of having a tumor that comprises cancer stem cells. In some embodiments, the subject has one or more clinical markers associated with having or being at risk of having a tumor that is chemo-resistant. [0123] In some embodiments, the subject has been previously treated with one or more chemotherapy drugs. In some such embodiments, the subject exhibits one or more clinical signs that the tumor has recurred or relapsed. [0124] In some embodiments, the subject has a tumor of a tissue type that is known to be prone to chemo-resistance. [0125] In some embodiments, the tumor is a solid tumor, e.g., a colon tumor. [0126] Compositions for administration to subjects generally comprise a self-assembled polypeptide complex as disclosed herein. In some embodiments, such compositions further comprise a pharmaceutically acceptable excipient. [0127] Compositions may be formulated for administration for any of a variety of routes of administration, including systemic routes (e.g., oral, inhalation, intranasal, intravenous, intraperitoneal, subcutaneous, or intramuscular administration). [0128] In some embodiments, the step of administering results in improvement in one or more clinical outcomes or metrics in the subject. [0129] In some embodiments, the step of administering results in slowing or inhibiting progression of the tumor, e.g., regression of the tumor. In some embodiments, the step of administering results in complete regression of the tumor. EXAMPLES Example 1. Construction and expression of DR5-targeting Multabodies [0130] This Example describes the generation of DR5-targeting Multabodies (MBs) comprising a combination of fusion proteins comprising a (1) human ferritin light chain or 24 IPTS/124242861.1
Attorney Docket No.90702160 subunit thereof and (2) a single-chain Fab (scFab) or a single chain Fc-dimer (scFc), fused via a linker, such as a (Glyn-Ser)m amino acid linker as described herein. [0131] Genes encoding fusion proteins (1) scFab of an anti-DR5 antibody (in this case, conatumumab) fused to the N-terminus of hFTL (aDR5-hFTL, SEQ ID NO:9), (2) scFab of an anti-DR5 antibody fused to the N-terminus of an N-half ferritin (aDR5-N_hFTL, SEQ ID NO:11), and (3) scFc-LLRAL (described further below) fused to the N-terminus of a C-half ferritin (scFc-LLRAL-C_hFTL, SEQ ID NO:13) were prepared, mixed at a molar ratio of 2:1:1 and transiently transfected into ExpiCHO-S cells for the production and formation of the DR5-targeting MBs. See FIG.1B. scFc-LLRAL is a single-chain Fc-dimer based on an IgG1 Fc and having the following Fc mutations: L234A, L235A, G236R, G237A, and A330L. The residue at position 329 is proline. (Numbering is according to the EU numbering scheme). [0132] The resulting Multabody is a DR5-targeting Multabody hereinafter referred to as Cona MB IgG1 LLRAL. Example 2. Therapeutic effect of DR5-targeting Multabodies in a chemo-resistant xenograft mouse model [0133] The therapeutic effect of an exemplary Multabody generated as described in Example 1 was evaluated in a chemo-resistant xenograft model. HCT-15 (colon adenocarcinoma) cells are known to be intrinsically resistant to chemotherapy drugs including paclitaxel, docetaxel, vincristine, doxorubicin, satraplatin, and oxaliplatin. [0134] 5 x 106 HCT-15 cells were injected subcutaneously in the flank of Balb/c SCID mice. Tumors were allowed to grow to an average size of 200 mm3. Mice were sorted into one of three groups (vehicle, parent IgG (conatumumab), or Cona MB IgG1 LLRAL) such that the mean tumor volumes were equal across groups. Mice received 5 mg/kg parent IgG, 5 mg/kg Cona MB IgG1 LLRAL, or vehicle via intraperitoneal (i.p.) injection once weekly for two weeks. Tumor volume was measured twice weekly using calipers. [0135] FIG.2A is a plot that depicts tumor volumes of mice in various groups over time since tumor injection. The red arrows indicate treatment time points. “MB” indicates the Cona MB IgG1 LLRAL group. [0136] As shown in FIG.2A, treatment with Cona MB IgG1 LLRAL caused regression of established tumors for a period before tumors began to grow again. When tumors in Cona MB IgG1 LLRAL-treated mice grew again, tumor growth was nevertheless suppressed 25 IPTS/124242861.1
Attorney Docket No.90702160 relative to the growth of tumors in the control (vehicle) group. Tumor growth in the parent IgG-treated group appeared indistinguishable from that of the vehicle group. [0137] Cona MB IgG1 LLRAL-treated mice also showed a statistically significant (p<0.0001) improved survival relative to the vehicle or parent IgG-treated mice. (See FIG. 2B, which depicts a plot of event-free survival over time for the three groups.) [0138] These results suggest that Cona MB IgG1 LLRAL demonstrated therapeutic efficacy and improved survival in a chemo-resistant tumor model which was also resistant to treatment with the parent IgG administered at the same dosage. Example 3. Dose range efficacy of a DR5-targeting Multabody in a chemo-resistant xenograft mouse model [0139] The dose range efficacy of Cona IgG1 MB LLRAL was also explored in the same chemo-resistant xenograft model used in Example 2. [0140] 5 x 106 HCT-15 cells were injected subcutaneously in the flank of Balb/c SCID mice. Tumors were allowed to grow to an average size of 200 mm3. Mice were sorted into one of five groups (vehicle or Cona MB IgG1 LLRAL at 0.1 mg/kg, 0.25 mg/kg, 1 mg/kg, or 5 mg/kg per dose) such that the mean tumor volumes were equal across the groups. Mice received treatment or vehicle via intraperitoneal (i.p.) injection once weekly for three weeks. Tumor volume was measured twice weekly using calipers. Blood samples were obtained throughout the experiment as shown by the red arrows in FIG.3, which depicts the timeline for these experiments. [0141] FIG.4A is a plot that depicts tumor volumes of mice in various groups over time since the first dose. “MB” indicates the Cona MB IgG1 LLRAL group. As shown in FIG. 4A, treatment with Cona MB IgG1 LLRAL at 0.25 mg/kg, 1 mg/kg/ and 5 mg/kg doses slowed tumor progression in that these treatment groups showed significant improvement over the vehicle group, with the 1 mg/kg treatment group appearing to have comparable treatment efficacy to that of the 5 mg/kg group. [0142] FIG.4B is a plot that depicts that amount of Cona MB IgG1 LLRAL detectable in blood samples collected at various timepoints after the first dose was administered. Cona MB IgG1 LLRAL was detectable at all time points tested in the 0.25 mg/kg, 1 mg/kg/ and 5 mg/kg Cona MB IgG1 LLRAL treatment groups. 26 IPTS/124242861.1
Attorney Docket No.90702160 [0143] These results demonstrate that Cona MB IgG1 LLRAL exhibited therapeutic efficacy at multiple doses tested, including comparable efficacy at a dose level that was five- fold lower than that tested in Example 2. Example 4. Penetration of large chemo-resistant tumors and induction of apoptosis by a Multabody [0144] Exemplary Multabodies generated as described in Example 1 were evaluated for their ability to penetrate large tumors and induce apoptosis in a chemo-resistant xenograft model. [0145] 5 x 106 HCT-15 cells were injected subcutaneously in the flank of Balb/c SCID mice. Tumors were allowed to grow until well established (~31 days). Tumor volumes were estimated using calipers. Mice were randomly assigned to a vehicle or treatment groups such that the average tumor size was the same across the two groups, about 400 mm3 in each group. Mice were then administered vehicle or 5 mg/kg Cona MB IgG1 LLRAL by intraperitoneal injection Blood samples were collected 24 hours after injection of vehicle or Cona MB IgG1 LLRAL, and tumors were harvested for subsequent histological analyses. FIG.5 depicts a schematic and timeline for these experiments. [0146] Tumors were fixed in formalin, embedded in paraffin, and sectioned. Tumor sections were stained immunohistochemically for cleaved caspase-3, a marker of apoptosis. Representative images of stained tissue sections are shown in FIGs.6A and 6B (vehicle- treated mice) and FIGs.6C and 6D (Cona MB IgG1 LLRAL-treated mice). As shown in these figures, few apoptotic cells were detected in tumor sections from vehicle-treated mice. In contrast, tissue sections from Cona MB IgG1 LLRAL-treated mice contained many apoptotic cells throughout the tumor including deep within the core of the tumor, away from the tumor margin (see stained cells in FIGs.6C and 6D) [0147] These results confirm that Cona MB IgG1 LLRAL induced apoptosis of tumor cells in the core of the tumor. Moreover, these results confirm that Multabodies are able to penetrate into the core of large established tumors. SEQUENCE LISTING Underlining within fusion sequences indicate linker sequences. Bolding within fusion sequences indicate ferritin or ferritin subunit sequences. 27 IPTS/124242861.1
Attorney Docket No.90702160 Within variable region sequences, underlining and bolding together indicate complementary determining regions sequences. Boxed and bolded residues indicate residues that are mutated relative to a reference molecule, e.g. relative to an IgG1 Fc. SEQ ID NO:1 hFTL MSSQIRQNYSTDVEAAVNSLVNLYLQASYTYLSLGFYFDRDDVALEGVSHFFRELAEEKREG YERLLKMQNQRGGRALFQDIKKPAEDEWGKTPDAMKAAMALEKKLNQALLDLHALGSARTDP HLCDFLETHFLDEEVKLIKKMGDHLTNLHRLGGPEAGLGEYLFERLTLRHD SEQ ID NO:2 N_hFTL MSSQIRQNYSTDVEAAVNSLVNLYLQASYTYLSLGFYFDRDDVALEGVSHFFRELAEEKREG YERLLKMQNQRGGRALFQDIKKPAEDEW SEQ ID NO:3 C_hFTL GKTPDAMKAAMALEKKLNQALLDLHALGSARTDPHLCDFLETHFLDEEVKLIKKMGDHLTNL HRLGGPEAGLGEYLFERLTLRHD SEQ ID NO:4 IgG1 Fc DKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGV EVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPR EPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFL YSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK SEQ ID NO:5 IgG1 scFc DKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGV EVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPR EPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFL YSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGKGGGGSGGGGSGGGGSGGGGSG GGGSGGGGSGGGGSGGGGSGGGGSGGGGSGGGGSGGGGSGGGGSGGGGSDKTHTCPPCPAPE LLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQ YNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREE 28 IPTS/124242861.1
Attorney Docket No.90702160 MTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQ GNVFSCSVMHEALHNHYTQKSLSLSPGK SEQ ID NO:6 Cona LC EIVLTQSPGTLSLSPGERATLSCRASQGISRSYLAWYQQKPGQAPSLLIYGASSRATGIPDR FSGSGSGTDFTLTISRLEPEDFAVYYCQQFGSSPWTFGQGTKVEIKRTVAAPSVFIFPPSDE QLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKAD YEKHKVYACEVTHQGLSSPVTKSFNRGEC SEQ ID NO:7 Cona HC QVQLQESGPGLVKPSQTLSLTCTVSGGSISSGDYFWSWIRQLPGKGLEWIGHIHNSGTTYYN PSLKSRVTISVDTSKKQFSLRLSSVTAADTAVYYCARDRGGDYYYGMDVWGQGTTVTVSSAS TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYS LSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHTCPPCPAPELLGGPSVFLF PPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSV LTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTC LVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMH EALHNHYTQKSLSLSPGK SEQ ID NO:8 Cona scFab EIVLTQSPGTLSLSPGERATLSCRASQGISRSYLAWYQQKPGQAPSLLIYGASSRATGIPDR FSGSGSGTDFTLTISRLEPEDFAVYYCQQFGSSPWTFGQGTKVEIKRTVAAPSVFIFPPSDE QLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKAD YEKHKVYACEVTHQGLSSPVTKSFNRGECGGGGSGGGGSGGGGSGGGGSGGGGSGGGGSGGG GSGGGGSGGGGSGGGGSGGGGSGGGGSGGGGSGGGGSQVQLQESGPGLVKPSQTLSLTCTVS GGSISSGDYFWSWIRQLPGKGLEWIGHIHNSGTTYYNPSLKSRVTISVDTSKKQFSLRLSSV TAADTAVYYCARDRGGDYYYGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGC LVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKP SNTKVDKKVEPKSCD 29 IPTS/124242861.1
Attorney Docket No.90702160 SEQ ID NO:9 aDR5-hFTL LEEIVLTQSPGTLSLSPGERATLSCRASQGISRSYLAWYQQKPGQAPSLLIYGASSRATGIP DRFSGSGSGTDFTLTISRLEPEDFAVYYCQQFGSSPWTFGQGTKVEIKRTVAAPSVFIFPPS DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSK ADYEKHKVYACEVTHQGLSSPVTKSFNRGECGGGGSGGGGSGGGGSGGGGSGGGGSGGGGSG GGGSGGGGSGGGGSGGGGSGGGGSGGGGSGGGGSGGGGSQVQLQESGPGLVKPSQTLSLTCT VSGGSISSGDYFWSWIRQLPGKGLEWIGHIHNSGTTYYNPSLKSRVTISVDTSKKQFSLRLS SVTAADTAVYYCARDRGGDYYYGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAAL GCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNH KPSNTKVDKKVEPKSCDGGGGSGGGGSGGGGSGGGGSGGGGSGGMSSQIRQNYSTDVEAAVN SLVNLYLQASYTYLSLGFYFDRDDVALEGVSHFFRELAEEKREGYERLLKMQNQRGGRALFQ DIKKPAEDEWGKTPDAMKAAMALEKKLNQALLDLHALGSARTDPHLCDFLETHFLDEEVKLI KKMGDHLTNLHRLGGPEAGLGEYLFERLTLRHD SEQ ID NO: 10 aDR5-hFTL, alternative sequence EIVLTQSPGTLSLSPGERATLSCRASQGISRSYLAWYQQKPGQAPSLLIYGASSRATGIPDR FSGSGSGTDFTLTISRLEPEDFAVYYCQQFGSSPWTFGQGTKVEIKRTVAAPSVFIFPPSDE QLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKAD YEKHKVYACEVTHQGLSSPVTKSFNRGECGGGGSGGGGSGGGGSGGGGSGGGGSGGGGSGGG GSGGGGSGGGGSGGGGSGGGGSGGGGSGGGGSGGGGSQVQLQESGPGLVKPSQTLSLTCTVS GGSISSGDYFWSWIRQLPGKGLEWIGHIHNSGTTYYNPSLKSRVTISVDTSKKQFSLRLSSV TAADTAVYYCARDRGGDYYYGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGC LVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKP SNTKVDKKVEPKSCDGGGGSGGGGSGGGGSGGGGSGGGGSGGSSQIRQNYSTDVEAAVNSLV NLYLQASYTYLSLGFYFDRDDVALEGVSHFFRELAEEKREGYERLLKMQNQRGGRALFQDIK KPAEDEWGKTPDAMKAAMALEKKLNQALLDLHALGSARTDPHLCDFLETHFLDEEVKLIKKM GDHLTNLHRLGGPEAGLGEYLFERLTLRHD SEQ ID NO:11 aDR5-N_hFTL EIVLTQSPGTLSLSPGERATLSCRASQGISRSYLAWYQQKPGQAPSLLIYGASSRATGIPDR FSGSGSGTDFTLTISRLEPEDFAVYYCQQFGSSPWTFGQGTKVEIKRTVAAPSVFIFPPSDE QLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKAD 30 IPTS/124242861.1
Attorney Docket No.90702160 YEKHKVYACEVTHQGLSSPVTKSFNRGECGGGGSGGGGSGGGGSGGGGSGGGGSGGGGSGGG GSGGGGSGGGGSGGGGSGGGGSGGGGSGGGGSGGGGSQVQLQESGPGLVKPSQTLSLTCTVS GGSISSGDYFWSWIRQLPGKGLEWIGHIHNSGTTYYNPSLKSRVTISVDTSKKQFSLRLSSV TAADTAVYYCARDRGGDYYYGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGC LVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKP SNTKVDKKVEPKSCDGGGGSGGGGSGGGGSGGGGSGGGGSGGMSSQIRQNYSTDVEAAVNSL VNLYLQASYTYLSLGFYFDRDDVALEGVSHFFRELAEEKREGYERLLKMQNQRGGRALFQDI KKPAEDEW SEQ ID NO: 12 aDR5-N_hFTL, alternative sequence EIVLTQSPGTLSLSPGERATLSCRASQGISRSYLAWYQQKPGQAPSLLIYGASSRATGIPDR FSGSGSGTDFTLTISRLEPEDFAVYYCQQFGSSPWTFGQGTKVEIKRTVAAPSVFIFPPSDE QLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKAD YEKHKVYACEVTHQGLSSPVTKSFNRGECGGGGSGGGGSGGGGSGGGGSGGGGSGGGGSGGG GSGGGGSGGGGSGGGGSGGGGSGGGGSGGGGSGGGGSQVQLQESGPGLVKPSQTLSLTCTVS GGSISSGDYFWSWIRQLPGKGLEWIGHIHNSGTTYYNPSLKSRVTISVDTSKKQFSLRLSSV TAADTAVYYCARDRGGDYYYGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGC LVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKP SNTKVDKKVEPKSCDGGGGSGGGGSGGGGSGGGGSGGGGSGGSSQIRQNYSTDVEAAVNSLV NLYLQASYTYLSLGFYFDRDDVALEGVSHFFRELAEEKREGYERLLKMQNQRGGRALFQDIK KPAEDEW
YNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALGLPIEKTISKAKGQPREPQVYTLPPSREE MTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQ GNVFSCSVMHEALHNHYTQKSLSLSPGKGGGGSGGGGSGGGGSGGGGSGGGGSGGGKTPDAM 31 IPTS/124242861.1
Attorney Docket No.90702160 KAAMALEKKLNQALLDLHALGSARTDPHLCDFLETHFLDEEVKLIKKMGDHLTNLHRLGGPE AGLGEYLFERLTLRHD SEQ ID NO:14 human DR5 (GenBank accession no. AAB67109.1) MEQRGQNAPA ASGARKRHGP GPREARGARP GPRVPKTLVL VVAAVLLLVS AESALITQQD LAPQQRAAPQ QKRSSPSEGL CPPGHHISED GRDCISCKYG QDYSTHWNDL LFCLRCTRCD SGEVELSPCT TTRNTVCQCE EGTFREEDSP EMCRKCRTGC PRGMVKVGDC TPWSDIECVH KESGIIIGVT VAAVVLIVAV FVCKSLLWKK VLPYLKGICS GGGGDPERVD RSSQRPGAED NVLNEIVSIL QPTQVPEQEM EVQEPAEPTG VNMLSPGESE HLLEPAEAER SQRRRLLVPA NEGDPTETLR QCFDDFADLV PFDSWEPLMR KLGLMDNEIK VAKAEAAGHR DTLYTMLIKW VNKTGRDASV HTLLDALETL GERLAKQKIE DHLLSSGKFM YLEGNADSAM S SEQ ID NO:15 human DR5 (GenBank accession no. AAB71412.1) MEQRGQNAPA ASGARKRHGP GPREARGARP GLRVPKTLVL VVAAVLLLVS AESALITQQD LAPQQRVAPQ QKRSSPSEGL CPPGHHISED GRDCISCKYG QDYSTHWNDL LFCLRCTRCD SGEVELSPCT TTRNTVCQCE EGTFREEDSP EMCRKCRTGC PRGMVKVGDC TPWSDIECVH KESGIIIGVT VAAVVLIVAV FVCKSLLWKK VLPYLKGICS GGGGDPERVD RSSQRPGAED NVLNEIVSIL QPTQVPEQEM EVQEPAEPTG VNMLSPGESE HLLEPAEAER SQRRRLLVPA NEGDPTETLR QCFDDFADLV PFDSWEPLMR KLGLMDNEIK VAKAEAAGHR DTLYTMLIKW VNKTGRDASV HTLLDALETL GERLAKQKIE DHLLSSGKFM YLEGNADSAM S SEQ ID NO:16 human DR5 (GenBank accession no. AAC01565.1) MEQRGQNAPA ASGARKRHGP GPREARGARP GLRVPKTLVL VVAAVLLLVS AESALITQQD LAPQQRVAPQ QKRSSPSEGL CPPGHHISED GRDCISCKYG QDYSTHWNDL LFCLRCTRCD SGEVELSPCT TTRNTVCQCE EGTFREEDSP EMCRKCRTGC PRGMVKVGDC TPWSDIECVH KESGIIIGVT VAAVVLIVAV FVCKSLLWKK VLPYLKGICS GGGGDPERVD RSSQRPGAED NVLNEIVSIL QPTQVPEQEM EVQEPAEPTG VNMLSPGESE HLLEPAEAER SQRRRLLVPA NEGDPTETLR QCFDDFADLV PFDSWEPLMR KLGLMDNEIK VAKAEAAGHR DTLYTMLIKW VNKTGRDASV HTLLDALETL GERLAKQKIE DHLLSSGKFM YLEGNADSAM S SEQ ID NO:17 human DR5 (GenBank accession no. AAB67103.1) MEQRGQNAPA ASGARKRHGP GPREARGARP GLRVPKTLVL VVAAVLLLVS AESALITQQD LAPQQRAAPQ QKRSSPSEGL CPPGHHISED GRDCISCKYG QDYSTHWNDL LFCLRCTRCD SGEVELSPCT TTRNTVCQCE EGTFREEDSP EMCRKCRTGC PRGMVKVGDC TPWSDIECVH KESGIIIGVT VAAVVLIVAV FVCKSLLWKK VLPYLKGICS GGGGDPERVD RSSQRPGAED NVLNEIVSIL QPTQVPEQEM EVQEPAEPTG VNMLSPGESE HLLEPAEAER SQRRRLLVPA 32 IPTS/124242861.1
Attorney Docket No.90702160 NEGDPTETLR QCFDDFADLV PFDSWEPLMR KLGLMDNEIK VAKAEAAGHR DTLYTMLIKW VNKTGRDASV HTLLDALETL GERLAKQKIE DHLLSSGKFM YLEGNADSAL S SEQ ID NO:18 VL from Conatumumab EIVLTQSPGTLSLSPGERATLSCRASQGISRSYLAWYQQKPGQAPSLLIYGASSRATGIPDR FSGSGSGTDFTLTISRLEPEDFAVYYCQQFGSSPWTFGQGTKVEIK SEQ ID NO:19 VH from Conatumumab QVQLQESGPGLVKPSQTLSLTCTVSGGSISSGDYFWSWIRQLPGKGLEWIGHIHNSGTTYYN PSLKSRVTISVDTSKKQFSLRLSSVTAADTAVYYCARDRGGDYYYGMDVWGQGTTVTVSS SEQ ID NO:20 CDR-L1 from Conatumumab RASQGISRSYLA SEQ ID NO:21 CDR-L2 from Conatumumab GASSRAT SEQ ID NO:22 CDR-L3 from Conatumumab QQFGSSPWT SEQ ID NO:23 CDR-H1 from Conatumumab GGSISSGDYFWS SEQ ID NO:24 CDR-H2 from Conatumumab HIHNSGTTYYNPSLKS SEQ ID NO:25 CDR-H3 from Conatumumab DRGGDYYYGMDV SEQ ID NO:26 VL from Tigatuzumab DIQMTQSPSSLSASVGDRVTITCKASQDVGTAVAWYQQKPGKAPKLLIYWASTRHTGVPSRF SGSGSGTDFTLTISSLQPEDFATYYCQQYSSYRTFGQGTKVEIK SEQ ID NO:27 VH from Tigatuzumab VQLVESGGGLVQPGGSLRLSCAASGFTFSSYVMSWVRQAPGKGLEWVATISSGGSYTYYPDS VKGRFTISRDNAKNTLYLQMNSLRAEDTAVYYCARRGDSMITTDYWGQGTLVTVSS SEQ ID NO:28 CDR-L1 from Tigatuzumab 33 IPTS/124242861.1
Attorney Docket No.90702160 KASQDVGTAVA SEQ ID NO:29 CDR-L2 from Tigatuzumab WASTRHT SEQ ID NO:30 CDR-L3 from Tigatuzumab QQYSSYRT SEQ ID NO:31 CDR-H1 from Tigatuzumab GFTFSSYVMS SEQ ID NO:32 CDR-H2 from Tigatuzumab TISSGGSYTYYPDSVKG SEQ ID NO:33 CDR-H3 from Tigatuzumab RGDSMITTDY SEQ ID NO:34 VL from Drozitumab SELTQDPAVSVALGQTVRITCSGDSLRSYYASWYQQKPGQAPVLVIYGANNRPSGIPDRFSG SSSGNTASLTITGAQAEDEADYYCNSADSSGNHVVFGGGTKLTVL SEQ ID NO:35 VH from Drozitumab EVQLVQSGGGVERPGGSLRLSCAASGFTFDDYAMSWVRQAPGKGLEWVSGINWQGGSTGYAD SVKGRVTISRDNAKNSLYLQMNSLRAEDTAVYYCAKILGAGRGWYFDYWGKGTTVTVSS SEQ ID NO:36 CDR-L1 from Drozitumab SGDSLRSYYAS SEQ ID NO:37 CDR-L2 from Drozitumab GANNRPS SEQ ID NO:38 CDR-L3 from Drozitumab NSADSSGNHVV SEQ ID NO:39 CDR-H1 from Drozitumab 34 IPTS/124242861.1
Attorney Docket No.90702160 GFTFDDYAMS SEQ ID NO:40 CDR-H2 from Drozitumab INWQGGSTGYADSVKG SEQ ID NO:41 CDR-H3 from Drozitumab ILGAGRGWYFDY SEQ ID NO:42 VL from Lexatumumab SELTQDPAVSVALGQTVRITCQGDSLRSYYASWYQQKPGQAPVLVIYGKNNRPSGIPDRFSG SSSGNTASLTITGAQAEDEADYYCNSRDSSGNHVVFGGGTKLTVL SEQ ID NO:43 VH from Lexatumumab EVQLVQSGGGVERPGGSLRLSCAASGFTFDDYGMSWVRQAPGKGLEWVSGINWNGGSTGYAD SVKGRVTISRDNAKNSLYLQMNSLRAEDTAVYYCAKILGAGRGWYFDLWGKGTTVTVSS SEQ ID NO:44 CDR-L1 from Lexatumumab QGDSLRSYYAS SEQ ID NO:45 CDR-L2 from Lexatumumab GKNNRPS SEQ ID NO:46 CDR-L3 from Lexatumumab NSRDSSGNHVV SEQ ID NO:47 CDR-H1 from Lexatumumab GFTFDDYGMS SEQ ID NO:48 CDR-H2 from Lexatumumab INWNGGSTGYADSVKG SEQ ID NO:49 CDR-H3 from Lexatumumab ILGAGRGWYFDL SEQ ID NO:50 GS linker sequence GGGGS 35 IPTS/124242861.1
Attorney Docket No.90702160 NUMBERED EMBODIMENTS [0148] Embodiment 1: A method of treating a subject who has or is at risk of having a chemo-resistant tumor, the method comprising a step of administering to the subject a pharmaceutical composition comprising a self-assembled polypeptide complex to the subject, wherein the self-assembled polypeptide complex comprises: a plurality of first fusion polypeptides, each first fusion polypeptide comprising (1) an antibody or antibody fragment that is capable of binding to a tumor-associated antigen expressed on the chemo-resistant tumor and (2) a nanocage monomer or subunit thereof, wherein said step of administering results in slowing, inhibiting progression of, or regression of the tumor. [0149] Embodiment 2: The method of embodiment 1, wherein the complex further comprises: a plurality of second fusion polypeptides, each second fusion polypeptide comprising (1) an Fc polypeptide and (2) a nanocage monomer or subunit thereof. [0150] Embodiment 3: The method of embodiment 2, wherein each second fusion polypeptide comprises the Fc polypeptide linked to the nanocage monomer or subunit thereof via an amino acid linker. [0151] Embodiment 4: The method of embodiment 3, wherein the amino acid linker comprises a (GnS)m linker. [0152] Embodiment 5: The method of embodiment 4, wherein the (GnS)m linker is a (GGGGS)m (SEQ ID NO:50) linker. [0153] Embodiment 6: The method of any one of embodiments 2-5, wherein the Fc polypeptide comprises a single-chain Fc (scFc) comprising two Fc chains, wherein the two Fc chains are linked via an amino acid linker. [0154] Embodiment 7: The method of embodiment 6, wherein the amino acid linker that links the two Fc chains comprises a (GnS)m linker. [0155] Embodiment 8: The method of embodiment 12, wherein the (GnS)m linker is a (GGGGS)m (SEQ ID NO:50) linker. [0156] Embodiment 9: The method of any one of embodiments 2-8, wherein the Fc polypeptide comprises an IgG1 Fc chain. [0157] Embodiment 10: The method of embodiment 9, wherein the IgG1 Fc chain comprises (1) an amino acid residue other than glycine at position 237; and (2) a proline residue at position 329, according to EU numbering. 36 IPTS/124242861.1
Attorney Docket No.90702160 [0158] Embodiment 11: The method of embodiment 10, wherein the IgG1 Fc chain comprises an alanine at position 237 according to EU numbering. [0159] Embodiment 12: The method of embodiment 10 or 11, wherein the IgG1 Fc chain comprises: an alanine at position 234, an alanine at position 235, an arginine at position 236, and a leucine at position 330, according to EU numbering. [0160] Embodiment 13: The method of any one of embodiments 1-12, wherein the nanocage monomer or subunit thereof is a ferritin monomer or subunit thereof. [0161] Embodiment 14: The method of embodiment 13, wherein the ferritin monomer or subunit thereof is a ferritin light chain or subunit thereof. [0162] Embodiment 15: The method of embodiment 13 or 14, wherein the ferritin monomer or subunit thereof is a human ferritin or subunit thereof. [0163] Embodiment 16: The method of any one of embodiments 13-15, wherein the self- assembled polypeptide complex does not comprise any ferritin heavy chains or subunits of ferritin heavy chains. [0164] Embodiment 17: The method of any one of embodiments 13-16, wherein at least a portion of the plurality of first fusion polypeptides and/or a portion of the plurality of second fusion polypeptides are fusion polypeptides which each comprise a ferritin monomer subunit. [0165] Embodiment 18: The method of embodiment 17, wherein (a) each first fusion polypeptide comprises a C-half-ferritin, and each second fusion polypeptide comprises an N- half-ferritin; or (b) each first fusion polypeptide comprises an N-half ferritin, and each second fusion polypeptide comprises a C-half-ferritin. [0166] Embodiment 19: The method of embodiment 18, wherein the self-assembled polypeptide complex is characterized by a 1:1 ratio of first fusion polypeptides to second fusion polypeptides. [0167] Embodiment 20: The method of any one of embodiments 1-19, wherein the total number of fusion polypeptides in each self-assembled polypeptide complex is at least 24. [0168] Embodiment 21: The method of claim 20, wherein the total number of fusion polypeptides in each self-assembled polypeptide complex is at least 32. [0169] Embodiment 22: The method of any one of embodiments 1-19, wherein the total number of fusion polypeptides in each self-assembled polypeptide complex is about 24. [0170] Embodiment 23: The method of any one of embodiments 1-19, wherein the total number of fusion polypeptides in each self-assembled polypeptide complex is about 32. 37 IPTS/124242861.1
Attorney Docket No.90702160 [0171] Embodiment 24: The method of any one of embodiments 1-19, wherein the total number of fusion polypeptides in each self-assembled polypeptide complex is between 24 and 48. [0172] Embodiment 25: The method of any one of embodiments 1-24, wherein, within each first fusion polypeptide, the antibody or antibody fragment is linked to the N-terminus of the nanocage monomer or subunit thereof. [0173] Embodiment 26: The method of any one of embodiments 1-25, wherein each first fusion polypeptide comprises (1) a Fab fragment and (2) a nanocage monomer or subunit thereof. [0174] Embodiment 27: The method of any one of embodiments 1-26, wherein each first fusion polypeptide does not comprise any antibody CH2 or CH3 domains. [0175] Embodiment 28: The method of any one of embodiments 1-27, wherein the tumor- associated antigen is a TNF receptor superfamily member. [0176] Embodiment 29: The method of embodiment 28, wherein the TNF receptor superfamily member is a death receptor. [0177] Embodiment 30: The method of embodiment 29, wherein the death receptor is DR5. [0178] Embodiment 31: The method of embodiment 30, wherein the antibody or antibody fragment is conatumumab, tigatuzumab, lexatumumab, drozitumab, or a DR5-binding fragment of any of the foregoing. [0179] Embodiment 32: The method of embodiment 31, wherein the antibody or antibody fragment is conatumumab or a DR5-binding fragment thereof. [0180] Embodiment 33: The method of embodiment 31, wherein the antibody or antibody fragment comprises (1) a heavy chain comprising CDR-H1, CDR-H2, and CDR-H3 and (2) a light chain comprising CDR-L1, CDR-L2, and CDR-L3, wherein (a) (i) the CDR-H1 has a sequence of SEQ ID NO:23 or a sequence differing by one or two amino acids therefrom; (ii) the CDR-H2 has a sequence of SEQ ID NO:24 or a sequence differing by one or two amino acids therefrom; (iii) the CDR-H3 has a sequence of SEQ ID NO:25 or a sequence differing by one or two amino acids therefrom; 38 IPTS/124242861.1
Attorney Docket No.90702160 (iv) the CDR-L1 has a sequence of SEQ ID NO:20 or a sequence differing by one or two amino acids therefrom; (v) the CDR-L2 has a sequence of SEQ ID NO:21 or a sequence differing by one or two amino acids therefrom; and (vi) the CDR-L3 has a sequence of SEQ ID NO:22 or a sequence differing by one or two amino acids therefrom; (b) (i) the CDR-H1 has a sequence of SEQ ID NO:31 or a sequence differing by one or two amino acids therefrom; (ii) the CDR-H2 has a sequence of SEQ ID NO:32 or a sequence differing by one or two amino acids therefrom; (iii) the CDR-H3 has a sequence of SEQ ID NO:33 or a sequence differing by one or two amino acids therefrom; (iv) the CDR-L1 has a sequence of SEQ ID NO:28 or a sequence differing by one or two amino acids therefrom; (v) the CDR-L2 has a sequence of SEQ ID NO:29 or a sequence differing by one or two amino acids therefrom; and (vi) the CDR-L3 has a sequence of SEQ ID NO:30 or a sequence differing by one or two amino acids thereof; (c) (i) the CDR-H1 has a sequence of SEQ ID NO:39 or a sequence differing by one or two amino acids therefrom; (ii) the CDR-H2 has a sequence of SEQ ID NO:40 or a sequence differing by one or two amino acids therefrom; (iii) the CDR-H3 has a sequence of SEQ ID NO:41 or a sequence differing by one or two amino acids therefrom; (iv) the CDR-L1 has a sequence of SEQ ID NO:36 or a sequence differing by one or two amino acids therefrom; (v) the CDR-L2 has a sequence of SEQ ID NO:37 or a sequence differing by one or two amino acids therefrom; and 39 IPTS/124242861.1
Attorney Docket No.90702160 (vi) the CDR-L3 has a sequence of SEQ ID NO:38 or a sequence differing by one or two amino acids therefrom; or (d) (i) the CDR-H1 has a sequence of SEQ ID NO:47 or a sequence differing by one or two amino acids therefrom; (ii) the CDR-H2 has a sequence of SEQ ID NO:48 or a sequence differing by one or two amino acids therefrom; (iii) the CDR-H3 has a sequence of SEQ ID NO:49 or a sequence differing by one or two amino acids therefrom; (iv) the CDR-L1 has a sequence of SEQ ID NO:44 or a sequence differing by one or two amino acids therefrom; (v) the CDR-L2 has a sequence of SEQ ID NO:45 or a sequence differing by one or two amino acids therefrom; and (vi) the CDR-L3 has a sequence of SEQ ID NO:46 or a sequence differing by one or two amino acids therefrom. [0181] Embodiment 34: The method of embodiment 33, wherein the antibody fragment comprises (1) a heavy chain comprising CDR-H1, CDR-H2, and CDR-H3 and (2) a light chain comprising CDR-L1, CDR-L2, and CDR-L3, wherein (a) (i) the CDR-H1 has a sequence of SEQ ID NO:23, (ii) the CDR-H2 has a sequence of SEQ ID NO:24, (iii) the CDR-H3 has a sequence of SEQ ID NO:25, (iv) the CDR-L1 has a sequence of SEQ ID NO:20, (v) the CDR-L2 has a sequence of SEQ ID NO:21, and (vi) the CDR-L3 has a sequence of SEQ ID NO:22; (b) (i) the CDR-H1 has a sequence of SEQ ID NO:31, (ii) the CDR-H2 has a sequence of SEQ ID NO:32, (iii) the CDR-H3 has a sequence of SEQ ID NO:33, 40 IPTS/124242861.1
Attorney Docket No.90702160 (iv) the CDR-L1 has a sequence of SEQ ID NO:28, (v) the CDR-L2 has a sequence of SEQ ID NO:29, and (vi) the CDR-L3 has a sequence of SEQ ID NO:30; (c) (i) the CDR-H1 has a sequence of SEQ ID NO:39, (ii) the CDR-H2 has a sequence of SEQ ID NO:40, (iii) the CDR-H3 has a sequence of SEQ ID NO:41, (iv) the CDR-L1 has a sequence of SEQ ID NO:36, (v) the CDR-L2 has a sequence of SEQ ID NO:37, and (vi) the CDR-L3 has a sequence of SEQ ID NO:38; or (d) (i) the CDR-H1 has a sequence of SEQ ID NO:47, (ii) the CDR-H2 has a sequence of SEQ ID NO:48, (iii) the CDR-H3 has a sequence of SEQ ID NO:49, (iv) the CDR-L1 has a sequence of SEQ ID NO:44, (v) the CDR-L2 has a sequence of SEQ ID NO:45, and (vi) the CDR-L3 has a sequence of SEQ ID NO:46. [0182] Embodiment 35: The method of any one of embodiments 1-34, wherein the antibody fragment comprises (1) a heavy chain variable region having at least 85% identical to a reference VH sequence and (2) a light chain variable region having at least 85% identical to a reference VL sequence, wherein: (a) the reference VH sequence has a sequence of SEQ ID NO:19 and the reference VL sequence has a sequence of SEQ ID NO:18; (b) the reference VH sequence has a sequence of SEQ ID NO:27 and the reference VL sequence has a sequence of SEQ ID NO:26; (c) the reference VH sequence has a sequence of SEQ ID NO:35 and the reference VL sequence has a sequence of SEQ ID NO:34; or (d) the reference VH sequence has a sequence of SEQ ID NO:43 and the reference VL sequence has a sequence of SEQ ID NO:42. 41 IPTS/124242861.1
Attorney Docket No.90702160 [0183] Embodiment 36: The method of any one of embodiments 1-35, wherein the subject is a mammal. [0184] Embodiment 37: The method of embodiment 36, wherein the subject is a human. [0185] Embodiment 38: The method of any one of embodiments 1-37, wherein the tumor is a colon tumor. [0186] Embodiment 39: The method of any one of embodiments 1-38, wherein the subject has a chemo-resistant tumor. [0187] Embodiment 40: The method of any one of embodiments 1-39, wherein the chemo- resistant tumor is resistant to a taxane, a vinca alkaloid, an anthracycline, or any combination of the foregoing. [0188] Embodiment 41: The method of embodiment 40, wherein the chemo-resistant tumor is resistant to a taxane. [0189] Embodiment 42: The method of embodiment 41, wherein the taxane is paclitaxel, taxane, or both. [0190] Embodiment 43: The method of embodiment 40, 41, or 42, wherein the chemo- resistant tumor is resistant to a vinca alkaloid. [0191] Embodiment 44: The method of embodiment 43, wherein the vinca alkaloid is vincristine. [0192] Embodiment 45: The method of any one of embodiment 41-44, wherein the chemo-resistant tumor is resistant to an anthracycline. [0193] Embodiment 46: The method of embodiment 45, wherein the anthracycline is doxorubicin. [0194] Embodiment 47: The method of any one of embodiment 41-46, wherein the chemo-resistant tumor is resistant to a platinum-containing compound. [0195] Embodiment 48: The method of embodiment 47, wherein the platinum-containing compound is satraplatin, oxaliplatin, or both. [0196] Embodiment 49: The method of any one of embodiments 1-46, wherein the administering comprises administration by a systemic route. [0197] Embodiment 50: The method of embodiment 47, wherein the systemic route comprises subcutaneous, intravenous, intramuscular, inhalation, or intranasal administration. 42 IPTS/124242861.1
Attorney Docket No.90702160 [0198] Embodiment 51: The method of any one of embodiments 1-48, wherein the step of administering comprises administering more than one dose of the pharmaceutical composition. [0199] Embodiment 52: The method of embodiment 49, wherein the step of administering comprises administering the pharmaceutical composition once a week for at least two weeks. [0200] Embodiment 53: The method of embodiment 50, wherein the step of administering comprises administering the pharmaceutical composition once a week for at least three weeks. [0201] Embodiment 54: A method of treating a subject who has a chemo-resistant tumor or is at risk of having a chemo-resistant tumor, the method comprising a step of administering a pharmaceutical composition comprising a self- assembled polypeptide complex to the subject, wherein the self-assembled polypeptide complex comprises: (a) a plurality of first fusion polypeptides, each first fusion polypeptide comprising (1) an antibody fragment that is capable of binding to DR5 and (2) a ferritin monomer or subunit thereof; and (b) a plurality of second fusion polypeptides, each second fusion polypeptide comprising (1) an scFc and (2) a ferritin monomer or subunit thereof, and, wherein the scFc comprises two IgG1 Fc chains, each IgG1 Fc chain comprising: an alanine at position 234, an alanine at position 235, an arginine at position 236, an alanine at position 237, a proline at position 329, and a leucine at position 330, according to EU numbering, wherein said step of administering results in slowing, inhibiting progression of, or regression of the tumor. EQUIVALENTS / OTHER EMBODIMENTS [0202] While the invention has been described in connection with specific embodiments thereof, it will be understood that it is capable of further modifications and this application is intended to cover any variations, uses, or adaptations of the invention following, in general, the principles of the invention and including such departures from the present disclosure that 43 IPTS/124242861.1
Attorney Docket No.90702160 come within known or customary practice within the art to which the invention pertains and may be applied to the essential features herein before set forth. 44 IPTS/124242861.1
Claims
Attorney Docket No.90702160 CLAIMS 1. Use of a pharmaceutical composition comprising a self-assembled polypeptide complex to treat a subject having or at risk of having a chemo-resistant tumor, wherein the self-assembled polypeptide complex comprises: a plurality of first fusion polypeptides, each first fusion polypeptide comprising (1) an antibody or antibody fragment that is capable of binding to a tumor-associated antigen expressed on the chemo-resistant tumor and (2) a nanocage monomer or subunit thereof. 2. The use of claim 1, wherein the complex further comprises: a plurality of second fusion polypeptides, each second fusion polypeptide comprising (1) an Fc polypeptide and (2) a nanocage monomer or subunit thereof. 3. The use of claim 2, wherein each second fusion polypeptide comprises the Fc polypeptide linked to the nanocage monomer or subunit thereof via an amino acid linker. 4. The use of claim 3, wherein the amino acid linker comprises a (GnS)m linker. 5. The use of claim 4, wherein the (GnS)m linker is a (GGGGS)m (SEQ ID NO:50) linker. 6. The use of any one of claims 2-5, wherein the Fc polypeptide comprises a single- chain Fc (scFc) comprising two Fc chains, wherein the two Fc chains are linked via an amino acid linker. 7. The use of claim 6, wherein the amino acid linker that links the two Fc chains comprises a (GnS)m linker. 8. The use of claim 12, wherein the (GnS)m linker is a (GGGGS)m (SEQ ID NO:50) linker. 45 IPTS/124242861.1
Attorney Docket No.90702160 9. The use of any one of claims 2-8, wherein the Fc polypeptide comprises an IgG1 Fc chain. 10. The use of claim 9, wherein the IgG1 Fc chain comprises (1) an amino acid residue other than glycine at position 237; and (2) a proline residue at position 329, according to EU numbering. 11. The use of claim 10, wherein the IgG1 Fc chain comprises an alanine at position 237 according to EU numbering. 12. The use of claim 10 or 11, wherein the IgG1 Fc chain comprises: an alanine at position 234, an alanine at position 235, an arginine at position 236, and a leucine at position 330, according to EU numbering. 13. The use of any one of claims 1-12, wherein the nanocage monomer or subunit thereof is a ferritin monomer or subunit thereof. 14. The use of claim 13, wherein the ferritin monomer or subunit thereof is a ferritin light chain or subunit thereof. 15. The use of claim 13 or 14, wherein the ferritin monomer or subunit thereof is a human ferritin or subunit thereof. 16. The use of any one of claims 13-15, wherein the self-assembled polypeptide complex does not comprise any ferritin heavy chains or subunits of ferritin heavy chains. 17. The use of any one of claims 13-16, wherein at least a portion of the plurality of first fusion polypeptides and/or a portion of the plurality of second fusion polypeptides are fusion polypeptides which each comprise a ferritin monomer subunit. 18. The use of claim 17, wherein (a) each first fusion polypeptide comprises a C-half-ferritin, and each second fusion polypeptide comprises an N-half-ferritin; or 46 IPTS/124242861.1
Attorney Docket No.90702160 (b) each first fusion polypeptide comprises an N-half ferritin, and each second fusion polypeptide comprises a C-half-ferritin. 19. The use of claim 18, wherein the self-assembled polypeptide complex is characterized by a 1:1 ratio of first fusion polypeptides to second fusion polypeptides. 20. The use of any one of claims 1-19, wherein the total number of fusion polypeptides in each self-assembled polypeptide complex is at least 24. 21. The use of claim 20, wherein the total number of fusion polypeptides in each self- assembled polypeptide complex is at least 32. 22. The use of any one of claims 1-19, wherein the total number of fusion polypeptides in each self-assembled polypeptide complex is about 24. 23. The use of any one of claims 1-19, wherein the total number of fusion polypeptides in each self-assembled polypeptide complex is about 32. 24. The use of any one of claims 1-19, wherein the total number of fusion polypeptides in each self-assembled polypeptide complex is between 24 and 48. 25. The use of any one of claims 1-24, wherein, within each first fusion polypeptide, the antibody or antibody fragment is linked to the N-terminus of the nanocage monomer or subunit thereof. 26. The use of any one of claims 1-25, wherein each first fusion polypeptide comprises (1) a Fab fragment and (2) a nanocage monomer or subunit thereof. 27. The use of any one of claims 1-26, wherein each first fusion polypeptide does not comprise any antibody CH2 or CH3 domains. 28. The use of any one of claims 1-27, wherein the tumor-associated antigen is a TNF receptor superfamily member. 47 IPTS/124242861.1
Attorney Docket No.90702160 29. The use of claim 28, wherein the TNF receptor superfamily member is a death receptor. 30. The use of claim 29, wherein the death receptor is DR5. 31. The use of claim 30, wherein the antibody or antibody fragment is conatumumab, tigatuzumab, lexatumumab, drozitumab, or a DR5-binding fragment of any of the foregoing. 32. The use of claim 31, wherein the antibody or antibody fragment is conatumumab or a DR5-binding fragment thereof. 33. The use of claim 31, wherein the antibody or antibody fragment comprises (1) a heavy chain comprising CDR-H1, CDR-H2, and CDR-H3 and (2) a light chain comprising CDR-L1, CDR-L2, and CDR-L3, wherein (a) (i) the CDR-H1 has a sequence of SEQ ID NO:23 or a sequence differing by one or two amino acids therefrom; (ii) the CDR-H2 has a sequence of SEQ ID NO:24 or a sequence differing by one or two amino acids therefrom; (iii) the CDR-H3 has a sequence of SEQ ID NO:25 or a sequence differing by one or two amino acids therefrom; (iv) the CDR-L1 has a sequence of SEQ ID NO:20 or a sequence differing by one or two amino acids therefrom; (v) the CDR-L2 has a sequence of SEQ ID NO:21 or a sequence differing by one or two amino acids therefrom; and (vi) the CDR-L3 has a sequence of SEQ ID NO:22 or a sequence differing by one or two amino acids therefrom; (b) (i) the CDR-H1 has a sequence of SEQ ID NO:31 or a sequence differing by one or two amino acids therefrom; 48 IPTS/124242861.1
Attorney Docket No.90702160 (ii) the CDR-H2 has a sequence of SEQ ID NO:32 or a sequence differing by one or two amino acids therefrom; (iii) the CDR-H3 has a sequence of SEQ ID NO:33 or a sequence differing by one or two amino acids therefrom; (iv) the CDR-L1 has a sequence of SEQ ID NO:28 or a sequence differing by one or two amino acids therefrom; (v) the CDR-L2 has a sequence of SEQ ID NO:29 or a sequence differing by one or two amino acids therefrom; and (vi) the CDR-L3 has a sequence of SEQ ID NO:30 or a sequence differing by one or two amino acids therefrom; (c) (i) the CDR-H1 has a sequence of SEQ ID NO:39 or a sequence differing by one or two amino acids therefrom; (ii) the CDR-H2 has a sequence of SEQ ID NO:40 or a sequence differing by one or two amino acids therefrom; (iii) the CDR-H3 has a sequence of SEQ ID NO:41 or a sequence differing by one or two amino acids therefrom; (iv) the CDR-L1 has a sequence of SEQ ID NO:36 or a sequence differing by one or two amino acids therefrom; (v) the CDR-L2 has a sequence of SEQ ID NO:37 or a sequence differing by one or two amino acids therefrom; and (vi) the CDR-L3 has a sequence of SEQ ID NO:38 or a sequence differing by one or two amino acids therefrom; or (d) (i) the CDR-H1 has a sequence of SEQ ID NO:47 or a sequence differing by one or two amino acids therefrom; (ii) the CDR-H2 has a sequence of SEQ ID NO:48 or a sequence differing by one or two amino acids therefrom; 49 IPTS/124242861.1
Attorney Docket No.90702160 (iii) the CDR-H3 has a sequence of SEQ ID NO:49 or a sequence differing by one or two amino acids therefrom; (iv) the CDR-L1 has a sequence of SEQ ID NO:44 or a sequence differing by one or two amino acids therefrom; (v) the CDR-L2 has a sequence of SEQ ID NO:45 or a sequence differing by one or two amino acids therefrom; and (vi) the CDR-L3 has a sequence of SEQ ID NO:46 or a sequence differing by one or two amino acids therefrom. 34. The use of claim 33, wherein the antibody fragment comprises (1) a heavy chain comprising CDR-H1, CDR-H2, and CDR-H3 and (2) a light chain comprising CDR- L1, CDR-L2, and CDR-L3, wherein (a) (i) the CDR-H1 has a sequence of SEQ ID NO:23, (ii) the CDR-H2 has a sequence of SEQ ID NO:24, (iii) the CDR-H3 has a sequence of SEQ ID NO:25, (iv) the CDR-L1 has a sequence of SEQ ID NO:20, (v) the CDR-L2 has a sequence of SEQ ID NO:21, and (vi) the CDR-L3 has a sequence of SEQ ID NO:22; (b) (i) the CDR-H1 has a sequence of SEQ ID NO:31, (ii) the CDR-H2 has a sequence of SEQ ID NO:32, (iii) the CDR-H3 has a sequence of SEQ ID NO:33, (iv) the CDR-L1 has a sequence of SEQ ID NO:28, (v) the CDR-L2 has a sequence of SEQ ID NO:29, and (vi) the CDR-L3 has a sequence of SEQ ID NO:30; (c) (i) the CDR-H1 has a sequence of SEQ ID NO:39, (ii) the CDR-H2 has a sequence of SEQ ID NO:40, (iii) the CDR-H3 has a sequence of SEQ ID NO:41, (iv) the CDR-L1 has a sequence of SEQ ID NO:36, (v) the CDR-L2 has a sequence of SEQ ID NO:37, and (vi) the CDR-L3 has a sequence of SEQ ID NO:38; 50 IPTS/124242861.1
Attorney Docket No.90702160 or (d) (i) the CDR-H1 has a sequence of SEQ ID NO:47, (ii) the CDR-H2 has a sequence of SEQ ID NO:48, (iii) the CDR-H3 has a sequence of SEQ ID NO:49, (iv) the CDR-L1 has a sequence of SEQ ID NO:44, (v) the CDR-L2 has a sequence of SEQ ID NO:45, and (vi) the CDR-L3 has a sequence of SEQ ID NO:46. 35. The use of any one of claims 1-34, wherein the antibody fragment comprises (1) a heavy chain variable region having at least 85% identical to a reference VH sequence and (2) a light chain variable region having at least 85% identical to a reference VL sequence, wherein: (a) the reference VH sequence has a sequence of SEQ ID NO:19 and the reference VL sequence has a sequence of SEQ ID NO:18; (b) the reference VH sequence has a sequence of SEQ ID NO:27 and the reference VL sequence has a sequence of SEQ ID NO:26; (c) the reference VH sequence has a sequence of SEQ ID NO:35 and the reference VL sequence has a sequence of SEQ ID NO:34; or (d) the reference VH sequence has a sequence of SEQ ID NO:43 and the reference VL sequence has a sequence of SEQ ID NO:42. 36. The use of any one of claims 1-35, wherein the subject is a mammal. 37. The use of claim 36, wherein the subject is a human. 38. The use of any one of claims 1-37, wherein the tumor is a colon tumor. 39. The use of any one of claims 1-38, wherein the subject has a chemo-resistant tumor. 51 IPTS/124242861.1
Attorney Docket No.90702160 40. The use of any one of claims 1-39, wherein the chemo-resistant tumor is resistant to a taxane, a vinca alkaloid, an anthracycline, or any combination of the foregoing. 41. The use of claim 40, wherein the chemo-resistant tumor is resistant to a taxane. 42. The use of claim 41, wherein the taxane is paclitaxel, taxane, or both. 43. The use of claim 40, 41, or 42, wherein the chemo-resistant tumor is resistant to a vinca alkaloid. 44. The use of claim 43, wherein the vinca alkaloid is vincristine. 45. The use of any one of claims 41-44, wherein the chemo-resistant tumor is resistant to an anthracycline. 46. The use of claim 45, wherein the anthracycline is doxorubicin. 47. The use of any one of claims 41-46, wherein the chemo-resistant tumor is resistant to a platinum-containing compound. 48. The use of claim 47, wherein the platinum-containing compound is satraplatin, oxaliplatin, or both. 49. The use of any one of claims 1-46, wherein the administering comprises administration by a systemic route. 50. The use of claim 47, wherein the systemic route comprises subcutaneous, intravenous, intramuscular, inhalation, or intranasal administration. 51. The use of any one of claims 1-48, wherein the subject is administered more than one dose of the pharmaceutical composition. 52 IPTS/124242861.1
Attorney Docket No.90702160 52. The use of claim 49, wherein the subject is administered the pharmaceutical composition once a week for at least two weeks. 53. The use of claim 50, wherein the subject is administered the pharmaceutical composition once a week for at least three weeks. 54. The use of any one of claims 1-53, wherein said use results in slowing, inhibiting progression of, or regression of the tumor. 55. Use of a pharmaceutical composition comprising a self-assembled polypeptide complex to treat a subject who has or is at risk of having a chemo-resistant tumor, wherein the self-assembled polypeptide complex comprises: (a) a plurality of first fusion polypeptides, each first fusion polypeptide comprising (1) an antibody fragment that is capable of binding to DR5 and (2) a ferritin monomer or subunit thereof; and (b) a plurality of second fusion polypeptides, each second fusion polypeptide comprising (1) an scFc and (2) a ferritin monomer or subunit thereof, and, wherein the scFc comprises two IgG1 Fc chains, each IgG1 Fc chain comprising: an alanine at position 234, an alanine at position 235, an arginine at position 236, an alanine at position 237, a proline at position 329, and a leucine at position 330, according to EU numbering. 56. The use of claim 55, wherein said use results in slowing, inhibiting progression of, or regression of the tumor. 57. Use of a self-assembled polypeptide complex in the manufacture of a medicament to treat a chemo-resistant tumor, wherein the self-assembled polypeptide complex comprises: a plurality of first fusion polypeptides, each first fusion polypeptide comprising (1) an antibody or antibody fragment that is capable of binding to a tumor-associated antigen expressed on the chemo-resistant tumor and (2) a nanocage monomer or subunit thereof. 53 IPTS/124242861.1
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