US20230242655A1 - Interferon-associated antigen binding proteins and uses thereof - Google Patents

Interferon-associated antigen binding proteins and uses thereof Download PDF

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US20230242655A1
US20230242655A1 US17/756,803 US202017756803A US2023242655A1 US 20230242655 A1 US20230242655 A1 US 20230242655A1 US 202017756803 A US202017756803 A US 202017756803A US 2023242655 A1 US2023242655 A1 US 2023242655A1
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antigen binding
interferon
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Antoine ALAM
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Evotec International GmbH
Sanofi SA
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    • 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
    • A61K39/395—Antibodies; Immunoglobulins; Immune serum, e.g. antilymphocytic serum
    • A61K39/39533—Antibodies; Immunoglobulins; Immune serum, e.g. antilymphocytic serum against materials from animals
    • A61K39/39541—Antibodies; Immunoglobulins; Immune serum, e.g. antilymphocytic serum against materials from animals against normal tissues, cells
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/2878—Immunoglobulins [IG], 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
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/12—Antivirals
    • A61P31/20—Antivirals for DNA viruses
    • 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
    • C07K14/52—Cytokines; Lymphokines; Interferons
    • C07K14/555—Interferons [IFN]
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • 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
    • A61K38/00—Medicinal preparations containing peptides
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/55—Fab or Fab'
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
    • C07K2317/565—Complementarity determining region [CDR]
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/33—Fusion polypeptide fusions for targeting to specific cell types, e.g. tissue specific targeting, targeting of a bacterial subspecies

Definitions

  • the present invention relates to novel interferon-associated antigen binding proteins based on the agonistic antiCD40 antibody CP870,893 as well as nucleic acids, vectors and vector systems encoding such interferon-associated antigen binding proteins.
  • the present invention also relates to compositions comprising such interferon-associated antigen binding proteins, nucleic acids, vectors and vector systems.
  • the novel interferon-associated antigen binding proteins afford beneficial improvements over the current state of the art, for example in that they effectively disrupt viral replication and thereby reduce HBV viral load.
  • the present invention also provides medical uses of such interferon-associated antigen binding proteins, nucleic acids, vectors, vector systems and compositions, e.g., in the treatment of hepatitis B virus (HBV) infection and/or for decreasing one or more symptoms of HBV infection in a subject.
  • the present invention further provides host cells comprising such nucleic acids, vectors and vector systems as well as methods of making the interferon-associated antigen binding proteins according to the invention using said host cells.
  • HBV infects more than 300 million people worldwide and is a common cause of liver disease and liver cancer (Liang (2009) Hepatology 49:S13).
  • HBV is a small DNA virus with unusual features similar to retroviruses, which replicates through an RNA intermediate (pre-genomic RNA, pgRNA) and can integrate into the host genome.
  • pgRNA pre-genomic RNA
  • the unique features of the HBV replication cycle confer a distinct ability of the virus to persist in infected cells.
  • HBV infection leads to a wide spectrum of liver disease ranging from acute (including fulminant hepatic failure) to chronic hepatitis, cirrhosis and hepatocellular carcinoma.
  • Acute HBV infection can be either asymptomatic or present with symptomatic acute hepatitis.
  • Novel methods for treating HBV infection by modulating HBV infection in a cell are needed.
  • methods for effectively disrupting viral replication, reducing HBV viral load of HBV-infected cells, reducing transcription of covalently closed circular HBV DNA in HBV-infected cells, and/or reducing the amount of pre-genomic HBV RNA in HBV-infected cells are needed.
  • the invention relates to an interferon-associated antigen binding protein comprising (I) an agonistic anti-CD40 antibody or an agonistic antigen binding fragment thereof, and (II) an Interferon (IFN) or a functional fragment thereof, wherein the agonistic anti-CD40 antibody, or the agonistic antigen binding fragment thereof, comprises
  • the IFN or the functional fragment thereof is selected from the group consisting of a Type I IFN, a Type II IFN and a Type III IFN, or a functional fragment thereof.
  • the Type I IFN, or the functional fragment thereof is IFN ⁇ or IFN ⁇ , or a functional fragment thereof.
  • the IFN or the functional fragment thereof is IFN ⁇ 2a, or a functional fragment thereof.
  • the IFN ⁇ 2a comprises the sequence as set forth in SEQ ID NO 17, or a sequence at least 90% identical thereto.
  • the IFN or the functional fragment thereof is IFN ⁇ , or a functional fragment thereof.
  • the IFN ⁇ comprises the sequence as set forth in SEQ ID NO 14, or a sequence at least 90% identical thereto.
  • the IFN or the functional fragment thereof is fused to a light chain of the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof.
  • the IFN or the functional fragment thereof is fused to a C-terminus of a light chain of the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof.
  • the IFN or the functional fragment thereof is fused to a heavy chain of the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof.
  • the IFN or the functional fragment thereof is fused to a C-terminus of a heavy chain of the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof.
  • the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof, and the IFN or the functional fragment thereof are fused to each other via a linker.
  • the linker comprises a sequence as set forth in SEQ ID NO 20, SEQ ID NO 21, SEQ ID NO 24, SEQ ID NO 25 or SEQ ID NO 26.
  • the interferon-associated antigen binding protein comprises a sequence selected from the group consisting of SEQ ID NO 28, SEQ ID NO 29, SEQ ID NO 30, SEQ ID NO 31, SEQ ID NO 32, SEQ ID NO 33, SEQ ID NO 34, SEQ ID NO 35, SEQ ID NO 36, SEQ ID NO 37, SEQ ID NO 38, SEQ ID NO 39, SEQ ID NO 40, SEQ ID NO 41, SEQ ID NO 42, SEQ ID NO 43, SEQ ID NO 44, SEQ ID NO 45, SEQ ID NO 46 and SEQ ID NO 47.
  • the interferon-associated antigen binding protein is an interferon-fused agonistic anti-CD40 antibody or an interferon-fused agonistic antigen binding fragment thereof comprising one of the sequence combinations disclosed in Table 8.
  • the invention relates to a nucleic acid encoding the interferon-associated antigen binding protein according to the invention.
  • the nucleic acid further encodes a secretory signal peptide.
  • the invention relates to a vector comprising said nucleic acid.
  • the invention relates to a vector system comprising
  • the invention relates to a composition, preferably a pharmaceutical composition, comprising an interferon-associated antigen binding protein, a nucleic acid, a vector, or a vector system according to the invention.
  • the invention relates to a host cell comprising a nucleic acid, a vector, or a vector system according to the invention.
  • the invention relates to a method of making an interferon-associated antigen binding protein according to the invention, comprising culturing said host cell and recovering said interferon-associated antigen binding protein.
  • the invention relates to an interferon-associated antigen binding protein, a nucleic acid, a vector, a vector system, or a composition according to the invention for use as a medicament.
  • the invention relates to an interferon-associated antigen binding protein, a nucleic acid, a vector, a vector system, or a composition according to the invention for use in treating hepatitis B virus (HBV) infection and/or for decreasing one or more symptoms of HBV infection in a subject.
  • HBV hepatitis B virus
  • FIG. 1 This schematic drawing depicts exemplary interferon-associated antigen binding protein formats.
  • the interferon-associated antigen binding protein is an interferon-fused agonistic anti-CD40 antibody or an interferon-fused agonistic antigen binding fragment thereof.
  • IFNs are associated via linkers to different positions on the antibody or the antigen binding fragment thereof: N-terminal or C-terminal part of the light chain (LC) or the heavy chain (HC).
  • LC light chain
  • HC heavy chain
  • IFNs are chosen from Type I, Type II and Type III interferon families.
  • FIG. 2 A depicts an exemplary map of a pcDNA3.1 plasmid encoding SEQ ID NO 32 under the control of the pCMV promoter.
  • the nucleic acid sequence encoding for SEQ ID NO 32 (SEQ ID NO 59) is also shown on the right. Italic: signal peptide sequence; black color: CP870,893 heavy chain coding sequence; underlined: HL linker coding sequence; bold: IFN ⁇ coding sequence.
  • FIG. 2 B shows examples of SDS PAGE in reduced conditions of some IFAs, with IFN ⁇ or IFN ⁇ fused either at the heavy chain or the light chain. Migration of the parental CP870,893 is also shown on the left.
  • FIGS. 3 A- 3 B graphically depict a dose dependent effect of a number of IFA molecules with IFN ⁇ fusions on activating the CD40-mediated NF ⁇ B pathway reporter assay in HEK-BlueTM CD40L cells.
  • FIG. 3 A shows examples of anti-CD40 activities for IFAs with IFN ⁇ fused to the C-terminal part of the heavy chain (HC).
  • FIG. 3 B shows examples of anti-CD40 activities for IFAs with IFN ⁇ fused to the N-terminal part of the LC (IFA34) or the HC (IFA36) and the corresponding fusions on the C-terminal part (IFA35 and IFA37). Purification yield of the latter group of IFAs was very low, thus to test their activity, the supernatants from HEK transfected cells were used and serially diluted to evaluate the anti-CD40 activity on HEK-BlueTM CD40L cells.
  • FIGS. 3 C- 3 D graphically depict a dose dependent effect of a number of IFA molecules with IFN ⁇ fusions on activating the Type I IFN- pathway in reporter HEK-Blue-IFN- ⁇ / ⁇ cells.
  • FIG. 3 C shows examples of IFN activity for IFAs with IFN ⁇ fused to the C-terminal part of the HC.
  • FIG. 3 D shows examples of IFN activity for IFAs with IFN ⁇ fused to the N-terminal part of the LC (IFA34) or the HC (IFA36) and the corresponding fusions on the C-terminal part (IFA35 and IFA37).
  • the same supernatants from HEK transfected cells as in FIG. 3 B were used and serially diluted to evaluate the IFN activity.
  • Parental antibody CP870,893 was used as negative control and recombinant human IFN ⁇ was used as positive control.
  • NS Non Stimulated.
  • FIG. 4 A graphically depicts a dose effect of a number of IFA molecules with IFN ⁇ fusions on activating the CD40-mediated NF ⁇ B pathway reporter assay in HEK-BlueTM CD40L cells.
  • FIG. 4 B graphically depicts a dose effect of a number of IFA molecules with IFN ⁇ fusions on activating the Type I IFN-mediated pathway in reporter HEK-Blue-IFN- ⁇ / ⁇ cells.
  • the activity of Pegasys is indicated in the insert in the lower right corner.
  • FIG. 4 C graphically depicts the effect of IFA molecules with IFN ⁇ fusions and HL linker on HC (IFA38) or LC (IFA39) on activating the CD40-mediated NF ⁇ B pathway reporter assay in HEK-BlueTM CD40L cells.
  • FIG. 4 D graphically depicts the effect of IFA38 and IFA39 on activation of the Type I IFN-pathway in reporter HEK-Blue-IFN ⁇ / ⁇ cells.
  • FIG. 5 depicts the effect of IFN ⁇ based IFAs in a dose dependent manner on HBeAg release from primary hepatocytes infected with HBV.
  • IFA1, IFA12 fusion of IFN ⁇ to the C-terminus of LC via HL or RL linkers, respectively.
  • IFA2 and IFA13 fusion of IFN ⁇ _C17S to the C-terminus of the LC via HL or RL linkers, respectively.
  • FIG. 6 A depicts the effect of IFA25, IFA26 and IFA27 in a dose dependent manner on HBeAg release from primary human hepatocytes infected by HBV.
  • FIG. 6 B depicts the effect of IFA28, IFA29 and IFA30 in a dose dependent manner on HBeAg release from primary human hepatocytes infected by HBV.
  • FIG. 6 C depicts a dose response anti-viral activity (HBeAg release) of IFAs with HL linker (IFA38 and IFA39) on HBV-infected PHHs.
  • FIGS. 6 D- 6 H depict a dose response anti-viral activity of 4 IFA molecules with fusion to IFN ⁇ via a peptide linker on primary human hepatocytes infected with HBV.
  • FIG. 6 D Cartoon illustrating the study design.
  • FIG. 6 E Effect of IFAs on HBeAg release in comparison to Pegasys.
  • FIG. 6 F Effect of IFAs on HBsAg release in comparison to Pegasys.
  • FIG. 6 G Effect of IFAs on pgRNA levels in comparison to Pegasys.
  • FIG. 6 H Effect of IFAs on CXCL10 release in comparison to Pegasys.
  • FIG. 7 depicts results from an in vitro Cytokines Release Assay of Human Whole Blood Cells (WBCs): Example of data obtained after stimulation of WBCs from 4 healthy volunteer donors. WBC were left Non-Stimulated (NS), treated with LPS (10 ng/mL) or with IFA1 (1 ⁇ g/mL) for 24 h. Supernatants were collected and submitted to cytokines release quantification using the MSD u-Plex kit for human cytokines. Results represent the mean of two independent stimulations from each donor. The profile of CXCL10 (IP10), IL6, IL1 ⁇ and TNF ⁇ are shown.
  • IP10 CXCL10
  • Tables 9a-b These tables summarize data obtained after in vitro stimulation of whole blood cells (WBCs) obtained from healthy volunteers. Each IFA was tested on WBCs from four different donors. WBCs were left Non-Treated (NT), treated with LPS (10 ng/mL) or with IFAs (1 ⁇ g/mL) for 24 h. Supernatants were collected and submitted to cytokines release quantification using the MSD u-Plex kit for human cytokines. Results represent the mean of two independent stimulations from each donor and are expressed in pg/mL (nd: not detected).
  • FIG. 8 Pharmacokinetic profile of IFA25, IFA26, IFA27, IFA28, IFA29, and IFA30 after 0.5 mg/kg (IFAs) or 0.3 mg/kg (Pegasys) intravenous bolus injection to mice. Data expressed as mean +/- SD on semi-logarithmic scale. Samples were collected up to 10 days after administration. ELISA assay using anti-IFN ⁇ as secondary antibody for quantification method was used for IFA27, IFA29 and IFA30 ( FIG. 8 A ) and for IFA25, IFA26 and IFA28 ( FIG. 8 B ). ELISA assay using anti-IgG2 as secondary antibody for quantification method was used for IFA25 and IFA27 ( FIG. 8 C ). FIG. 8 D : Pegasys quantification was done using human IFN ⁇ matched antibody pairs. The marked line (LLOQ) denotes the limit of detection for the Pegasys assay.
  • Table 10A PK Report Summary: PK parameters for CP870,893, IFA27, IFA29 and IFA30 following single intravenous administration of 0.5 mg/kg to male CD1 Swiss mice. PK parameters for CP870,893 were explored in a 7-day experiment and those for IFA27, IFA29 and IFA30 in 10-day experiments (quantification for IFA27 was performed using 2 different ELISA approaches).
  • Table 10B PK parameters for CP870,893, Pegasys and for three different IFAs (IFA25, IFA26 and IFA28) following single intravenous bolus administration of 0.5 mg/kg to male CD1 Swiss mice.
  • PK parameters for CP870,893 and IFA25, IFA26, IFA28 and Pegasys were explored in 21-day experiments (quantification for IFA25 was performed using 2 different ELISA approaches).
  • FIG. 9 A depicts CD40 agonistic activity in a dose dependent manner of IFA50 and IFA51 with no Fc region in comparison to the parental anti-CD40 antibody in reporter HEK-BlueTM CD40L cells.
  • FIG. 9 B depicts the IFN ⁇ activity in a dose dependent manner of IFA50 and IFA51 in reporter HEK-BlueTM hIFN- ⁇ / ⁇ cells.
  • FIG. 9 C Effect of IFA50 and IFA51 on HBeAg release from HBV-infected PHHs.
  • FIG. 10 A depicts CD40 agonistic activity in a dose dependent manner of IFNs based IFA49, in comparison to parental anti-CD40 antibody, in HEK-BlueTM CD40L reporter cells.
  • IFA49 corresponds to fusion of IFN ⁇ to the HC via a peptide linker.
  • FIG. 10 B depicts the IFN activity in a dose dependent manner of IFA49 on reporter HEK-BlueTM hIFN- ⁇ / ⁇ reporter cells which are activated by Type I interferons.
  • FIG. 10 C Effect of IFA49 on HbeAg release from HBV-infected PHHs.
  • FIG. 11 A depicts CD40 agonistic activity in a dose dependent manner of IFN ⁇ based IFA46, in comparison to parental anti-CD40 antibody, in HEK-BlueTM CD40L reporter cells.
  • IFA46 corresponds to fusion of IFN ⁇ to the LC via a peptide linker.
  • FIG. 11 B depicts the IFN activity in a dose dependent manner of IFA46 on reporter HEK-BlueTM hIFN- ⁇ / ⁇ reporter cells which are activated by Type I interferons.
  • FIG. 11 C Effect of IFA46 on HbeAg release from HBV-infected PHHs.
  • FIG. 12 A depicts CD40 agonistic activity in a dose dependent manner of IFN ⁇ based IFAs (IFA42 and IFA43), in comparison to parental anti-CD40 antibody, in HEK-BlueTM CD40L reporter cells.
  • IFA42 corresponds to fusion of IFN ⁇ to the LC via a peptide linker
  • IFA43 correspond to fusion of IFN ⁇ to the HC via a peptide linker.
  • FIG. 12 B depicts the IFN activity in a dose dependent manner of IFA42 and IFA43 in reporter HEK-Blue-hIFN ⁇ cells.
  • FIG. 12 C Effect of IFA42 and IFA43 on HbeAg release from HBV-infected PHHs.
  • FIG. 13 A depicts CD40 agonistic activity in a dose dependent manner of IFN ⁇ , based IFAs (IFA44 and IFA45), in comparison to parental anti-CD40 antibody, in HEK-BlueTM CD40L reporter cells.
  • IFA44 corresponds to fusion of IFN ⁇ to the LC via a peptide linker
  • IFA45 correspond to fusion of IFN ⁇ to the HC via a peptide linker.
  • FIG. 13 B depicts the IFN activity in a dose dependent manner of IFA44 and IFA45 in reporter HEK-Blue-hIFN ⁇ , cells.
  • FIG. 13 C Effect of the IFN ⁇ based IFAs (IFA44 and IFA45) on HbeAg release from HBV-infected PHHs.
  • the present invention is based in part on the discovery of a therapy that is based on the use of “interferon-associated antigen-binding proteins”, variants or derivatives thereof comprising (I) an agonistic anti-CD40 antibody or an agonistic antigen binding fragment thereof, and (II) an interferon (IFN) or a functional fragment thereof in hepatitis B virus (HBV) therapy.
  • “interferon-associated antigen-binding proteins” variants or derivatives thereof comprising (I) an agonistic anti-CD40 antibody or an agonistic antigen binding fragment thereof, and (II) an interferon (IFN) or a functional fragment thereof in hepatitis B virus (HBV) therapy.
  • interferon-associated antigen-binding proteins inhibit transcription of hepatitis B virus covalently closed circular DNA (cccDNA) into pre-genomic HBV RNA (pgRNA) in HBV-infected cells, inhibit release of hepatitis B e-antigen (HBeAg) from HBV-infected cells, and enhance the IFN pathway in uninfected and HBV infected hepatocytes, in particular in uninfected and HBV infected primary human hepatocytes and in a synergistic fashion.
  • HBV therapy comprising administering an interferon-associated antigen-binding protein to an HBV-infected cell, or a subject infected with HBV, is provided.
  • CD40 refers to “Cluster of differentiation 40”, a member of the tumor necrosis factor receptor (TNFR) superfamily.
  • CD40 is a costimulatory protein found on antigen presenting cells (e.g., B cells, dendritic cells, monocytes), hematopoietic precursors, endothelial cells, smooth muscle cells, epithelial cells, as well as the majority of human tumors (Grewal & Flavell, Ann. Rev. Immunol., 1996, 16: 111-35; Toes & Schoenberger, Seminars in Immunology, 1998, 10(6): 443-8).
  • antigen presenting cells e.g., B cells, dendritic cells, monocytes
  • hematopoietic precursors hematopoietic precursors
  • endothelial cells smooth muscle cells
  • epithelial cells as well as the majority of human tumors (Grewal & Flavell, Ann. Rev. Immunol., 1996, 16: 111-
  • CD40L The binding of the natural ligand CD154 (CD40L) on T H cells to CD40 activates antigen presenting cells and induces a variety of downstream effects.
  • the TNF-receptor associated factor adaptor proteins TRAF1, TRAF2, TRAF6 and TRAF5 interact with CD40 and serve as mediators of the signal transduction.
  • CD40 signaling activates both the canonical and the noncanonical NF- ⁇ B pathways.
  • the term “antibody” refers to immunoglobulin molecules comprising four polypeptide chains, two heavy (H) chains and two light (L) chains inter-connected by disulfide bonds, as well as multimers thereof (e.g., IgM).
  • Each heavy chain comprises a heavy chain variable region (abbreviated VH or V H ) and a heavy chain constant region (CH or C H ).
  • the heavy chain constant region comprises three domains, CH1, CH2 and CH3.
  • Each light chain comprises a light chain variable region (abbreviated VL or V L ) and a light chain constant region (CL or C L ).
  • the light chain constant region comprises one domain (CL1).
  • VH and VL regions can be further subdivided into regions of hypervariability, termed “complementarity determining regions (CDRs)”, interspersed with regions that are more conserved, termed “framework regions” (FR).
  • CDRs complementarity determining regions
  • FR frame regions
  • Each VH and VL is composed of three CDRs and four FRs, arranged from amino-terminus to carboxy-terminus in the following order: FR1, CDR1, FR2, CDR2, FR3, CDR3, FR4.
  • Framework regions can aid in maintaining the proper conformation of the CDRs to promote binding between the antigen binding region and an antigen.
  • immunoglobulin G a tetrameric glycoprotein.
  • each tetramer is composed of two identical pairs of polypeptide chains, each pair having one light (about 25 kDa) and one heavy chain (about 50-70 kDa).
  • the amino-terminal portion of each chain includes a variable region of about 100 to 110 or more amino acids primarily responsible for antigen recognition.
  • the carboxy-terminal portion of each chain defines a constant region primarily responsible for effector function.
  • Immunoglobulins can be assigned to different classes depending on the amino acid sequence of the constant domain of their heavy chains.
  • Heavy chains are classified as mu ( ⁇ ), delta ( ⁇ ), gamma ( ⁇ ), alpha ( ⁇ ), and epsilon ( ⁇ ), and define the antibody’s isotype as IgM, IgD, IgG, IgA, and IgE, respectively.
  • Several of these may be further divided into subclasses or isotypes, e.g. IgG1, IgG2, IgG3, IgG4, IgA1 and IgA2.
  • Different isotypes have different effector functions; for example, IgG1 and IgG3 isotypes have antibody-dependent cellular cytotoxicity (ADCC) activity.
  • ADCC antibody-dependent cellular cytotoxicity
  • the agonistic antiCD40 antibodies or agonistic antigen binding fragments thereof comprised in the interferon-associated antigen binding proteins according to the invention are of the IgG class.
  • the agonistic antiCD40 antibodies or agonistic antigen binding fragments thereof comprised in the interferon-associated antigen binding proteins according to the invention are of the IgG1 or IgG3 subclasses.
  • the agonistic antiCD40 antibodies or agonistic antigen binding fragments thereof comprised in the interferon-associated antigen binding proteins according to the invention are of the IgG1 subclass.
  • the agonistic antiCD40 antibodies or agonistic antigen binding fragments thereof comprised in the interferon-associated antigen binding proteins according to the invention are of the IgG2 or IgG4 subclasses. In specifically preferred embodiments, the agonistic antiCD40 antibodies or agonistic antigen binding fragments thereof comprised in the interferon-associated antigen binding proteins according to the invention are of the IgG2 subclass.
  • the agonistic antiCD40 antibodies or agonistic antigen binding fragments thereof comprised in the interferon-associated antigen binding proteins according to the invention comprise a light chain of the ⁇ class.
  • the agonistic antiCD40 antibodies or agonistic antigen binding fragments thereof comprised in the interferon-associated antigen binding proteins according to the invention comprise a light chain of the ⁇ class.
  • the variable and constant regions are joined by a “J” region of about 12 or more amino acids, wherein the heavy chain additionally includes a “D” region of about 10 more amino acids. See generally, Fundamental Immunology, Ch. 7 (Paul, W., ed., 2nd ed. Raven Press, N.Y. (1989)).
  • antibody further includes, but is not limited to, monoclonal antibodies, bispecific antibodies, minibodies, domain antibodies, synthetic antibodies (sometimes referred to as “antibody mimetics”), chimeric antibodies, humanized antibodies, human antibodies, and fragments thereof, respectively.
  • antibody mimetics sometimes referred to as “antibody mimetics”
  • antibody includes, in addition to antibodies comprising two full-length heavy chains and two full-length light chains, derivatives, variants, antigen binding fragments, and muteins thereof, examples of which are described below.
  • the term “agonistic CD40 antibody” or “agonistic anti-CD40 antibody” refers to an antibody that binds to CD40 and mediates CD40 signaling. In a preferred embodiment, it binds to human CD40. As described below, binding to CD40 may be determined using surface plasmon resonance, preferably using the BIAcore® system.
  • the agonistic anti-CD40 antibody may increase one or more CD40 activities by at least about 20% when added to a cell, tissue or organism expressing CD40. In some embodiments, the antibody activates CD40 activity by at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, or at least 85%.
  • CD40 activity of the agonistic anti-CD40 antibody may be measured using a whole blood surface molecule upregulation assay or using an in vitro reporter cell assay, e.g., using HEK-BlueTM CD40L cells (InvivoGen Cat. #: hkb-cd40), as described in greater detail in Example I.
  • HEK-BlueTM CD40L cells InvivoGen Cat. #: hkb-cd40
  • SEAP NF ⁇ B-inducible secreted embryonic alkaline phosphatase construct to measure the activity of CD40 agonists. Stimulation of CD40 leads to NF ⁇ B activation and thus to production of SEAP, which can be detected in the supernatant using chromogenic substrates such as QUANTI-BlueTM.
  • the interferon-associated antigen binding proteins activate both the CD40 and an IFN pathway.
  • the interferon-associated antigen binding protein activates the CD40 pathway with an EC 50 of less than 400, 300, 200, 150, 100, 70, 60, 50, 40, 30, 25, 20, or 15 ng/mL.
  • the interferon-associated antigen binding protein activates the CD40 pathway with an EC 50 ranging from 10 to 200 ng/mL.
  • the interferon-associated antigen binding protein activates the CD40 pathway with an EC 50 ranging from 10 to 50 ng/mL, preferably 10 to 30 ng/mL.
  • agonistic antigen binding fragment of an agonistic anti-CD40 antibody refers to a fragment of an agonistic anti-CD40 antibody that retains one or more functional activities of the original antibody, such as the ability to bind to and act as an agonist of CD40 signaling in a cell, e.g., it mediates CD40 pathway signaling. Such fragment may compete with the intact antibody for binding to CD40.
  • Agonistic antigen binding fragments of an agonistic anti-CD40 antibody can be produced by recombinant DNA techniques, or can be produced by enzymatic or chemical cleavage of an anti-CD40 antibody.
  • Agonistic antigen binding fragments include, but are not limited to, a Fab fragment, a diabody (heavy chain variable domain on the same polypeptide as a light chain variable domain, connected via a short peptide linker that is too short to permit pairing between the two domains on the same chain), a Fab′ fragment, a F(ab′) 2 fragment, a Fv fragment, domain antibodies and single-chain antibodies, and can be derived from any mammalian source, including but not limited to human, mouse, rat, camelid or rabbit.
  • variable region refers to a portion of the light and/or heavy chains of an antibody, typically including approximately the amino-terminal 120 to 130 amino acids in the heavy chain and about 100 to 110 amino terminal amino acids in the light chain. Variable regions of different antibodies differ extensively in amino acid sequence even among antibodies derived from the same species or of the same class.
  • Exemplary V L and V H domain sequences of the agonistic anti-CD40 antibody CP870,893 are shown in Table 1.
  • the variable region of an antibody typically determines specificity of a particular antibody for its target as it contains the CDRs.
  • Table 1 also shows exemplary CDR sequences of the agonistic anti-CD40 antibody CP870,893.
  • Delineation of a CDR and identification of residues comprising the binding site of an antibody may be accomplished by solving the structure of the antibody and/or solving the structure of the antibody-ligand complex. This can be accomplished by any of a variety of techniques known to those skilled in the art, such as X-ray crystallography. Various methods of analysis can be employed to identify or approximate the CDR regions. Examples of such methods include, but are not limited to, the Kabat definition, the Chothia definition, the AbM definition and the contact definition.
  • the Kabat definition is a standard for numbering the residues in an antibody and is typically used to identify CDR regions. See, e.g., Johnson & Wu, Nucleic Acids Res., 28: 214-8 (2000).
  • the Chothia definition is similar to the Kabat definition, but the Chothia definition takes into account positions of certain structural loop regions. See, e.g., Chothia et al., J. Mol. Biol., 196: 901-17 (1986); Chothia et al., Nature, 342: 877-83 (1989).
  • the AbM definition uses an integrated suite of computer programs produced by Oxford Molecular Group that model antibody structure.
  • the AbM definition models the tertiary structure of an antibody from primary sequence using a combination of knowledge databases and ab initio methods, such as those described by Samudrala et al., “Ab Initio Protein Structure Prediction Using a Combined Hierarchical Approach,” in PROTEINS, Structure, Function and Genetics Suppl., 3:194-198 (1999).
  • the contact definition is based on an analysis of the available complex crystal structures. See, e.g., MacCallum et al., J. Mol. Biol., 5:732-45 (1996).
  • the complementarity determining regions (CDRs) of the light and heavy chain variable regions of an agonistic anti-CD40 antibody, or an agonistic antigen binding fragment thereof can be grafted to framework regions (FRs) from the same, or another, species.
  • the CDRs of the light and heavy chain variable regions of an agonistic anti-CD40 antibody, or an agonistic antigen binding fragment thereof can be grafted to consensus human FRs.
  • consensus human FRs in certain embodiments, FRs from several human heavy chain or light chain amino acid sequences are aligned to identify a consensus amino acid sequence.
  • the FRs of the heavy chain or light chain of an agonistic anti-CD40 antibody, or an agonistic antigen binding fragment thereof are replaced with the FRs from a different heavy chain or light chain.
  • rare amino acids in the FRs of the heavy and light chains of an agonistic anti-CD40 antibody, or an agonistic antigen binding fragment thereof are not replaced, while the rest of the FR amino acids are replaced. Rare amino acids are specific amino acids that are in positions in which they are not usually found in FRs.
  • the grafted variable regions from an agonistic anti-CD40 antibody, or an agonistic antigen binding fragment thereof can be used with a constant region that is different from the constant region of an agonistic anti-CD40 antibody, or an agonistic antigen binding fragment thereof.
  • the grafted variable regions are part of a single chain Fv antibody. CDR grafting is described, e.g., in U.S. Pat. Nos.
  • An “Fc” region typically comprises two heavy chain fragments comprising the C H 2 and C H 3 domains of an antibody.
  • the two heavy chain fragments are held together by two or more disulfide bonds and by hydrophobic interactions of the C H 3 domains.
  • a “Fab fragment” comprises one full-length light chain as well as the C H 1 and variable regions of one heavy chain (the combination of the V H and C H 1 regions is referred to herein as “fab region heavy chain”).
  • a “Fab′ fragment” comprises one light chain and a portion of one heavy chain that contains the VH domain and the C H 1 domain and also the region between the C H 1 and C H 2 domains, such that an interchain disulfide bond can be formed between the two heavy chains of two Fab′ fragments to form an F(ab′) 2 molecule.
  • a “F(ab′) 2 fragment” contains two light chains and two heavy chains containing a portion of the constant region between the C H 1 and C H 2 domains, such that an interchain disulfide bond is formed between the two heavy chains.
  • a F(ab′) 2 fragment thus is composed of two Fab′ fragments that are held together by a disulfide bond between the two heavy chains.
  • the “Fv region” comprises the variable regions from both the heavy and light chains, but lacks the constant regions.
  • Single-chain antibodies are Fv molecules in which the heavy and light chain variable regions have been connected by a flexible linker to form a single polypeptide chain, which forms an antigen binding region.
  • Single chain antibodies are discussed in detail in International Patent Application Publication No. WO 88/01649 and U.S. Pat. Nos. 4,946,778 and No. 5,260,203, the disclosures of which are incorporated by reference.
  • a “domain antibody” is an immunologically functional immunoglobulin fragment containing only the variable region of a heavy chain or the variable region of a light chain.
  • two or more V H regions are covalently joined with a peptide linker to create a bivalent domain antibody.
  • the two V H regions of a bivalent domain antibody can target the same or different antigens.
  • An antibody or antigen binding protein such as an interferon-associated antigen binding protein according to the invention, preferably binds to its target antigen with a dissociation constant (K d ) of ⁇ 10 -7 M.
  • the antibody or antigen binding protein binds its antigen with “high affinity” when the K d is ⁇ 5 ⁇ 10 -9 M, and with “very high affinity” when the K d is ⁇ 5 ⁇ 10 -10 M. More preferably, the antibody or antigen binding protein has a K d of ⁇ 10 -9 M.
  • the off-rate is ⁇ 1 ⁇ 10 -5 .
  • the antibody or antigen binding protein will bind to human CD40 with a K d of between about 10 -9 M and 10 -13 M, and in yet another embodiment the antibody or antigen binding protein will bind with a K d ⁇ 5 ⁇ 10 -10 .
  • any or all of the antigen binding fragments can bind to CD40.
  • said constants are determined using surface plasmon resonance, more preferably using the BIAcore® system.
  • surface plasmon resonance means an optical phenomenon that allows for the analysis of real-time biospecific interactions by detection of alterations in protein concentrations within a biosensor matrix, for example using the BIAcore® system (BIAcore International AB, a GE Healthcare company, Uppsala, Sweden and Piscataway, N.J.). For further descriptions, see Jönsson et al. (1993) Ann. Biol. Clin. 51:19-26.
  • K on means the on rate constant for association of a binding protein (e.g., an antibody or antigen binding protein) to the antigen to form the, e.g., antigen binding protein/antigen complex.
  • K on also means “association rate constant”, or “ka”, as is used interchangeably herein.
  • association rate constant or “ka”, as is used interchangeably herein. This value indicating the binding rate of a binding protein to its target antigen or the rate of complex formation between a binding protein, e.g., an antibody or an antigen binding protein, and antigen also is shown by the equation below:
  • K off means the off rate constant for dissociation, or “dissociation rate constant”, of a binding protein (e.g., an antibody or antigen binding protein) from the, e.g., antigen binding protein/antigen complex as is known in the art.
  • This value indicates the dissociation rate of a binding protein, e.g., an antibody or an antigen binding protein, from its target antigen or separation of Ab-Ag complex over time into free antibody and antigen as shown by the equation below:
  • K d and “equilibrium dissociation constant” means the value obtained in a titration measurement at equilibrium, or by dividing the dissociation rate constant (K off ) by the association rate constant (K on ).
  • the association rate constant, the dissociation rate constant and the equilibrium dissociation constant are used to represent the binding affinity of a binding protein (e.g., an antibody or an antigen binding protein) to an antigen.
  • Methods for determining association and dissociation rate constants are well known in the art. Using fluorescence-based techniques offers high sensitivity and the ability to examine samples in physiological buffers at equilibrium.
  • BIAcore® biological interaction analysis
  • KinExA® Kineetic Exclusion Assay
  • An antigen binding protein according to the invention may bind to one target with an affinity at least one order of magnitude, preferably at least two orders of magnitude higher than for a second target.
  • target refers to a molecule or a portion of a molecule capable of being bound by an antigen binding protein.
  • a target can have one or more epitopes. It will therefore be understood that the target may serve as “antigen” for the “antigen binding protein” of the present invention.
  • epitope includes any determinant capable of being bound by an antigen binding protein, such as an antibody.
  • An epitope is a region of an antigen that is bound by an antigen binding protein that targets that antigen, and when the antigen is a protein, includes specific amino acids that directly contact the antigen binding protein. Most often, epitopes reside on proteins, but in some instances can reside on other kinds of molecules, such as nucleic acids.
  • Epitope determinants can include chemically active surface groupings of molecules such as amino acids, sugar side chains, phosphoryl or sulfonyl groups, and can have specific three-dimensional structural characteristics, and/or specific charge characteristics.
  • antibodies specific for a particular target antigen will preferentially/specifically recognize an epitope on the target antigen in a complex mixture of proteins and/or macromolecules.
  • the agonistic anti-CD40 antibody, or the agonistic antigen binding fragment thereof forming part (I) of the interferon-associated antigen binding proteins of the invention comprises three light chain complementarity determining regions (CDRs) that are at least 90% identical to the CDRL1, CDRL2 and CDRL3 sequences within SEQ ID NO 3; and three heavy chain CDRs that are at least 90% identical to the CDRH1, CDRH2 and CDRH3 sequences within SEQ ID NO 6.
  • CDRs light chain complementarity determining regions
  • the agonistic anti-CD40 antibody, or the agonistic antigen binding fragment thereof may also comprise three light chain complementarity determining regions (CDRs) that are identical to the CDRL1, CDRL2 and CDRL3 sequences within SEQ ID NO 3; and three heavy chain CDRs that are identical to the CDRH1, CDRH2 and CDRH3 sequences within SEQ ID NO 6.
  • each CDR is defined in accordance with the Kabat definition, the Chothia definition, the AbM definition, or the contact definition of CDR; preferably wherein each CDR is defined in accordance with the CDR definition of Kabat or the CDR definition of Chothia.
  • each CDR is defined in accordance with the Kabat definition.
  • each CDR is defined in accordance with the Chothia definition.
  • the agonistic anti-CD40 antibody, or the agonistic antigen binding fragment thereof forming part (I) of the interferon-associated antigen binding proteins of the invention comprises (a) a heavy chain or a fragment thereof comprising a complementarity determining region (CDR) CDRH1 that is at least 90%, at least 95%, at least 98% or at least 99% identical to SEQ ID NO 56, a CDRH2 that is at least 90%, at least 95%, at least 98% or at least 99% identical to SEQ ID NO 57, and a CDRH3 that is at least 90%, at least 95%, at least 98% or at least 99% identical to SEQ ID NO 58; and (b) a light chain or a fragment thereof comprising a CDRL1 that is at least 90%, at least 95%, at least 98% or at least 99% identical to SEQ ID NO 52, a CDRL2 that is at least 90%, at least 95%, at least 98% or at least 99% identical to SEQ ID NO 53, and
  • the agonistic anti-CD40 antibody, or the agonistic antigen binding fragment thereof comprises (a) a heavy chain or a fragment thereof comprising a complementarity determining region (CDR) CDRH1 that is identical to SEQ ID NO 56, a CDRH2 that is identical to SEQ ID NO 57, and a CDRH3 that is identical to SEQ ID NO 58; and (b) a light chain or a fragment thereof comprising a CDRL1 that is identical to SEQ ID NO 52, a CDRL2 that is identical to SEQ ID NO 53, and a CDRL3 that is identical to SEQ ID NO 54.
  • CDR complementarity determining region
  • the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof, comprises a light chain variable region V L comprising the sequence as set forth in SEQ ID NO 51, or a sequence at least 90%, at least 95%, at least 98% or at least 99% identical thereto; and/or a heavy chain variable region V H comprising the sequence as set forth in SEQ ID NO 55, or a sequence at least 90%, at least 95%, at least 98% or at least 99% identical thereto.
  • the interferon-associated antigen binding proteins of the invention may also comprise an agonistic anti-CD40 antibody or an agonistic antigen binding fragment thereof, comprising a Fab region heavy chain comprising an amino acid sequence as set forth in SEQ ID NO 12, or a sequence at least 90%, at least 95%, at least 98% or at least 99% identical thereto.
  • the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof comprises a light chain (LC) that comprises a sequence as set forth in SEQ ID NO 3, or a sequence at least 90%, at least 95%, at least 98% or at least 99% identical thereto; and/or a heavy chain (HC) that comprises a sequence selected from the group consisting of SEQ ID NO 6, SEQ ID NO 9, SEQ ID NO 49, SEQ ID NO 12 and SEQ ID NO 50, or a sequence at least 90%, at least 95%, at least 98% or at least 99% identical thereto.
  • LC light chain
  • HC heavy chain
  • the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof comprises a light chain (LC) that comprises a sequence as set forth in SEQ ID NO 3, or a sequence at least 90%, at least 95%, at least 98% or at least 99% identical thereto; and/or a heavy chain (HC) that comprises a sequence as set forth in SEQ ID NO 6, or a sequence at least 90%, at least 95%, at least 98% or at least 99% identical thereto.
  • LC light chain
  • HC heavy chain
  • the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof comprises a light chain (LC) that comprises a sequence as set forth in SEQ ID NO 3, or a sequence at least 90%, at least 95%, at least 98% or at least 99% identical thereto; and/or a heavy chain (HC) that comprises a sequence as set forth in SEQ ID NO 9, or a sequence at least 90%, at least 95%, at least 98% or at least 99% identical thereto.
  • LC light chain
  • HC heavy chain
  • the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof comprises a light chain (LC) that comprises a sequence as set forth in SEQ ID NO 3, or a sequence at least 90%, at least 95%, at least 98% or at least 99% identical thereto; and/or a heavy chain (HC) that comprises a sequence as set forth in SEQ ID NO 49, or a sequence at least 90%, at least 95%, at least 98% or at least 99% identical thereto.
  • LC light chain
  • HC heavy chain
  • the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof comprises a light chain (LC) that comprises a sequence as set forth in SEQ ID NO 3, or a sequence at least 90%, at least 95%, at least 98% or at least 99% identical thereto; and/or a heavy chain (HC) that comprises a sequence as set forth in SEQ ID NO 12, or a sequence at least 90%, at least 95%, at least 98% or at least 99% identical thereto.
  • LC light chain
  • HC heavy chain
  • the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof comprises a light chain (LC) that comprises a sequence as set forth in SEQ ID NO 3, or a sequence at least 90%, at least 95%, at least 98% or at least 99% identical thereto; and/or a heavy chain (HC) that comprises a sequence as set forth in SEQ ID NO 50, or a sequence at least 90%, at least 95%, at least 98% or at least 99% identical thereto.
  • LC light chain
  • HC heavy chain
  • a “variant” of a polypeptide comprises an amino acid sequence wherein one, two, three, four, five or more amino acid residues are inserted into, deleted from and/or substituted into the amino acid sequence relative to another polypeptide sequence.
  • the variant comprises up to ten insertions, deletions and/or substitutions, more preferably up to eight insertions, deletions and/or substitutions. More specifically, the variant may comprise up to ten, more preferably up to eight insertions. The variant may also comprise up to ten, more preferably up to eight deletions. In even more preferred embodiments, the variant comprises up to ten substitutions, most preferably up to eight substitutions. In some embodiments, these substitutions are conservative amino acid substitution as described below.
  • a “variant” of a polynucleotide sequence comprises one or more mutations within the polynucleotide sequence relative to another polynucleotide sequence, wherein one, two, three, four, five or more nucleic acid residues are inserted into, deleted from and/or substituted into the nucleic acid sequence.
  • the variant comprises up to ten insertions, deletions and/or substitutions, more preferably up to eight insertions, deletions and/or substitutions. More specifically, the variant may comprise up to ten, more preferably up to eight insertions. The variant may also comprise up to ten, more preferably up to eight deletions.
  • the variant comprises up to ten substitutions, most preferably up to eight substitutions.
  • Said one, two, three, four, five or more mutations can cause one, two, three, four, five or more amino acid exchanges within the amino acid sequence the variant encodes for as compared to another amino acid sequence (i.e. a “non-silent mutation”).
  • Variants also include nucleic acid sequences wherein one, two, three, four, five or more codons have been replaced by their synonyms which does not cause an amino acid exchange and is thus called a “silent mutation”.
  • identity refers to a relationship between the sequences of two or more polypeptide molecules or two or more nucleic acid molecules, as determined by aligning and comparing the sequences. “Percent identity” means the percent of identical residues between the amino acids or nucleotides in the compared molecules and is calculated based on the size of the smallest of the molecules being compared. Preferably, identity is determined over the full length of a sequence. It is understood that the expression “at least 80% identical”, includes embodiments wherein the claimed sequence is at least 85%, at least 90%, at least 95%, at least 98% or at least 99% identical to the reference sequence.
  • the expression “at least 90 % identical” includes embodiments wherein the claimed sequence is 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 the reference sequence.
  • gaps in alignments are preferably addressed by a particular mathematical model or computer program (i.e., an “algorithm”).
  • Methods that can be used to calculate the identity of the aligned nucleic acids or polypeptides include those described in Computational Molecular Biology, (Lesk, A. M., ed.), 1988, New York: Oxford University Press; Biocomputing Informatics and Genome Projects, (Smith, D. W., ed.), 1993, New York: Academic Press; Computer Analysis of Sequence Data, Part I, (Griffin, A. M., and Griffin, H.
  • the sequences being compared are typically aligned in a way that gives the largest match between the sequences.
  • One example of a computer program that can be used to determine percent identity is the GCG program package, which includes GAP (Devereux et al., 1984, Nucl. Acid Res . 12:387; Genetics Computer Group, University of Wisconsin, Madison, WI).
  • GAP is used to align the two polypeptides or polynucleotides for which the percent sequence identity is to be determined.
  • the sequences are aligned for optimal matching of their respective amino acid or nucleotide (the “matched span”, as determined by the algorithm).
  • a gap opening penalty (which is calculated as 3 ⁇ the average diagonal, wherein the “average diagonal” is the average of the diagonal of the comparison matrix being used; the “diagonal” is the score or number assigned to each perfect amino acid match by the particular comparison matrix) and a gap extension penalty (which is usually 1 ⁇ 10 times the gap opening penalty), as well as a comparison matrix such as PAM 250 or BLOSum 62 are used in conjunction with the algorithm.
  • a standard comparison matrix (see, Dayhoff et al., 1978, Atlas of Protein Sequence and Structure 5:345-352 for the PAM 250 comparison matrix; Henikoff et al., 1992, Proc. Natl. Acad. Sci. U.S.A. 89:10915-10919 for the BLOSum 62 comparison matrix) is also used by the algorithm.
  • Certain alignment schemes for aligning two amino acid sequences may result in matching of only a short region of the two sequences, and this small aligned region may have very high sequence identity even though there is no significant relationship between the two full-length sequences. Accordingly, the selected alignment method (GAP program) can be adjusted if so desired to result in an alignment that spans at least 50 or at least 100, preferably the entire length, of contiguous amino acids of the target polypeptide.
  • amino acid residues can encompass non-naturally occurring amino acid residues, which are typically incorporated by chemical peptide synthesis rather than by synthesis in biological systems. These include peptidomimetics and other reversed or inverted forms of amino acid moieties.
  • Naturally occurring residues can be divided into classes based on common side chain properties:
  • non-conservative substitutions can involve the exchange of a member of one of these classes for a member from another class.
  • substituted residues can be introduced, for example, into regions of a human antibody that are homologous with non-human antibodies, or into the non-homologous regions of the molecule.
  • the hydropathic index of amino acids can be considered.
  • Each amino acid has been assigned a hydropathic index on the basis of its hydrophobicity and charge characteristics. They are: isoleucine (+4.5); valine (+4.2); leucine (+3.8); phenylalanine (+2.8); cysteine/cystine (+2.5); methionine (+1.9); alanine (+1.8); glycine (-0.4); threonine (-0.7); serine (-0.8); tryptophan (-0.9); tyrosine (-1.3); proline (-1.6); histidine (-3.2); glutamate (-3.5); glutamine (-3.5); aspartate (-3.5); asparagine (-3.5); lysine (-3.9); and arginine (-4.5).
  • hydropathic amino acid index in conferring interactive biological function on a protein is understood in the art. Kyte et al., J. Mol. Biol., 157:105-131 (1982). It is known that certain amino acids can be substituted for other amino acids having a similar hydropathic index or score and still retain a similar biological activity. In making changes based upon the hydropathic index, in certain embodiments, the substitution of amino acids whose hydropathic indices are within ⁇ 2 is included. In certain embodiments, those which are within ⁇ 1 are included, and in certain embodiments, those within ⁇ 0.5 are included.
  • the substitution of like amino acids can be made effectively on the basis of hydrophilicity.
  • the greatest local average hydrophilicity of a protein as governed by the hydrophilicity of its adjacent amino acids, correlates with its immunogenicity and antigenicity, i.e., with a biological property of the protein.
  • hydrophilicity values have been assigned to these amino acid residues: arginine (+3.0); lysine (+3.0); aspartate (+3.0 ⁇ 1); glutamate (+3.0 ⁇ 1); serine (+0.3); asparagine (+0.2); glutamine (+0.2); glycine (0); threonine (-0.4); proline (-0.5 ⁇ 1); alanine (-0.5); histidine (-0.5); cysteine (-1.0); methionine (-1.3); valine (-1.5); leucine (-1.8); isoleucine (-1.8); tyrosine (-2.3); phenylalanine (-2.5) and tryptophan (-3.4).
  • the substitution of amino acids whose hydrophilicity values are within ⁇ 2 is included, in certain embodiments, those which are within ⁇ 1 are included, and in certain embodiments, those within ⁇ 0.5 are included.
  • a skilled artisan will be able to determine suitable variants of the interferon-associated antigen binding proteins as set forth herein using well-known techniques.
  • one skilled in the art can identify suitable areas of the molecule that may be changed without destroying activity by targeting regions not believed to be important for activity.
  • even areas that can be important for biological activity or for structure can be subject to conservative amino acid substitutions without destroying the biological activity or without adversely affecting the polypeptide structure.
  • One skilled in the art can also analyze the three-dimensional structure and amino acid sequence in relation to that structure in similar proteins or protein domains. In view of such information, one skilled in the art can predict the alignment of amino acid residues of interferon-associated antigen binding protein, an antibody or an antigen binding fragment thereof or an interferon or a functional fragment thereof as described herein with respect to its three dimensional structure. In certain embodiments, one skilled in the art can choose not to make radical changes to amino acid residues predicted to be on the surface of the protein, since such residues can be involved in important interactions with other molecules. Moreover, one skilled in the art can generate test variants containing a single amino acid substitution at each desired amino acid residue. The variants can then be screened using activity assays known to those skilled in the art.
  • variants can be used to gather information about suitable variants. For example, if one discovered that a change to a particular amino acid residue resulted in destroyed, undesirably reduced, or unsuitable activity, variants with such a change can be avoided. In other words, based on information gathered from such experiments, one skilled in the art can readily determine the amino acids where further substitutions should be avoided either alone or in combination with other mutations.
  • amino acid substitutions are those which: (1) reduce susceptibility to proteolysis, (2) reduce susceptibility to oxidation, (3) alter binding affinity for forming protein complexes, (4) alter binding affinities, and/or (5) confer or modify other physicochemical or functional properties on such polypeptides.
  • single or multiple amino acid substitutions in certain embodiments, conservative amino acid substitutions can be made in the naturally-occurring sequence (in certain embodiments, in the portion of the polypeptide outside the domain(s) forming intermolecular contacts).
  • a conservative amino acid substitution typically may not substantially change the structural characteristics of the parent sequence (e.g., a replacement amino acid should not tend to break a helix that occurs in the parent sequence, or disrupt other types of secondary structure that characterizes the parent sequence).
  • a replacement amino acid should not tend to break a helix that occurs in the parent sequence, or disrupt other types of secondary structure that characterizes the parent sequence.
  • Examples of art-recognized polypeptide secondary and tertiary structures are described in Proteins, Structures and Molecular Principles (Creighton, Ed., W. H. Freeman and Company, New York (1984)); Introduction to Protein Structure (C. Branden & J. Tooze, eds., Garland Publishing, New York, N.Y. (1991)); and Thornton et al., Nature, 354:105 (1991), which are each incorporated herein by reference.
  • derivative refers to a molecule that includes a chemical modification other than an insertion, deletion, or substitution of amino acids (or nucleic acids).
  • derivatives comprise covalent modifications, including, but not limited to, chemical bonding with polymers, lipids, or other organic or inorganic moieties.
  • a chemically modified interferon-associated antigen binding protein can have a greater circulating half-life than an interferon-associated antigen binding protein that is not chemically modified.
  • a chemically modified interferon-associated antigen binding protein can have improved targeting capacity for desired cells, tissues, and/or organs.
  • a derivative interferon-associated antigen binding protein is covalently modified to include one or more water-soluble polymer attachments, including, but not limited to, polyethylene glycol, polyoxyethylene glycol, or polypropylene glycol. See, e.g., U.S. Pat. Nos: 4,640,835, 4,496,689, 4,301,144, 4,670,417,4,791,192 and 4,179,337.
  • a derivative interferon-associated antigen binding protein comprises one or more polymer, including, but not limited to, monomethoxy-polyethylene glycol, dextran, cellulose, or other carbohydrate based polymers, poly-(N-vinyl pyrrolidone)-polyethylene glycol, propylene glycol homopolymers, a polypropylene oxide/ethylene oxide co-polymer, polyoxyethylated polyols (e.g., glycerol) and polyvinyl alcohol, as well as mixtures of such polymers.
  • polymer including, but not limited to, monomethoxy-polyethylene glycol, dextran, cellulose, or other carbohydrate based polymers, poly-(N-vinyl pyrrolidone)-polyethylene glycol, propylene glycol homopolymers, a polypropylene oxide/ethylene oxide co-polymer, polyoxyethylated polyols (e.g., glycerol) and poly
  • a derivative of an interferon-associated antigen binding protein as described herein is covalently modified with polyethylene glycol (PEG) subunits.
  • PEG polyethylene glycol
  • one or more water-soluble polymer is bonded at one or more specific position, for example at the amino terminus, of a derivative.
  • one or more water-soluble polymer is randomly attached to one or more side chains of a derivative.
  • PEG is used to improve the therapeutic capacity of the interferon-associated antigen binding protein. Certain such methods are discussed, for example, in U.S. Pat. No. 6,133,426, which is hereby incorporated by reference for any purpose.
  • interferon-associated antigen binding protein variants include glycosylation variants wherein the number and/or type of glycosylation site has been altered compared to the amino acid sequences of a parent polypeptide.
  • protein variants comprise a greater number of N-linked glycosylation sites than the native protein.
  • protein variants comprise a lesser number of N-linked glycosylation sites than the native protein.
  • An N-linked glycosylation site is characterized by the sequence: Asn-X-Ser or Asn-X-Thr, wherein the amino acid residue designated as X can be any amino acid residue except proline. The substitution of amino acid residues to create this sequence provides a potential new site for the addition of an N-linked carbohydrate chain.
  • substitutions which eliminate this sequence will remove an existing N-linked carbohydrate chain.
  • a rearrangement of N-linked carbohydrate chains wherein one, two, three, four, five or more N-linked glycosylation sites (typically those that are naturally occurring) are eliminated and one or more new N-linked sites are created.
  • Additional preferred variants include cysteine variants wherein one or more cysteine residues are deleted from or substituted for another amino acid (e.g., serine) as compared to the parent amino acid sequence.
  • Cysteine variants can be useful when antibodies must be refolded into a biologically active conformation such as after the isolation of insoluble inclusion bodies. Cysteine variants generally have fewer cysteine residues than the native protein, and typically have an even number to minimize interactions resulting from unpaired cysteines.
  • hepatitis B virus or “HBV” refers to the double stranded DNA virus that causes hepatitis B, which belongs to a family of closely related DNA viruses called the Hepadnaviruses. Hepadnaviruses have a strong preference for infecting liver cells, but small amounts of hepadnaviral DNA can be found in kidney, pancreas, and mononuclear cells. However, infection at these sites is not linked to extra hepatic disease.
  • the HBV virion i.e., the Dane particle, consists of an outer lipid envelope and an icosahedral nucleocapsid core composed of protein.
  • the nucleocapsid encloses the viral DNA and a DNA polymerase that has reverse transcriptase activity similar to retroviruses.
  • the outer envelope contains embedded proteins, which are involved in viral binding of, and entry into, susceptible cells.
  • the virus is one of the smallest enveloped animal viruses with a virion diameter of 42 nm, but pleomorphic forms exist, including filamentous and spherical bodies lacking a core.
  • HBV surface antigen
  • HBeAg splice variant HBeAg
  • DNA polymerase DNA polymerase
  • Hbx HBV is one of a few known non-retroviral viruses which employ reverse transcription as a part of its replication process.
  • the HBV nucleocapsid contains a relatively small and partially duplex 3.2 kb circular DNA, viral polymerase and core protein.
  • the genome has only four long open reading frames.
  • the pre-S-S (pre-surface-surface) region of the genome encodes the three viral surface antigens by differential initiation of translation at each of three in-frame initiation codons.
  • HBeAg The most abundant protein of HBV is the 24 kD S protein (which is known as HBsAg).
  • the pre-C-C (pre-core-core) region encodes HBcAg (HBV core Antigen) and HBeAg (HBV e Antigen).
  • HBeAg is not required for viral replication and plays no role in viral assembly but is nevertheless a useful indicator of active viral replication.
  • HBeAg Since HBeAg is secreted by HBV-infected hepatocytes, it can be detected in the blood via standard diagnostic tests (such as ELISA) and is thus used as a laboratory marker for a viremic HBV infection (Testoni et al., Serum hepatitis B core-related antigen (HBcrAg) correlates with covalently closed circular DNA. J. Hepatol. 2019, 70, 615-625. http://dx.doi.org/10.1016/j.jhep.2018.11.030).
  • the P-coding region is specific for the viral polymerase, a multifunctional enzyme involved in DNA synthesis and RNA encapsidation.
  • the X open reading frame encodes the viral X protein (HBx), which modulates host-cell signal transduction and can directly and indirectly affect host and viral gene expression.
  • HBV The life cycle of HBV is believed to begin when the virus attaches to the host cell membrane via its envelope proteins. It has been suggested that HBV binds to a receptor on the plasma membrane that is predominantly expressed on human hepatocytes via the pre-S1 domain of the large envelope protein as an initial step in HBV infection. However, the nature of the receptor remains controversial. Then, the viral membrane fuses with the cell membrane and the viral genome is released into the cells.
  • Replication of HBV can be regulated by a variety of factors, including hormones, growth factors, and cytokines.
  • the cellular DNA repair machinery convert the partial double-stranded DNA (dsDNA; also called relaxed circular HBV DNA (rcDNA)), genome into covalently closed circular DNA (cccDNA).
  • dsDNA partial double-stranded DNA
  • rcDNA relaxed circular HBV DNA
  • cccDNA covalently closed circular DNA
  • the resulting cccDNA is the template for host RNA Pol-II for further transcription of pre-genomic RNA and sub-genomic RNA (Allweiss L and Dandri M, The Role of cccDNA in HBV Maintenance. Viruses 2017, 9(6): 156; doi:10.3390/v9060156; Nur K.
  • the pre-genomic RNA is bifunctional, serving as both the template for viral DNA synthesis and as the messenger for pre-C, C, and P translation.
  • the sub-genomic RNAs function exclusively for translation of the envelope and X protein. All viral RNA is transported to the cytoplasm, where its translation yields the viral envelope, core, and polymerase proteins, as well as HBx and HBcAg.
  • HBV core particles are assembled in the cytosol and during this process, a single molecule of pre-genomic RNA is incorporated into the assembling viral core.
  • RNA Once the viral RNA is encapsidated, reverse transcription begins. The synthesis of the two viral DNA strands is sequential. The first DNA strand is made from the encapsidated RNA template; during or after the synthesis of this strand, the RNA template is degraded and the synthesis of the second DNA strand proceeds, with the use of the newly made first DNA strand as a template.
  • Some cores bearing the mature genome are transported back to the nucleus, where their newly minted DNA genomes can be converted to cccDNA to maintain a stable intranuclear pool of transcriptional templates.
  • HBV surface antigen (HBsAg) proteins are initially synthesized and polymerized in the rough endoplasmic reticulum. These proteins are transported to the post-ER and pre-Golgi compartments, where budding of the nucleocapsid follows. The assembled HBV virion and sub-viral particles are transported to the Golgi for further modification of glycans of the surface proteins, and then are secreted out of the host cell to finish the life cycle.
  • the interferon-associated antigen binding proteins, the nucleic acids, vectors, vector systems, methods and compositions described herein can be used to treat HBV infection.
  • “treat HBV infection” and “treatment of HBV infection” refers to one or more of: (i) reducing HBV viral load / viral titer; (ii) reducing the transcription of cccDNA; (iii) reducing the level of pre-genomic RNA in cells; (iv) decreasing one or more HBV-related disorders; and (v) decreasing one or more HBV-related symptoms in a subject.
  • viral load and “viral titer” refer to the number of viral particles in a cell, an organ or a bodily fluid such as blood or serum. Viral load or viral titer is often expressed as viral particles, or infectious particles per mL depending on the type of assay. Today, viral load is usually measured using international units per milliliter (IU/mL). Viral load or viral titer may alternatively be determined as so-called viral genome equivalent. A higher viral burden, titer, or viral load often correlates with the severity of an active viral infection. Accordingly, reducing the viral load or viral titer correlates with a reduced number of infectious viral particles, e.g., in the serum.
  • Viral load is usually determined using nucleic acid amplification based tests (NATs or NAATss).
  • NAT/NAAT tests utilize, for example, PCR, (quantitative) reverse transcription polymerase chain reaction (RT-PCR or qRT-PCR), nucleic acid sequence based amplification (NASBA) or probe-based assays.
  • Real-time PCR assays for hepatitis B virus DNA quantification are described, e.g., in Liu et al., Virol J 14, 94 (2017) doi:10.1186/s12985-017-0759-8. Due to the ease of detection of viral DNA using PCR, the viral load is useful in clinical settings to monitor success during treatment.
  • a viral load of >10,000 copies/mL (2,000 IU/mL) is a strong risk predictor of hepatocellular carcinoma, independent of HBeAg status.
  • patient and “subject” are used interchangeably and include human and non-human animal subjects, preferably human subjects, as well as those with formally diagnosed disorders, those without formally recognized disorders, those receiving medical attention, those at risk of developing the disorders, etc.
  • the interferon-associated antigen binding protein, the nucleic acids, vectors, vector systems, methods and compositions described herein can be used to reduce the HBV viral load / viral titer in an HBV-infected cell (such as in a cell culture, in an HBV-infected organ or in an HBV-infected patient).
  • HBV viral load / viral titer may be reduced by about 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% compared to an untreated HBV-infected cell culture or to the same patient before treatment.
  • HBV viral load / viral titer is reduced by at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90% or at least 95%.
  • HBV viral load / viral titer is reduced by at least 35%, more preferably by at least 50%.
  • viral load / viral titer is determined by PCR or qRT-PCR.
  • the interferon-associated antigen binding protein, the nucleic acids, vectors, vector systems, methods and compositions described herein can be used to reduce transcription of HBV cccDNA in an HBV-infected cell (such as in a cell culture, in an HBV-infected organ or in an HBV-infected patient).
  • cccDNA transcription may be reduced by about 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% compared to an untreated HBV-infected cell culture or to the same patient before treatment.
  • transcription of HBV cccDNA is reduced by at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90% or at least 95%.
  • transcription of HBV cccDNA is reduced by at least 35%, more preferably by at least 50%.
  • transcription of HBV cccDNA is determined by PCR or qPCR.
  • the interferon-associated antigen binding protein, the nucleic acids, vectors, vector systems, methods and compositions described herein can be used to reduce the level of pre-genomic HBV RNA in an HBV-infected cell (such as in a cell culture, in an HBV-infected organ or in an HBV-infected patient).
  • Pre-genomic HBV RNA levels may be reduced by about 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% compared to an untreated HBV-infected cell culture or to the same patient before treatment.
  • the level of pre-genomic HBV RNA is reduced by at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90% or at least 95%.
  • the level of pre-genomic HBV RNA is reduced by at least 35%, more preferably by at least 50%.
  • the level of pre-genomic HBV RNA is determined by qRT-PCR.
  • HBV-related disorder refers to a disorder that results from infection of a subject by HBV.
  • HBV-related disorders include, but are not limited to acute hepatitis, chronic hepatitis, icteric hepatitis, fulminant hepatitis, sub-fulminant hepatitis, and symptoms and/or complications arising from any of these disorders.
  • an “HBV-related symptom,” a “symptom of HBV infection” or an “HBV-related complication” includes one or more physical dysfunctions related to HBV infection.
  • HBV symptoms and complications include, but are not limited to, cirrhosis, hepatocellular carcinoma (HCC), membranous glomerulonephritis (MGN), death, acute necrotizing vasculitis (polyarteritis nodosa), membranous glomerulonephritis, papular acrodermatitis of childhood (Gianotti-Crosti syndrome), HBV-associated nephropathy (e.g., membranous glomerulonephritis), immune-mediated hematological disorders (e.g., essential mixed cryoglobulinemia, aplastic anemia), portal hypertension, ascites, encephalopathy, jaundice, pruritus, pale stools, steatorrhea, polyarteritis nodosa, glomerular
  • IFN refers to a cytokine, or derivative thereof, that is typically produced and released by cells in response to the presence of a pathogen or a tumor cell.
  • IFNs include type I IFNs (e.g., IFN ⁇ , IFN ⁇ , IFN ⁇ , IFN ⁇ , IFN ⁇ , IFN ⁇ and IFN ⁇ ), type II IFNs (e.g., IFN ⁇ ) and type III IFNs (e.g., IFN ⁇ 1, IFN ⁇ 2 and IFN ⁇ 3).
  • IFN includes without limitation full-length IFN, a variant or a derivative thereof (e.g., a chemically (e.g., PEGylated) modified derivative or mutein), or a functionally active fragment thereof, that retains one or more signaling activities of a full-length IFN.
  • a functional fragment refers to a fragment of a substance that retains one or more functional activities of the original substance.
  • a functional fragment of an interferon refers to a fragment of an interferon that retains an IFN function as described herein, e.g., it mediates IFN pathway signaling.
  • the IFN may increase one or more IFN receptor activities by at least about 20% when added to a cell, tissue or organism expressing a cognate IFN receptor (IFNAR for IFN ⁇ , IFNBR for IFN ⁇ , etc).
  • the interferon activates IFN receptor activity by at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, or at least 85%.
  • the activity of the IFN i.e., the “IFN activity” may be measured, e.g., using an in vitro reporter cell assay, e.g., using HEK-BlueTM IFN- ⁇ / ⁇ cells (InvivoGen, Cat.
  • HEK-BlueTM IFN- ⁇ (InvivoGen, Cat. #: hkb-ifnl) or HEK-BlueTM Dual IFN-y cells (InvivoGen, Cat. #: hkb-ifng), as described in greater detail in Example I.
  • These reporter cells were generated by stable transfection of HEK293 cells with human IFN receptor genes and an IFN-stimulated response element-controlled secreted embryonic alkaline phosphatase (SEAP) construct to measure the activity of IFNs.
  • SEAP IFN-stimulated response element-controlled secreted embryonic alkaline phosphatase construct to measure the activity of IFNs.
  • HEK-BlueTM IFN-cells are designed to monitor the activation of the JAK/STAT/ISGF3 pathways induced by type I, type II or type III interferons. Activation of these pathways induces the production and release of SEAP.
  • the interferon-associated antigen binding proteins activate both the CD40 and an IFN pathway.
  • the interferon-associated antigen binding protein activates the IFN pathway with an EC 50 of less than 100, 60, 50, 40, 30, 20, 10, or 1 ng/mL, preferably with an EC 50 of less than 11 ng/mL, more preferably with an EC 50 of less than 6 ng/mL.
  • the IFN pathway is the IFN ⁇ (interferon alpha), IFN ⁇ (interferon beta), IFN ⁇ (interferon epsilon), IFN ⁇ (interferon omega), IFN ⁇ (interferon gamma), or IFN ⁇ (interferon lambda) pathway.
  • an interferon-associated antigen binding protein as described herein comprises full-length IFN, a variant or a derivative thereof (e.g., a chemically (e.g., PEGylated) modified derivative or mutein), or a functionally active fragment thereof, that retains one or more signaling activities of a full-length IFN.
  • the IFN is a human IFN.
  • an interferon-associated antigen binding protein as described herein comprises an IFN or a functional fragment thereof selected from the group consisting of a Type I IFN, a Type II IFN and a Type III IFN, or a functional fragment thereof.
  • the IFN or the functional fragment thereof is a Type I IFN, or a functional fragment thereof.
  • the type I IFN or the functional fragment thereof is IFN ⁇ , IFN ⁇ , IFN ⁇ or IFN ⁇ , or a functional fragment thereof.
  • the type I IFN or the functional fragment thereof is IFN ⁇ or IFN ⁇ , or a functional fragment thereof.
  • the type I IFN or the functional fragment thereof is IFN ⁇ , or a functional fragment thereof.
  • the type I IFN or the functional fragment thereof is IFN ⁇ , or a functional fragment thereof.
  • the type I IFN or the functional fragment thereof is IFN ⁇ , or a functional fragment thereof.
  • the type I IFN or the functional fragment thereof is IFN ⁇ , or a functional fragment thereof.
  • the type I IFN or the functional fragment thereof is IFN ⁇ , or a functional fragment thereof.
  • the type I IFN or the functional fragment thereof is IFN ⁇ , or a functional fragment thereof.
  • the IFN or the functional fragment thereof is IFN ⁇ , IFN ⁇ , IFN ⁇ , IFN ⁇ , IFN ⁇ or IFN ⁇ , or a functional fragment thereof.
  • the IFN or a functional fragment thereof is IFN ⁇ or IFN ⁇ , or a functional fragment thereof.
  • the IFN or the functional fragment thereof is IFN ⁇ , or a functional fragment thereof. In more specific embodiments, the IFN or functional fragment thereof is IFN ⁇ 2a, or a functional fragment thereof.
  • the IFN ⁇ 2a may comprise the sequence as set forth in SEQ ID NO 17, or a sequence at least 90% identical thereto.
  • the IFN or the functional fragment thereof is IFN ⁇ , or a functional fragment thereof.
  • the IFN ⁇ may comprise the sequence as set forth in SEQ ID NO 14, or a sequence at least 90% identical thereto.
  • the IFN ⁇ or the functional fragment thereof may comprise one or two amino acid substitution(s) relative to SEQ ID NO 14, selected from C17S and N80Q.
  • the IFN ⁇ or the functional fragment thereof comprises the amino acid substitution C17S relative to SEQ ID NO 14.
  • the IFN ⁇ comprises the amino acid sequence as set forth in SEQ ID NO 15.
  • the IFN ⁇ comprises the amino acid substitutions C17S and N80Q relative to SEQ ID NO 14.
  • the IFN ⁇ comprises the amino acid sequence as set forth in SEQ ID NO 16.
  • the IFN or the functional fragment thereof is IFN ⁇ or IFN ⁇ , or a functional fragment thereof.
  • the IFN or functional fragment thereof is IFN ⁇ , or a functional fragment thereof.
  • the IFN ⁇ comprises the sequence as set forth in SEQ ID NO 19, or a sequence at least 90% identical thereto.
  • the IFN or functional fragment thereof is IFN ⁇ , or a functional fragment thereof.
  • the IFN ⁇ or the functional fragment thereof is IFN ⁇ 2, or a functional fragment thereof.
  • the IFN ⁇ 2 may comprise the sequence as set forth in SEQ ID NO 18, or a sequence at least 90% identical thereto.
  • the IFN or the functional fragment thereof is IFN ⁇ , or a functional fragment thereof.
  • the IFN ⁇ may comprise the sequence as set forth in SEQ ID NO 61, or a sequence at least 90% identical thereto.
  • the IFN or the functional fragment thereof is IFN ⁇ , or a functional fragment thereof.
  • the IFN ⁇ may comprise the sequence as set forth in SEQ ID NO 60, or a sequence at least 90% identical thereto.
  • the expression level of one or more IFN signaling pathway biomarkers is altered, i.e., upregulated or downregulated, in an HBV-infected cell treated with an interferon-associated antigen binding protein described herein.
  • the expression level of one or more IFN pathway biomarkers is upregulated in an HBV-infected cell treated with an interferon-associated antigen binding protein described herein.
  • a “biomarker” is to be understood as a characteristic that is objectively measured and evaluated as an indicator of normal biological processes, pathogenic processes, or pharmacologic responses to a therapeutic intervention.
  • a suitable IFN pathway biomarker featured herein is a chemokine, e.g., a C-X-C chemokine, selected from the group consisting of CXCL9, CXCL10 and CXCL11.
  • a suitable biomarker induced by the IFN pathway is CXCL9, CXCL10 and/or CXCL11, and also the interferon stimulated gene ISG20.
  • Cytokine induction or release may be quantified using techniques known in the art, such as ELISA. Alternatively, induction may also be determined using RNA-based assays such as RNAseq or qRT-PCR.
  • upregulation may refer to an at least at 1.5-fold, at least 2-fold, at least 2.5-fold, at least 3-fold, at least 4-fold, at least 5-fold or at least 10-fold increased expression or secretion of these cytokines.
  • the expression level of pro-inflammatory cytokines is not significantly upregulated in human Whole Blood cells upon treatment with an interferon-associated antigen binding protein of the invention.
  • the expression level of IL10 is not significantly upregulated in human Whole Blood cells upon treatment with an interferon-associated antigen binding protein of the invention.
  • the expression level of IL1 ⁇ is not significantly upregulated in human Whole Blood cells upon treatment with an interferon-associated antigen binding protein of the invention.
  • the expression level of IL2 is not significantly upregulated in an HBV-infected cell upon treatment with an interferon-associated antigen binding protein of the invention.
  • the expression levels of IL10 and IL1 ⁇ are not significantly upregulated in an HBV-infected cell upon treatment with an interferon-associated antigen binding protein of the invention. In some embodiments, the expression levels of IL10 and IL2 are not significantly upregulated in an HBV-infected cell upon treatment with an interferon-associated antigen binding protein of the invention. In some embodiments, the expression levels of IL1 ⁇ and IL2 are not significantly upregulated in an HBV-infected cell upon treatment with an interferon-associated antigen binding protein of the invention. In some embodiments, the expression levels of IL10, IL1 ⁇ and IL2 are not significantly upregulated in an HBV-infected cell upon treatment with an interferon-associated antigen binding protein of the invention.
  • association generally refers to a covalent or non-covalent linkage of two (or more) molecules. Associated proteins are created by joining two or more distinct peptides or proteins, resulting in a protein with one or more functional properties derived from each of the original proteins. In the context of the present invention, the interferon-associated antigen binding proteins activate both the CD40 and an IFN pathway.
  • An associated protein encompasses monomeric and multimeric, e.g., dimeric, trimeric, tetrameric or the like, complexes of distinct associated or fused proteins.
  • non-covalent linkage results from strong interactions between two protein surface regions, usually via ionic, Van-der-Waals, and/or hydrogen bond interactions.
  • Covalent linkage requires the presence of actual chemical bonds, such as peptide bonds, disulphide bridges, etc.
  • the term “fused” as used herein generally refers to the joining of two or more distinct peptides or proteins in a covalent fashion via a peptide bond.
  • a “fused protein” refers to single protein created by joining two or more distinct peptides or proteins via a peptide bond with one or more functional properties derived from each of the original proteins.
  • two or more distinct peptides or proteins may be fused to one another via one or more peptide linkers (“L”).
  • an interferon-associated antigen binding protein is a protein comprising an agonistic anti-CD40 antibody or an agonistic antigen binding fragment thereof and an IFN or a functional fragment thereof.
  • the IFN or the functional fragment thereof is non-covalently associated with the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof. In more specific embodiments, the IFN or the functional fragment thereof is non-covalently associated with the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof via ionic, Van-der-Waals, and/or hydrogen bond interactions.
  • the IFN or the functional fragment thereof is covalently associated with the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof.
  • the IFN or the functional fragment thereof is fused to the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof.
  • the IFN or the functional fragment thereof may be fused to a light chain of the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof.
  • the IFN or the functional fragment thereof is fused to the N-terminus of a light chain of the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof.
  • the IFN or the functional fragment thereof is fused to the C-terminus of a light chain of the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof.
  • the IFN or the functional fragment thereof may be also be fused to a heavy chain of the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof.
  • the IFN or the functional fragment thereof is fused to the N-terminus of a heavy chain of the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof.
  • the IFN or the functional fragment thereof is fused to the C-terminus of a heavy chain of the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof.
  • the agonistic anti-CD40 antibody or an agonistic antigen binding fragment thereof, and the IFN or the functional fragment thereof may be fused to each other via a linker.
  • linker refers to any moiety that covalently joins one or more agonistic anti-CD40 antibody or an agonistic antigen binding fragment thereof to one or more interferon, or a functional fragment thereof.
  • a linker is a peptide linker.
  • peptide linker refers to a peptide adapted to link two or more moieties.
  • a peptide linker referred to herein may have one or more of the properties outlined in the following. The sequences of peptide linker according to certain exemplary embodiments are set forth in Table 7.
  • a peptide linker may have any length, i.e., comprise any number of amino acid residues.
  • the linker comprises at least 1, at least 2, at least 3, at least 4, at least 5 amino acids.
  • the linker may comprise at least 4 amino acids.
  • the linker may comprise at least 11 amino acids.
  • the linker may comprise at least 12 amino acids.
  • the linker may comprise at least 13 amino acids.
  • the linker may comprise at least 15 amino acids.
  • the linker may comprise at least 20 amino acids.
  • the linker may comprise at least 21 amino acids.
  • the linker may comprise at least 24 amino acids.
  • a linker is typically long enough to provide an adequate degree of flexibility to prevent the linked moieties from interfering with each other’s activity, e.g., the ability of a moiety to bind to a receptor.
  • the linker comprises up to 10, up to 20, up to 30, up to 40, up to 50, up to 60, up to 70, up to 80, up to 90, or up to 100 amino acids.
  • the linker may comprise up to 80 amino acids.
  • the linker may comprise up to 40 amino acids.
  • the linker may comprise up to 24 amino acids.
  • the linker may comprise up to 21 amino acids.
  • the linker may comprise up to 20 amino acids.
  • the linker may comprise up to 15 amino acids.
  • the linker may comprise up to 13 amino acids.
  • the linker may comprise up to 12 amino acids.
  • the linker may comprise up to 11 amino acids.
  • the linker may comprise up to 4 amino acids.
  • the linker is selected from the group comprising rigid, flexible and/or helix-forming linkers. It is understood that helix-forming linkers can also be rigid linkers, since an ⁇ -helix has less degrees of freedom than a peptide assuming a more random-coil conformation.
  • the linker is a rigid linker.
  • An exemplary rigid linker comprises a sequence as set forth in SEQ ID NO 20. Further exemplary rigid linkers comprise a sequence as set forth in SEQ ID NO 22 or SEQ ID NO 23.
  • the linker is a helix-forming linker. Exemplary helix-forming linkers comprise a sequence as set forth in SEQ ID NO 22 or SEQ ID NO 23.
  • the linker is a flexible linker. Exemplary flexible linkers comprise a sequence as set forth in SEQ ID NO 21, SEQ ID NO 24, SEQ ID NO 25 or SEQ ID NO 26.
  • the linker can also have different chemical properties.
  • a linker can be selected from acidic, basic or neutral linkers.
  • acidic linkers contain one or more acidic amino acid, such as Asp or Glu.
  • Basic linkers typically contain one or more basic amino acids, such as Arg, His and Lys. Both types of amino acids are very hydrophilic.
  • the linker is an acidic linker.
  • Exemplary acidic linkers comprise a sequence as set forth in SEQ ID NO 22 or SEQ ID NO 23.
  • the linker is a basic linker.
  • the linker is a neutral linker.
  • Exemplary neutral linkers comprise a sequence as set forth in SEQ ID NO 20, SEQ ID NO 21, SEQ ID NO 24, SEQ ID NO 25 or SEQ ID NO 26.
  • the linker is Gly-Ser or a Gly-Ser-Thr linker composed of multiple glycine, serine and, where applicable, threonine residues.
  • the linker comprises the amino acids glycine and serine.
  • the linker comprises the sequence as set forth in SEQ ID NO 21, SEQ ID NO 24, SEQ ID NO 25, SEQ ID NO 26.
  • the linker further comprises the amino acid threonine.
  • the linker comprises the sequence as set forth in SEQ ID NO 21.
  • the interferon-associated antigen binding protein comprises a linker comprising a sequence selected from the sequences as set forth in SEQ ID NOs 20 to 26, preferably from the sequences as set forth in SEQ ID NO 24, SEQ ID NO 25 or SEQ ID NO 26.
  • the linker comprises a sequence as set forth in SEQ ID NO 24.
  • the linker comprises a sequence as set forth in SEQ ID NO 25.
  • the linker comprises a sequence as set forth in SEQ ID NO 26.
  • the interferon-associated antigen binding protein comprises no amino acids other than those forming (I) said agonistic anti-CD40 antibody, or agonistic antigen binding fragment thereof and (II) said IFN or functional fragment thereof.
  • the interferon-associated antigen binding protein comprises no amino acids other than those forming (I) said agonistic anti-CD40 antibody, or agonistic antigen binding fragment thereof, (II) said IFN or functional fragment thereof and (III) said linker.
  • the IFN or a functional fragment thereof is fused to the C-terminus of a heavy chain of the agonistic anti-CD40 antibody, or the agonistic antigen binding fragment thereof, via the linker, as set forth in Table 3A or Table 3B.
  • the heavy chain of the agonistic anti-CD40 antibody, or the agonistic antigen binding fragment thereof may comprise a sequence as set forth in SEQ ID NO 6, SEQ ID NO 9, SEQ ID NO 12, SEQ ID NO 48 or SEQ ID NO 49.
  • the IFN ⁇ 2a may comprise the sequence as set forth in SEQ ID NO 17.
  • the IFN ⁇ may comprise the sequence as set forth in SEQ ID NO 14, SEQ ID NO 15 or SEQ ID NO 16.
  • the IFN ⁇ may comprise the sequence as set forth in SEQ ID NO 14.
  • the IFN ⁇ _C17S may comprise the sequence as set forth in SEQ ID NO 15.
  • the IFN ⁇ _C17S,N80Q may comprise the sequence as set forth in SEQ ID NO 16.
  • the IFN ⁇ may comprise the sequence as set forth in SEQ ID NO 19.
  • the IFN ⁇ 2 may comprise the sequence as set forth in SEQ ID NO 18.
  • the IFN ⁇ may comprise the sequence as set forth in SEQ ID NO 61.
  • the IFN ⁇ may comprise the sequence as set forth in SEQ ID NO 60.
  • the linkers referred to are those listed in Table 7.
  • the interferon-associated antigen binding protein further comprises a light chain of an agonistic anti-CD40 antibody, or an agonistic antigen binding fragment thereof.
  • a heavy chain comprises a sequence as set forth in SEQ ID NO 6, SEQ ID NO 9, SEQ ID NO 12, SEQ ID NO 48, or SEQ ID NO 49 and a light chain comprises a sequence as set forth in SEQ ID NO 3.
  • the IFN or a functional fragment thereof is fused to the N-terminus of a heavy chain of the agonistic anti-CD40 antibody, or the agonistic antigen binding fragment thereof, via the linker, as set forth in Table 4A or Table 4B.
  • the heavy chain of the agonistic anti-CD40 antibody, or the agonistic antigen binding fragment thereof may comprise a sequence as set forth in SEQ ID NO 6, SEQ ID NO 9, SEQ ID NO 12, SEQ ID NO 48, SEQ ID NO 49 or SEQ ID NO 50.
  • the IFN ⁇ 2a may comprise the sequence as set forth in SEQ ID NO 17.
  • the IFN ⁇ may comprise the sequence as set forth in SEQ ID NO 14, SEQ ID NO 15 or SEQ ID NO 16.
  • the IFN ⁇ may comprise the sequence as set forth in SEQ ID NO 14.
  • the IFN ⁇ _C17S may comprise the sequence as set forth in SEQ ID NO 15.
  • the IFN ⁇ _C17S,N80Q may comprise the sequence as set forth in SEQ ID NO 16.
  • the IFN ⁇ may comprise the sequence as set forth in SEQ ID NO 19.
  • the IFN ⁇ 2 may comprise the sequence as set forth in SEQ ID NO 18.
  • the IFN ⁇ may comprise the sequence as set forth in SEQ ID NO 61.
  • the IFN ⁇ may comprise the sequence as set forth in SEQ ID NO 60.
  • the linkers referred to are those listed in Table 7.
  • the interferon-associated antigen binding protein further comprises a light chain of an agonistic anti-CD40 antibody, or an agonistic antigen binding fragment thereof.
  • a heavy chain comprises a sequence as set forth in SEQ ID NO 6, SEQ ID NO 9, SEQ ID NO 12, SEQ ID NO 48, SEQ ID NO 49 or SEQ ID NO 50 and a light chain comprises a sequence as set forth in SEQ ID NO 3.
  • the IFN is fused to the C-terminus of a light chain of the agonistic anti-CD40 antibody, or the agonistic antigen binding fragment thereof, via the linker, as set forth in Table 5A or Table 5B.
  • the light chain of the agonistic anti-CD40 antibody, or the agonistic antigen binding fragment thereof may comprise a sequence as set forth in SEQ ID NO 3.
  • the IFN ⁇ 2a may comprise the sequence as set forth in SEQ ID NO 17.
  • the IFN ⁇ may comprise the sequence as set forth in SEQ ID NO 14, SEQ ID NO 15 or SEQ ID NO 16.
  • the IFN ⁇ may comprise the sequence as set forth in SEQ ID NO 14.
  • the IFN ⁇ _C17S may comprise the sequence as set forth in SEQ ID NO 15.
  • the IFN ⁇ _C17S,N80Q may comprise the sequence as set forth in SEQ ID NO 16.
  • the IFN ⁇ may comprise the sequence as set forth in SEQ ID NO 19.
  • the IFN ⁇ 2 may comprise the sequence as set forth in SEQ ID NO 18.
  • the IFN ⁇ may comprise the sequence as set forth in SEQ ID NO 61.
  • the IFN ⁇ may comprise the sequence as set forth in SEQ ID NO 60.
  • the linkers referred to are those listed in Table 7.
  • the interferon-associated antigen binding protein further comprises a heavy chain of an agonistic anti-CD40 antibody, or an agonistic antigen binding fragment thereof.
  • a light chain comprises a sequence as set forth in SEQ ID NO 3 and a heavy chain comprises a sequence as set forth in SEQ ID NO 6, SEQ ID NO 9, SEQ ID NO 49, SEQ ID NO 48, SEQ ID NO 50 or SEQ ID NO 12.
  • the IFN is fused to the N-terminus of a light chain of the agonistic anti-CD40 antibody, or the agonistic antigen binding fragment thereof, via the linker, as set forth in Table 6A or Table 6B.
  • the light chain of the agonistic anti-CD40 antibody, or the agonistic antigen binding fragment thereof may comprise a sequence as set forth in SEQ ID NO 3.
  • the IFN ⁇ 2a may comprise the sequence as set forth in SEQ ID NO 17.
  • the IFN ⁇ may comprise the sequence as set forth in SEQ ID NO 14, SEQ ID NO 15 or SEQ ID NO 16.
  • the IFN ⁇ may comprise the sequence as set forth in SEQ ID NO 14.
  • the IFN ⁇ _C17S may comprise the sequence as set forth in SEQ ID NO 15.
  • the IFN ⁇ _C17S,N80Q may comprise the sequence as set forth in SEQ ID NO 16.
  • the IFN ⁇ may comprise the sequence as set forth in SEQ ID NO 19.
  • the IFN ⁇ 2 may comprise the sequence as set forth in SEQ ID NO 18.
  • the IFN ⁇ may comprise the sequence as set forth in SEQ ID NO 61.
  • the IFN ⁇ may comprise the sequence as set forth in SEQ ID NO 60.
  • the linkers referred to are those listed in Table 7.
  • the interferon-associated antigen binding protein further comprises a heavy chain of an agonistic anti-CD40 antibody, or an agonistic antigen binding fragment thereof.
  • a light chain comprises a sequence as set forth in SEQ ID NO 3 and a heavy chain comprises a sequence as set forth in SEQ ID NO 6, SEQ ID NO 9, SEQ ID NO 49, SEQ ID NO 48, SEQ ID NO 12 or SEQ ID NO 50.
  • the interferon-associated antigen binding protein comprises an interferon-fused agonistic anti-CD40 antibody or an interferon-fused agonistic antigen binding fragment thereof comprising a sequence selected from SEQ ID NOs 28-47. In other exemplary embodiments, the interferon-associated antigen binding protein comprises an interferon-fused agonistic antiCD40 antibody or an interferon-fused agonistic antigen binding fragment thereof comprising a sequence selected from SEQ ID NOs 62-69.
  • the interferon-associated antigen binding protein is an interferon-fused agonistic anti-CD40 antibody or an interferon-fused agonistic antigen binding fragment thereof comprising a sequence selected from SEQ ID NOs 28-47.
  • the interferon-associated antigen binding protein is an interferon-fused agonistic anti-CD40 antibody or an interferon-fused agonistic antigen binding fragment thereof comprising a sequence selected from SEQ ID NOs 62-69.
  • the interferon-associated antigen binding protein comprises an interferon-fused agonistic anti-CD40 antibody or an interferon-fused agonistic binding fragment thereof comprising a sequence as set forth in SEQ ID NO 62.
  • the interferon-associated antigen binding protein is an interferon-fused agonistic anti-CD40 antibody or an interferon-fused agonistic binding fragment thereof comprising a sequence as set forth in SEQ ID NO 62.
  • the interferon-associated antigen binding protein comprises an interferon-fused agonistic anti-CD40 antibody or an interferon-fused agonistic binding fragment thereof comprising a sequence as set forth in SEQ ID NO 63.
  • the interferon-associated antigen binding protein is an interferon-fused agonistic anti-CD40 antibody or an interferon-fused agonistic binding fragment thereof comprising a sequence as set forth in SEQ ID NO 63.
  • the interferon-associated antigen binding protein comprises an interferon-fused agonistic anti-CD40 antibody or an interferon-fused agonistic binding fragment thereof comprising a sequence as set forth in SEQ ID NO 64.
  • the interferon-associated antigen binding protein is an interferon-fused agonistic anti-CD40 antibody or an interferon-fused agonistic binding fragment thereof comprising a sequence as set forth in SEQ ID NO 64.
  • the interferon-associated antigen binding protein comprises an interferon-fused agonistic anti-CD40 antibody or an interferon-fused agonistic binding fragment thereof comprising a sequence as set forth in SEQ ID NO 65.
  • the interferon-associated antigen binding protein is an interferon-fused agonistic anti-CD40 antibody or an interferon-fused agonistic binding fragment thereof comprising a sequence as set forth in SEQ ID NO 65.
  • the interferon-associated antigen binding protein comprises an interferon-fused agonistic anti-CD40 antibody or an interferon-fused agonistic binding fragment thereof comprising a sequence as set forth in SEQ ID NO 66.
  • the interferon-associated antigen binding protein is an interferon-fused agonistic anti-CD40 antibody or an interferon-fused agonistic binding fragment thereof comprising a sequence as set forth in SEQ ID NO 66.
  • the interferon-associated antigen binding protein comprises an interferon-fused agonistic anti-CD40 antibody or an interferon-fused agonistic binding fragment thereof comprising a sequence as set forth in SEQ ID NO 67.
  • the interferon-associated antigen binding protein is an interferon-fused agonistic anti-CD40 antibody or an interferon-fused agonistic binding fragment thereof comprising a sequence as set forth in SEQ ID NO 67.
  • the interferon-associated antigen binding protein comprises an interferon-fused agonistic anti-CD40 antibody or an interferon-fused agonistic binding fragment thereof comprising a sequence as set forth in SEQ ID NO 68.
  • the interferon-associated antigen binding protein is an interferon-fused agonistic anti-CD40 antibody or an interferon-fused agonistic binding fragment thereof comprising a sequence as set forth in SEQ ID NO 68.
  • the interferon-associated antigen binding protein comprises an interferon-fused agonistic anti-CD40 antibody or an interferon-fused agonistic binding fragment thereof comprising a sequence as set forth in SEQ ID NO 69.
  • the interferon-associated antigen binding protein is an interferon-fused agonistic anti-CD40 antibody or an interferon-fused agonistic binding fragment thereof comprising a sequence as set forth in SEQ ID NO 69.
  • the interferon-associated antigen binding protein comprises an interferon-fused agonistic anti-CD40 antibody or an interferon-fused agonistic antigen binding fragment thereof comprising a sequence selected from SEQ ID NO 38, SEQ ID NO 39, SEQ ID NO 40, SEQ ID NO 41, SEQ ID NO 42 or SEQ ID NO 43.
  • the interferon-associated antigen binding protein is an interferon-fused agonistic anti-CD40 antibody or an interferon-fused agonistic antigen binding fragment thereof comprising a sequence selected from SEQ ID NO 38, SEQ ID NO 39, SEQ ID NO 40, SEQ ID NO 41, SEQ ID NO 42 or SEQ ID NO 43.
  • the interferon-associated antigen binding protein comprises an interferon-fused agonistic anti-CD40 antibody or an interferon-fused agonistic binding fragment thereof comprising a sequence as set forth in SEQ ID NO 38.
  • the interferon-associated antigen binding protein is an interferon-fused agonistic antiCD40 antibody or an interferon-fused agonistic binding fragment thereof comprising a sequence as set forth in SEQ ID NO 38.
  • the interferon-associated antigen binding protein comprises an interferon-fused agonistic anti-CD40 antibody or an interferon-fused agonistic binding fragment thereof comprising a sequence as set forth in SEQ ID NO 39.
  • the interferon-associated antigen binding protein is an interferon-fused agonistic antiCD40 antibody or an interferon-fused agonistic binding fragment thereof comprising a sequence as set forth in SEQ ID NO 39.
  • the interferon-associated antigen binding protein comprises an interferon-fused agonistic anti-CD40 antibody or an interferon-fused agonistic binding fragment thereof comprising a sequence as set forth in SEQ ID NO 40.
  • the interferon-associated antigen binding protein is an interferon-fused agonistic antiCD40 antibody or an interferon-fused agonistic binding fragment thereof comprising a sequence as set forth in SEQ ID NO 40.
  • the interferon-associated antigen binding protein comprises an interferon-fused agonistic anti-CD40 antibody or an interferon-fused agonistic binding fragment thereof comprising a sequence as set forth in SEQ ID NO 41.
  • the interferon-associated antigen binding protein is an interferon-fused agonistic antiCD40 antibody or an interferon-fused agonistic binding fragment thereof comprising a sequence as set forth in SEQ ID NO 41.
  • the interferon-associated antigen binding protein comprises an interferon-fused agonistic anti-CD40 antibody or an interferon-fused agonistic binding fragment thereof comprising a sequence as set forth in SEQ ID NO 42.
  • the interferon-associated antigen binding protein is an interferon-fused agonistic antiCD40 antibody or an interferon-fused agonistic binding fragment thereof comprising a sequence as set forth in SEQ ID NO 42.
  • the interferon-associated antigen binding protein comprises an interferon-fused agonistic anti-CD40 antibody or an interferon-fused agonistic binding fragment thereof comprising a sequence as set forth in SEQ ID NO 43.
  • the interferon-associated antigen binding protein is an interferon-fused agonistic antiCD40 antibody or an interferon-fused agonistic binding fragment thereof comprising a sequence as set forth in SEQ ID NO 43.
  • the interferon-associated antigen binding proteins described herein are interferon-fused antigen binding proteins comprising polypeptides derived from those specified in Table 8, in particular Table 8A or Table 8B, more particularly Table 8A below, and especially from the polypeptides of SEQ ID NO 38, SEQ ID NO 39, SEQ ID NO 40, SEQ ID NO 41, SEQ ID NO 42 or SEQ ID NO 43 above.
  • the interferon-associated antigen binding proteins described herein are interferon-fused antigen binding proteins consisting of polypeptides derived from those specified in Table 8, in particular Table 8A or Table 8B, more particularly Table 8A below, and especially from the polypeptides of SEQ ID NO 38, SEQ ID NO 39, SEQ ID NO 40, SEQ ID NO 41, SEQ ID NO 42 or SEQ ID NO 43 above.
  • the interferon-fused antibody comprises the sequences as set forth in SEQ ID NO 38 and SEQ ID NO 3.
  • the interferon-fused antibody comprises the sequences as set forth in SEQ ID NO 39 and SEQ ID NO 3.
  • the interferon-fused antibody comprises the sequences as set forth in SEQ ID NO 40 and SEQ ID NO 3. In other more preferred embodiments, the interferon-fused antibody comprises the sequences as set forth in SEQ ID NO 41 and SEQ ID NO 9. In other more preferred embodiments, the interferon-fused antibody comprises the sequences as set forth in SEQ ID NO 42 and SEQ ID NO 9. In other more preferred embodiments, the interferon-fused antibody comprises the sequences as set forth in SEQ ID NO 43 and SEQ ID NO 9. A
  • a combination of polynucleotides encoding an interferon-associated antigen binding protein is provided. Methods of making an interferon-associated antigen binding protein comprising expressing these polynucleotides are also provided.
  • a nucleic acid encoding an IFN or a functional fragment thereof being fused to an agonistic anti-CD40 antibody or an agonistic antigen binding fragment thereof, as disclosed herein is provided.
  • the nucleic acid is encoding an IFN or a functional fragment thereof fused to an agonistic anti-CD40 antibody or an agonistic antigen binding fragment thereof according to any of the sequences set forth in SEQ ID NOs 62 to 69, or a nucleic acid sequence at least 80%, at least 85%, at least 90%, at least 95%, at least 98% or at least 99% identical to a nucleic acid encoding any of these sequences.
  • said nucleic acid is at least 95%, at least 98% or at least 99% identical to a nucleic acid encoding any of SEQ ID NOs 62 to 69.
  • the nucleic acid is encoding an IFN or a functional fragment thereof fused to an agonistic anti-CD40 antibody or an agonistic antigen binding fragment thereof according to any of the sequences set forth in SEQ ID NOs 28 to 47, or a nucleic acid sequence at least 80%, at least 85%, at least 90%, at least 95%, at least 98% or at least 99% identical to a nucleic acid encoding any of these sequences.
  • said nucleic acid is at least 95%, at least 98% or at least 99% identical to a nucleic acid encoding any of SEQ ID NOs 28 to 47.
  • nucleic acid encodes an IFN or a functional fragment thereof being fused to a light chain of the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof
  • the nucleic acid may further encode a heavy chain of the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof.
  • the heavy chain of the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof comprises a sequence as set forth in SEQ ID NO 6, SEQ ID NO 7, SEQ ID NO 8, SEQ ID NO 9, SEQ ID NO 10, SEQ ID NO 11, SEQ ID NO 12, SEQ ID NO 13, SEQ ID NO 48, SEQ ID NO 49, or SEQ ID NO 50, or a nucleic acid sequence at least 80%, at least 85%, at least 90%, at least 95%, at least 98% or at least 99% identical to a nucleic acid encoding any of these sequences.
  • said nucleic acid is at least 95%, at least 98% or at least 99% identical to a nucleic acid encoding SEQ ID NO 6, SEQ ID NO 7, SEQ ID NO 8, SEQ ID NO 9, SEQ ID NO 10, SEQ ID NO 11, SEQ ID NO 12, SEQ ID NO 13, SEQ ID NO 48, SEQ ID NO 49, or SEQ ID NO 50.
  • the nucleic acid may further encode a light chain of the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof.
  • the light chain of the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof comprises a sequence as set forth in SEQ ID NO 3, SEQ ID NO 4 or SEQ ID NO 5, or a nucleic acid sequence at least 80%, at least 85%, at least 90%, at least 95%, at least 98% or at least 99% identical to a nucleic acid encoding any of these sequences.
  • said nucleic acid is at least 95%, at least 98% or at least 99% identical to a nucleic acid encoding SEQ ID NO 3, SEQ ID NO 4 or SEQ ID NO 5.
  • the nucleic acids described herein may comprise a sequence encoding a sequence to increase the yield (e.g. a solubility tag) or facilitate purification of the expressed proteins (i.e., a purification tag).
  • Purification tags are known to a person skilled in the art and may be selected from glutathione S-transferase (GST) tags, maltose binding protein (MBP) tags, calmodulin binding peptide (CBP) tags, intein-chitin binding domain (intein-CBD) tags, Streptavidin/Biotin-based tags (such as biotinylation signal peptide (BCCP) tags, Streptavidin-binding peptide (SBP) tags, His-patch ThioFusion tags, tandem affinity purification (TAP) tags, Small ubiquitin-like modifier (SUMO) tags, HaloTag® (Promega), Profinity eXactTM system (Bio-Rad).
  • GST glutathione S-transferase
  • the purification tag may be a polyhistidine tag (e.g., a His 6 -, His 7 -, His 8 -, His 9 - or His 10 -tag).
  • the purification tag may be a Strep-tag (e.g., a Strep-tag® or a Strep-tag II®; IBA Life Sciences).
  • the purification tag may be a maltose binding protein (MBP) tag.
  • MBP maltose binding protein
  • the nucleic acid sequence may further comprise a sequence encoding a cleavage site for removal of the purification tag.
  • cleavage sequences are known to a person skilled in the art and may be selected from a sequence recognized and cleaved by an endoprotease or an exoprotease.
  • an endoprotease for the removal of a purification tag may be selected from: Enteropeptidase, Thrombin, Factor Xa, TEV protease or Rhinovirus 3C protease.
  • an exoprotease for the removal of a purification tag may be selected from: Carboxypeptidase A, Carboxypeptidase B or DAPase.
  • the protease for the removal of a purification tag is TEV protease.
  • the nucleic acid comprises a sequence encoding a His 6 -tag and a TEV cleavage site.
  • said nucleic acid comprises a sequence encoding a sequence as set forth in SEQ ID NO 27.
  • the nucleic acid molecules of the invention may also comprise a sequence encoding a signal peptide.
  • the skilled person is aware of the various signal peptides available to direct the expressed protein to the desired site of folding, assembly and/or maturation as well as to effect secretion of the final protein into the medium to facilitate downstream processing.
  • the signal peptide is a secretory signal peptide.
  • the encoded signal peptide may comprise a sequence as set forth in SEQ ID NO: 1 or SEQ ID NO: 2.
  • the signal peptide comprises the sequence as set forth in SEQ ID NO: 1.
  • the signal peptide comprises the sequence as set forth in SEQ ID NO: 2.
  • Signal peptide 1 was used for synthesis of the polypeptide sequences as set forth in SEQ ID NO 28, SEQ ID NO 29, SEQ ID NO 30, SEQ ID NO 31, SEQ ID NO 32, SEQ ID NO 33, SEQ ID NO 34, SEQ ID NO 35, SEQ ID 36, SEQ ID NO 37, SEQ ID NO 44, SEQ ID NO 45, SEQ ID NO 46, SEQ ID NO 47 or SEQ ID NO 50.
  • Such signal peptide that is initially present at the N-terminus of the respective sequence of the polypeptide is cleaved during synthesis.
  • Signal peptide 2 (SEQ ID NO 2) was used for synthesis of the polypeptide sequences as set forth in SEQ ID NO 38, SEQ ID NO 39, SEQ ID NO 40, SEQ ID NO 41, SEQ ID NO 42 and SEQ ID NO 43. Such signal peptide that is initially present at the N-terminus of the respective sequence of the polypeptide is cleaved during synthesis.
  • polynucleotides encoding an IFN or a functional fragment thereof being fused to the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof as disclosed herein are typically inserted in an expression vector for introduction into host cells that may be used to produce the desired quantity of the claimed interferon-associated antigen binding proteins. Accordingly, in certain aspects, the invention provides expression vectors comprising polynucleotides disclosed herein and host cells comprising these vectors and polynucleotides.
  • vectors used in accordance with the present invention as a vehicle for introducing into and expressing a desired gene in a cell.
  • vectors may easily be selected from the group consisting of plasmids, phages, viruses and retroviruses.
  • vectors compatible with the present invention will comprise a selection marker, appropriate restriction sites to facilitate cloning of the desired gene and the ability to enter and/or replicate in eukaryotic or prokaryotic cells.
  • one class of vector utilizes DNA elements which are derived from animal viruses such as bovine papilloma virus, polyoma virus, adenovirus, vaccinia virus, baculovirus, retroviruses (RSV, MMTV or MOMLV), or SV40 virus.
  • Others involve the use of polycistronic systems with internal ribosome binding sites.
  • cells which have integrated the DNA into their chromosomes may be selected by introducing one or more markers which allow selection of transfected host cells. The marker may provide for prototrophy to an auxotrophic host, biocide resistance (e.g., antibiotics) or resistance to heavy metals such as copper.
  • the selectable marker gene can either be directly linked to the DNA sequences to be expressed, or introduced into the same cell by co-transformation. Additional elements may also be needed for optimal synthesis of mRNA. These elements may include signal sequences, splice signals, as well as transcriptional promoters, enhancers, and termination signals. In some embodiments the cloned variable region genes, one of them fused with a gene encoding an IFN or a functional fragment thereof, are inserted into an expression vector along with the heavy and light chain constant region genes (such as human genes) synthesized as discussed above.
  • a vector system of the invention may comprise more than one vector.
  • a vector system may comprise a first vector for the expression of an IFN or a functional fragment thereof fused to a light chain of the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof and a second vector for expression of a heavy chain of the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof.
  • such a vector system may comprise a first vector for the expression of an IFN or a functional fragment thereof fused to a heavy chain of the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof and a second vector for expression of a light chain of the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof.
  • an interferon-associated antigen binding protein as described herein may be expressed using polycistronic constructs.
  • multiple gene products of interest such as those encoding an IFN or a functional fragment thereof being fused to a heavy chain of an agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof and encoding a light chain of said antibody, or those encoding an IFN or a functional fragment thereof being fused to a light chain of an agonistic anti-CD40 antibody or an agonistic antigen binding fragment thereof and encoding a heavy chain of said antibody or an agonistic antigen binding fragment thereof may be produced from a single polycistronic construct.
  • IRES internal ribosome entry site
  • the expression vector may be introduced into an appropriate host cell. That is, the host cell may be transformed.
  • Introduction of a plasmid into the host cell can be accomplished by various techniques well known to those of skill in the art. These include, but are not limited to, transfection (including electrophoresis and electroporation), protoplast fusion, calcium phosphate precipitation, cell fusion with enveloped DNA, microinjection, and infection with intact virus. See, e.g., Ridgway, A. A. G. “Mammalian Expression Vectors” Chapter 24.2, pp. 470-472 Vectors, Rodriguez and Denhardt, Eds.
  • the transformed cells are grown under conditions appropriate to the production of the light chains and heavy chains, and assayed for heavy and/or light chain protein synthesis.
  • exemplary assay techniques include enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (RIA), or fluorescence-activated cell sorter analysis (FACS), immunohistochemistry and the like.
  • transformation shall be used in a broad sense to refer to the introduction of DNA into a recipient host cell that changes the genotype and consequently results in a change in the recipient cell.
  • host cells refer to cells that have been transformed with vectors constructed using recombinant DNA techniques and encoding at least one heterologous gene.
  • the terms “cell” and “cell culture” are used interchangeably to denote the source of the interferon-associated antigen binding protein unless it is clearly specified otherwise.
  • recovery of polypeptide from the “cells” may mean either from spun down whole cells, or from the cell culture containing both the medium and the suspended cells.
  • the host cell line used for expression of an interferon-associated antigen binding protein is of eukaryotic or prokaryotic origin.
  • expression may include the transcription and translation of more than one polypeptide chain (such as a heavy and a light chain of the antibody moiety of an interferon-associated antigen binding protein), which associate to form the final interferon-associated antigen binding protein.
  • the host cell line used for expression of an interferon-associated antigen binding protein is of bacterial origin.
  • the host cell line used for expression of an interferon-associated antigen binding protein is of mammalian origin; those skilled in the art can determine particular host cell lines which are best suited for the desired gene product to be expressed therein.
  • Exemplary host cell lines include, but are not limited to, CHO K1 GS knockout from Horizon, DG44 and DUXB11 (Chinese Hamster Ovary lines, DHFR minus), HELA (human cervical carcinoma), CVI (monkey kidney line), COS (a derivative of CVI with SV40 T antigen), R1610 (Chinese hamster fibroblast) BALBC/3T3 (mouse fibroblast), HAK (hamster kidney line), SP2/O (mouse myeloma), BFA-1c1BPT (bovine endothelial cells), RAJI (human lymphocyte), HEK 293 (human kidney).
  • HEK FS S11/ 254 cells may be used.
  • CHO K1 GS from Horizon may be used.
  • the cell line provides for altered glycosylation, e.g., afucosylation, of the antibody expressed therefrom (e.g., PER.C6® (Crucell) or FUT8-knock-out CHO cell lines (POTELLIGENTTM cells) (Biowa, Princeton, NJ)).
  • NS0 cells may be used. Host cell lines are typically available from commercial services, the American Tissue Culture Collection or from published literature.
  • the host used for expression of an interferon-associated antigen binding protein is a non-human transgenic animal or transgenic plant.
  • Interferon-associated antigen binding proteins of the invention can also be produced transgenically through the generation of a non-human animal (e.g., mammal) or plant that is transgenic for the sequences of interest and production of the interferon-associated antigen binding protein in a recoverable form therefrom.
  • interferon-associated antigen binding proteins can be produced in, and recovered from, the milk of goats, cows, or other mammals. See, e.g., U.S. Pat. Nos 5,827,690, 5,756,687, 5,750,172, and 5,741,957.
  • Exemplary plant hosts are Nicotiana , Arabidopsis , duckweed, corn, wheat, potato, etc.
  • non-human transgenic animals or plants are produced by introducing one or more nucleic acid molecules encoding an interferon-associated antigen binding protein of the invention into the animal or plant by standard transgenic techniques. See Hogan and U.S. Pat. 6,417,429.
  • the transgenic cells used for making the transgenic animal can be embryonic stem cells or somatic cells.
  • the transgenic non-human organisms can be chimeric, nonchimeric heterozygotes, and nonchimeric homozygotes.
  • the transgenic non-human animals have a targeted disruption and replacement by a targeting construct that encodes the sequence(s) of interest.
  • the interferon-associated antigen binding proteins may be made in any transgenic animal.
  • the non-human animals are mice, rats, sheep, pigs, goats, cattle or horses.
  • the non-human transgenic animal expresses said interferon-associated antigen binding proteins in blood, milk, urine, saliva, tears, mucus and other bodily fluids.
  • tissue culture conditions include homogeneous suspension culture, e.g., in an airlift reactor or in a continuous stirrer reactor, or immobilized or entrapped cell culture, e.g., in hollow fibers, microcapsules, on agarose microbeads or ceramic cartridges.
  • a solution of an interferon-associated antigen binding protein can be purified by the customary chromatography methods, for example gel filtration, ion-exchange chromatography, chromatography over DEAE-cellulose and/or (immuno-) affinity chromatography.
  • One or more genes encoding an interferon-associated antigen binding protein can also be expressed in non-mammalian cells such as bacteria or yeast or plant cells.
  • non-mammalian cells such as bacteria or yeast or plant cells.
  • various unicellular non-mammalian microorganisms such as bacteria can also be transformed; i.e. those capable of being grown in cultures or fermentation.
  • Bacteria which are susceptible to transformation, include members of the enterobacteriaceae, such as strains of Escherichia coli or Salmonella ; Bacillaceae , such as Bacillus subtilis ; Pneumococcus ; Streptococcus , and Haemophilus influenzae .
  • interferon-associated antigen binding proteins when expressed in bacteria, interferon-associated antigen binding proteins according to the invention or components thereof (i.e., agonistic anti-CD40 antibodies or agonistic antigen binding fragments thereof, and IFNs or functional fragments of IFNs) can become part of inclusion bodies.
  • the desired interferon-associated antigen binding proteins may then need to be isolated, optionally also refolded, and purified.
  • Saccharomyces cerevisiae or common baker’s yeast, is the most commonly used among eukaryotic microorganisms although a number of other strains are commonly available.
  • Saccharomyces the plasmid YRp7, for example, (Stinchcomb et al., Nature, 282:39 (1979); Kingsman et al., Gene, 7:141 (1979); Tschemper et al., Gene, 10:157 (1980)) is commonly used.
  • This plasmid already contains the TRP1 gene, which provides a selection marker for a mutant strain of yeast lacking the ability to grow in tryptophan, for example ATCC No. 44076 or PEP4-1 (Jones, Genetics, 85:12 (1977)).
  • the presence of the trp1 lesion as a characteristic of the yeast host cell genome then provides an effective environment for detecting transformation by growth in the absence of tryptophan.
  • a nucleic acid sequence encoding an interferon-associated antigen binding protein can be inserted into a vector and used as a therapeutic vector, e.g., a vector that expresses an interferon-associated antigen binding protein of the invention.
  • a therapeutic vector e.g., a vector that expresses an interferon-associated antigen binding protein of the invention.
  • suitable, functional expression constructs and therapeutic expression vectors is known to one of ordinary skill in the art.
  • the interferon-associated antigen binding protein may be administered to a subject by means of genetic delivery with RNA or DNA sequences, a vector or vector system encoding the interferon-associated antigen binding protein.
  • Therapeutic vectors can be delivered to a subject by, for example, intravenous injection, local administration (see U.S. Pat. No. 5,328,470) or by stereotactic injection (see, e.g., Chen et al., PNAS 91:3054-3057 (1994)).
  • the pharmaceutical preparation of a therapeutic vector can include the vector in an acceptable diluent.
  • An interferon-associated antigen binding protein encoding nucleic acid, or nucleic acids can be incorporated into a gene construct to be used as a part of a therapy protocol to deliver nucleic acids encoding an interferon-associated antigen binding protein.
  • Expression vectors for in vivo transfection and expression of an interferon-associated antigen binding protein are provided.
  • Expression constructs of such components may be administered in any biologically effective carrier, e.g., any formulation or composition capable of effectively delivering the component nucleic acid sequence to cells in vivo, as are known to one of ordinary skill in the art.
  • Approaches include, but are not limited to, insertion of the subject nucleic acid sequence(s) in viral vectors including, but not limited to, recombinant retroviruses, adenovirus, adeno-associated virus and herpes simplex virus-1, recombinant bacterial or eukaryotic plasmids and the like.
  • Retrovirus vectors and adeno-associated viral vectors can be used as a recombinant delivery system for the transfer of exogenous nucleic acid sequences in vivo, particularly into humans.
  • Such vectors provide efficient delivery of genes into cells, and the transferred nucleic acids can be stably integrated into the chromosomal DNA of the host.
  • a replication-defective retrovirus can be packaged into virions, which can be used to infect a target cell through the use of a helper virus by standard techniques.
  • retroviruses include pLJ, pZIP, pWE and pEM, which are known to those of ordinary skill in the art.
  • suitable packaging virus lines include *Crip, *Cre, *2 and *Am. (See, for example, Eglitis, et al., Science 230:1395-1398 (1985); Danos and Mulligan, Proc. Natl. Acad. Sci.
  • adenovirus-derived delivery vectors are provided.
  • the genome of an adenovirus can be manipulated such that it encodes and expresses a gene product of interest but is inactivated in terms of its ability to replicate in a normal lytic viral life cycle. See, for example, Berkner, et al., BioTechniques 6:616 (1988); Rosenfeld, et al., Science 252:431-434 (1991); and Rosenfeld, et al., Cell 68:143-155 (1992).
  • Suitable adenoviral vectors derived from the adenovirus strain Ad type 5 d1324 or other strains of adenovirus are known to those of ordinary skill in the art.
  • Recombinant adenoviruses can be advantageous in certain circumstances in that they are not capable of infecting non-dividing cells and can be used to infect a wide variety of cell types, including epithelial cells (Rosenfeld, et al. (1992), supra).
  • the virus particle is relatively stable and amenable to purification and concentration and, as above, can be modified so as to affect the spectrum of infectivity.
  • introduced adenoviral DNA (and foreign DNA contained therein) is not integrated into the genome of a host cell, but remains episomal, thereby avoiding potential problems that can occur as a result of insertional mutagenesis in situ where introduced DNA becomes integrated into the host genome (e.g., retroviral DNA).
  • the carrying capacity of the adenoviral genome for foreign DNA is large (up to 8 kilobases) relative to other delivery vectors (Berkner, et al. (1998), supra; Haj-Ahmand and Graham, J. Virol. 57:267 (1986)).
  • AAV adeno-associated virus
  • AAV is a naturally occurring defective virus that requires another virus, such as an adenovirus or a herpes virus, as a helper virus for efficient replication and a productive life cycle.
  • AAV is also one of the few viruses that may integrate its DNA into non-dividing cells, and exhibits a high frequency of stable integration (see for example Flotte, et al., Am. J. Respir. Cell. Mol. Biol.
  • Vectors containing as little as 300 base pairs of AAV can be packaged and can integrate. Space for exogenous DNA is limited to about 4.5 kb.
  • An AAV vector such as that described in Tratschin, et al., Mol. Cell. Biol. 5:3251-3260 (1985) can be used to introduce DNA into cells.
  • a variety of nucleic acids have been introduced into different cell types using AAV vectors (see for example Hermonat, et al., Proc. Natl. Acad. Sci.
  • non-viral methods can also be employed to cause expression of a nucleic acid sequence encoding an interferon-associated antigen binding protein in the tissue of a subject.
  • Most non-viral methods of gene transfer rely on normal mechanisms used by mammalian cells for the uptake and intracellular transport of macromolecules.
  • non-viral delivery systems rely on endocytic pathways for the uptake of the subject gene by the targeted cell.
  • Exemplary delivery systems of this type include liposomal derived systems, poly-lysine conjugates, and artificial viral envelopes.
  • Other embodiments include plasmid injection systems such as are described in Meuli, et al., J. Invest. Dermatol. 116 (1):131-135 (2001); Cohen, et al., Gene Ther 7 (22):1896-905 (2000); or Tam, et al., Gene Ther. 7 (21):1867-74 (2000).
  • the delivery systems can be introduced into a subject by any of a number of methods, each of which is familiar in the art.
  • a pharmaceutical preparation of the delivery system can be introduced systemically, e.g., by intravenous injection.
  • Specific transduction of the protein in the target cells occurs predominantly from specificity of transfection provided by the delivery vehicle, cell-type or tissue-type expression due to the transcriptional regulatory sequences controlling expression of the receptor gene, or a combination thereof.
  • initial delivery of the recombinant gene is more limited with introduction into the animal being quite localized.
  • the delivery vehicle can be introduced by catheter (see, U.S. Pat. No. 5,328,470) or by stereotactic injection (e.g., Chen, et al., PNAS 91: 3054-3057 (1994)).
  • the pharmaceutical preparation of the therapeutic construct can consist essentially of the delivery system in an acceptable diluent, or can comprise a slow release matrix in which the delivery vehicle is imbedded.
  • the complete delivery system can be produced intact from recombinant cells, e.g., retroviral vectors, the pharmaceutical preparation can comprise one or more cells, which produce the delivery system.
  • the invention provides methods of treating a patient in need thereof (e.g., a patient infected with HBV) comprising administering an effective amount of an interferon-associated antigen binding protein, or a nucleic acid sequence (e.g., mRNA) that encodes an interferon-associated antigen binding protein, as disclosed herein.
  • a patient in need thereof e.g., a patient infected with HBV
  • a nucleic acid sequence e.g., mRNA
  • the invention also provides for a use of an interferon-associated antigen binding protein, or a nucleic acid sequence (e.g., mRNA) that encodes an interferon-associated antigen binding protein, as disclosed herein, in the preparation of a medicament.
  • the invention provides for a use of an interferon-associated antigen binding protein, or a nucleic acid sequence (e.g., mRNA) that encodes an interferon-associated antigen binding protein, as disclosed herein, in the preparation of a medicament for the treatment of disorders and/or symptoms, e.g., HBV-related disorders and/or HBV-related symptoms.
  • the present invention provides kits and methods for the treatment of disorders and/or symptoms, e.g., HBV-related disorders and/or HBV-related symptoms, in a mammalian subject in need of such treatment.
  • the subject is a human.
  • interferon-associated antigen binding proteins, or nucleic acid sequences that encode them, of the present invention are useful in a number of different applications.
  • the subject interferon-associated antigen binding proteins, or nucleic acid sequences that encode them are useful for reducing HBeAg release from an HBV-infected cell.
  • the interferon-associated antigen binding proteins of the invention reduce HBeAg release by primary hepatocytes in vitro by at least 10% at 1 ng/mL, at least 20% at 1 ng/mL, at least 30 % at 1 ng/mL, at least 40% at 1 ng/mL, at least 50% at 1 ng/mL, at least 60 % at 1 ng/mL, at least 70% at 1 ng/mL, at least 80% at 1 ng/mL, or at least 85% at 1 ng/mL. In some embodiments, the interferon-associated antigen binding proteins of the invention reduce HBeAg release by primary hepatocytes in vitro by at least 12% at 1 ng/mL.
  • the interferon-associated antigen binding proteins of the invention reduce HBeAg release by primary hepatocytes in vitro by up to 90% at 1 ng/mL.
  • the interferon-associated antigen binding protein reduces HBeAg release with an EC 50 of less than 30 ng/mL, preferably with an EC 50 of less than 10 ng/mL, more preferably with an EC 50 of less than 1 ng/mL.
  • the subject interferon-associated antigen binding proteins, or nucleic acid sequences that encode them are useful for reducing pgRNA transcription of cccDNA in an HBV-infected cell.
  • the subject interferon-associated antigen binding proteins, or nucleic acid sequences that encode them are useful for reducing one or more symptoms and/or complications associated with HBV infection, as described herein (infra).
  • the subject interferon-associated antigen binding proteins, or nucleic acid sequences that encode them are useful for reducing one or more disorders, symptoms and/or complications associated with chronic HBV infection, e.g., chronic inflammation of the liver (chronic hepatitis), leading to cirrhosis over a period of several years; hepatocellular carcinoma (HCC); development of membranous glomerulonephritis (MGN); risk of death; acute necrotizing vasculitis (polyarteritis nodosa), membranous glomerulonephritis, and papular acrodermatitis of childhood (Gianotti-Crosti syndrome); HBV-associated nephropathy (e.g., membranous glomerulonephritis); immune-mediated hematological disorders (e.g., essential mixed cryoglobulinemia, aplastic anemia); and the like.
  • chronic HBV infection e.g., chronic inflammation of the liver (chronic hepatit
  • the subject interferon-associated antigen binding proteins, or nucleic acid sequences that encode them are useful for reducing one or more symptoms and/or complications associated with acute HBV infection, e.g., acute viral hepatitis (which begins with general ill-health, loss of appetite, nausea, vomiting, body aches, mild fever, and dark urine, and then progresses to development of jaundice, fulminant hepatic failure, and/or serum-sickness-like syndrome); loss of appetite; joint and muscle pain; low-grade fever; stomach pain; nausea; vomiting; jaundice; bloated stomach; and the like.
  • acute viral hepatitis which begins with general ill-health, loss of appetite, nausea, vomiting, body aches, mild fever, and dark urine, and then progresses to development of jaundice, fulminant hepatic failure, and/or serum-sickness-like syndrome
  • loss of appetite joint and muscle pain
  • low-grade fever stomach pain
  • nausea nausea
  • vomiting jaundice
  • this invention also relates to a method of treating one or more disorders, symptoms and/or complications associated with HBV infection in a human or other animal by administering to such human or animal an effective, non-toxic amount of an interferon-associated antigen binding protein, or a nucleic acid sequence that encodes it.
  • an effective, non-toxic amount of an interferon-associated antigen binding protein, or a nucleic acid sequence that encodes it would be for the purpose of treating HBV infection.
  • a “therapeutically active amount” of an interferon-associated antigen binding protein of the present invention may vary according to factors such as the disease stage (e.g., acute vs. chronic), age, sex, medical complications (e.g., HIV co-infection, immunosuppressed conditions or diseases) and weight of the subject, and the ability of the interferon-associated antigen binding protein to elicit a desired response in the subject.
  • the dosage regimen may be adjusted to provide the optimum therapeutic response. For example, several divided doses may be administered daily, or the dose may be proportionally reduced as indicated by the exigencies of the therapeutic situation.
  • compositions provided in the current invention may be used to prophylactically treat non-infected cells or therapeutically treat any HBV-infected cells comprising an antigenic marker that allows for the targeting of the HBV-infected cells by an interferon-associated antigen binding protein.
  • the interferon-associated antigen binding proteins of the invention or nucleic acid sequences (including vectors or vector systems) that encode them are comprised in a pharmaceutical composition.
  • Methods of preparing and administering interferon-associated antigen binding proteins, or nucleic acid sequences that encode them, of the current invention to a subject are well known to or can be readily determined by those skilled in the art using this specification and the knowledge in the art as a guide.
  • the route of administration of the interferon-associated antigen binding proteins, or nucleic acid sequences that encode them, of the current invention may be oral, parenteral, by inhalation or topical.
  • a form for administration would be a solution for injection, in particular for intravenous or intraarterial injection or drip.
  • a suitable pharmaceutical composition for injection may comprise a buffering agent (e.g. acetate, phosphate or citrate buffer), a surfactant (e.g. polysorbate), optionally a stabilizing agent (e.g. human albumin), etc.
  • the buffering agent is acetate.
  • the buffering agent is formate.
  • the buffering agent is citrate.
  • the surfactant may be selected from the list comprising pluronics, PEG, sorbitan esters, polysorbates, triton, tromethamine, lecithin, cholesterol and tyloxapal.
  • the surfactant is polysorbate.
  • the surfactant is polysorbate 20, polysorbate 40, polysorbate 60, polysorbate 80 or polysorbate 100, preferably polysorbate 20 or polysorbate 80.
  • the interferon-associated antigen binding proteins, or nucleic acid sequences that encode them can be delivered directly to the site of the adverse cellular population (e.g., the liver) thereby increasing the exposure of the diseased tissue to the therapeutic agent.
  • Preparations for parenteral administration include sterile aqueous or non-aqueous solutions, suspensions, and emulsions.
  • non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate.
  • Aqueous carriers include water, alcoholic/aqueous solutions, emulsions or suspensions, including saline and buffered media.
  • pharmaceutically acceptable carriers include, but are not limited to, 0.01-0.1 M, e.g., 0.05 M phosphate buffer, or 0.8% saline.
  • compositions suitable for injectable use include sterile aqueous solutions (where water-soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions.
  • the composition must be sterile and should be fluid to the extent that easy syringability exists. It should be stable under the conditions of manufacture and storage and will typically be preserved against the contaminating action of microorganisms, such as bacteria and fungi.
  • the carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (e.g., glycerol, propylene glycol, and liquid polyethylene glycol, and the like), and suitable mixtures thereof.
  • the proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants.
  • Prevention of the action of microorganisms can be achieved by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, ascorbic acid, thimerosal and the like.
  • isotonic agents will be included, for example, sugars, polyalcohols, such as mannitol, sorbitol, or sodium chloride in the composition.
  • Prolonged absorption of the injectable compositions can be brought about by including in the composition an agent which delays absorption, for example, aluminum monostearate and gelatin.
  • sterile injectable solutions can be prepared by incorporating an active compound such as an interferon-associated antigen binding protein, or a nucleic acid sequence encoding said interferon-associated antigen binding protein, of the present invention by itself or in combination with other active agents in the required amount in an appropriate solvent with one or a combination of ingredients enumerated herein, as required, followed by filtered sterilization.
  • an active compound such as an interferon-associated antigen binding protein, or a nucleic acid sequence encoding said interferon-associated antigen binding protein, of the present invention by itself or in combination with other active agents in the required amount in an appropriate solvent with one or a combination of ingredients enumerated herein, as required, followed by filtered sterilization.
  • dispersions are prepared by incorporating the active compound into a sterile vehicle, which contains a basic dispersion medium and the required other ingredients from those enumerated above.
  • exemplary methods of preparation include vacuum drying and freeze-drying, which yields a powder of an active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.
  • the preparations for injections are processed, filled into containers such as ampules, bags, bottles, syringes or vials, and sealed under aseptic conditions according to methods known in the art. Further, the preparations may be packaged and sold in the form of a kit. Such articles of manufacture will typically have labels or package inserts indicating that the associated compositions are useful for treating a subject suffering from HBV infection.
  • Effective doses of the compositions of the present invention, for the treatment of the above described HBV infection-related conditions vary depending upon many different factors, including means of administration, target site, physiological state of the patient, whether the patient is human or an animal, other medications administered, and whether treatment is prophylactic or therapeutic.
  • the patient is a human, but non-human mammals including transgenic mammals, in particular non-human primates, can also be treated.
  • Treatment dosages may be titrated using routine methods known to those of skill in the art to optimize safety and efficacy.
  • the dosage can range, e.g., from about 0.0001 to about 100 mg/kg, and more usually about 0.01 to about 5 mg/kg (e.g., about 0.02 mg/kg, about 0.25 mg/kg, about 0.5 mg/kg, about 0.75 mg/kg, about 1 mg/kg, about 2 mg/kg, etc.), of the host body weight.
  • dosages can be about 1 mg/kg body weight or about 10 mg/kg body weight or within the range of about 1 to about 10 mg/kg, e.g., at least about 1 mg/kg. Doses intermediate in the above ranges are also intended to be within the scope of the current invention.
  • Subjects can be administered such doses daily, on alternative days, weekly or according to any other schedule determined by empirical analysis.
  • An exemplary treatment entails administration in multiple dosages over a prolonged period, for example, of at least six months. Additional exemplary treatment regimens entail administration about once per every two weeks or about once a month or about once every 3 to 6 months.
  • Exemplary dosage schedules include about 1 to about 10 mg/kg or about 15 mg/kg on consecutive days, about 30 mg/kg on alternate days or about 60 mg/kg weekly.
  • Interferon-associated antigen binding proteins, or nucleic acid sequences expressing any of these can be administered on multiple occasions. Intervals between single dosages can be weekly, monthly or yearly. Intervals can also be irregular as indicated by measuring blood levels of interferon-associated antigen binding proteins of components thereof in the patient. Alternatively, interferon-associated antigen binding proteins, or nucleic acid sequences expressing any of these can be administered as a sustained release formulation, in which case less frequent administration is required. Dosage and frequency vary depending on the half-life of the interferon-associated antigen binding proteins in the patient.
  • half-life or “t 1 ⁇ 2 ”, as referred to herein, relates to the stability and/or the rate of excretion of a compound, such as the interferon-associated antigen binding proteins of the invention.
  • the half-life of a compound is usually measured in the serum and denotes the time after administration that the serum concentration is 50% of the serum concentration at the time of administration.
  • the interferon-associated antigen binding proteins of the invention are characterized by a long serum half-life in mice.
  • the half-life of the interferon-associated antigen binding protein is at least 50 h, at least 60 h, at least 70 h, at least 80 h, at least 90 h or at least 100 h.
  • the half-life of the interferon-associated antigen binding protein is at least 100 h.
  • the half-life of the interferon-associated antigen binding protein in mice ranges from 116 to 158 h.
  • the half-life of a protein is related to its clearance.
  • volume of distribution refers to the theoretical volume that would be necessary to contain the total amount of an administered compound such as the interferon-associated antigen binding protein of the invention at the same concentration that it is observed in the blood plasma and relates to the distribution of said compound between plasma and the rest of the body after oral or parenteral dosing.
  • the volume of distribution Vss of the interferon-associated antigen binding protein is below 500 mL/kg, below 400 mL/kg, below 300 mL/kg, below 200 mL/kg, or below 100 mL/kg.
  • the volume of distribution Vss of the interferon-associated antigen binding protein is below 100 mL/kg. In some embodiments, the volume of distribution Vss of the interferon-associated antigen binding protein in mice ranges from 50 to 98 mL/kg.
  • systemic exposure Another related pharmacokinetic parameter is the systemic exposure.
  • systemic exposure AUC or “area under the curve” refer to the integral of the concentration-time curve.
  • Systemic exposure might be represented by plasma (serum or blood) concentrations or the AUCs of parent compound and/or metabolite(s).
  • the interferon-associated antigen binding proteins of the invention circulate in the blood with higher systemic exposure (AUC (0-inf)) than their parental antibody (CP870,893).
  • the systemic exposure of the interferon-associated antigen binding protein is at least 600 ⁇ g*h/mL, at least 700 ⁇ g*h/mL, at least 800 ⁇ g*h/mL, at least 900 ⁇ g*h/mL or at least 1000 ⁇ g*h/mL, preferably at least 1000 ⁇ g*h/mL.
  • the systemic exposure of the interferon-associated antigen binding protein in mice ranges from 1033 ⁇ g*h/mL to 1793 ⁇ g*h/mL.
  • an interferon-associated antigen binding protein of the present invention may be administered in a pharmaceutically effective amount for the in vivo treatment of mammalian disorders.
  • an interferon-associated antigen binding protein will be formulated to facilitate administration and promote stability of the active agent.
  • a pharmaceutical composition in accordance with the present invention can comprise a pharmaceutically acceptable, non-toxic, sterile carrier such as physiological saline, nontoxic buffers, preservatives and the like.
  • a pharmaceutically effective amount of an interferon-associated antigen binding protein typically is an amount sufficient to mediate one or more of: a reduction of HBeAg release from an HBV-infected cell; a reduction of pgRNA transcription in an HBV-infected cell; and a stimulation of the IFN signaling pathway in an infected cell.
  • the pharmaceutical compositions of the present invention may be administered in single or multiple doses to provide for a pharmaceutically effective amount of the interferon-associated antigen binding protein.
  • interferon-associated antigen binding proteins may be administered to a human or other animal in accordance with the aforementioned methods of treatment in an amount sufficient to produce a therapeutic effect.
  • the interferon-associated antigen binding proteins, or nucleic acid sequences expressing any of them can be administered to such human or other animal in a conventional dosage form prepared by combining the interferon-associated antigen binding proteins, or nucleic acid sequences expressing any of them, with a conventional pharmaceutically acceptable carrier or diluent according to known techniques.
  • the form and character of the pharmaceutically acceptable carrier or diluent is dictated by the amount of active ingredient with which it is to be combined, the route of administration and other well-known variables.
  • a cocktail comprising one or more species of interferon-associated antigen binding proteins, or nucleic acid sequences expressing any of them, described in the current invention may prove to be effective.
  • FIG. 2 A depicts an exemplary map of a pcDNA3.1 plasmid encoding Seq ID NO 32 under the control of the pCMV promoter.
  • the Freestyle 293-F cells (Invitrogen) were transiently cotransfected with plasmids encoding both HC and LC at a HC/LC ratio of 4/6. Six days after transfection, the supernatant was collected, centrifuged and filtered through 0.22 ⁇ m filters. Purification process was performed in two purification steps, on AktaExpress chromatography system (GE Healthcare) using Protein A MabSelect Sure 5 mL 1.6/2.5 cm column (GE Healthcare) at a Flow rate of 5 mL/min. Sample binding was done in D-PBS1X pH 7.5 buffer, and elution with Glycine/HCl 0.1 M pH 3.0 buffer.
  • Elution peak was stored in a loop then injected on HiTrap desalting 26/10 column (GE Healthcare) with a flow rate of 10 mL/min in D-PBS1XpH 7.5 buffer. Elution peak was collected on a 96-well microplate (2 mL fractions). Pool was performed according to the UV peak profile.
  • HEK-BlueTM CD40L cells InvivoGen Cat. #: hkb-cd40
  • HEK-BlueTM IFN- ⁇ / ⁇ cells InvivoGen, Cat. #: hkb-ifn ⁇
  • HEK-BlueTM CD40L cells were generated by stable transfection of HEK293 cells with the human CD40 gene and a NF ⁇ B-inducible Secreted Embryonic Alkaline Phosphatase (SEAP) construct (Invivogen) to measure the bioactivity of CD40 agonists. Stimulation of CD40 leads to NF ⁇ B induction and then production of SEAP, which is detected in the supernatant using QUANTI-BlueTM (Invivogen, Cat. # rep-qbs2).
  • SEAP Secreted Embryonic Alkaline Phosphatase
  • HEK-BlueTM IFN-cells are designed to monitor the activation of the JAK/STAT/ISGF3 pathways induced by type I-IFNs. Activation of this pathway induces the production and release of SEAP. Levels of SEAP are readily assessable in the supernatant using QUANTI-BlueTM.
  • HEK-BlueTM IFN- ⁇ / ⁇ are used to monitor the activity of human IFN ⁇ or IFN ⁇ .
  • Cells were seeded in 96-well plates (50,000 cells per well) and stimulated with the indicated concentration for each IFA or controls and incubated at 37° C. for 24 h. Supernatants were then collected and levels of SEAP were quantified after incubation of the supernatant for about 30 min with QuantiBlueTM and Optical Density (O.D.) assessment at 620 nm on an Ensight plate reader or PheraStar (Lab Biotech).
  • QuantiBlueTM and Optical Density (O.D.) assessment at 620 nm on an Ensight plate reader or PheraStar (Lab Biotech).
  • HEK-BlueTM Dual IFN-y cells (InvivoGen, Cat. #: hkb-ifng) or HEK-BlueTM IFN- ⁇ , (InvivoGen, Cat. #: hkb-ifnl) may be used to respectively monitor the activity of type II- and type III-IFNs.
  • HEK-BlueTM IFN- ⁇ cells are designed to monitor the activity of IFN ⁇ .
  • HEK-BlueTM Dual IFN-y cells allow the detection of bioactive human IFN ⁇ .
  • FIG. 3 shows examples of dose responses of IFAs, where IFN ⁇ or a mutated version thereof as specified in Table 7 was fused to the HC as indicated in Table 7, on HEK-BlueTM CD40L ( FIGS. 3 A- 3 B ) and HEK-BlueTM IFN- ⁇ / ⁇ cells ( FIGS. 3 C- 3 D ).
  • Agonistic anti-CD40 activities of IFAs are summarized in Table 8 and examples are shown in FIG. 3 A and FIG. 3 B . Results indicate that all tested IFAs are functional to activate both the CD40 pathway and the IFN- ⁇ / ⁇ pathway in a dose dependent manner.
  • the EC 50 values for agonistic CD40 are ranging from 11.1 ng/mL to 192 ng/mL (Table 8).
  • the mean EC 50 value for the parental antibody is 48 ng/mL and 57 ng/mL in the experiment shown in FIG. 3 .
  • IFAs with the IFN fused to the N-terminus of the HC or the LC were also able to activate the CD40 pathway, but the precise EC 50 values could not be determined for these IFAs since the activity was directly determined from the supernatant and not using purified proteins ( FIG. 3 B ).
  • the IFN activity of various IFAs is summarized in Table 8 and examples are shown in FIGS. 3 C to 3 D .
  • the IFN activity is variable depending on the linker sequence with EC 50 values ranging from 0.14 ng/mL to 4.5 ng/mL ( FIG. 3 C and Table 8).
  • FIG. 3 D shows that IFAs with IFN ⁇ fused to the N-terminal part exhibit high IFN activity.
  • the parental antibody used as negative control did not show any activity, whereas recombinant IFN ⁇ did show a strong dose-dependent response.
  • FIG. 4 shows examples of dose responses of IFAs, where IFN ⁇ was fused to the HC or the LC as indicated in Table 7, on HEK-BlueTM CD40L ( FIG. 4 A and FIG. 4 C ) and HEK-BlueTM IFN- ⁇ / ⁇ cells ( FIG. 4 B and FIG. 4 D ).
  • Results indicate that all tested IFAs are functional to activate both the CD40 pathway and the IPN ⁇ / ⁇ pathway in a dose-dependent manner.
  • the potency on CD40 pathway was reproducibly higher than that of the parental antibody.
  • the EC 50 values for IFN ⁇ -based IFAs ranged from 11.1 ng/mL to 22.7 ng/mL and the EC 50 for CP870,893 ranged from 30 ng/mL to 80 ng/mL (mean EC 50 value: 48 ng/mL).
  • the IFN activity of IFAs is variable depending on the linker sequence with EC 50 values ranging from 1.6 ng/mL to 5.1 ng/mL.
  • PEGylated IFN ⁇ 2a (Pegasys®) was also active in a dose-dependent manner with an EC 50 value of around 1 ng/mL.
  • Suitable constructs according to the invention can also be interferon-associated antigen binding proteins without an Fc region.
  • a construct encoding the heavy chain of the fab fragment of CP870,893 fused to a TEV-His tag was designed (SEQ ID NO 50) and cloned into the expression plasmid pcDNA3.1. This construct is cotransfected in HEK cells as described earlier, with LCs fused via different linkers to different IFNs such as SEQ ID NO 28, SEQ ID NO 29, SEQ ID NO 34, SEQ ID NO 35, SEQ ID NO 36, SEQ ID NO 37, SEQ ID NO 41, SEQ ID NO 42, or SEQ ID NO 43.
  • Proteins and/or supernatants are evaluated in reporter cells and/or their effect on HBV infection in PHHs. It will be understood by one of skill in the art that constructs for use in therapy will no longer contain the TEV-His tag. These constructs are likewise embodiments of the invention. Interferon-associated antigen binding proteins without the Fc part will be active against HBV infection. Two IFAs were then produced and their functional characterization is described in Example V: IFA50: (SEQ ID NO 41) + (SEQ ID NO 50) and IFA51: (SEQ ID NO 42) + (SEQ ID NO 50).
  • PHH cells were plated in 96-well plates (70,000 cells/well) in William’s E GlutaMAX media (32551-020, Gibco) supplemented with 10% fetal calf serum (FCS) (SH30066.02, Hyclone), insulin (19278-5ML, Sigma), hydrocortisone (H2270-100MG, Sigma) and Penicillin/Streptomycin (15140, Gibco).
  • FCS fetal calf serum
  • H2270-100MG hepatocytes
  • Penicillin/Streptomycin 15140, Gibco
  • HBV e-antigen (HBeAg) levels in the cell culture supernatant were measured using ELISA as described by the manufacturer and results expressed in PEI Units (HBeAg CLIA 96T/K: CL0312-2; Autobio) or in luminescence.
  • Quantification of the HBsAg in the supernatant was carried out by following the protocol of the AutoBio HBsAg CLIA kit (# CL0310-2), the main steps were: first the samples were diluted 1 ⁇ 5 in 1X PBS. Then 50 ⁇ L of standards, controls, and diluted samples were placed in the wells. 50 ⁇ L of “Enzyme conjugate” solution were added to each well, followed by an incubation of one hour at 37° C. Subsequently, the plates were washed 6 times with 300 ⁇ L of washing solution from the kit using the plate washer.
  • the qPCR technique was used to compare the level of expression of pgRNA from infected cells treated with test compounds.
  • pgRNA quantification from infected cells was done in 96-well plates with the QuantStudio 12 K Flex.
  • the cDNA was obtained by RT, followed by qPCR with TaqMan Fast Virus assay in one step (ThermoFisher cat# 4444434).
  • the results were processed by the ⁇ Ct method and normalized with the housekeeping gene GUSB in duplex.
  • the pgRNA was amplified using the following primers and probe: (forward: CCTCACCATACTGCACTCA, reverse: GAGGGAGTTCTTCTTCTAGG, AGTGTGGATTCGCACTCCTCCAGC as a probe).
  • the GUSB gene was amplified using the TaqMan assay from Thermo Fisher (Hs99999908-ml).
  • CXCL10 release was assessed using an ELISA kit according to the manufacturer’s instruction (BioLegend 439904). Samples were diluted 1/50 and luminescence was assessed on an EnSight microplate reader at 450 nm.
  • FIG. 6 shows that these IFAs are very potent on HBV infection with EC 50 values ranging from 0.06 ng/mL to 0.2 ng/mL for IFAs with IFN ⁇ 2a fused at the C-terminus of the HC (IFA25: 0.16 ng/mL, IFA26: 0.1 ng/mL; IFA27: 0.06 ng/mL; and IFA38: ⁇ 0.2 ng/mL ( ⁇ 2.2 pM); FIG. 6 A and FIG.
  • results indicate that all tested IFAs were able to inhibit HbeAG and HBsAG release as well as pgRNA expression in a dose dependent manner. Pegasys alone was only able to inhibit HBeAG release and reduce pgRNA levels. In this respect, IFAs are at least 2 logs more active than Pegasys on viral parameters. Surprisingly, although all tested IFAs showed a dose dependent inhibition of HBsAg release, no reduction was observed with Pegasys even at the highest concentration. Analysis of CXCL10, a biomarker of the IFN pathway, showed that IFAs are also much more potent than Pegasys.
  • WBC ex vivo stimulation assay was used to investigate release of cytokines following IFA stimulation.
  • WBC were collected from four healthy donors, diluted 1 ⁇ 3 in RPMI1640 (72400-021, Gibco) and distributed in sterile reaction tubes (300 ⁇ l). Cells were left unstimulated, stimulated with LPS (LipoPolySaccharide) K12 (tlrl-eklps, Invivogen) at 10 ng/mL as a positive control or with IFAs at 1 ⁇ g/ml and incubated for 24 h at 37° C. Supernatants were then collected and frozen at -20° C. until the day of analysis.
  • LPS LipoPolySaccharide
  • K12 tlrl-eklps, Invivogen
  • MSD assay Human pro-inflammatory cytokines were analyzed using multiplexing MSD assay (K15067L-4) which measures Tumor Necrosis Factor (TNF)- ⁇ , Interleukin (IL)-1 ⁇ , IL-2, IL-6, IL-8, IL-10, IL-12/IL-23p40 and IFN ⁇ . MSD plates were analyzed on the 1300 MESO QuickPlex SQ120 apparatus (MSD).
  • MSD Tumor Necrosis Factor
  • FIG. 7 depicts exemplary results from an in vitro Cytokine Release Assessment of Human WBC either non-stimulated, treated with LPS or with IFA1.
  • TMB Tetramethylbenzidin, TebuBio; TMBW-1000-01
  • TMB Tetramethylbenzidin, TebuBio
  • TMBW-1000-01 Tetramethylbenzidin, TebuBio
  • the reaction was stopped by adding 1 M HCl. Plates were read at 450-650 nm with an Ensight plate reader (Perkin Elmer). Quantification of Pegasys was assessed using similar protocol steps but using human IFN- ⁇ matched antibody pairs from eBioscience/Invitrogen. Capture was performed using 100 ⁇ L of human anti-IFN ⁇ antibody (eBioscience/Invitrogen; BMS216MST), at 1 ⁇ g/mL in sodium carbonate (0.05 M,pH 9.6, C-3041, Sigma). For the detection, a secondary anti-IFN ⁇ conjugate HRP antibody (1/1000, Affymetrix eBioscience/BMS216MST; 15501707) in PBS -0.05% Tween20 - 1% Milk was applied.
  • CP870,893, IFA25, IFA26, IFA27, IFA28, IFA29 and IFA30 were administrated at 0.5 mg/kg and Pegasys at 0.3 mg/kg i.v. bolus to male CD1-Swiss mice and blood samples were collected at different time points.
  • Examples of quantification of circulating molecules using the ELISA approach described above and revealed with anti-IFN ⁇ -conjugated HRP are shown in FIGS. 8 A and 8 B
  • examples of quantification revealed with anti-IgG2-conjugated HRP are shown in FIG. 8 C ;
  • Pegasys quantification is shown in FIG. 8 D .
  • PK parameters for CP870,893 were explored in a 7-day experiment and those for IFA27, IFA29 and IFA30 in 10-day experiments (quantification for IFA27 was performed using 2 different ELISA approaches).
  • Table 10B the PK parameters for CP870,893 and IFA25, IFA26, IFA28 and Pegasys were explored in 21-day experiments (quantification for IFA25 was performed using 2 different ELISA approaches).
  • the pharmacokinetic profiles of IFAs are characterized by a long serum half-life ranging from 116 to 218 h (Table 10A and Table 10B). Very similar PK profiles were obtained for the 6 tested IFAs with high circulating level even ten days after single dose administration.
  • the pharmacokinetic parameters summarized in Table 10A/B indicate that these IFAs surprisingly circulate in the blood with higher systemic exposure (AUC (0-inf)) ranging from 1033 ⁇ g.h/mL to 2552 ⁇ g.h/mL for IFAs in comparison to 590 or 797 ⁇ g.h/mL, respectively, for the parental antibody CP870,893 (up to 3.2 fold), also reflecting lower clearance values for IFAs.
  • the volume of distribution Vss was low and ranked from 50 to 105 mL/kg, slightly higher than the plasma vascular volume (50 mL/kg) in this species.
  • the clearance was ranked as low (0.28 to 0.49 mL/h/kg).
  • the clearance of Pegasys (1.4 mL/hr/kg) is up to 7 fold higher than clearance of IFAs (e.g., 0.2 mL/hr/kg for IFA27) demonstrating a higher systemic exposure of IFAs.
  • IFN ⁇ was linked to the LC part with a (G4S)2 (IFA50) or (G4S)3 (IFA51) linker.
  • IFA49 IFN epsilon
  • IFA46 IFN omega; IFN ⁇
  • IFA46 IFN omega
  • FIG. 11 A Evaluation on HEK-BlueTM hIFN- ⁇ / ⁇ cells (which are in fact activated by any type I interferon) showed that IFA46 is also able to activate the IFN-I-pathways ( FIG. 11 B ).
  • EC 50 values are reported in Table 8B.
  • IFA46 was also tested on HBV infection in primary hepatocytes and showed similar activity to Pegasys ( FIG. 11 C ).
  • IFN ⁇ type II Interferon
  • IFN lambda type III Interferon
  • IFA44 and IFA45 were tested in a single dose in comparison to Pegasys on HBV infection in primary hepatocytes as described earlier. Results indicate that both types of IFAs reduce HbeAg release by 65% and 78%, respectively. Under these condition Pegasys inhibited HbeAg release by 81%. These results indicate that IFAs with type III IFN are active on HBV infection with EC 50 values for both tested IFAs ⁇ 10 nM ( FIG. 13 C ).
  • the present invention also relates to the following items:
  • An interferon-associated antigen binding protein comprising
  • interferon-associated antigen binding protein according to item 1, wherein the HC comprises the sequence as set forth in SEQ ID NO 6, or a sequence at least 90% identical thereto.
  • interferon-associated antigen binding protein according to item 1, wherein the HC comprises the sequence as set forth in SEQ ID NO 48, or a sequence at least 90% identical thereto.
  • interferon-associated antigen binding protein according to any one of the preceding items, wherein the IFN or the functional fragment thereof is a human interferon.
  • interferon-associated antigen binding protein according to any one of the preceding items, wherein the IFN or the functional fragment thereof is selected from the group consisting of a Type I IFN, a Type II IFN and a Type III IFN, or a functional fragment thereof.
  • interferon-associated antigen binding protein according to any one of the preceding items, wherein the IFN or the functional fragment thereof is a Type I IFN, or a functional fragment thereof.
  • interferon-associated antigen binding protein according to item 8, wherein the type I IFN or the functional fragment thereof is IFN ⁇ , IFN ⁇ , IFN ⁇ , or IFN ⁇ , or a functional fragment thereof.
  • interferon-associated antigen binding protein according to item 8, wherein the type I IFN or the functional fragment thereof is IFN ⁇ or IFN ⁇ , or a functional fragment thereof.
  • interferon-associated antigen binding protein according to item 8, wherein the type I IFN or the functional fragment thereof is IFN ⁇ , or a functional fragment thereof.
  • interferon-associated antigen binding protein according to item 8, wherein the type I IFN or the functional fragment thereof is IFN ⁇ , or a functional fragment thereof.
  • interferon-associated antigen binding protein according to any one of the items 1 to 6, wherein the IFN or the functional fragment thereof is IFN ⁇ , IFN ⁇ , IFN ⁇ , IFN ⁇ , IFN ⁇ or IFN ⁇ , or a functional fragment thereof.
  • interferon-associated antigen binding protein according to item 13, wherein the IFN or the functional fragment thereof is IFN ⁇ or IFN ⁇ , or a functional fragment thereof.
  • interferon-associated antigen binding protein according to item 14, wherein the IFN or the functional fragment thereof is IFN ⁇ , or a functional fragment thereof.
  • interferon-associated antigen binding protein according to item 15, wherein the IFN or functional fragment thereof is IFN ⁇ 2a, or a functional fragment thereof.
  • interferon-associated antigen binding protein according to item 16, wherein the IFN ⁇ 2a comprises the sequence as set forth in SEQ ID NO 17, or a sequence at least 90% identical thereto.
  • interferon-associated antigen binding protein according to item 14, wherein the IFN or the functional fragment thereof is IFN ⁇ , or a functional fragment thereof.
  • interferon-associated antigen binding protein according to item 18, wherein the IFN ⁇ comprises the sequence as set forth in SEQ ID NO 14, or a sequence at least 90% identical thereto.
  • interferon-associated antigen binding protein according to item 18, wherein the IFN ⁇ or the functional fragment thereof comprises one or two amino acid substitution(s) relative to SEQ ID NO 14, selected from C17S and N80Q.
  • interferon-associated antigen binding protein according to item 20, wherein the IFN ⁇ or the functional fragment thereof comprises the amino acid substitution C17S relative to SEQ ID NO 14.
  • interferon-associated antigen binding protein according to item 21, wherein the IFN ⁇ comprises the amino acid sequence as set forth in SEQ ID NO 15.
  • interferon-associated antigen binding protein according to item 20, wherein the IFN ⁇ or the functional fragment thereof comprises the amino acid substitutions C17S and N80Q relative to SEQ ID NO 14.
  • interferon-associated antigen binding protein according to item 23, wherein the IFN ⁇ comprises the amino acid sequence as set forth in SEQ ID NO 16.
  • interferon-associated antigen binding protein according to item 13, wherein the IFN or a functional fragment thereof is IFN ⁇ or IFN ⁇ , or a functional fragment thereof.
  • interferon-associated antigen binding protein according to item 26, wherein the IFN ⁇ comprises the sequence as set forth in SEQ ID NO 19, or a sequence at least 90% identical thereto.
  • interferon-associated antigen binding protein according to item 28, wherein the IFN ⁇ or the functional fragment thereof is IFN ⁇ 2, or a functional fragment thereof.
  • interferon-associated antigen binding protein according to item 29, wherein the IFN ⁇ 2 comprises the sequence as set forth in SEQ ID NO 18, or a sequence at least 90% identical thereto.
  • interferon-associated antigen binding protein according to any one of the preceding items, wherein the IFN or the functional fragment thereof is non-covalently associated with the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof.
  • interferon-associated antigen binding protein according to item 31, wherein the IFN or the functional fragment thereof is non-covalently associated with the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof via ionic, Van-der-Waals, and/or hydrogen bond interactions.
  • interferon-associated antigen binding protein according to any one of items 1 to 30, wherein the IFN or the functional fragment thereof is covalently associated with the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof.
  • interferon-associated antigen binding protein according to item 33, wherein the IFN or the functional fragment thereof is fused to the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof.
  • interferon-associated antigen binding protein according to item 34, wherein the IFN or the functional fragment thereof is fused to a light chain of the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof.
  • interferon-associated antigen binding protein according to item 35, wherein the IFN or the functional fragment thereof is fused to the N-terminus of the light chain of the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof.
  • interferon-associated antigen binding protein according to item 35, wherein the IFN or the functional fragment thereof is fused to the C-terminus of the light chain of the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof.
  • interferon-associated antigen binding protein according to item 34, wherein the IFN or the functional fragment thereof is fused to a heavy chain of the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof.
  • interferon-associated antigen binding protein according to item 38, wherein the IFN or the functional fragment thereof is fused to the N-terminus of the heavy chain of the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof.
  • interferon-associated antigen binding protein according to item 38, wherein the IFN or the functional fragment thereof is fused to the C-terminus of the heavy chain of the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof.
  • interferon-associated antigen binding protein according to any one of items 34 to 40, wherein the agonistic anti-CD40 antibody or an agonistic antigen binding fragment thereof, and the IFN or the functional fragment thereof are fused to each other via a linker.
  • interferon-associated antigen binding protein according to item 41, wherein the interferon-associated antigen binding protein comprises no amino acids other than those forming (I) said agonistic anti-CD40 antibody, or agonistic antigen binding fragment thereof, (II) said IFN or functional fragment thereof and (III) said linker.
  • interferon-associated antigen binding protein according to any one of items 1 to 41, wherein the interferon-associated antigen binding protein comprises no amino acids other than those forming (I) said agonistic anti-CD40 antibody, or agonistic antigen binding fragment thereof and (II) said IFN or functional fragment thereof.
  • interferon-associated antigen binding protein according to item 44, wherein the linker comprises at least 1, at least 2, at least 3, at least 4, or at least 5 amino acids.
  • interferon-associated antigen binding protein according to item 45, wherein the linker comprises at least 20 amino acids.
  • interferon-associated antigen binding protein according to item 45, wherein the linker comprises at least 24 amino acids.
  • interferon-associated antigen binding protein according to item 44, wherein the linker comprises up to 10, up to 20, up to 30, up to 40, up to 50, up to 60, up to 70, up to 80, up to 90, or up to 100 amino acids.
  • interferon-associated antigen binding protein according to item 54, wherein the linker comprises up to 20 amino acids.
  • interferon-associated antigen binding protein according to item 54, wherein the linker comprises up to 15 amino acids.
  • interferon-associated antigen binding protein according to item 54, wherein the linker comprises up to 13 amino acids.
  • interferon-associated antigen binding protein according to item 54, wherein the linker comprises up to 12 amino acids.
  • interferon-associated antigen binding protein according to any one of items 44 to 64, wherein the linker is selected from the group comprising acidic, basic and neutral linkers.
  • interferon-associated antigen binding protein according to item 65 or 66, wherein the linker comprises a sequence as set forth in SEQ ID NO 22 or SEQ ID NO 23.
  • interferon-associated antigen binding protein according to item 65 or 69, wherein the linker comprises a sequence as set forth in SEQ ID NO 20, SEQ ID NO 21, SEQ ID NO 24, SEQ ID NO 25 or SEQ ID NO 26.
  • interferon-associated antigen binding protein according to any one of items 44 to 70, wherein the linker is selected from the group comprising rigid, flexible and helix-forming linkers.
  • interferon-associated antigen binding protein according to item 71 or 72, wherein the linker comprises a sequence as set forth in SEQ ID NO 20, SEQ ID NO 22 or SEQ ID NO 23.
  • interferon-associated antigen binding protein according to item 71 or 74, wherein the linker comprises a sequence as set forth in SEQ ID NO 21, SEQ ID NO 24, SEQ ID NO 25 or SEQ ID NO 26.
  • interferon-associated antigen binding protein according to item 71 or 76, wherein the linker comprises a sequence as set forth in SEQ ID NO 22 or SEQ ID NO 23.
  • interferon-associated antigen binding protein according to any one of items 44 to 66, 68, 69, 71, 72, 74 or 76, wherein the linker comprises the amino acids glycine and serine.
  • interferon-associated antigen binding protein according to item 78, wherein the linker comprises the sequence as set forth in SEQ ID NO 21, SEQ ID NO 24, SEQ ID NO 25, or SEQ ID NO 26.
  • interferon-associated antigen binding protein according to item 78, wherein the linker further comprises the amino acid threonine.
  • interferon-associated antigen binding protein according to item 80, wherein the linker comprises the sequence as set forth in SEQ ID NO 21.
  • interferon-associated antigen binding protein according to item 44, wherein the linker comprises a sequence selected from the sequences as set forth in SEQ ID NOs 20 to 26.
  • interferon-associated antigen binding protein according to item 82, wherein the linker comprises a sequence selected from the sequences as set forth in SEQ ID NO 24, SEQ ID NO 25 or SEQ ID NO 26.
  • interferon-associated antigen binding protein according to item 83, wherein the linker comprises a sequence as set forth in SEQ ID NO 24.
  • interferon-associated antigen binding protein according to item 83, wherein the linker comprises a sequence as set forth in SEQ ID NO 25.
  • interferon-associated antigen binding protein according to item 83, wherein the linker comprises a sequence as set forth in SEQ ID NO 26.
  • interferon-associated antigen binding protein according to any one of items 41, 42 or 44 to 86, wherein the IFN or a functional fragment thereof is fused to the C-terminus of a heavy chain of the agonistic anti-CD40 antibody, or the agonistic antigen binding fragment thereof, via the linker as set forth in Table 3, in particular Table 3A or Table 3B, more particularly Table 3A.
  • the interferon-associated antigen binding protein according to item 87, wherein the heavy chain of the agonistic anti-CD40 antibody, or the agonistic antigen binding fragment thereof, comprises a sequence as set forth in SEQ ID NO 6, SEQ ID NO 9, SEQ ID NO 49, SEQ ID NO 48, or SEQ ID NO 12.
  • interferon-associated antigen binding protein according to items 87 or 88, wherein the IFN ⁇ 2a comprises the sequence as set forth in SEQ ID NO 17.
  • interferon-associated antigen binding protein according to items 87 or 88, wherein the IFN ⁇ comprises the sequence as set forth in SEQ ID NO 14, SEQ ID NO 15 or SEQ ID NO 16.
  • interferon-associated antigen binding protein according to item 90, wherein the IFN ⁇ comprises the sequence as set forth in SEQ ID NO 14.
  • interferon-associated antigen binding protein according to item 90, wherein the IFN ⁇ comprises the sequence as set forth in SEQ ID NO 15.
  • interferon-associated antigen binding protein according to item 90, wherein the IFN ⁇ comprises the sequence as set forth in SEQ ID NO 16.
  • interferon-associated antigen binding protein according to item 87 or 88, wherein the IFN ⁇ comprises the sequence as set forth in SEQ ID NO 19.
  • interferon-associated antigen binding protein according to item 87 or 88, wherein the IFN ⁇ 2 comprises the sequence as set forth in SEQ ID NO 18.
  • interferon-associated antigen binding protein according to any one of items 87 to 95, wherein the interferon-associated antigen binding protein further comprises a light chain of an agonistic anti-CD40 antibody, or an agonistic antigen binding fragment thereof.
  • interferon-associated antigen binding protein according to item 96, wherein the light chain comprises a sequence as set forth in SEQ ID NO 3.
  • interferon-associated antigen binding protein according to any one of items 41, 42 or 44 to 86, wherein the IFN or a functional fragment thereof is fused to the N-terminus of a heavy chain of the agonistic anti-CD40 antibody, or the agonistic antigen binding fragment thereof, via the linker as set forth in Table 4, in particular Table 4A or Table 4B, more particularly Table 4A.
  • the interferon-associated antigen binding protein according to item 98 wherein the heavy chain of the agonistic anti-CD40 antibody, or the agonistic antigen binding fragment thereof, comprises a sequence as set forth in SEQ ID NO 6, SEQ ID NO 9, SEQ ID NO 12, SEQ ID NO 48, SEQ ID NO 49 or SEQ ID NO 50, preferably a sequence as set forth in SEQ ID NO 6, SEQ ID NO 9, SEQ ID NO 12, SEQ ID NO 48 or SEQ ID NO 49.
  • interferon-associated antigen binding protein according to items 98 or 99, wherein the IFN ⁇ 2a comprises the sequence as set forth in SEQ ID NO 17.
  • interferon-associated antigen binding protein according to items 98 or 99, wherein the IFN ⁇ comprises the sequence as set forth in SEQ ID NO 14, SEQ ID NO 15 or SEQ ID NO 16.
  • interferon-associated antigen binding protein according to item 101, wherein the IFN ⁇ comprises the sequence as set forth in SEQ ID NO 14.
  • interferon-associated antigen binding protein according to item 101, wherein the IFN ⁇ comprises the sequence as set forth in SEQ ID NO 15.
  • interferon-associated antigen binding protein according to item 101, wherein the IFN ⁇ comprises the sequence as set forth in SEQ ID NO 16.
  • interferon-associated antigen binding protein according to items 98 or 99, wherein the IFN ⁇ comprises the sequence as set forth in SEQ ID NO 19.
  • interferon-associated antigen binding protein according to items 98 or 99, wherein the IFN ⁇ 2 comprises the sequence as set forth in SEQ ID NO 18.
  • interferon-associated antigen binding protein according to any one of items 98 to 106, wherein the interferon-associated antigen binding protein further comprises a light chain of an agonistic anti-CD40 antibody, or an agonistic antigen binding fragment thereof.
  • interferon-associated antigen binding protein according to item 107, wherein the light chain comprises a sequence as set forth in SEQ ID NO 3.
  • interferon-associated antigen binding protein according to any one of items 41, 42 or 44 to 86, wherein the IFN or a functional fragment thereof is fused to the C-terminus of a light chain of the agonistic anti-CD40 antibody, or the agonistic antigen binding fragment thereof, via the linker as set forth in Table 5, in particular Table 5A or Table 5B, more particularly Table 5A.
  • interferon-associated antigen binding protein according to item 109, wherein the light chain of the agonistic anti-CD40 antibody, or the agonistic antigen binding fragment thereof, comprises a sequence as set forth in SEQ ID NO 3.
  • interferon-associated antigen binding protein according to items 109 or 110, wherein the IFN ⁇ 2a comprises the sequence as set forth in SEQ ID NO 17.
  • interferon-associated antigen binding protein according to items 109 or 110, wherein the IFN ⁇ comprises the sequence as set forth in SEQ ID NO 14, SEQ ID NO 15 or SEQ ID NO 16.
  • interferon-associated antigen binding protein according to item 112, wherein the IFN ⁇ comprises the sequence as set forth in SEQ ID NO 14.
  • interferon-associated antigen binding protein according to item 112, wherein the IFN ⁇ comprises the sequence as set forth in SEQ ID NO 15.
  • interferon-associated antigen binding protein according to item 112, wherein the IFN ⁇ comprises the sequence as set forth in SEQ ID NO 16.
  • interferon-associated antigen binding protein according to items 109 or 110, wherein the IFN ⁇ comprises the sequence as set forth in SEQ ID NO 19.
  • interferon-associated antigen binding protein according to items 109 or 110, wherein the IFN ⁇ 2 comprises the sequence as set forth in SEQ ID NO 18.
  • interferon-associated antigen binding protein according to any one of items 109 to 117, wherein the interferon-associated antigen binding protein further comprises a heavy chain of an agonistic anti-CD40 antibody, or an agonistic antigen binding fragment thereof.
  • interferon-associated antigen binding protein according to item 118, wherein the heavy chain of the agonistic anti-CD40 antibody comprises a sequence as set forth in SEQ ID NO 6, SEQ ID NO 9, SEQ ID NO 12, SEQ ID NO 48, SEQ ID NO 49 or SEQ ID NO 50, preferably a sequence as set forth in SEQ ID NO 6, SEQ ID NO 9, SEQ ID NO 12, SEQ ID NO 48 or SEQ ID NO 49.
  • interferon-associated antigen binding protein according to any one of items 41, 42 or 44 to 86, wherein the IFN is fused to the N-terminus of a light chain of the agonistic anti-CD40 antibody, or the agonistic antigen binding fragment thereof, via the linker as set forth in Table 6, in particular Table 6A or Table 6B, more particularly Table 6A.
  • interferon-associated antigen binding protein according to item 120, wherein the light chain of the agonistic anti-CD40 antibody, or the agonistic antigen binding fragment thereof, comprises a sequence as set forth in SEQ ID NO 3.
  • interferon-associated antigen binding protein according to items 120 or 121, wherein the IFN ⁇ 2a comprises the sequence as set forth in SEQ ID NO 17.
  • interferon-associated antigen binding protein according to items 120 or 121, wherein the IFN ⁇ comprises the sequence as set forth in SEQ ID NO 14, SEQ ID NO 15 or SEQ ID NO 16.
  • interferon-associated antigen binding protein according to item 123, wherein the IFN ⁇ comprises the sequence as set forth in SEQ ID NO 14.
  • interferon-associated antigen binding protein according to item 123, wherein the IFN ⁇ comprises the sequence as set forth in SEQ ID NO 15.
  • interferon-associated antigen binding protein according to item 123, wherein the IFN ⁇ comprises the sequence as set forth in SEQ ID NO 16.
  • interferon-associated antigen binding protein according to items 120 or 121, wherein the IFN ⁇ comprises the sequence as set forth in SEQ ID NO 19.
  • interferon-associated antigen binding protein according to items 120 or 121, wherein the IFN ⁇ 2 comprises the sequence as set forth in SEQ ID NO 18.
  • interferon-associated antigen binding protein according to any one of items 120 to 128, wherein the interferon-associated antigen binding protein further comprises a heavy chain of an anti-CD40 antibody, or an agonistic antigen binding fragment thereof.
  • interferon-associated antigen binding protein according to item 129, wherein the heavy chain of the agonistic anti-CD40 antibody comprises a sequence as set forth in SEQ ID NO 6, SEQ ID NO 9, SEQ ID NO 12, SEQ ID NO 48, SEQ ID NO 49 or SEQ ID NO 50, preferably a sequence as set forth in SEQ ID NO 6, SEQ ID NO 9, SEQ ID NO 12, SEQ ID NO 48 or SEQ ID NO 49.
  • interferon-associated antigen binding protein according to any one of items 1 to 130, wherein the interferon-associated antigen binding protein comprises a sequence selected from SEQ ID NO 28, SEQ ID NO 29, SEQ ID NO 30, SEQ ID NO 31, SEQ ID NO 32, SEQ ID NO 33, SEQ ID NO 34, SEQ ID NO 35, SEQ ID NO 36, SEQ ID NO 37, SEQ ID NO 38, SEQ ID NO 39, SEQ ID NO 40, SEQ ID NO 41, SEQ ID NO 42, SEQ ID NO 43, SEQ ID NO 44, SEQ ID NO 45, SEQ ID NO 46 and SEQ ID NO 47.
  • interferon-associated antigen binding protein according to item 131, wherein the interferon-associated antigen binding protein comprises a sequence selected from SEQ ID NO 38, SEQ ID NO 39, SEQ ID NO 40, SEQ ID NO 41, SEQ ID NO 42 or SEQ ID NO 43.
  • interferon-associated antigen binding protein according to items 131 or 132, wherein the interferon-associated antigen binding protein is an interferon-fused agonistic anti-CD40 antibody or an interferon-fused agonistic antigen binding fragment thereof comprising one of the sequence combinations disclosed in Table 8, in particular Table 8A or Table 8B, more particularly Table 8A.
  • interferon-associated antigen binding protein according to item 133, wherein the interferon-associated antigen binding protein is an interferon-fused agonistic anti-CD40 antibody or an interferon-fused agonistic antigen binding fragment thereof comprising the sequences as set forth in SEQ ID NO 38 and SEQ ID NO 3.
  • interferon-associated antigen binding protein according to item 133, wherein the interferon-associated antigen binding protein is an interferon-fused agonistic anti-CD40 antibody or an interferon-fused agonistic antigen binding fragment thereof comprising the sequences as set forth in SEQ ID NO 39 and SEQ ID NO 3.
  • interferon-associated antigen binding protein according to item 133, wherein the interferon-associated antigen binding protein is an interferon-fused agonistic anti-CD40 antibody or an interferon-fused agonistic antigen binding fragment thereof comprising the sequences as set forth in SEQ ID NO 40 and SEQ ID NO 3.
  • interferon-associated antigen binding protein according to item 133, wherein the interferon-associated antigen binding protein is an interferon-fused agonistic anti-CD40 antibody or an interferon-fused agonistic antigen binding fragment thereof comprising the sequences as set forth in SEQ ID NO 41 and SEQ ID NO 9.
  • interferon-associated antigen binding protein according to item 133, wherein the interferon-associated antigen binding protein is an interferon-fused agonistic anti-CD40 antibody or an interferon-fused agonistic antigen binding fragment thereof comprising the sequences as set forth in SEQ ID NO 42 and SEQ ID NO 9.
  • interferon-associated antigen binding protein according to item 133, wherein the interferon-associated antigen binding protein is an interferon-fused agonistic anti-CD40 antibody or an interferon-fused agonistic antigen binding fragment thereof comprising the sequences as set forth in SEQ ID NO 43 and SEQ ID NO 9.
  • interferon-associated antigen binding protein according to any one of items 1 to 139, wherein the interferon-associated antigen binding protein activates both the CD40 and an IFN pathway.
  • interferon-associated antigen binding protein according to item 140, wherein CD40 activity is determined using a whole blood surface molecule upregulation assay or an in vitro reporter cell assay.
  • interferon-associated antigen binding protein according to item 141, wherein CD40 activity is determined using an in vitro reporter cell assay, optionally using HEK-BlueTM CD40L cells.
  • interferon-associated antigen binding protein according to any one of items 140 to 142, wherein the interferon-associated antigen binding protein activates the CD40 pathway with an EC 50 of less than 400, 300, 200, 150, 100, 70, 60, 50, 40, 30, 25, 20, or 15 ng/mL.
  • interferon-associated antigen binding protein according to item 143, wherein the interferon-associated antigen binding protein activates the CD40 pathway with an EC 50 ranging from 10 to 200 ng/mL.
  • interferon-associated antigen binding protein according to item 144, wherein the interferon-associated antigen binding protein activates the CD40 pathway with an EC 50 ranging from 10 to 50 ng/mL, preferably 10 to 30 ng/mL.
  • interferon-associated antigen binding protein according to any one of items 140 to 145, wherein the interferon-associated antigen binding protein activates the IFN pathway with an EC 50 of less than 100, 60, 50, 40, 30, 20, 10, or 1 ng/mL.
  • interferon-associated antigen binding protein according to any one of items 140 to 146, wherein the interferon-associated antigen binding protein activates the IFN pathway with an EC 50 of less than 11 ng/mL, preferably less than 6 ng/mL.
  • interferon-associated antigen binding protein according to any one of items 140 to 147, wherein the IFN pathway is the IFN ⁇ , IFN ⁇ , IFN ⁇ , IFN ⁇ , IFN ⁇ or IFN ⁇ pathway.
  • interferon-associated antigen binding protein according to item 148, wherein IFN ⁇ activity is determined using an in vitro reporter cell assay, optionally using HEK-BlueTM IFN- ⁇ / ⁇ cells.
  • interferon-associated antigen binding protein according to item 148, wherein IFN ⁇ activity is determined using an in vitro reporter cell assay, optionally using HEK-BlueTM IFN- ⁇ / ⁇ cells.
  • interferon-associated antigen binding protein according to item 148, wherein IFN ⁇ activity is determined using an in vitro reporter cell assay, optionally using HEK-BlueTM Dual IFN-y cells.
  • interferon-associated antigen binding protein according to item 148, wherein IFN ⁇ activity is determined using an in vitro reporter cell assay, optionally using HEK-BlueTM IFN- ⁇ cells.
  • interferon-associated antigen binding protein according to any one of the preceding items, wherein the interferon-associated antigen binding protein reduces HBeAg release by primary hepatocytes in vitro by at least 12% at 1 ng/mL.
  • interferon-associated antigen binding protein for the use of item 153, wherein the interferon-associated antigen binding protein reduces HBeAg release by primary hepatocytes in vitro by up to 90% at 1 ng/mL.
  • interferon-associated antigen binding protein according to item 153, wherein the interferon-associated antigen binding protein reduces HBeAg release with an EC 50 of less than 30 ng/mL.
  • interferon-associated antigen binding protein according to item 155, wherein the interferon-associated antigen binding protein reduces HBeAg release with an EC 50 of less than 10 ng/mL.
  • interferon-associated antigen binding protein according to item 156, wherein the interferon-associated antigen binding protein reduces HBeAg release with an EC 50 of less than 1 ng/mL.
  • interferon-associated antigen binding protein according to item 156, wherein the interferon-associated antigen binding protein reduces HBeAg release with an EC 50 of less than 0.1 ng/mL.
  • interferon-associated antigen binding protein according to any one of the preceding items, wherein the interferon-associated antigen binding protein is capable of upregulating the expression level of one or more IFN pathway biomarkers in an HBV-infected cell, preferably at least 1.5-fold, more preferably at least 2-fold, most preferably at least 3-fold.
  • interferon-associated antigen binding protein according to item 159, wherein the IFN pathway biomarker is a chemokine.
  • interferon-associated antigen binding protein according to item 160, wherein the IFN pathway biomarker is the interferon stimulated gene ISG20.
  • interferon-associated antigen binding protein according to item 160, wherein the IFN pathway biomarker is a C-X-C chemokine, selected from the group consisting of CXCL9, CXCL10 and CXCL11.
  • interferon-associated antigen binding protein according to item 162, wherein the IFN pathway biomarker is CXCL10.
  • interferon-associated antigen binding protein according to any one of the preceding items, wherein the interferon-associated antigen binding protein does not significantly upregulate the expression level of one or more of IL10, IL1 ⁇ and IL2 in an HBV-infected cell.
  • interferon-associated antigen binding protein according to any one of the preceding items, wherein the systemic exposure of the interferon-associated antigen binding protein is increased compared to antibody CP870,893, preferably by at least 10%, more preferably by at least 15%, most preferably by at least 25%.
  • interferon-associated antigen binding protein according to any one of the preceding items, wherein the systemic exposure of the interferon-associated antigen binding protein is at least 1000 ⁇ g ⁇ h/mL.
  • interferon-associated antigen binding protein according to item 166, wherein the systemic exposure of the interferon-associated antigen binding protein ranges from 1033 ⁇ g ⁇ h/mL to 1793 ⁇ g ⁇ h/mL.
  • interferon-associated antigen binding protein according to any one of the preceding items, wherein the half-life of the interferon-associated antigen binding protein is at least 100 h.
  • interferon-associated antigen binding protein according to item 168, wherein the half-life of the interferon-associated antigen binding protein ranges from 116 to 158 h.
  • interferon-associated antigen binding protein according to any one of the preceding items, wherein the clearance rate of the interferon-associated antigen binding protein is below 0.5 mL/h/kg.
  • interferon-associated antigen binding protein according to item 170, wherein the clearance of the interferon-associated antigen binding protein ranges from 0.28 to 0.49 mL/h/kg.
  • interferon-associated antigen binding protein according to any one of the preceding items, wherein the volume of distribution Vss of the interferon-associated antigen binding protein is below 100 mL/kg.
  • interferon-associated antigen binding protein according to item 172, wherein the volume of distribution Vss of the interferon-associated antigen binding protein ranges from 50 to 98 mL/kg.
  • interferon-associated antigen binding protein according to any one of the preceding items, wherein the interferon-associated antigen binding protein is suitable for administration to a subject in need thereof by means of genetic delivery with nucleic acid sequences encoding the interferon-associated antigen binding protein, or a vector or vector system encoding the interferon-associated antigen binding protein.
  • nucleic acid according to item 176 encoding the IFN or the functional fragment thereof being fused to the light chain of the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof, and further encoding a heavy chain of the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof.
  • nucleic acid according to item 177 wherein the heavy chain of the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof comprises a sequence as set forth in SEQ ID NO 6, SEQ ID NO 7, SEQ ID NO 8, SEQ ID NO 9, SEQ ID NO 10, SEQ ID NO 11, SEQ ID NO 12, SEQ ID NO 13, SEQ ID NO 48, SEQ ID NO 49 or SEQ ID NO 50, or a nucleic acid sequence at least 95% identical to a nucleic acid encoding any of these sequences.
  • nucleic acid according to item 176 encoding the IFN or the functional fragment thereof being fused to the heavy chain of the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof, and further encoding a light chain of the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof.
  • nucleic acid according to item 179 wherein the light chain of the agonistic anti-CD40 antibody or the agonistic antigen binding fragment thereof comprises a sequence as set forth in SEQ ID NO 3, SEQ ID NO 4 or SEQ ID NO 5, or a nucleic acid sequence at least 95% identical to a nucleic acid encoding any of these sequences.
  • nucleic acid according to items 175 to 181, wherein the nucleic acid further encodes a purification tag.
  • nucleic acid according to items 182 or 183, wherein the nucleic acid further encodes a cleavage site to cleave off the purification tag.
  • nucleic acid according to item 184 wherein the nucleic acid comprises a sequence encoding the amino acid sequence as set forth in SEQ ID NO 27.
  • nucleic acid according to items 175 to 185, wherein the nucleic acid further encodes a signal peptide.
  • nucleic acid according to item 186 or 187, wherein the signal peptide comprises the sequence as set forth in SEQ ID NO: 1 or SEQ ID NO: 2.
  • nucleic acid according to item 188, wherein the signal peptide comprises the sequence as set forth in SEQ ID NO: 1.
  • nucleic acid according to item 188, wherein the signal peptide comprises the sequence as set forth in SEQ ID NO: 2.
  • a vector or a vector system comprising the nucleic acid according to any one of items 175 to 190.
  • a vector system comprising
  • a vector system comprising
  • a composition comprising the interferon-associated antigen binding protein according to any one of items 1 to 174, the nucleic acid according to any one of items 175 to 190, the vector according to item 191 or the vector system according to any one of items 191 to 193.
  • composition according to item 194 wherein the composition is a pharmaceutical composition.
  • composition according to item 195 wherein the pharmaceutical composition is suitable for oral, parenteral, or topical administration or for administration by inhalation.
  • composition according to item 196 wherein the pharmaceutical composition is suitable for oral administration.
  • composition according to item 196 wherein the pharmaceutical composition is suitable for topical administration.
  • composition according to item 196 wherein the pharmaceutical composition is suitable for administration by inhalation.
  • composition according to item 196 wherein the pharmaceutical composition is suitable for parenteral administration.
  • composition according to item 200 wherein the pharmaceutical composition is suitable for intravenous, intraarterial, intraperitoneal, intramuscular, subcutaneous, rectal or vaginal administration.
  • composition according to item 201, wherein the pharmaceutical composition is suitable for injection, preferably for intravenous or intraarterial injection or drip.
  • composition according to any one of items 195 to 202 comprising at least one buffering agent.
  • composition according to item 203 wherein the buffering agent is acetate, formate or citrate.
  • composition according to any one of items 195 to 207, wherein the pharmaceutical formulation comprises a surfactant.
  • composition according to item 208 wherein the surfactant is selected from the list comprising pluronics, PEG, sorbitan esters, polysorbates, triton, tromethamine, lecithin, cholesterol and tyloxapal.
  • the surfactant is selected from the list comprising pluronics, PEG, sorbitan esters, polysorbates, triton, tromethamine, lecithin, cholesterol and tyloxapal.
  • composition according to item 210, wherein the surfactant is polysorbate 20, polysorbate 40, polysorbate 60, polysorbate 80 or polysorbate 100.
  • composition according to item 211, wherein the surfactant is polysorbate 20.
  • composition according to item 211, wherein the surfactant is polysorbate 80.
  • composition according to any one of items 195 to 213 comprising a stabilizing agent, optionally wherein the stabilizing agent is albumin.
  • a host cell comprising the nucleic acid according to any one of items 175 to 190, the vector according to item 191 or the vector system according to any one of items 191 to 193.
  • a non-human transgenic animal or transgenic plant comprising the nucleic acid according to any one of items 175 to 190, the vector according to item 191 or the vector system according to any one of items 191 to 193, wherein the non-human transgenic animal or transgenic plant expresses said nucleic acid.
  • interferon-associated antigen binding protein according to any one of items 1 to 174, the nucleic acid according to any one of items 175 to 190, the vector according to item 191, the vector system according to any one of items 191 to 193 or the composition according to any one of items 195 to 214 for use as a medicament.
  • interferon-associated antigen binding protein according to any one of items 1 to 174, the nucleic acid according to any one of items 175 to 190, the vector according to item 191, the vector system according to any one of items 191 to 193 or the composition according to any one of items 195 to 214 for use in treating hepatitis B virus (HBV) infection and/or for decreasing one or more symptoms of HBV infection in a patient.
  • HBV hepatitis B virus
  • interferon-associated antigen binding protein, the nucleic acid, the vector, the vector system or the composition for the use of item 220, wherein treating hepatitis B virus (HBV) infection comprises decreasing one or more symptoms of HBV infection in the patient.
  • HBV hepatitis B virus
  • interferon-associated antigen binding protein according to any one of items 1 to 174, the nucleic acid according to any one of items 175 to 190, the vector according to item 191, the vector system according to any one of items 191 to 193 or the composition according to any one of items 195 to 214 for use in reducing the HBV viral load in an HBV-infected cell culture or an HBV-infected patient compared to an untreated HBV-infected cell culture or to the same patient before treatment.
  • interferon-associated antigen binding protein according to any one of items 1 to 174, the nucleic acid according to any one of items 175 to 190, the vector according to item 191, the vector system according to any one of items 191 to 193 or the composition according to any one of items 195 to 214 for use in reducing the HBV viral titer in an HBV-infected cell culture or an HBV-infected patient compared to an untreated HBV-infected cell culture or to the same patient before treatment.
  • interferon-associated antigen binding protein the nucleic acid, the vector, the vector system or the composition for the use of item 225, wherein the HBV viral titer is reduced by about 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%.
  • interferon-associated antigen binding protein according to any one of items 1 to 174, the nucleic acid according to any one of items 175 to 190, the vector according to item 191, the vector system according to any one of items 191 to 193 or the composition according to any one of items 195 to 214 for use in reducing transcription of HBV cccDNA in an HBV-infected cell culture or an HBV-infected patient compared to an untreated HBV-infected cell culture or to the same patient before treatment.
  • interferon-associated antigen binding protein the nucleic acid, the vector, the vector system or the composition for the use of item 228, wherein transcription of cccDNA is reduced by about 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%.
  • interferon-associated antigen binding protein the nucleic acid, the vector, the vector system or the composition for the use of item 228 or 229, wherein cccDNA transcription is determined by qPCR.
  • interferon-associated antigen binding protein according to any one of items 1 to 174, the nucleic acid according to any one of items 175 to 190, the vector according to item 191, the vector system according to any one of items 191 to 193 or the composition according to any one of items 195 to 214 for use in reducing the level of pre-genomic HBV RNA in an HBV-infected cell culture or an HBV-infected patient compared to an untreated HBV-infected cell culture or to the same patient before treatment.

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